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Sample records for profiles selective identification

  1. Latent Class Symptom Profiles of Selective Mutism: Identification and Linkage to Temperamental and Social Constructs.

    Science.gov (United States)

    Diliberto, Rachele; Kearney, Christopher A

    2017-11-21

    Selective mutism (SM) is a stable, debilitating psychiatric disorder in which a child fails to speak in most public situations. Considerable debate exists as to the typology of this population, with empirically-based studies pointing to possible dimensions of anxiety, oppositionality, and communication problems, among other aspects. Little work has juxtaposed identified symptom profiles with key temperamental and social constructs often implicated in SM. The present study examined a large, diverse, non-clinical, international sample of children aged 6-10 years with SM to empirically identify symptom profiles and to link these profiles to key aspects of temperament (i.e., emotionality, shyness, sociability, activity) and social functioning (i.e., social problems, social competence). Exploratory and confirmatory factor analysis revealed anxiety/distress, oppositionality, and inattention domains. In addition, latent class analysis revealed nuanced profiles labeled as (1) moderately anxious, oppositional, and inattentive, (2) highly anxious, and moderately oppositional and inattentive, and (3) mildly to moderately anxious, and mildly oppositional and inattentive. Class 2 was the most impaired group and was associated with greater emotionality, shyness, and social problems. Class 3 was the least impaired group and was associated with better sociability and social competence and activity. Class 1 was largely between the other classes, demonstrating less shyness and social problems than Class 2. The results help confirm previous findings of anxiety and oppositional profiles among children with SM but that nuanced classes may indicate subtle variations in impairment. The results have implications not only for subtyping this population but also for refining assessment and case conceptualization strategies and pursuing personalized and perhaps less lengthy treatment.

  2. Selective structural source identification

    Science.gov (United States)

    Totaro, Nicolas

    2018-04-01

    In the field of acoustic source reconstruction, the inverse Patch Transfer Function (iPTF) has been recently proposed and has shown satisfactory results whatever the shape of the vibrating surface and whatever the acoustic environment. These two interesting features are due to the virtual acoustic volume concept underlying the iPTF methods. The aim of the present article is to show how this concept of virtual subsystem can be used in structures to reconstruct the applied force distribution. Some virtual boundary conditions can be applied on a part of the structure, called virtual testing structure, to identify the force distribution applied in that zone regardless of the presence of other sources outside the zone under consideration. In the present article, the applicability of the method is only demonstrated on planar structures. However, the final example show how the method can be applied to a complex shape planar structure with point welded stiffeners even in the tested zone. In that case, if the virtual testing structure includes the stiffeners the identified force distribution only exhibits the positions of external applied forces. If the virtual testing structure does not include the stiffeners, the identified force distribution permits to localize the forces due to the coupling between the structure and the stiffeners through the welded points as well as the ones due to the external forces. This is why this approach is considered here as a selective structural source identification method. It is demonstrated that this approach clearly falls in the same framework as the Force Analysis Technique, the Virtual Fields Method or the 2D spatial Fourier transform. Even if this approach has a lot in common with these latters, it has some interesting particularities like its low sensitivity to measurement noise.

  3. Used Fuel Cask Identification through Neutron Profile

    Energy Technology Data Exchange (ETDEWEB)

    Rauch, Eric Benton [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-11-20

    Currently, most spent fuel is stored near reactors. An interim consolidated fuel storage facility would receive fuel from multiple sites and store it in casks on site for decades. For successful operation of such a facility there is need for a way to restore continuity of knowledge if lost as well as a method that will indicate state of fuel inside the cask. Used nuclear fuel is identifiable by its radiation emission, both gamma and neutron. Neutron emission from fission products, multiplication from remaining fissile material, and the unique distribution of both in each cask produce a unique neutron signature. If two signatures taken at different times do not match, either changes within the fuel content or misidentification of a cask occurred. It was found that identification of cask loadings works well through the profile of emitted neutrons in simulated real casks. Even casks with similar overall neutron emission or average counts around the circumference can be distinguished from each other by analyzing the profile. In conclusion, (1) identification of unaltered casks through neutron signature profile is viable; (2) collecting the profile provides insight to the condition and intactness of the fuel stored inside the cask; and (3) the signature profile is stable over time.

  4. Molecular Identification, Enzyme Assay, and Metabolic Profiling of Trichoderma spp.

    Science.gov (United States)

    Bae, Soo-Jung; Park, Young-Hwan; Bae, Hyeun-Jong; Jeon, Junhyun; Bae, Hanhong

    2017-06-28

    The goal of this study was to identify and characterize selected Trichoderma isolates by metabolic profiling and enzyme assay for evaluation of their potential as biocontrol agents against plant pathogens. Trichoderma isolates were obtained from the Rural Development Administration Genebank Information Center (Wanju, Republic of Korea). Eleven Trichoderma isolates were re-identified using ribosomal DNA internal transcribed spacer (ITS) regions. ITS sequence results showed new identification of Trichoderma isolates. In addition, metabolic profiling of the ethyl acetate extracts of the liquid cultures of five Trichoderma isolates that showed the best anti- Phytophthora activities was conducted using gas chromatography-mass spectrometry. Metabolic profiling revealed that Trichoderma isolates shared common metabolites with well-known antifungal activities. Enzyme assays indicated strong cell walldegrading enzyme activities of Trichoderma isolates. Overall, our results indicated that the selected Trichoderma isolates have great potential for use as biocontrol agents against plant pathogens.

  5. On active current selection for Lagrangian profilers

    DEFF Research Database (Denmark)

    Jouffroy, Jerome; Zhou, Qiuyang; Zielinski, Oliver

    2013-01-01

    simple and computationally-efficient control strategies to actively select and use ocean currents so that a profiler can autonomously reach a desired destination. After briefly presenting a typical profiler and possible mechanical modifications for a coastal environment, we introduce simple mathematical...... models for the profiler and the currents it will use. We then present simple feedback controllers that, using the direction of the currents and taking into account the configuration of the environment (coastal or deep-sea), is able to steer the profiler to any desired horizontal location. To illustrate...

  6. Commodity profiles for selected metals

    International Nuclear Information System (INIS)

    Svoboda, O.; Wilson, B.M.

    1985-01-01

    This report describes the basic characteristics of 35 metals and gives the prices and production of these metals for the period 1979 to 1983/4. The description of each metal includes the ore grades and reserves, the major minerals in which the metal occurs, and the discovery, selected physical properties, sources, uses, substitutes, and effects on the environment of the metal. Graphs showing price and production cover the period 1950 to 1984, and possible future developments in these areas are forecast for each metal until the year 2000

  7. IDENTIFICATION AND SELECTION OF SIX SIGMA PROJECTS

    Directory of Open Access Journals (Sweden)

    Abdalhkeim FA. Flifel

    2017-04-01

    Full Text Available Six Sigma is a well-structured and proven methodology for improving organizational performance. It helps achieving the goals of the organization through the use of project-driven approach. The implementation of Six sigma approach depends on proper identification and selection of projects, moreover, the selection of right Six sigma projects is one of the critical success factors of six sigma efforts. The paper provides the sources for the identification of potential projects, top down and bottom up approaches, the process of selection of projects, guidelines that assist the selection of appropriate projects, selection criteria which must be precisely chosen in accordance with the objectives, needs and capabilities of the organization as well as sophisticated techniques and tools recommended in the literature for the selection of projects.

  8. Identification of Biomarkers of Impaired Sensory Profiles among Autistic Patients

    Science.gov (United States)

    El-Ansary, Afaf; Hassan, Wail M.; Qasem, Hanan; Das, Undurti N.

    2016-01-01

    Background Autism is a neurodevelopmental disorder that displays significant heterogeneity. Comparison of subgroups within autism, and analyses of selected biomarkers as measure of the variation of the severity of autistic features such as cognitive dysfunction, social interaction impairment, and sensory abnormalities might help in understanding the pathophysiology of autism. Methods and Participants In this study, two sets of biomarkers were selected. The first included 7, while the second included 6 biomarkers. For set 1, data were collected from 35 autistic and 38 healthy control participants, while for set 2, data were collected from 29 out of the same 35 autistic and 16 additional healthy subjects. These markers were subjected to a principal components analysis using either covariance or correlation matrices. Moreover, libraries composed of participants categorized into units were constructed. The biomarkers used include, PE (phosphatidyl ethanolamine), PS (phosphatidyl serine), PC (phosphatidyl choline), MAP2K1 (Dual specificity mitogen-activated protein kinase kinase 1), IL-10 (interleukin-10), IL-12, NFκB (nuclear factor-κappa B); PGE2 (prostaglandin E2), PGE2-EP2, mPGES-1 (microsomal prostaglandin synthase E-1), cPLA2 (cytosolic phospholipase A2), 8-isoprostane, and COX-2 (cyclo-oxygenase-2). Results While none of the studied markers correlated with CARS and SRS as measure of cognitive and social impairments, six markers significantly correlated with sensory profiles of autistic patients. Multiple regression analysis identifies a combination of PGES, mPGES-1, and PE as best predictors of the degree of sensory profile impairment. Library identification resulted in 100% correct assignments of both autistic and control participants based on either set 1 or 2 biomarkers together with a satisfactory rate of assignments in case of sensory profile impairment using different sets of biomarkers. Conclusion The two selected sets of biomarkers were effective to

  9. On Active Current Selection for Lagrangian Profilers

    Directory of Open Access Journals (Sweden)

    J. Jouffroy

    2013-01-01

    Full Text Available Autonomous Lagrangian profilers are now widely used as measurement and monitoring platforms, notably in observation programs as Argo. In a typical mode of operation, the profilers drift passively at their parking depthbefore making a vertical profile to go back to the surface. This paperpresents simple and computationally-efficient control strategies to activelyselect and use ocean currents so that a profiler can autonomously reach adesired destination. After briefly presenting a typical profiler andpossible mechanical modifications for a coastal environment, we introducesimple mathematical models for the profiler and the currents it will use. Wethen present simple feedback controllers that, using the direction of thecurrents and taking into account the configuration of the environment(coastal or deep-sea, is able to steer the profiler to any desiredhorizontal location. To illustrate the approach, a few results are presentedusing both simulated currents and real current velocity profiles from theNorth Sea.

  10. Effect of cooking methods on the micronutrient profile of selected ...

    African Journals Online (AJOL)

    Effect of cooking methods on the micronutrient profile of selected vegetables: okra fruit ( Abelmoshcus esculentus ), fluted pumpkin ( Telfairia occidentalis ), African spinach ( Amarantus viridis ), and scent leaf ( Ocumum gratissimum.

  11. Line profile variations in selected Seyfert galaxies

    International Nuclear Information System (INIS)

    Kollatschny, W; Zetzl, M; Ulbrich, K

    2010-01-01

    Continua as well as the broad emission lines in Seyfert 1 galaxies vary in different galaxies with different amplitudes on typical timescales of days to years. We present the results of two independent variability campaigns taken with the Hobby-Eberly Telescope. We studied in detail the integrated line and continuum variations in the optical spectra of the narrow-line Seyfert galaxy Mrk 110 and the very broad-line Seyfert galaxy Mrk 926. The broad-line emitting region in Mrk 110 has radii of four to 33 light-days as a function of the ionization degree of the emission lines. The line-profile variations are matched by Keplerian disk models with some accretion disk wind. The broad-line region in Mrk 926 is very small showing an extension of two to three light-days only. We could detect a structure in the rms line-profiles as well as in the response of the line profile segments of Mrk 926 indicating the BLR is structured.

  12. European securitization and biometric identification: the uses of genetic profiling.

    Science.gov (United States)

    Johnson, Paul; Williams, Robin

    2007-01-01

    The recent loss of confidence in textual and verbal methods for validating the identity claims of individual subjects has resulted in growing interest in the use of biometric technologies to establish corporeal uniqueness. Once established, this foundational certainty allows changing biographies and shifting category memberships to be anchored to unchanging bodily surfaces, forms or features. One significant source for this growth has been the "securitization" agendas of nation states that attempt the greater control and monitoring of population movement across geographical borders. Among the wide variety of available biometric schemes, DNA profiling is regarded as a key method for discerning and recording embodied individuality. This paper discusses the current limitations on the use of DNA profiling in civil identification practices and speculates on future uses of the technology with regard to its interoperability with other biometric databasing systems.

  13. A simple data base for identification of risk profiles

    Energy Technology Data Exchange (ETDEWEB)

    Munganahalli, D.

    1996-12-31

    Sedco Forex is a drilling contractor that operates approximately 80 rigs on land and offshore worldwide. The HSE management system developed by Sedco Forex is an effort to prevent accidents and minimize losses. An integral part of the HSE management system is establishing risk profiles and thereby minimizing risk and reducing loss exposures. Risk profiles are established based on accident reports, potential accident reports and other risk identification reports (RIR) like the Du Pont STOP system. A rig could fill in as many as 30 accident reports, 30 potential accident reports and 500 STOP cards each year. Statistics are important for an HSE management system, since they are indicators of success or failure of HSE systems. It is however difficult to establish risk profiles based on statistical information, unless tools are available at the rig site to aid with the analysis. Risk profiles are then used to identify important areas in the operation that may require specific attention to minimize the loss exposure. Programs to address the loss exposure can then be identified and implemented with either a local or corporate approach. In January 1995, Sedco Forex implemented a uniform HSE Database on all the rigs worldwide. In one year companywide, the HSE database would contain information on approximately 500 accident and potential accident reports, and 10,000 STOP cards. This paper demonstrates the salient features of the database and describes how it has helped in establishing key risk profiles. It also shows a recent example of how risk profiles have been established at the corporate level and used to identify the key contributing factors to hands and finger injuries. Based on this information, a campaign was launched to minimize the frequency of occurrence and associated loss attributed to hands and fingers accidents.

  14. Antimicrobial susceptibility profile of selected bacteraemic ...

    African Journals Online (AJOL)

    Extended-spectrum 13-lactamase (ESBL) production was determined in selected species of Enterobacteriaceae irrespective of source. Results. The overall prevalence of ampicillin resistance in blood culture isolates of E. coli (N = 471) was 84%, and 20% were resistant to the fluoroquinolones. Considerable geographical ...

  15. Identification, Selection, and Enrichment of Cardiomyocyte Precursors

    Directory of Open Access Journals (Sweden)

    Bianca Ferrarini Zanetti

    2013-01-01

    Full Text Available The large-scale production of cardiomyocytes is a key step in the development of cell therapy and tissue engineering to treat cardiovascular diseases, particularly those caused by ischemia. The main objective of this study was to establish a procedure for the efficient production of cardiomyocytes by reprogramming mesenchymal stem cells from adipose tissue. First, lentiviral vectors expressing neoR and GFP under the control of promoters expressed specifically during cardiomyogenesis were constructed to monitor cell reprogramming into precardiomyocytes and to select cells for amplification and characterization. Cellular reprogramming was performed using 5′-azacytidine followed by electroporation with plasmid pOKS2a, which expressed Oct4, Sox2, and Klf4. Under these conditions, GFP expression began only after transfection with pOKS2a, and less than 0.015% of cells were GFP+. These GFP+ cells were selected for G418 resistance to find molecular markers of cardiomyocytes by RT-PCR and immunocytochemistry. Both genetic and protein markers of cardiomyocytes were present in the selected cells, with some variations among them. Cell doubling time did not change after selection. Together, these results indicate that enrichment with vectors expressing GFP and neoR under cardiomyocyte-specific promoters can produce large numbers of cardiomyocyte precursors (CMPs, which can then be differentiated terminally for cell therapy and tissue engineering.

  16. Choosing face: The curse of self in profile image selection.

    Science.gov (United States)

    White, David; Sutherland, Clare A M; Burton, Amy L

    2017-01-01

    People draw automatic social inferences from photos of unfamiliar faces and these first impressions are associated with important real-world outcomes. Here we examine the effect of selecting online profile images on first impressions. We model the process of profile image selection by asking participants to indicate the likelihood that images of their own face ("self-selection") and of an unfamiliar face ("other-selection") would be used as profile images on key social networking sites. Across two large Internet-based studies (n = 610), in line with predictions, image selections accentuated favorable social impressions and these impressions were aligned to the social context of the networking sites. However, contrary to predictions based on people's general expertise in self-presentation, other-selected images conferred more favorable impressions than self-selected images. We conclude that people make suboptimal choices when selecting their own profile pictures, such that self-perception places important limits on facial first impressions formed by others. These results underscore the dynamic nature of person perception in real-world contexts.

  17. Stress identification in steam generator tubes from profile measurements

    International Nuclear Information System (INIS)

    Andrieux, S.; Voldoire, F.

    1993-01-01

    An identification method devoted to the determination of stresses in tubes, by means of profile measurements, provided by on site non-destructive evaluations, is presented here. From the only available data (the radial displacement w on the inner wall), the computation of the strains, and consequently the stresses in the elastoplastic range, is made within the framework of the shell theory. For this purpose, we need to determine the associated curvature w'': this step is an ill-posed problem, because of the lack of continuity with respect to the discrete data. This difficulty is overridden by means of an appropriate regularization procedure. The predictive ability of the method has been tested by comparison with direct simulations; we present an industrial application. (author)

  18. Anxiety and oppositional behavior profiles among youth with selective mutism.

    Science.gov (United States)

    Diliberto, Rachele A; Kearney, Christopher A

    2016-01-01

    Selective mutism (SM) is a debilitating condition in which a child does not speak in social situations where speech is expected. The clinical conceptualization of SM has been debated historically, with evidence pointing partly to anxious and oppositional behavior profiles. Behavioral characteristics were examined in a clinical sample of 57 youth formally diagnosed with selective mutism. Parents rated children across internalizing and externalizing behaviors on the Child Behavior Checklist. Eighteen highly rated items were subjected to exploratory and then confirmatory factor analysis. Anxiety and oppositional behavior factors were derived. The anxious behavior profile was associated with social anxiety disorder symptoms, social problems, and aggressive behaviors but not oppositional defiant disorder symptoms. The oppositional behavior profile was associated with aggressive behaviors, oppositional defiant disorder symptoms, social problems, and inversely to social anxiety disorder symptoms. Results are consistent with emerging research regarding subgroups of children with SM. Behavior profiles are discussed as well with respect to assessment and treatment implications. Readers will learn about the nature of children with selective mutism as well as behaviors that differentiate anxious and oppositional behavior profiles. Items that comprise anxious and oppositional behavior profiles are presented. These item profiles may have ramifications for assessment and treatment. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. 5-HT7 Receptor Antagonists with an Unprecedented Selectivity Profile.

    Science.gov (United States)

    Ates, Ali; Burssens, Pierre; Lorthioir, Olivier; Lo Brutto, Patrick; Dehon, Gwenael; Keyaerts, Jean; Coloretti, Francis; Lallemand, Bénédicte; Verbois, Valérie; Gillard, Michel; Vermeiren, Céline

    2018-04-23

    Selective leads: In this study, we generated a new series of serotonin 5-HT 7 receptor antagonists. Their synthesis, structure-activity relationships, and selectivity profiles are reported. This series includes 5-HT 7 antagonists with unprecedented high selectivity for the 5-HT 7 receptor, setting the stage for lead optimization of drugs acting on a range of neurological targets. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Feature extraction and sensor selection for NPP initiating event identification

    International Nuclear Information System (INIS)

    Lin, Ting-Han; Wu, Shun-Chi; Chen, Kuang-You; Chou, Hwai-Pwu

    2017-01-01

    Highlights: • A two-stage feature extraction scheme for NPP initiating event identification. • With stBP, interrelations among the sensors can be retained for identification. • With dSFS, sensors that are crucial for identification can be efficiently selected. • Efficacy of the scheme is illustrated with data from the Maanshan NPP simulator. - Abstract: Initiating event identification is essential in managing nuclear power plant (NPP) severe accidents. In this paper, a novel two-stage feature extraction scheme that incorporates the proposed sensor type-wise block projection (stBP) and deflatable sequential forward selection (dSFS) is used to elicit the discriminant information in the data obtained from various NPP sensors to facilitate event identification. With the stBP, the primal features can be extracted without eliminating the interrelations among the sensors of the same type. The extracted features are then subjected to a further dimensionality reduction by selecting the sensors that are most relevant to the events under consideration. This selection is not easy, and a combinatorial optimization technique is normally required. With the dSFS, an optimal sensor set can be found with less computational load. Moreover, its sensor deflation stage allows sensors in the preselected set to be iteratively refined to avoid being trapped into a local optimum. Results from detailed experiments containing data of 12 event categories and a total of 112 events generated with a Taiwan’s Maanshan NPP simulator are presented to illustrate the efficacy of the proposed scheme.

  1. Unnatural selection: talent identification and development in sport.

    Science.gov (United States)

    Abbott, Angela; Button, Chris; Pepping, Gert-Jan; Collins, Dave

    2005-01-01

    The early identification of talented individuals has become increasingly important across many performance domains. Current talent identification (TI) schemes in sport typically select on the basis of discrete, unidimensional measures at unstable periods in the athlete's development. In this article, the concept of talent is revised as a complex, dynamical system in which future behaviors emerge from an interaction of key performance determinants such as psychological behaviors, motor abilities, and physical characteristics. Key nonlinear dynamics concepts are related to TI approaches such as sensitivity to initial conditions, transitions, and exponential behavioral distributions. It is concluded that many TI models place an overemphasis on early identification rather than the development of potentially talented performers. A generic model of talent identification and development is proposed that addresses these issues and provides direction for future research.

  2. Meaning identification and meaning selection for general language monolingual dictionaries

    DEFF Research Database (Denmark)

    Bergenholtz, Henning; Agerbo, Heidi

    2014-01-01

    The traditional way for lexicographers to deal with polysemy in dictionaries is by applying the terms lumping and splitting. We will not follow this tradition. Instead, we argue that the identification and selection of meaning items (= polysems) should be treated in the same way as the identifica......The traditional way for lexicographers to deal with polysemy in dictionaries is by applying the terms lumping and splitting. We will not follow this tradition. Instead, we argue that the identification and selection of meaning items (= polysems) should be treated in the same way...... to references in the world (in this contribution called things), followed by a formulation of the identified meaning items which can be used for reception situations. Not always – as in the case of lemma selection – will all the identified meaning items be included in the dictionary. The selection of identified...... meaning items will depend on the genuine purpose of the dictionary....

  3. Antibiotic profiles of bacteria isolated on selective campylobacter media

    Science.gov (United States)

    The objective of this study was to determine antibiotic profiles of non-Campylobacter bacteria recovered on selective Campylobacter media. Broiler carcasses were obtained from a processing facility, and whole-carcass rinses were performed by shaking carcasses in plastic bags with 200 mL of distilled...

  4. Flies selected for longevity retain a young gene expression profile

    DEFF Research Database (Denmark)

    Sarup, Pernille Merete; Sørensen, Peter; Loeschcke, Volker

    2011-01-01

      We investigated correlated responses in the transcriptomes of longevity-selected lines of Drosophila melanogaster to identify pathways that affect life span in metazoan systems. We evaluated the gene expression profile in young, middle-aged, and old male flies, finding that 530 genes were...

  5. Documentation and Nutritional profile of some selected food plants ...

    African Journals Online (AJOL)

    Documentation and Nutritional profile of some selected food plants of Otwal and Ngai sun counties Oyam District, Northern Uganda. ... However, it should be noted that there is a general decline in the consumption of wild plants, despite the apparent high nutritional values. The conservation of wild food plants is not taking ...

  6. An Identification Key for Selecting Methods for Sustainability Assessments

    Directory of Open Access Journals (Sweden)

    Michiel C. Zijp

    2015-03-01

    Full Text Available Sustainability assessments can play an important role in decision making. This role starts with selecting appropriate methods for a given situation. We observed that scientists, consultants, and decision-makers often do not systematically perform a problem analyses that guides the choice of the method, partly related to a lack of systematic, though sufficiently versatile approaches to do so. Therefore, we developed and propose a new step towards method selection on the basis of question articulation: the Sustainability Assessment Identification Key. The identification key was designed to lead its user through all important choices needed for comprehensive question articulation. Subsequently, methods that fit the resulting specific questions are suggested by the key. The key consists of five domains, of which three determine method selection and two the design or use of the method. Each domain consists of four or more criteria that need specification. For example in the domain “system boundaries”, amongst others, the spatial and temporal scales are specified. The key was tested (retrospectively on a set of thirty case studies. Using the key appeared to contribute to improved: (i transparency in the link between the question and method selection; (ii consistency between questions asked and answers provided; and (iii internal consistency in methodological design. There is latitude to develop the current initial key further, not only for selecting methods pertinent to a problem definition, but also as a principle for associated opportunities such as stakeholder identification.

  7. Selecting foils for identification lineups: matching suspects or descriptions?

    Science.gov (United States)

    Tunnicliff, J L; Clark, S E

    2000-04-01

    Two experiments directly compare two methods of selecting foils for identification lineups. The suspect-matched method selects foils based on their match to the suspect, whereas the description-matched method selects foils based on their match to the witness's description of the perpetrator. Theoretical analyses and previous results predict an advantage for description-matched lineups both in terms of correctly identifying the perpetrator and minimizing false identification of innocent suspects. The advantage for description-matched lineups should be particularly pronounced if the foils selected in suspect-matched lineups are too similar to the suspect. In Experiment 1, the lineups were created by trained police officers, and in Experiment 2, the lineups were constructed by undergraduate college students. The results of both experiments showed higher suspect-to-foil similarity for suspect-matched lineups than for description-matched lineups. However, neither experiment showed a difference in correct or false identification rates. Both experiments did, however, show that there may be an advantage for suspect-matched lineups in terms of no-pick and rejection responses. From these results, the endorsement of one method over the other seems premature.

  8. Is there a link between selectivity and binding thermodynamics profiles?

    Science.gov (United States)

    Tarcsay, Ákos; Keserű, György M

    2015-01-01

    Thermodynamics of ligand binding is influenced by the interplay between enthalpy and entropy contributions of the binding event. The impact of these binding free energy components, however, is not limited to the primary target only. Here, we investigate the relationship between binding thermodynamics and selectivity profiles by combining publicly available data from broad off-target assay profiling and the corresponding thermodynamics measurements. Our analysis indicates that compounds binding their primary targets with higher entropy contributions tend to hit more off-targets compared with those ligands that demonstrated enthalpy-driven binding. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Occupational Heat Stress Profiles in Selected Workplaces in India

    OpenAIRE

    Venugopal, Vidhya; Chinnadurai, Jeremiah S.; Lucas, Rebekah A. I.; Kjellstrom, Tord

    2016-01-01

    Health and productivity impacts from occupational heat stress have significant ramifications for the large workforce of India. This study profiled occupational heat stress impacts on the health and productivity of workers in select organized and unorganized Indian work sectors. During hotter and cooler seasons, Wet Bulb Globe Temperatures (WBGT) were used to quantify the risk of heat stress, according to International workplace guidelines. Questionnaires assessed workers' perceived health and...

  10. Identification of salivary Lactobacillus rhamnosus species by DNA profiling and a specific probe.

    Science.gov (United States)

    Richard, B; Groisillier, A; Badet, C; Dorignac, G; Lonvaud-Funel, A

    2001-03-01

    The Lactobacillus genus has been shown to be associated with the dental carious process, but little is known about the species related to the decay, although Lactobacillus rhamnosus is suspected to be the most implicated species. Conventional identification methods based on biochemical criteria lead to ambiguous results, since the Lactobacillus species found in saliva are phenotypically close. To clarify the role of this genus in the evolution of carious disease, this work aimed to find a rapid and reliable method for identifying the L. rhamnosus species. Methods based on hybridization with DNA probes and DNA amplification by PCR were used. The dominant salivary Lactobacillus species (reference strains from the ATCC) were selected for this purpose as well as some wild strains isolated from children's saliva. DNA profiling using semirandom polymorphic DNA amplification (semi-RAPD) generated specific patterns for L. rhamnosus ATCC 7469. The profiles of all L. rhamnosus strains tested were similar and could be grouped; these strains shared four common fragments. Wild strains first identified with classic methods shared common patterns with the L. rhamnosus species and could be reclassified. One fragment of the profile was purified, cloned, used as a probe and found to be specific to the L. rhamnosus species. These results may help to localize this species within its ecological niche and to elucidate the progression of the carious process.

  11. Phytochemical profile of morphologically selected yerba-mate progenies

    Directory of Open Access Journals (Sweden)

    Alice Teresa Valduga

    2016-02-01

    Full Text Available ABSTRACT Yerba-mate (Ilex paraguariensis St. Hil is a native South American species. Plant progenies are populations that differ in terms of their productivity, morphology and phytochemical profile. This study aimed to determine the concentration of primary and secondary metabolites, such as antioxidants, in leaves, of yerba-mate progenies selected based on morphological characteristics. We evaluated the centesimal composition of secondary metabolites in the leaves of five yerba-mate plants. Methylxanthines and phenolic compounds were determined by UPLC-PDA, and antioxidant activity by measuring DPPH scavenging. Significant differences were found in centesimal composition and the contents of caffeine, theobromine, rutin and chlorogenic acid, as well as antioxidant activities, in selected progenies. The IC50 values were correlated with the chlorogenic acid levels (r2 = 0.5242 and soluble content (r2 = 0.7686. The morphological characteristics observed in yerba-mate leaves can be used as a tool for plant selection, to obtain matrices with different phytochemical profiles as a genetic material source.

  12. Identification and selection of initiating events for experimental fusion facilities

    International Nuclear Information System (INIS)

    Cadwallader, L.C.

    1989-01-01

    This paper describes the current approaches used in probabilistic risk assessment (PRA) to identify and select accident initiating events for study in either probabilistic safety analysis or PRA. Current methods directly apply to fusion facilities as well as other types of industries, such as chemical processing and nuclear fission. These identification and selection methods include the Master Logic Diagram, historical document review, system level Failure Modes and Effects Analysis, and others. A combination of the historical document review, such as Safety Analysis Reports and fusion safety studies, and the Master Logic Diagram with appropriate quality assurance reviews, is suggested for standardizing US fusion PRA effects. A preliminary set of generalized initiating events applicable to fusion facilities derived from safety document review is presented as a framework to start from for the historical document review and Master Logic Diagram approach. Fusion designers should find this list useful for their design reviews. 29 refs., 2 tabs

  13. Identification and selection of initiating events for experimental fusion facilities

    International Nuclear Information System (INIS)

    Cadwallader, L.C.

    1989-01-01

    This paper describes the current approaches used in probabilistic risk assessment (PRA) to identify and select accident initiating events for study in either probabilistic safety analysis or PRA. Current methods directly apply to fusion facilities as well as other types of industries, such as chemical processing and nuclear fission. These identification and selection methods include the Master Logic Diagram, historical document review, system level Failure Modes and Effects Analysis, and others. A combination of the historical document review, such as Safety Analysis Reports and fusion safety studies, and the Master Logic Diagram with appropriate quality assurance reviews, is suggested for standardizing U.S. fusion PRA efforts. A preliminary set of generalized initiating events applicable to fusion facilities derived from safety document review is presented as a framework to start from for the historical document review and Master Logic Diagram approach. Fusion designers should find this list useful for their design reviews. 29 refs., 1 tab

  14. Identification of a myometrial molecular profile for dystocic labor.

    LENUS (Irish Health Repository)

    Brennan, Donal J

    2011-01-01

    The most common indication for cesarean section (CS) in nulliparous women is dystocia secondary to ineffective myometrial contractility. The aim of this study was to identify a molecular profile in myometrium associated with dystocic labor.

  15. Automatic identification approach for high-performance liquid chromatography-multiple reaction monitoring fatty acid global profiling.

    Science.gov (United States)

    Tie, Cai; Hu, Ting; Jia, Zhi-Xin; Zhang, Jin-Lan

    2015-08-18

    Fatty acids (FAs) are a group of lipid molecules that are essential to organisms. As potential biomarkers for different diseases, FAs have attracted increasing attention from both biological researchers and the pharmaceutical industry. A sensitive and accurate method for globally profiling and identifying FAs is required for biomarker discovery. The high selectivity and sensitivity of high-performance liquid chromatography-multiple reaction monitoring (HPLC-MRM) gives it great potential to fulfill the need to identify FAs from complicated matrices. This paper developed a new approach for global FA profiling and identification for HPLC-MRM FA data mining. Mathematical models for identifying FAs were simulated using the isotope-induced retention time (RT) shift (IRS) and peak area ratios between parallel isotope peaks for a series of FA standards. The FA structures were predicated using another model based on the RT and molecular weight. Fully automated FA identification software was coded using the Qt platform based on these mathematical models. Different samples were used to verify the software. A high identification efficiency (greater than 75%) was observed when 96 FA species were identified in plasma. This FAs identification strategy promises to accelerate FA research and applications.

  16. Isolation, identification and antimicrobial suscep- tibility profiles of ...

    African Journals Online (AJOL)

    determine the in vitro antimicrobial resistance profiles of the isolates. A to- tal of 266 samples ... meats), cross contamination through direct contact of foods to contaminated surfaces such as stainless steel, hanging ... of contaminated milk and meat products (Endrias Zewdu and Cornelius 2009), through mutation, acquisition ...

  17. Orientation selective neural network for cosmic muon identification

    International Nuclear Information System (INIS)

    Abramowicz, H.; Tel Aviv Univ.; Horn, D.; Naftaly, U.; Sahar-Pikielny, C.

    1997-01-01

    We discuss a novel method for identification of a linear pattern of pixels on a two-dimensional grid. Motivated by principles employed by the visual cortex, we construct orientation selective neurons in a neural network that performs this task. The method is then applied to a sample of data collected with the ZEUS detector at HERA in order to identify cosmic muons that leave a linear pattern of signals in the segmented uranium-scintillator calorimeter. A two dimensional representation of the relevant part of the detector is used. The algorithm performs well in the presence of noise and pixels with limited efficiency. Given its architecture, this system becomes a good candidate for fast pattern recognition in parallel processing devices. (orig.)

  18. Identification of recently selected mutations driven by artificial selection in hanwoo (korean cattle).

    Science.gov (United States)

    Lim, Dajeong; Gondro, Cedric; Park, Hye Sun; Cho, Yong Min; Chai, Han Ha; Seong, Hwan Hoo; Yang, Bo Suk; Hong, Seong Koo; Chang, Won Kyung; Lee, Seung Hwan

    2013-05-01

    Hanwoo have been subjected over the last seventy years to intensive artificial selection with the aim of improving meat production traits such as marbling and carcass weight. In this study, we performed a signature of selection analysis to identify recent positive selected regions driven by a long-term artificial selection process called a breeding program using whole genome SNP data. In order to investigate homozygous regions across the genome, we estimated iES (integrated Extended Haplotype Homozygosity SNP) for the each SNPs. As a result, we identified two highly homozygous regions that seem to be strong and/or recent positive selection. Five genes (DPH5, OLFM3, S1PR1, LRRN1 and CRBN) were included in this region. To go further in the interpretation of the observed signatures of selection, we subsequently concentrated on the annotation of differentiated genes defined according to the iES value of SNPs localized close or within them. We also described the detection of the adaptive evolution at the molecular level for the genes of interest. As a result, this analysis also led to the identification of OLFM3 as having a strong signal of selection in bovine lineage. The results of this study indicate that artificial selection which might have targeted most of these genes was mainly oriented towards improvement of meat production.

  19. Identification of Recently Selected Mutations Driven by Artificial Selection in Hanwoo (Korean Cattle

    Directory of Open Access Journals (Sweden)

    Dajeong Lim

    2013-05-01

    Full Text Available Hanwoo have been subjected over the last seventy years to intensive artificial selection with the aim of improving meat production traits such as marbling and carcass weight. In this study, we performed a signature of selection analysis to identify recent positive selected regions driven by a long-term artificial selection process called a breeding program using whole genome SNP data. In order to investigate homozygous regions across the genome, we estimated iES (integrated Extended Haplotype Homozygosity SNP for the each SNPs. As a result, we identified two highly homozygous regions that seem to be strong and/or recent positive selection. Five genes (DPH5, OLFM3, S1PR1, LRRN1 and CRBN were included in this region. To go further in the interpretation of the observed signatures of selection, we subsequently concentrated on the annotation of differentiated genes defined according to the iES value of SNPs localized close or within them. We also described the detection of the adaptive evolution at the molecular level for the genes of interest. As a result, this analysis also led to the identification of OLFM3 as having a strong signal of selection in bovine lineage. The results of this study indicate that artificial selection which might have targeted most of these genes was mainly oriented towards improvement of meat production.

  20. Prospective identification of malaria parasite genes under balancing selection.

    Directory of Open Access Journals (Sweden)

    Kevin K A Tetteh

    Full Text Available Endemic human pathogens are subject to strong immune selection, and interrogation of pathogen genome variation for signatures of balancing selection can identify important target antigens. Several major antigen genes in the malaria parasite Plasmodium falciparum have shown such signatures in polymorphism-versus-divergence indices (comparing with the chimpanzee parasite P. reichenowi, and in allele frequency based indices.To compare methods for prospective identification of genes under balancing selection, 26 additional genes known or predicted to encode surface-exposed proteins of the invasive blood stage merozoite were first sequenced from a panel of 14 independent P. falciparum cultured lines and P. reichenowi. Six genes at the positive extremes of one or both of the Hudson-Kreitman-Aguade (HKA and McDonald-Kreitman (MK indices were identified. Allele frequency based analysis was then performed on a Gambian P. falciparum population sample for these six genes and three others as controls. Tajima's D (TjD index was most highly positive for the msp3/6-like PF10_0348 (TjD = 1.96 as well as the positive control ama1 antigen gene (TjD = 1.22. Across the genes there was a strong correlation between population TjD values and the relative HKA indices (whether derived from the population or the panel of cultured laboratory isolates, but no correlation with the MK indices.Although few individual parasite genes show significant evidence of balancing selection, analysis of population genomic and comparative sequence data with the HKA and TjD indices should discriminate those that do, and thereby identify likely targets of immunity.

  1. Software Assisted Profiling of Dentition in Human Identification

    Directory of Open Access Journals (Sweden)

    Hina Mehrotra

    2018-01-01

    Full Text Available Forensic odontology is the integral part of forensic science that utilizes unique characteristics of human dentition. Dental remains withstand degradation bet­ter than other human remains. This study was aimed to determine the human identity by using the various predetermined parameters of dental morphology us­ing their digital smile photographs and confirming by means of Adobe Photoshop CC software. The study also aimed to compare and identify the most used pa­rameter of the dental morphology in the human iden­tification process.  This retrospective study was conducted in the Department of Oral & Maxillofacial Pathology, Mi­crobiology and Forensic Odontology, I.T.S Dental College Hospital & Research Centre, Greater Noida, UP, India. A sample of 50 subjects (25 males and 25 females aged between 20 and 40 years were included in the study. Two sequential techniques were followed. Dental casts and pictures were analyzed by 3 blind observers by comparison of dental traits and then were confirmed by superimposition using Adobe Photoshop CC. Positive identification was achieved by application of the 2 techniques. ICC Multiple Raters and ICC Two Raters were applied to analyze the stratum of agreement between the observers. By analyzing the parameters specified by three blind observers, the combination of Central and Lateral Incisor morphology was the most used parameter in the identification process. When the records are unavailable, dental comparison of postmortem findings with antemortem photographs of people displaying uncommon dental features visible in smiles taken from photographs may increase the probability of identification.  Keywords: Forensic Science, Forensic Odontology, Smile, Photograph, Antemortem, Postmortem.

  2. Friend or Foe? Fake Profile Identification in Online Social Networks

    OpenAIRE

    Fire, Michael; Kagan, Dima; Elyashar, Aviad; Elovici, Yuval

    2013-01-01

    The amount of personal information unwillingly exposed by users on online social networks is staggering, as shown in recent research. Moreover, recent reports indicate that these networks are infested with tens of millions of fake users profiles, which may jeopardize the users' security and privacy. To identify fake users in such networks and to improve users' security and privacy, we developed the Social Privacy Protector software for Facebook. This software contains three protection layers,...

  3. Word Embeddings to Enhance Twitter Gang Member Profile Identification

    OpenAIRE

    Wijeratne, Sanjaya; Balasuriya, Lakshika; Doran, Derek; Sheth, Amit

    2016-01-01

    Gang affiliates have joined the masses who use social media to share thoughts and actions publicly. Interestingly, they use this public medium to express recent illegal actions, to intimidate others, and to share outrageous images and statements. Agencies able to unearth these profiles may thus be able to anticipate, stop, or hasten the investigation of gang-related crimes. This paper investigates the use of word embeddings to help identify gang members on Twitter. Building on our previous wo...

  4. New Technologies for Rapid Bacterial Identification and Antibiotic Resistance Profiling.

    Science.gov (United States)

    Kelley, Shana O

    2017-04-01

    Conventional approaches to bacterial identification and drug susceptibility testing typically rely on culture-based approaches that take 2 to 7 days to return results. The long turnaround times contribute to the spread of infectious disease, negative patient outcomes, and the misuse of antibiotics that can contribute to antibiotic resistance. To provide new solutions enabling faster bacterial analysis, a variety of approaches are under development that leverage single-cell analysis, microfluidic concentration and detection strategies, and ultrasensitive readout mechanisms. This review discusses recent advances in this area and the potential of new technologies to enable more effective management of infectious disease.

  5. mRNA profiling for the identification of blood-Results of a collaborative EDNAP exercise

    DEFF Research Database (Denmark)

    Haas, Cordula; Hanson, E; Bär, W

    2010-01-01

    of the laboratories had no prior experience with RNA. Despite some expected variation in sensitivity between laboratories, the method proved to be reproducible and sensitive using different analysis strategies. The results of this collaborative exercise support the potential use of mRNA profiling as an alternative......A collaborative exercise on mRNA profiling for the identification of blood was organized by the European DNA Profiling Group (EDNAP). Seven blood samples and one blood dilution series were analyzed by the participating laboratories for the reportedly blood-specific markers HBB, SPTB and PBGD, using...

  6. mRNA profiling for the identification of blood--Results of a collaborative EDNAP exercise

    DEFF Research Database (Denmark)

    Haas, C.; Hanson, E.; Bär, W.

    2011-01-01

    of the laboratories had no prior experience with RNA. Despite some expected variation in sensitivity between laboratories, the method proved to be reproducible and sensitive using different analysis strategies. The results of this collaborative exercise support the potential use of mRNA profiling as an alternative......A collaborative exercise on mRNA profiling for the identification of blood was organized by the European DNA Profiling Group (EDNAP). Seven blood samples and one blood dilution series were analyzed by the participating laboratories for the reportedly blood-specific markers HBB, SPTB and PBGD, using...

  7. Vibrating Profile in the Aerodynamic Tunnel — Identification of the Start of Flutter

    Czech Academy of Sciences Publication Activity Database

    Kozánek, Jan; Vlček, Václav; Zolotarev, Igor

    2014-01-01

    Roč. 3, č. 4 (2014), s. 317-323 ISSN 2164-6457 R&D Projects: GA ČR GA13-10527S Institutional support: RVO:61388998 Keywords : profile in airflow * Mach numbers * limits of the aeroelastic stability * spectral identification Subject RIV: BI - Acoustics

  8. Towards Selective Tidal-Stream Transport for Lagrangian profilers

    DEFF Research Database (Denmark)

    Jouffroy, Jerome; Zhou, Qiuyang; Zielinski, Oliver

    2011-01-01

    Autonomous Lagrangian profilers are widely used as measurement and monitoring platforms. In their current mode of operation, the profilers usually drift passively at their parking depth before making a vertical profile to go back to the surface. This paper presents a control strategy to actively...

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

    Science.gov (United States)

    Murugaiyan, Jayaseelan; Roesler, Uwe

    2017-01-01

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

  11. Occupational Heat Stress Profiles in Selected Workplaces in India.

    Science.gov (United States)

    Venugopal, Vidhya; Chinnadurai, Jeremiah S; Lucas, Rebekah A I; Kjellstrom, Tord

    2015-12-29

    Health and productivity impacts from occupational heat stress have significant ramifications for the large workforce of India. This study profiled occupational heat stress impacts on the health and productivity of workers in select organized and unorganized Indian work sectors. During hotter and cooler seasons, Wet Bulb Globe Temperatures (WBGT) were used to quantify the risk of heat stress, according to International workplace guidelines. Questionnaires assessed workers' perceived health and productivity impacts from heat stress. A total of 442 workers from 18 Indian workplaces participated (22% and 78% from the organized and unorganized sector, respectively). Overall 82% and 42% of workers were exposed to higher than recommended WBGT during hotter and cooler periods, respectively. Workers with heavy workloads reported more heat-related health issues (chi square = 23.67, p ≤ 0.001) and reduced productivity (chi square = 15.82, p ≤ 0.001), especially the outdoor workers. Heat-rashes, dehydration, heat-syncope and urinogenital symptoms were self-reported health issues. Cited reasons for productivity losses were: extended-work hours due to fatigue/exhaustion, sickness/hospitalization and wages lost. Reducing workplace heat stress will benefit industries and workers via improving worker health and productivity. Adaptation and mitigation measures to tackle heat stress are imperative to protect the present and future workforce as climate change progresses.

  12. Occupational Heat Stress Profiles in Selected Workplaces in India

    Science.gov (United States)

    Venugopal, Vidhya; Chinnadurai, Jeremiah S.; Lucas, Rebekah A. I.; Kjellstrom, Tord

    2015-01-01

    Health and productivity impacts from occupational heat stress have significant ramifications for the large workforce of India. This study profiled occupational heat stress impacts on the health and productivity of workers in select organized and unorganized Indian work sectors. During hotter and cooler seasons, Wet Bulb Globe Temperatures (WBGT) were used to quantify the risk of heat stress, according to International workplace guidelines. Questionnaires assessed workers’ perceived health and productivity impacts from heat stress. A total of 442 workers from 18 Indian workplaces participated (22% and 78% from the organized and unorganized sector, respectively). Overall 82% and 42% of workers were exposed to higher than recommended WBGT during hotter and cooler periods, respectively. Workers with heavy workloads reported more heat-related health issues (chi square = 23.67, p ≤ 0.001) and reduced productivity (chi square = 15.82, p ≤ 0.001), especially the outdoor workers. Heat-rashes, dehydration, heat-syncope and urinogenital symptoms were self-reported health issues. Cited reasons for productivity losses were: extended-work hours due to fatigue/exhaustion, sickness/hospitalization and wages lost. Reducing workplace heat stress will benefit industries and workers via improving worker health and productivity. Adaptation and mitigation measures to tackle heat stress are imperative to protect the present and future workforce as climate change progresses. PMID:26729144

  13. Identification of a myometrial molecular profile for dystocic labor

    Science.gov (United States)

    2011-01-01

    Background The most common indication for cesarean section (CS) in nulliparous women is dystocia secondary to ineffective myometrial contractility. The aim of this study was to identify a molecular profile in myometrium associated with dystocic labor. Methods Myometrial biopsies were obtained from the upper incisional margins of nulliparous women undergoing lower segment CS for dystocia (n = 4) and control women undergoing CS in the second stage who had demonstrated efficient uterine action during the first stage of labor (n = 4). All patients were in spontaneous (non-induced) labor and had received intrapartum oxytocin to accelerate labor. RNA was extracted from biopsies and hybridized to Affymetrix HuGene U133A Plus 2 microarrays. Internal validation was performed using quantitative SYBR Green Real-Time PCR. Results Seventy genes were differentially expressed between the two groups. 58 genes were down-regulated in the dystocia group. Gene ontology analysis revealed 12 of the 58 down-regulated genes were involved in the immune response. These included (ERAP2, (8.67 fold change (FC)) HLA-DQB1 (7.88 FC) CD28 (2.60 FC), LILRA3 (2.87 FC) and TGFBR3 (2.1 FC)) Hierarchical clustering demonstrated a difference in global gene expression patterns between the samples from dystocic and non-dystocic labours. RT-PCR validation was performed on 4 genes ERAP2, CD28, LILRA3 and TGFBR3 Conclusion These findings suggest an underlying molecular basis for dystocia in nulliparous women in spontaneous labor. Differentially expressed genes suggest an important role for the immune response in dystocic labor and may provide important indicators for new diagnostic assays and potential intrapartum therapeutic targets. PMID:21999197

  14. Identification of a Myometrial Molecular Profile for Dystocic Labor

    LENUS (Irish Health Repository)

    Brennan, Donal J

    2011-10-16

    Abstract Background The most common indication for cesarean section (CS) in nulliparous women is dystocia secondary to ineffective myometrial contractility. The aim of this study was to identify a molecular profile in myometrium associated with dystocic labor. Methods Myometrial biopsies were obtained from the upper incisional margins of nulliparous women undergoing lower segment CS for dystocia (n = 4) and control women undergoing CS in the second stage who had demonstrated efficient uterine action during the first stage of labor (n = 4). All patients were in spontaneous (non-induced) labor and had received intrapartum oxytocin to accelerate labor. RNA was extracted from biopsies and hybridized to Affymetrix HuGene U133A Plus 2 microarrays. Internal validation was performed using quantitative SYBR Green Real-Time PCR. Results Seventy genes were differentially expressed between the two groups. 58 genes were down-regulated in the dystocia group. Gene ontology analysis revealed 12 of the 58 down-regulated genes were involved in the immune response. These included (ERAP2, (8.67 fold change (FC)) HLA-DQB1 (7.88 FC) CD28 (2.60 FC), LILRA3 (2.87 FC) and TGFBR3 (2.1 FC)) Hierarchical clustering demonstrated a difference in global gene expression patterns between the samples from dystocic and non-dystocic labours. RT-PCR validation was performed on 4 genes ERAP2, CD28, LILRA3 and TGFBR3 Conclusion These findings suggest an underlying molecular basis for dystocia in nulliparous women in spontaneous labor. Differentially expressed genes suggest an important role for the immune response in dystocic labor and may provide important indicators for new diagnostic assays and potential intrapartum therapeutic targets.

  15. [Identification of candidate genes and expression profiles, as doping biomarkers].

    Science.gov (United States)

    Paparini, A; Impagnatiello, F; Pistilli, A; Rinaldi, M; Gianfranceschi, G; Signori, E; Stabile, A M; Fazio, V; Rende, M; Romano Spica, V

    2007-01-01

    Administration of prohibited substances to enhance athletic performance represents an emerging medical, social, ethical and legal issue. Traditional controls are based on direct detection of substances or their catabolites. However out-of-competition doping may not be easily revealed by standard analytical methods. Alternative indirect control strategies are based on the evaluation of mid- and long-term effects of doping in tissues. Drug-induced long-lasting changes of gene expression may be taken as effective indicators of doping exposure. To validate this approach, we used real-time PCR to monitor the expression pattern of selected genes in human haematopoietic cells exposed to nandrolone, insulin-like growth factor I (IGF-I) or growth hormone (GH). Some candidate genes were found significantly and consistently modulated by treatments. Nandrolone up-regulated AR, ESR2 and PGR in K562 cells, and SRD5A1, PPARA and JAK2 in Jurkat cells; IGF-I up-regulated EPOR and PGR in HL60 cells, and SRD5A1 in Jurkat; GH up-regulated SRD5A1 and GHR in K562. GATA1 expression was down-regulated in IGF-1-treated HL60, ESR2 was down-regulated in nandrolone-treated Jurkat, and AR and PGR were down-regulated in GH-treated Jurkat. This pilot study shows the potential of molecular biology-based strategies in anti-doping controls.

  16. Panning for SNuRMs: using cofactor profiling for the rational discovery of selective nuclear receptor modulators.

    Science.gov (United States)

    Kremoser, Claus; Albers, Michael; Burris, Thomas P; Deuschle, Ulrich; Koegl, Manfred

    2007-10-01

    Drugs that target nuclear receptors are clinically, as well as commercially, successful. Their widespread use, however, is limited by an inherent propensity of nuclear receptors to trigger beneficial, as well as adverse, pharmacological effects upon drug activation. Hence, selective drugs that display reduced adverse effects, such as the selective estrogen receptor modulator (SERM) Raloxifene, have been developed by guidance through classical cell culture assays and animal trials. Full agonist and selective modulator nuclear receptor drugs, in general, differ by their ability to recruit certain cofactors to the receptor protein. Hence, systematic cofactor profiling is advancing into an approach for the rationally guided identification of selective NR modulators (SNuRMs) with improved therapeutic ratio.

  17. Stratigraphic Profiles for Selected Hanford Site Seismometer Stations and Other Locations

    Energy Technology Data Exchange (ETDEWEB)

    Last, George V. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2014-02-01

    Stratigraphic profiles were constructed for eight selected Hanford Site seismometer stations, five Hanford Site facility reference locations, and seven regional three-component broadband seismometer stations. These profiles provide interpretations of the subsurface layers to support estimation of ground motions from past earthquakes, and the prediction of ground motions from future earthquakes. In most cases these profiles terminated at the top of the Wanapum Basalt, but at selected sites profiles were extended down to the top of the crystalline basement. The composite one-dimensional stratigraphic profiles were based primarily on previous interpretations from nearby boreholes, and in many cases the nearest deep borehole is located kilometers away.

  18. A feature selection approach for identification of signature genes from SAGE data

    Directory of Open Access Journals (Sweden)

    Silva Paulo JS

    2007-05-01

    Full Text Available Abstract Background One goal of gene expression profiling is to identify signature genes that robustly distinguish different types or grades of tumors. Several tumor classifiers based on expression profiling have been proposed using microarray technique. Due to important differences in the probabilistic models of microarray and SAGE technologies, it is important to develop suitable techniques to select specific genes from SAGE measurements. Results A new framework to select specific genes that distinguish different biological states based on the analysis of SAGE data is proposed. The new framework applies the bolstered error for the identification of strong genes that separate the biological states in a feature space defined by the gene expression of a training set. Credibility intervals defined from a probabilistic model of SAGE measurements are used to identify the genes that distinguish the different states with more reliability among all gene groups selected by the strong genes method. A score taking into account the credibility and the bolstered error values in order to rank the groups of considered genes is proposed. Results obtained using SAGE data from gliomas are presented, thus corroborating the introduced methodology. Conclusion The model representing counting data, such as SAGE, provides additional statistical information that allows a more robust analysis. The additional statistical information provided by the probabilistic model is incorporated in the methodology described in the paper. The introduced method is suitable to identify signature genes that lead to a good separation of the biological states using SAGE and may be adapted for other counting methods such as Massive Parallel Signature Sequencing (MPSS or the recent Sequencing-By-Synthesis (SBS technique. Some of such genes identified by the proposed method may be useful to generate classifiers.

  19. The psychological selection profile for civil-military coordination ...

    African Journals Online (AJOL)

    from job incumbents to assess the relationship between performance and profile ... TO ASSESS APPLICANTS' ..... Knuth (1999) and Natsios (1995) characterised complex emergencies as a ..... Journal of Personality Assessment, 72 (3), pp.

  20. Comparison of Selective Attention and Intelligence Profile in Bilingual and Monolingual Adolescents

    Directory of Open Access Journals (Sweden)

    Rahim Yousefi

    2018-01-01

    Conclusion Learning a foreign language (e.g. English may be an effective factor in selective attention and intelligence profile of adolescents. Therefore, the role of learning a foreign language should be considered in selective attention and intelligence profile of adolescents.

  1. Novel identification strategy for ground coffee adulteration based on UPLC-HRMS oligosaccharide profiling.

    Science.gov (United States)

    Cai, Tie; Ting, Hu; Jin-Lan, Zhang

    2016-01-01

    Coffee is one of the most common and most valuable beverages. According to International Coffee Organization (ICO) reports, the adulteration of coffee for financial reasons is regarded as the most serious threat to the sustainable development of the coffee market. In this work, a novel strategy for adulteration identification in ground coffee was developed based on UPLC-HRMS oligosaccharide profiling. Along with integrated statistical analysis, 17 oligosaccharide composition were identified as markers for the identification of soybeans and rice in ground coffee. This strategy, validated by manual mixtures, optimized both the reliability and authority of adulteration identification. Rice and soybean adulterants present in ground coffee in amounts as low as 5% were identified and evaluated. Some commercial ground coffees were also successfully tested using this strategy. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Character Selection During Interactive Taxonomic Identification: “Best Characters”

    Directory of Open Access Journals (Sweden)

    Nadia Talent

    2014-03-01

    Full Text Available Software interfaces for interactive multiple-entry taxonomic identification (polyclaves sometimes provide a “best character” or “separation” coefficient, to guide the user to choose a character that could most effectively reduce the number of identification steps required. The coefficient could be particularly helpful when difficult or expensive tasks are needed for forensic identification, and in very large databases, uses that appear likely to increase in importance. Several current systems also provide tools to develop taxonomies or single-entry identification keys, with a variety of coefficients that are appropriate to that purpose. For the identification task, however, information theory neatly applies, and provides the most appropriate coefficient. To our knowledge, Delta-Intkey is the only currently available system that uses a coefficient related to information theory, and it is currently being reimplemented, which may allow for improvement. We describe two improvements to the algorithm used by Delta-Intkey. The first improves transparency as the number of remaining taxa decreases, by normalizing the range of the coefficient to [0,1]. The second concerns numeric ranges, which require consistent treatment of sub-intervals and their end-points. A stand-alone Bestchar program for categorical data is provided, in the Python and R languages. The source code is freely available and dedicated to the Public Domain.

  3. Oral tongue cancer gene expression profiling: Identification of novel potential prognosticators by oligonucleotide microarray analysis

    International Nuclear Information System (INIS)

    Estilo, Cherry L; Boyle, Jay O; Kraus, Dennis H; Patel, Snehal; Shaha, Ashok R; Wong, Richard J; Huryn, Joseph M; Shah, Jatin P; Singh, Bhuvanesh; O-charoenrat, Pornchai; Talbot, Simon; Socci, Nicholas D; Carlson, Diane L; Ghossein, Ronald; Williams, Tijaana; Yonekawa, Yoshihiro; Ramanathan, Yegnanarayana

    2009-01-01

    The present study is aimed at identifying potential candidate genes as prognostic markers in human oral tongue squamous cell carcinoma (SCC) by large scale gene expression profiling. The gene expression profile of patients (n=37) with oral tongue SCC were analyzed using Affymetrix HG-U95Av2 high-density oligonucleotide arrays. Patients (n=20) from which there were available tumor and matched normal mucosa were grouped into stage (early vs. late) and nodal disease (node positive vs. node negative) subgroups and genes differentially expressed in tumor vs. normal and between the subgroups were identified. Three genes, GLUT3, HSAL2, and PACE4, were selected for their potential biological significance in a larger cohort of 49 patients via quantitative real-time RT-PCR. Hierarchical clustering analyses failed to show significant segregation of patients. In patients (n=20) with available tumor and matched normal mucosa, 77 genes were found to be differentially expressed (P< 0.05) in the tongue tumor samples compared to their matched normal controls. Among the 45 over-expressed genes, MMP-1 encoding interstitial collagenase showed the highest level of increase (average: 34.18 folds). Using the criterion of two-fold or greater as overexpression, 30.6%, 24.5% and 26.5% of patients showed high levels of GLUT3, HSAL2 and PACE4, respectively. Univariate analyses demonstrated that GLUT3 over-expression correlated with depth of invasion (P<0.0001), tumor size (P=0.024), pathological stage (P=0.009) and recurrence (P=0.038). HSAL2 was positively associated with depth of invasion (P=0.015) and advanced T stage (P=0.047). In survival studies, only GLUT3 showed a prognostic value with disease-free (P=0.049), relapse-free (P=0.002) and overall survival (P=0.003). PACE4 mRNA expression failed to show correlation with any of the relevant parameters. The characterization of genes identified to be significant predictors of prognosis by oligonucleotide microarray and further validation by

  4. Molecular identification and genotyping of Microsporidia in selected hosts

    Czech Academy of Sciences Publication Activity Database

    Valenčáková, A.; Balent, P.; Ravaszová, P.; Horák, Aleš; Oborník, Miroslav; Halanová, M.; Malčeková, B.; Novotný, F.; Goldová, M.

    2012-01-01

    Roč. 110, č. 2 (2012), s. 689-693 ISSN 0932-0113 Institutional research plan: CEZ:AV0Z60220518 Keywords : ENCEPHALITOZOON-CUNICULI * RIBOSOMAL-RNA * SPECIES IDENTIFICATION * AIDS PATIENTS * PET RABBITS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.852, year: 2012

  5. Identification of Atuveciclib (BAY 1143572), the First Highly Selective, Clinical PTEFb/CDK9 Inhibitor for the Treatment of Cancer.

    Science.gov (United States)

    Lücking, Ulrich; Scholz, Arne; Lienau, Philip; Siemeister, Gerhard; Kosemund, Dirk; Bohlmann, Rolf; Briem, Hans; Terebesi, Ildiko; Meyer, Kirstin; Prelle, Katja; Denner, Karsten; Bömer, Ulf; Schäfer, Martina; Eis, Knut; Valencia, Ray; Ince, Stuart; von Nussbaum, Franz; Mumberg, Dominik; Ziegelbauer, Karl; Klebl, Bert; Choidas, Axel; Nussbaumer, Peter; Baumann, Matthias; Schultz-Fademrecht, Carsten; Rühter, Gerd; Eickhoff, Jan; Brands, Michael

    2017-11-08

    Selective inhibition of exclusively transcription-regulating PTEFb/CDK9 is a promising new approach in cancer therapy. Starting from lead compound BAY-958, lead optimization efforts strictly focusing on kinase selectivity, physicochemical and DMPK properties finally led to the identification of the orally available clinical candidate atuveciclib (BAY 1143572). Structurally characterized by an unusual benzyl sulfoximine group, BAY 1143572 exhibited the best overall profile in vitro and in vivo, including high efficacy and good tolerability in xenograft models in mice and rats. BAY 1143572 is the first potent and highly selective PTEFb/CDK9 inhibitor to enter clinical trials for the treatment of cancer. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  6. Identification of selection footprints on the X chromosome in pig.

    Directory of Open Access Journals (Sweden)

    Yunlong Ma

    Full Text Available Identifying footprints of selection can provide a straightforward insight into the mechanism of artificial selection and further dig out the causal genes related to important traits. In this study, three between-population and two within-population approaches, the Cross Population Extend Haplotype Homozygosity Test (XPEHH, the Cross Population Composite Likelihood Ratio (XPCLR, the F-statistics (Fst, the Integrated Haplotype Score (iHS and the Tajima's D, were implemented to detect the selection footprints on the X chromosome in three pig breeds using Illumina Porcine60K SNP chip. In the detection of selection footprints using between-population methods, 11, 11 and 7 potential selection regions with length of 15.62 Mb, 12.32 Mb and 9.38 Mb were identified in Landrace, Chinese Songliao and Yorkshire by XPEHH, respectively, and 16, 13 and 17 potential selection regions with length of 15.20 Mb, 13.00 Mb and 19.21 Mb by XPCLR, 4, 2 and 4 potential selection regions with length of 3.20 Mb, 1.60 Mb and 3.20 Mb by Fst. For within-population methods, 7, 10 and 9 potential selection regions with length of 8.12 Mb, 8.40 Mb and 9.99 Mb were identified in Landrace, Chinese Songliao and Yorkshire by iHS, and 4, 3 and 2 potential selection regions with length of 3.20 Mb, 2.40 Mb and 1.60 Mb by Tajima's D. Moreover, the selection regions from different methods were partly overlapped, especially the regions around 22∼25 Mb were detected under selection in Landrace and Yorkshire while no selection in Chinese Songliao by all three between-population methods. Only quite few overlap of selection regions identified by between-population and within-population methods were found. Bioinformatics analysis showed that the genes relevant with meat quality, reproduction and immune were found in potential selection regions. In addition, three out of five significant SNPs associated with hematological traits reported in our genome-wide association study were harbored in

  7. Identification of (R)-selective ω-aminotransferases by exploring evolutionary sequence space.

    Science.gov (United States)

    Kim, Eun-Mi; Park, Joon Ho; Kim, Byung-Gee; Seo, Joo-Hyun

    2018-03-01

    Several (R)-selective ω-aminotransferases (R-ωATs) have been reported. The existence of additional R-ωATs having different sequence characteristics from previous ones is highly expected. In addition, it is generally accepted that R-ωATs are variants of aminotransferase group III. Based on these backgrounds, sequences in RefSeq database were scored using family profiles of branched-chain amino acid aminotransferase (BCAT) and d-alanine aminotransferase (DAT) to predict and identify putative R-ωATs. Sequences with two profile analysis scores were plotted on two-dimensional score space. Candidates with relatively similar scores in both BCAT and DAT profiles (i.e., profile analysis score using BCAT profile was similar to profile analysis score using DAT profile) were selected. Experimental results for selected candidates showed that putative R-ωATs from Saccharopolyspora erythraea (R-ωAT_Sery), Bacillus cellulosilyticus (R-ωAT_Bcel), and Bacillus thuringiensis (R-ωAT_Bthu) had R-ωAT activity. Additional experiments revealed that R-ωAT_Sery also possessed DAT activity while R-ωAT_Bcel and R-ωAT_Bthu had BCAT activity. Selecting putative R-ωATs from regions with similar profile analysis scores identified potential R-ωATs. Therefore, R-ωATs could be efficiently identified by using simple family profile analysis and exploring evolutionary sequence space. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Assessment of microbial profile of selected proprietary broiler ...

    African Journals Online (AJOL)

    Bacterial and fungal isolates recovered include Escherichia coli, Staphylococcus albus, Bacillus subtilis, Micrococcus spp, Pseudomonas spp, Aspergillus fumigatus, A. flavus, A. niger, Fusarium spp, Mucor spp, and Penicillium notatum. Total microbial counts were significantly different (P<0.05) among the selected feed ...

  9. Metabolomic Profiling for Identification of Novel Potential Biomarkers in Cardiovascular Diseases

    Directory of Open Access Journals (Sweden)

    Maria G. Barderas

    2011-01-01

    Full Text Available Metabolomics involves the identification and quantification of metabolites present in a biological system. Three different approaches can be used: metabolomic fingerprinting, metabolic profiling, and metabolic footprinting, in order to evaluate the clinical course of a disease, patient recovery, changes in response to surgical intervention or pharmacological treatment, as well as other associated features. Characteristic patterns of metabolites can be revealed that broaden our understanding of a particular disorder. In the present paper, common strategies and analytical techniques used in metabolomic studies are reviewed, particularly with reference to the cardiovascular field.

  10. A Profile of Current Employee Training Practices in Selected Businesses and Industries in Southwest Virginia

    OpenAIRE

    Hundley, Katrina M.

    2003-01-01

    The purposes of this study were to (a) establish a profile of the current training practices of selected businesses and industries in Southwest Virginia; (b) identify the type of training methods these companies are choosing -- such as traditional classroom training or web-based training programs, and (c) identify how the training methods are selected. This profile established baseline data for current business and industry employee training programs. The population of this study include...

  11. Identification of Chinese medicinal fungus Cordyceps sinensis by depth-profiling mid-infrared photoacoustic spectroscopy

    Science.gov (United States)

    Du, Changwen; Zhou, Jianmin; Liu, Jianfeng

    2017-02-01

    With increased demand for Cordyceps sinensis it needs rapid methods to meet the challenge of identification raised in quality control. In this study Cordyceps sinensis from four typical natural habitats in China was characterized by depth-profiling Fourier transform infrared photoacoustic spectroscopy. Results demonstrated that Cordyceps sinensis samples resulted in typical photoacoustic spectral appearance, but heterogeneity was sensed in the whole sample; due to the heterogeneity Cordyceps sinensis was represented by spectra of four groups including head, body, tail and leaf under a moving mirror velocity of 0.30 cm s- 1. The spectra of the four groups were used as input of a probabilistic neural network (PNN) to identify the source of Cordyceps sinensis, and all the samples were correctly identified by the PNN model. Therefore, depth-profiling Fourier transform infrared photoacoustic spectroscopy provides novel and unique technique to identify Cordyceps sinensis, which shows great potential in quality control of Cordyceps sinensis.

  12. Selecting fillers on emotional appearance improves lineup identification accuracy.

    Science.gov (United States)

    Flowe, Heather D; Klatt, Thimna; Colloff, Melissa F

    2014-12-01

    Mock witnesses sometimes report using criminal stereotypes to identify a face from a lineup, a tendency known as criminal face bias. Faces are perceived as criminal-looking if they appear angry. We tested whether matching the emotional appearance of the fillers to an angry suspect can reduce criminal face bias. In Study 1, mock witnesses (n = 226) viewed lineups in which the suspect had an angry, happy, or neutral expression, and we varied whether the fillers matched the expression. An additional group of participants (n = 59) rated the faces on criminal and emotional appearance. As predicted, mock witnesses tended to identify suspects who appeared angrier and more criminal-looking than the fillers. This tendency was reduced when the lineup fillers matched the emotional appearance of the suspect. Study 2 extended the results, testing whether the emotional appearance of the suspect and fillers affects recognition memory. Participants (n = 1,983) studied faces and took a lineup test in which the emotional appearance of the target and fillers was varied between subjects. Discrimination accuracy was enhanced when the fillers matched an angry target's emotional appearance. We conclude that lineup member emotional appearance plays a critical role in the psychology of lineup identification. The fillers should match an angry suspect's emotional appearance to improve lineup identification accuracy. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  13. Identification of Biomarkers for Esophageal Squamous Cell Carcinoma Using Feature Selection and Decision Tree Methods

    Directory of Open Access Journals (Sweden)

    Chun-Wei Tung

    2013-01-01

    Full Text Available Esophageal squamous cell cancer (ESCC is one of the most common fatal human cancers. The identification of biomarkers for early detection could be a promising strategy to decrease mortality. Previous studies utilized microarray techniques to identify more than one hundred genes; however, it is desirable to identify a small set of biomarkers for clinical use. This study proposes a sequential forward feature selection algorithm to design decision tree models for discriminating ESCC from normal tissues. Two potential biomarkers of RUVBL1 and CNIH were identified and validated based on two public available microarray datasets. To test the discrimination ability of the two biomarkers, 17 pairs of expression profiles of ESCC and normal tissues from Taiwanese male patients were measured by using microarray techniques. The classification accuracies of the two biomarkers in all three datasets were higher than 90%. Interpretable decision tree models were constructed to analyze expression patterns of the two biomarkers. RUVBL1 was consistently overexpressed in all three datasets, although we found inconsistent CNIH expression possibly affected by the diverse major risk factors for ESCC across different areas.

  14. DYNAMIC FEATURE SELECTION FOR WEB USER IDENTIFICATION ON LINGUISTIC AND STYLISTIC FEATURES OF ONLINE TEXTS

    Directory of Open Access Journals (Sweden)

    A. A. Vorobeva

    2017-01-01

    Full Text Available The paper deals with identification and authentication of web users participating in the Internet information processes (based on features of online texts.In digital forensics web user identification based on various linguistic features can be used to discover identity of individuals, criminals or terrorists using the Internet to commit cybercrimes. Internet could be used as a tool in different types of cybercrimes (fraud and identity theft, harassment and anonymous threats, terrorist or extremist statements, distribution of illegal content and information warfare. Linguistic identification of web users is a kind of biometric identification, it can be used to narrow down the suspects, identify a criminal and prosecute him. Feature set includes various linguistic and stylistic features extracted from online texts. We propose dynamic feature selection for each web user identification task. Selection is based on calculating Manhattan distance to k-nearest neighbors (Relief-f algorithm. This approach improves the identification accuracy and minimizes the number of features. Experiments were carried out on several datasets with different level of class imbalance. Experiment results showed that features relevance varies in different set of web users (probable authors of some text; features selection for each set of web users improves identification accuracy by 4% at the average that is approximately 1% higher than with the use of static set of features. The proposed approach is most effective for a small number of training samples (messages per user.

  15. Identification of selective inhibitors of RET and comparison with current clinical candidates through development and validation of a robust screening cascade [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Amanda J. Watson

    2016-05-01

    Full Text Available RET (REarranged during Transfection is a receptor tyrosine kinase, which plays pivotal roles in regulating cell survival, differentiation, proliferation, migration and chemotaxis. Activation of RET is a mechanism of oncogenesis in medullary thyroid carcinomas where both germline and sporadic activating somatic mutations are prevalent.   At present, there are no known specific RET inhibitors in clinical development, although many potent inhibitors of RET have been opportunistically identified through selectivity profiling of compounds initially designed to target other tyrosine kinases. Vandetanib and cabozantinib, both multi-kinase inhibitors with RET activity, are approved for use in medullary thyroid carcinoma, but additional pharmacological activities, most notably inhibition of vascular endothelial growth factor - VEGFR2 (KDR, lead to dose-limiting toxicity. The recent identification of RET fusions present in ~1% of lung adenocarcinoma patients has renewed interest in the identification and development of more selective RET inhibitors lacking the toxicities associated with the current treatments.   In an earlier publication [Newton et al, 2016; 1] we reported the discovery of a series of 2-substituted phenol quinazolines as potent and selective RET kinase inhibitors. Here we describe the development of the robust screening cascade which allowed the identification and advancement of this chemical series.  Furthermore we have profiled a panel of RET-active clinical compounds both to validate the cascade and to confirm that none display a RET-selective target profile.

  16. Identification of physicochemical selective pressure on protein encoding nucleotide sequences

    Directory of Open Access Journals (Sweden)

    Sainudiin Raazesh

    2006-03-01

    Full Text Available Abstract Background Statistical methods for identifying positively selected sites in protein coding regions are one of the most commonly used tools in evolutionary bioinformatics. However, they have been limited by not taking the physiochemical properties of amino acids into account. Results We develop a new codon-based likelihood model for detecting site-specific selection pressures acting on specific physicochemical properties. Nonsynonymous substitutions are divided into substitutions that differ with respect to the physicochemical properties of interest, and those that do not. The substitution rates of these two types of changes, relative to the synonymous substitution rate, are then described by two parameters, γ and ω respectively. The new model allows us to perform likelihood ratio tests for positive selection acting on specific physicochemical properties of interest. The new method is first used to analyze simulated data and is shown to have good power and accuracy in detecting physicochemical selective pressure. We then re-analyze data from the class-I alleles of the human Major Histocompatibility Complex (MHC and from the abalone sperm lysine. Conclusion Our new method allows a more flexible framework to identify selection pressure on particular physicochemical properties.

  17. Iterative Selection of Unknown Weights in Direct Weight Optimization Identification

    Directory of Open Access Journals (Sweden)

    Xiao Xuan

    2014-01-01

    Full Text Available To the direct weight optimization identification of the nonlinear system, we add some linear terms about input sequences in the former linear affine function so as to approximate the nonlinear property. To choose the two classes of unknown weights in the more linear terms, this paper derives the detailed process on how to choose these unknown weights from theoretical analysis and engineering practice, respectively, and makes sure of their key roles between the unknown weights. From the theoretical analysis, the added unknown weights’ auxiliary role can be known in the whole process of approximating the nonlinear system. From the practical analysis, we learn how to transform one complex optimization problem to its corresponding common quadratic program problem. Then, the common quadratic program problem can be solved by the basic interior point method. Finally, the efficiency and possibility of the proposed strategies can be confirmed by the simulation results.

  18. Criteria of reaction identification and selection of badly measured events

    International Nuclear Information System (INIS)

    Linetskij, A.R.; Lyubarskij, G.Ya.; Sagalovich, N.E.

    1979-01-01

    Basing on photoemulsion methods of studying channels of multiparticle nuclear reactions the metrological characteristics of a physical technique are described in the process of its development. To increase the accuracy of reaction identification the technique for picture measuring has been complicated by introducing calibration measurements of tracks of stopped in the emulsion primary α-particles. Callibration measurements have support assumptions on energy oscillations of the primary beam and made possible the employment of actual values of this energy instead of rated one during mathematical processing. By using simulation reactions the effect of errors in determining the contraction ratio has been estimated. It has been found that rather a small error in determining the contraction (+-20%) results in additional casting-out 8-15% of measured events

  19. Gingival profiles in a select Asian cohort: A pilot study.

    Science.gov (United States)

    Lee, Wan Zhen; Ong, Marianne M A; Yeo, Alvin B-K

    2018-02-01

    The aim of the present study was to determine the facial gingival profiles of teeth with a healthy periodontium in an Asian population. A total of 51 patients with a healthy periodontium were examined. Gingival thickness (GT) and gingival width (GW) were assessed at the maxillary and mandibular incisors to the first molars. GT was measured by transgingival probing (GT-TGP), and probe visibility through the marginal gingiva (GT-TRAN) was assessed. Results between groups (anterior and posterior, tooth types) were analyzed using one-way analysis of variance and t-test. The mean age was 30.3±11.4 years, with 27 females and 24 males. The mean GT-TGP was 1.39±52 mm, while the mean GW was 4.59±1.34 mm. Considerable intra-individual and interindividual variation in GT (TGP and TRAN) was noted. GT increased from the anterior to posterior, and was thinnest at the mandibular centrals to the first premolars and maxillary canines. GT-TGP and GW were influenced by tooth type, plaque, recession, and TRAN, but not age, sex, or ethnicity. GW were recorded lowest at the mandibular canines and all premolars. Thin gingiva was recorded at 63.8%-92% (GT-TGPTGP and GT-TRAN. © 2017 John Wiley & Sons Australia, Ltd.

  20. Transcriptome profiling in imipenem-selected Acinetobacter baumannii.

    Science.gov (United States)

    Chang, Kai-Chih; Kuo, Han-Yueh; Tang, Chuan Yi; Chang, Cheng-Wei; Lu, Chia-Wei; Liu, Chih-Chin; Lin, Huei-Ru; Chen, Kuan-Hsueh; Liou, Ming-Li

    2014-09-26

    Carbapenem-resistance in Acinetobacter baumannii has gradually become a global challenge. To identify the genes involved in carbapenem resistance in A. baumannii, the transcriptomic responses of the completely sequenced strain ATCC 17978 selected with 0.5 mg/L (IPM-2 m) and 2 mg/L (IPM-8 m) imipenem were investigated using RNA-sequencing to identify differences in the gene expression patterns. A total of 88 and 68 genes were differentially expressed in response to IPM-2 m and IPM-8 m selection, respectively. Among the expressed genes, 50 genes were highly expressed in IPM-2 m, 30 genes were highly expressed in IPM-8 m, and 38 genes were expressed common in both strains. Six groups of genes were simultaneously expressed in IPM-2 m and IPM-8 m mutants. The three gene groups involved in DNA recombination were up-regulated, including recombinase, transposase and DNA repair, and beta-lactamase OXA-95 and homologous recombination. The remaining gene groups involved in biofilm formation were down-regulated, including quorum sensing, secretion systems, and the csu operon. The antibiotic resistance determinants, including RND efflux transporters and multidrug resistance pumps, were over-expressed in response to IPM-2 m selection, followed by a decrease in response to IPM-8 m selection. Among the genes over-expressed in both strains, blaOXA-95, previously clustered with the blaOXA-51-like family, showed 14-fold (IPM-2 m) to 330-fold (IPM-8 m) over-expression. The expression of blaOXA-95 in IPM-2 m and IPM-8 m cells was positively correlated with the rate of imipenem hydrolysis, as demonstrated through Liquid Chromatography-Mass Spectrometry/Mass Spectrometry, suggesting that blaOXA-95 plays a critical role in conferring carbapenem resistance. In addition, A. baumannii shows an inverse relationship between carbapenem resistance and biofilm production. Gene recombination and blaOXA-95 play critical roles in carbapenem resistance in A. baumannii. Taken together, the results of

  1. Identification of contributing factors to pedestrian overpass selection

    Directory of Open Access Journals (Sweden)

    Yao Wu

    2014-12-01

    Full Text Available In order to improve the efficiency of overpass and the safety level of pedestrian, this paper aims to investigate the contributing factors for selective preference of overpass. Eight overpasses were investigated in Xi’an, and a questionnaire was conducted by the pedestrians near the overpass. Totally, 1131 valid samples (873 used of overpasses and 258 non-used of overpasses were collected. Based on the data, a binary logit (BL model was developed to identify what and how the factors affect the selective preference of overpass. The BL model was calibrated by the maximum likelihood method. Likelihood ratio test and McFadden-R2 were used to analyze the goodness-of-fit of the model. The results show that the BL model has a reasonable goodness-of-fit, and the prediction accuracy of the BL model can reach 81.9%. The BL model showed that the selective preference of overpass was significantly influenced by eight factors, including gender, age, career, education level, license, detour wishes, detour distance, and crossing time. Besides, the odds ratios of significant factors were also analyzed to explain the impacts of the factors on selective preference of overpass.

  2. Selection, isolation, and identification of fungi for bioherbicide production

    Directory of Open Access Journals (Sweden)

    Angélica Rossana Castro de Souza

    Full Text Available Abstract Production of a bioherbicide for biological control of weeds requires a series of steps, from selection of a suitable microbial strain to final formulation. Thus, this study aimed to select fungi for production of secondary metabolites with herbicidal activity using biological resources of the Brazilian Pampa biome. Phytopathogenic fungi were isolated from infected tissues of weeds in the Pampa biome. A liquid synthetic culture medium was used for production of metabolites. The phytotoxicity of fungal metabolites was assessed via biological tests using the plant Cucumis sativus L., and the most promising strain was identified by molecular analysis. Thirty-nine fungi were isolated, and 28 presented some phytotoxic symptoms against the target plant. Fungus VP51 belonging to the genus Diaporthe showed the most pronounced herbicidal activity. The Brazilian Pampa biome is a potential resource for the development of new and sustainable chemical compounds for modern agriculture.

  3. RNA-Seq for gene identification and transcript profiling of three Stevia rebaudiana genotypes.

    Science.gov (United States)

    Chen, Junwen; Hou, Kai; Qin, Peng; Liu, Hongchang; Yi, Bin; Yang, Wenting; Wu, Wei

    2014-07-07

    Stevia (Stevia rebaudiana) is an important medicinal plant that yields diterpenoid steviol glycosides (SGs). SGs are currently used in the preparation of medicines, food products and neutraceuticals because of its sweetening property (zero calories and about 300 times sweeter than sugar). Recently, some progress has been made in understanding the biosynthesis of SGs in Stevia, but little is known about the molecular mechanisms underlying this process. Additionally, the genomics of Stevia, a non-model species, remains uncharacterized. The recent advent of RNA-Seq, a next generation sequencing technology, provides an opportunity to expand the identification of Stevia genes through in-depth transcript profiling. We present a comprehensive landscape of the transcriptome profiles of three genotypes of Stevia with divergent SG compositions characterized using RNA-seq. 191,590,282 high-quality reads were generated and then assembled into 171,837 transcripts with an average sequence length of 969 base pairs. A total of 80,160 unigenes were annotated, and 14,211 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. Gene sequences of all enzymes known to be involved in SG synthesis were examined. A total of 143 UDP-glucosyltransferase (UGT) unigenes were identified, some of which might be involved in SG biosynthesis. The expression patterns of eight of these genes were further confirmed by RT-QPCR. RNA-seq analysis identified candidate genes encoding enzymes responsible for the biosynthesis of SGs in Stevia, a non-model plant without a reference genome. The transcriptome data from this study yielded new insights into the process of SG accumulation in Stevia. Our results demonstrate that RNA-Seq can be successfully used for gene identification and transcript profiling in a non-model species.

  4. Simultaneous genomic identification and profiling of a single cell using semiconductor-based next generation sequencing

    Directory of Open Access Journals (Sweden)

    Manabu Watanabe

    2014-09-01

    Full Text Available Combining single-cell methods and next-generation sequencing should provide a powerful means to understand single-cell biology and obviate the effects of sample heterogeneity. Here we report a single-cell identification method and seamless cancer gene profiling using semiconductor-based massively parallel sequencing. A549 cells (adenocarcinomic human alveolar basal epithelial cell line were used as a model. Single-cell capture was performed using laser capture microdissection (LCM with an Arcturus® XT system, and a captured single cell and a bulk population of A549 cells (≈106 cells were subjected to whole genome amplification (WGA. For cell identification, a multiplex PCR method (AmpliSeq™ SNP HID panel was used to enrich 136 highly discriminatory SNPs with a genotype concordance probability of 1031–35. For cancer gene profiling, we used mutation profiling that was performed in parallel using a hotspot panel for 50 cancer-related genes. Sequencing was performed using a semiconductor-based bench top sequencer. The distribution of sequence reads for both HID and Cancer panel amplicons was consistent across these samples. For the bulk population of cells, the percentages of sequence covered at coverage of more than 100× were 99.04% for the HID panel and 98.83% for the Cancer panel, while for the single cell percentages of sequence covered at coverage of more than 100× were 55.93% for the HID panel and 65.96% for the Cancer panel. Partial amplification failure or randomly distributed non-amplified regions across samples from single cells during the WGA procedures or random allele drop out probably caused these differences. However, comparative analyses showed that this method successfully discriminated a single A549 cancer cell from a bulk population of A549 cells. Thus, our approach provides a powerful means to overcome tumor sample heterogeneity when searching for somatic mutations.

  5. The Role of Lipsticks and Blush Sticks in Genetic Profiling for Human Identification

    OpenAIRE

    Nouman Rasool; Ahmad Farooq

    2016-01-01

    The core objectives of the current study are to generate human DNA profiles from used lipsticks and blush sticks of various brands available in Pakistan. A total of 12 international and local brands of lipsticks and blush sticks were selected. The lipsticks and blush sticks were applied by twenty different healthy female volunteers of 21-30 years of age. The heads of used lipsticks and blush sticks were swabbed with dry sterile cotton swabs. The qualitative and quantitative analysis was done ...

  6. Selection and Evaluation of Chemical Indicators for Waste Stream Identification

    Science.gov (United States)

    DeVita, W. M.; Hall, J.

    2015-12-01

    Human and animal wastes pose a threat to the quality of groundwater, surface water and drinking water. This is especially of concern for private and public water supplies in agricultural areas of Wisconsin where land spreading of livestock waste occurs on thin soils overlaying fractured bedrock. Current microbial source tracking (MST) methods for source identification requires the use of polymerase chain reaction (PCR) techniques. Due to cost, these tests are often not an option for homeowners, municipalities or state agencies with limited resources. The Water and Environmental Analysis Laboratory sought to develop chemical methods to provide lower cost processes to determine sources of fecal waste using fecal sterols, pharmaceuticals (human and veterinary) and human care/use products in ground and surface waters using solid phase extraction combined with triple quadrupole mass spectrometry. The two separate techniques allow for the detection of fecal sterol and other chemical markers in the sub part per billion-range. Fecal sterol ratios from published sources were used to evaluate drinking water samples and wastewater from onsite waste treatment systems and municipal wastewater treatment plants. Pharmaceuticals and personal care products indicative of human waste included: acetaminophen, caffeine, carbamazepine, cotinine, paraxanthine, sulfamethoxazole, and the artificial sweeteners; acesulfame, saccharin, and sucralose. The bovine antibiotic sulfamethazine was also targeted. Well water samples with suspected fecal contamination were analyzed for fecal sterols and PPCPs. Results were compared to traditional MST results from the Wisconsin State Laboratory of Hygiene. Chemical indicators were found in 6 of 11 drinking water samples, and 5 of 11 were in support of MST results. Lack of detection of chemical indicators in samples contaminated with fecal waste supports the need for confirmatory methods and advancement of chemical indicator detection technologies.

  7. Identification and Selection of Major Carbon Dioxide Stream Compositions

    Energy Technology Data Exchange (ETDEWEB)

    Last, George V.; Schmick, Mary T.

    2011-06-30

    A critical component in the assessment of long-term risk from geologic sequestration of CO2 is the ability to predict mineralogical and geochemical changes within storage reservoirs due to rock-brine-CO2 reactions. Impurities and/or other constituents selected for co-sequestration can affect both the chemical and physical (e.g. density, viscosity, interfacial tension) behavior of CO2 in the deep subsurface. These impurities and concentrations are a function of both the industrial source(s) of the CO2, as well as the carbon capture technology used to extract the CO2 and produce a concentrated stream for geologic sequestration. This report summarizes the relative concentrations of CO2 and other constituents in exhaust gases from major non-energy related industrial sources of CO2. Assuming that carbon-capture technology would remove most of the incondensable gases N2, O2, and Ar, leaving SO2 and NOx as the main impurities, we selected four test fluid compositions for use in geochemical experiments. These included: 1) a pure CO2 stream representative of food grade CO2 used in most enhanced oil recovery projects: 2) a test fluid composition containing low concentrations (0.5 mole %) SO2 and NOx (representative of that generated from cement production), 3) a test fluid composition with higher concentrations (2.5 mole %) of SO2, and 4) and test fluid composition containing 3 mole % H2S.

  8. SELECTING SAGITTARIUS: IDENTIFICATION AND CHEMICAL CHARACTERIZATION OF THE SAGITTARIUS STREAM

    Energy Technology Data Exchange (ETDEWEB)

    Hyde, E. A. [University of Western Sydney, Locked Bag 1797, Penrith South DC, NSW 1797 (Australia); Keller, S. [Research School of Astronomy and Astrophysics, Australian National University, Canberra, ACT 2601 (Australia); Zucker, D. B. [Macquarie University, Physics and Astronomy, NSW 2109 (Australia); Ibata, R.; Siebert, A. [Observatoire astronomique de Strasbourg, Université de Strasbourg, CNRS, UMR 7550, 11 rue de l’Université, F-67000 Strasbourg (France); Lewis, G. F.; Conn, A. R. [Sydney Institute for Astronomy, School of Physics, The University of Sydney, NSW 2006 (Australia); Penarrubia, J. [ROE, The University of Edinburgh, Institute for Astronomy, Edinburgh EH9 3HJ (United Kingdom); Irwin, M.; Gilmore, G. [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); Lane, R. R. [Departamento de Astronomía Universidad de Concepción, Casilla 160 C, Concepción (Chile); Koch, A. [Landessternwarte, Zentrum für Astronomie der Universität Heidelberg, Königstuhl 12, D-69117 Heidelberg (Germany); Diakogiannis, F. I. [International Center for Radio Astronomy Research, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 (Australia); Martell, S., E-mail: E.Hyde@uws.edu.au [Department of Astrophysics, School of Physics, University of New South Wales, Sydney, NSW 2052 (Australia)

    2015-06-01

    Wrapping around the Milky Way, the Sagittarius stream is the dominant substructure in the halo. Our statistical selection method has allowed us to identify 106 highly likely members of the Sagittarius stream. Spectroscopic analysis of metallicity and kinematics of all members provides us with a new mapping of the Sagittarius stream. We find correspondence between the velocity distribution of stream stars and those computed for a triaxial model of the Milky Way dark matter halo. The Sagittarius trailing arm exhibits a metallicity gradient, ranging from −0.59 to −0.97 dex over 142°. This is consistent with the scenario of tidal disruption from a progenitor dwarf galaxy that possessed an internal metallicity gradient. We note high metallicity dispersion in the leading arm, causing a lack of detectable gradient and possibly indicating orbital phase mixing. We additionally report on a potential detection of the Sextans dwarf spheroidal in our data.

  9. Differential identification of Candida species and other yeasts by analysis of [35S]methionine-labeled polypeptide profiles

    International Nuclear Information System (INIS)

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

    1988-01-01

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

  10. The Role of Lipsticks and Blush Sticks in Genetic Profiling for Human Identification

    Directory of Open Access Journals (Sweden)

    Nouman Rasool

    2016-06-01

    Full Text Available The core objectives of the current study are to generate human DNA profiles from used lipsticks and blush sticks of various brands available in Pakistan. A total of 12 international and local brands of lipsticks and blush sticks were selected. The lipsticks and blush sticks were applied by twenty different healthy female volunteers of 21-30 years of age. The heads of used lipsticks and blush sticks were swabbed with dry sterile cotton swabs. The qualitative and quantitative analysis was done by real time polymerase chain reaction (PCR, using a Quantifiler® Duo DNA Quantification Kit on Real Time PCR ABI™ 7500. Samples were amplified for 16 STR loci using an AmpFlSTR® Identifiler® PCR amplification kit on Thermocycler ABI 9700. The amplified product was run on Applied Biosystems 3130™ Genetic Analyzer. The genetic profiles were analyzed on GeneMapper® ID-X software version 1.0. The quantification results showed that the yield of DNA obtained from lipstick samples was greater than that of DNA obtained from blush stick samples. The real-time PCR results showed that only 16% of cosmetic samples had shown inhibition. The DNA profiles obtained from all blush stick samples were of good quality compared to those from lipstick samples. No profile was obtained from one blush stick sample (DNA 0.001 ng/μL and four lipstick samples (DNA 0.001-0.003 ng/μL because the amount of DNA in each of these samples was less than the amount required for successful amplification. DNA profiles were successfully generated from most of the samples of various available brands of lipsticks and blush sticks. This is the first study proving that DNA profiles can be generated from various lip and face cosmetics.

  11. Narcissism as a predictor of motivations behind Facebook profile picture selection.

    Science.gov (United States)

    Kapidzic, Sanja

    2013-01-01

    The rising popularity of social networking sites raises the question of whether and how personality differences are manifested on them. The present study explores this topic through an analysis of the relationship between narcissism and motivations behind Facebook profile picture selection. A survey that assesses motivations emphasizing physical attractiveness, personality, and social ties was conducted with 288 undergraduate students. The study found narcissism to be a significant predictor of the motivation for selecting profile pictures that emphasize attractiveness and personality for both men and women. The findings are discussed in terms of the dynamic self-regulatory processing model of narcissism.

  12. Automatic feed phase identification in multivariate bioprocess profiles by sequential binary classification.

    Science.gov (United States)

    Nikzad-Langerodi, Ramin; Lughofer, Edwin; Saminger-Platz, Susanne; Zahel, Thomas; Sagmeister, Patrick; Herwig, Christoph

    2017-08-22

    In this paper, we propose a new strategy for retrospective identification of feed phases from online sensor-data enriched feed profiles of an Escherichia Coli (E. coli) fed-batch fermentation process. In contrast to conventional (static), data-driven multi-class machine learning (ML), we exploit process knowledge in order to constrain our classification system yielding more parsimonious models compared to static ML approaches. In particular, we enforce unidirectionality on a set of binary, multivariate classifiers trained to discriminate between adjacent feed phases by linking the classifiers through a one-way switch. The switch is activated when the actual classifier output changes. As a consequence, the next binary classifier in the classifier chain is used for the discrimination between the next feed phase pair etc. We allow activation of the switch only after a predefined number of consecutive predictions of a transition event in order to prevent premature activation of the switch and undertake a sensitivity analysis regarding the optimal choice of the (time) lag parameter. From a complexity/parsimony perspective the benefit of our approach is three-fold: i) The multi-class learning task is broken down into binary subproblems which usually have simpler decision surfaces and tend to be less susceptible to the class-imbalance problem. ii) We exploit the fact that the process follows a rigid feed cycle structure (i.e. batch-feed-batch-feed) which allows us to focus on the subproblems involving phase transitions as they occur during the process while discarding off-transition classifiers and iii) only one binary classifier is active at the time which keeps effective model complexity low. We further use a combination of logistic regression and Lasso (i.e. regularized logistic regression, RLR) as a wrapper to extract the most relevant features for individual subproblems from the whole set of high-dimensional sensor data. We train different soft computing classifiers

  13. Identification and selection of cases and controls in the Pneumonia Etiology Research for Child Health project

    NARCIS (Netherlands)

    Deloria-Knoll, Maria; Feikin, Daniel R.; Scott, J. Anthony G.; O'Brien, Katherine L.; DeLuca, Andrea N.; Driscoll, Amanda J.; Levine, Orin S.; Black, Robert E.; Bhutta, Zulfiqar A.; Campbell, Harry; Cherian, Thomas; Crook, Derrick W.; de Jong, Menno D.; Dowell, Scott F.; Graham, Stephen M.; Klugman, Keith P.; Lanata, Claudio F.; Madhi, Shabir A.; Martin, Paul; Nataro, James P.; Piazza, Franco M.; Qazi, Shamim A.; Zar, Heather J.; Baggett, Henry C.; Brooks, W. Abdullah; Chipeta, James; Ebruke, Bernard; Endtz, Hubert P.; Groome, Michelle; Hammitt, Laura L.; Howie, Stephen R. C.; Kotloff, Karen; Maloney, Susan A.; Moore, David; Otieno, Juliet; Seidenberg, Phil; Tapia, Milagritos; Thamthitiwat, Somsak; Thea, Donald M.; Zaman, Khaleque

    2012-01-01

    Methods for the identification and selection of patients (cases) with severe or very severe pneumonia and controls for the Pneumonia Etiology Research for Child Health (PERCH) project were needed. Issues considered include eligibility criteria and sampling strategies, whether to enroll hospital or

  14. Objective ARX Model Order Selection for Multi-Channel Human Operator Identification

    NARCIS (Netherlands)

    Roggenkämper, N; Pool, D.M.; Drop, F.M.; van Paassen, M.M.; Mulder, M.

    2016-01-01

    In manual control, the human operator primarily responds to visual inputs but may elect to make use of other available feedback paths such as physical motion, adopting a multi-channel control strategy. Hu- man operator identification procedures generally require a priori selection of the model

  15. Gene expression profiling in cervical cancer: identification of novel markers for disease diagnosis and therapy.

    LENUS (Irish Health Repository)

    Martin, Cara M

    2012-02-01

    Cervical cancer, a potentially preventable disease, remains the second most common malignancy in women worldwide. Human papillomavirus is the single most important etiological agent in cervical cancer. HPV contributes to neoplastic progression through the action of two viral oncoproteins E6 and E7, which interfere with critical cell cycle pathways, p53, and retinoblastoma. However, evidence suggests that HPV infection alone is insufficient to induce malignant changes and other host genetic variations are important in the development of cervical cancer. Advances in molecular biology and high throughput gene expression profiling technologies have heralded a new era in biomarker discovery and identification of molecular targets related to carcinogenesis. These advancements have improved our understanding of carcinogenesis and will facilitate screening, early detection, management, and personalised targeted therapy. In this chapter, we have described the use of high density microarrays to assess gene expression profiles in cervical cancer. Using this approach we have identified a number of novel genes which are differentially expressed in cervical cancer, including several genes involved in cell cycle regulation. These include p16ink4a, MCM 3 and 5, CDC6, Geminin, Cyclins A-D, TOPO2A, CDCA1, and BIRC5. We have validated expression of mRNA using real-time PCR and protein by immunohistochemistry.

  16. Profiling oil sands mixtures from industrial developments and natural groundwaters for source identification.

    Science.gov (United States)

    Frank, Richard A; Roy, James W; Bickerton, Greg; Rowland, Steve J; Headley, John V; Scarlett, Alan G; West, Charles E; Peru, Kerry M; Parrott, Joanne L; Conly, F Malcolm; Hewitt, L Mark

    2014-01-01

    The objective of this study was to identify chemical components that could distinguish chemical mixtures in oil sands process-affected water (OSPW) that had potentially migrated to groundwater in the oil sands development area of northern Alberta, Canada. In the first part of the study, OSPW samples from two different tailings ponds and a broad range of natural groundwater samples were assessed with historically employed techniques as Level-1 analyses, including geochemistry, total concentrations of naphthenic acids (NAs) and synchronous fluorescence spectroscopy (SFS). While these analyses did not allow for reliable source differentiation, they did identify samples containing significant concentrations of oil sands acid-extractable organics (AEOs). In applying Level-2 profiling analyses using electrospray ionization high resolution mass spectrometry (ESI-HRMS) and comprehensive multidimensional gas chromatography time-of-flight mass spectrometry (GC × GC-TOF/MS) to samples containing appreciable AEO concentrations, differentiation of natural from OSPW sources was apparent through measurements of O2:O4 ion class ratios (ESI-HRMS) and diagnostic ions for two families of suspected monoaromatic acids (GC × GC-TOF/MS). The resemblance between the AEO profiles from OSPW and from 6 groundwater samples adjacent to two tailings ponds implies a common source, supporting the use of these complimentary analyses for source identification. These samples included two of upward flowing groundwater collected <1 m beneath the Athabasca River, suggesting OSPW-affected groundwater is reaching the river system.

  17. Transcriptional Profiling and Identification of Heat-Responsive Genes in Perennial Ryegrass by RNA-Sequencing

    Directory of Open Access Journals (Sweden)

    Kehua Wang

    2017-06-01

    Full Text Available Perennial ryegrass (Lolium perenne is one of the most widely used forage and turf grasses in the world due to its desirable agronomic qualities. However, as a cool-season perennial grass species, high temperature is a major factor limiting its performance in warmer and transition regions. In this study, a de novo transcriptome was generated using a cDNA library constructed from perennial ryegrass leaves subjected to short-term heat stress treatment. Then the expression profiling and identification of perennial ryegrass heat response genes by digital gene expression analyses was performed. The goal of this work was to produce expression profiles of high temperature stress responsive genes in perennial ryegrass leaves and further identify the potentially important candidate genes with altered levels of transcript, such as those genes involved in transcriptional regulation, antioxidant responses, plant hormones and signal transduction, and cellular metabolism. The de novo assembly of perennial ryegrass transcriptome in this study obtained more total and annotated unigenes compared to previously published ones. Many DEGs identified were genes that are known to respond to heat stress in plants, including HSFs, HSPs, and antioxidant related genes. In the meanwhile, we also identified four gene candidates mainly involved in C4 carbon fixation, and one TOR gene. Their exact roles in plant heat stress response need to dissect further. This study would be important by providing the gene resources for improving heat stress tolerance in both perennial ryegrass and other cool-season perennial grass plants.

  18. A novel adjuvant to the resident selection process: the hartman value profile.

    Science.gov (United States)

    Cone, Jeffrey D; Byrum, C Stephen; Payne, Wyatt G; Smith, David J

    2012-01-01

    The goal of resident selection is twofold: (1) select candidates who will be successful residents and eventually successful practitioners and (2) avoid selecting candidates who will be unsuccessful residents and/or eventually unsuccessful practitioners. Traditional tools used to select residents have well-known limitations. The Hartman Value Profile (HVP) is a proven adjuvant tool to predicting future performance in candidates for advanced positions in the corporate setting. No literature exists to indicate use of the HVP for resident selection. The HVP evaluates the structure and the dynamics of an individual value system. Given the potential impact, we implemented its use beginning in 2007 as an adjuvant tool to the traditional selection process. Experience gained from incorporating the HVP into the residency selection process suggests that it may add objectivity and refinement in predicting resident performance. Further evaluation is warranted with longer follow-up times.

  19. Identification of Novel Translational Urinary Biomarkers for Acetaminophen-Induced Acute Liver Injury Using Proteomic Profiling in Mice

    NARCIS (Netherlands)

    van Swelm, Rachel P. L.; Laarakkers, Coby M. M.; van der Kuur, Ellen C.; Morava-Kozicz, Eva; Wevers, Ron A.; Augustijn, Kevin D.; Touw, Daan J.; Sandel, Maro H.; Masereeuw, Rosalinde; Russel, Frans G. M.

    2012-01-01

    Drug-induced liver injury (DILI) is the leading cause of acute liver failure. Currently, no adequate predictive biomarkers for DILI are available. This study describes a translational approach using proteomic profiling for the identification of urinary proteins related to acute liver injury induced

  20. Identification of new serum markers of pathological states by bioinformatic tools for the analysis of serum proteomics expression profiles

    International Nuclear Information System (INIS)

    Malorni, A.; Facchiano, A.

    2009-01-01

    We have developed new bioinformatic tools and strategies, aimed to the identification and characterization of proteins as markers of pathological states, for the analysis of data derived from protein expression profiles obtained by mass spectrometry techniques, for the study of structural and functional properties of the proteins, and for the analysis of data from omics approaches

  1. Nitrogen accumulation profiles of selected grain and vegetable crops: A bibliography (1940-1992)

    Energy Technology Data Exchange (ETDEWEB)

    Meischen, S.J.; Byrd, K.R.

    1994-10-01

    A bibliography of nitrogen accumulation profile data for 25 vegetable and grain crops reported between 1940 and 1992 is presented. The selected crops are asparagus, broccoli, brussels sprouts, cabbage, carrots, cauliflower, celery, corn, cotton, cucumber, field bean, field pea, garlic, lettuce, onions, and peppers.

  2. Refining the Classification of Children with Selective Mutism: A Latent Profile Analysis

    Science.gov (United States)

    Cohan, Sharon L.; Chavira, Denise A.; Shipon-Blum, Elisa; Hitchcock, Carla; Roesch, Scott C.; Stein, Murray B.

    2008-01-01

    The goal of this study was to develop an empirically derived classification system for selective mutism (SM) using parent-report measures of social anxiety, behavior problems, and communication delays. The sample consisted of parents of 130 children (ages 5-12) with SM. Results from latent profile analysis supported a 3-class solution made up of…

  3. When misery avoids company : Selective social comparisons to photographic online profiles

    NARCIS (Netherlands)

    Johnson, Benjamin K.; Knobloch-Westerwick, Silvia

    2017-01-01

    Social networking site usage may affect subjective well-being. Two experiments examined how selective exposure to profiles of other users facilitated mood management via self-enhancing social comparisons. In Study 1, when given detailed impression management cues, such as photographs and status

  4. Identification and Characterization of 293T Cell-Derived Exosomes by Profiling the Protein, mRNA and MicroRNA Components.

    Directory of Open Access Journals (Sweden)

    Jing Li

    Full Text Available Cell-derived exosomes are leading candidates for in vivo drug delivery carriers. In particular, exosomes derived from 293T cells are used most frequently, although exosome dosing has varied greatly among studies. Considering their biological origin, it is crucial to characterize the molecular composition of exosomes if large doses are to be administered in clinical settings. In this study, we present the first comprehensive analysis of the protein, messenger RNA and microRNA profiles of 293T cell-derived exosomes; then, we characterized these data using Gene Ontology annotation and Kyoto Encyclopedia for Genes and Genomes pathway analysis. Our study will provide the basis for the selection of 293T cell-derived exosome drug delivery systems. Profiling the exosomal signatures of 293T cells will lead to a better understanding of 293T exosome biology and will aid in the identification of any harmful factors in exosomes that could cause adverse clinical effects.

  5. Selecting lineup foils in eyewitness identification experiments: experimental control and real-world simulation.

    Science.gov (United States)

    Clark, S E; Tunnicliff, J L

    2001-06-01

    Experimental research on eyewitness identification follows a standard principle of experimental design. Perpetrator-present and perpetrator-absent lineups are constructed with the same foils, so that the two conditions are identical except for the presence or absence ofthe trueperpetrator ofthe crime. However, this aspect of the design simulates conditions that do not correspond to those of real criminal investigations. Specifically, these conditions can create perp-absent lineups in which the foils are selected based on their similarity to an unknown person--the real perpetrator. Analysis of the similarity relations predicts that when foils for perp-absent lineups are selected based on their match to the perpetrator the false identification rate will be lower than if the foils are selected based on their match to the innocent suspect. This prediction was confirmed in an experiment that compared these two perp-absent lineup conditions. These results suggest that false identification rates in previous experiments would have been higher if the foils had been selected based on their match to the innocent suspect, rather than the absent perpetrator.

  6. Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling

    DEFF Research Database (Denmark)

    Simonsen, Martin; Maetschke, S.R.; Ragan, M.A.

    2012-01-01

    Motivation: Phylogenetic profiling methods can achieve good accuracy in predicting protein–protein interactions, especially in prokaryotes. Recent studies have shown that the choice of reference taxa (RT) is critical for accurate prediction, but with more than 2500 fully sequenced taxa publicly......: We present three novel methods for automating the selection of RT, using machine learning based on known protein–protein interaction networks. One of these methods in particular, Tree-Based Search, yields greatly improved prediction accuracies. We further show that different methods for constituting...... phylogenetic profiles often require very different RT sets to support high prediction accuracy....

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

    Science.gov (United States)

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

    2016-09-16

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

  8. Fruit Phenolic Profiling: A New Selection Criterion in Olive Breeding Programs.

    Science.gov (United States)

    Pérez, Ana G; León, Lorenzo; Sanz, Carlos; de la Rosa, Raúl

    2018-01-01

    Olive growing is mainly based on traditional varieties selected by the growers across the centuries. The few attempts so far reported to obtain new varieties by systematic breeding have been mainly focused on improving the olive adaptation to different growing systems, the productivity and the oil content. However, the improvement of oil quality has rarely been considered as selection criterion and only in the latter stages of the breeding programs. Due to their health promoting and organoleptic properties, phenolic compounds are one of the most important quality markers for Virgin olive oil (VOO) although they are not commonly used as quality traits in olive breeding programs. This is mainly due to the difficulties for evaluating oil phenolic composition in large number of samples and the limited knowledge on the genetic and environmental factors that may influence phenolic composition. In the present work, we propose a high throughput methodology to include the phenolic composition as a selection criterion in olive breeding programs. For that purpose, the phenolic profile has been determined in fruits and oils of several breeding selections and two varieties ("Picual" and "Arbequina") used as control. The effect of three different environments, typical for olive growing in Andalusia, Southern Spain, was also evaluated. A high genetic effect was observed on both fruit and oil phenolic profile. In particular, the breeding selection UCI2-68 showed an optimum phenolic profile, which sums up to a good agronomic performance previously reported. A high correlation was found between fruit and oil total phenolic content as well as some individual phenols from the two different matrices. The environmental effect on phenolic compounds was also significant in both fruit and oil, although the low genotype × environment interaction allowed similar ranking of genotypes on the different environments. In summary, the high genotypic variance and the simplified procedure of the

  9. Identification of Protein Pupylation Sites Using Bi-Profile Bayes Feature Extraction and Ensemble Learning

    Directory of Open Access Journals (Sweden)

    Xiaowei Zhao

    2013-01-01

    Full Text Available Pupylation, one of the most important posttranslational modifications of proteins, typically takes place when prokaryotic ubiquitin-like protein (Pup is attached to specific lysine residues on a target protein. Identification of pupylation substrates and their corresponding sites will facilitate the understanding of the molecular mechanism of pupylation. Comparing with the labor-intensive and time-consuming experiment approaches, computational prediction of pupylation sites is much desirable for their convenience and fast speed. In this study, a new bioinformatics tool named EnsemblePup was developed that used an ensemble of support vector machine classifiers to predict pupylation sites. The highlight of EnsemblePup was to utilize the Bi-profile Bayes feature extraction as the encoding scheme. The performance of EnsemblePup was measured with a sensitivity of 79.49%, a specificity of 82.35%, an accuracy of 85.43%, and a Matthews correlation coefficient of 0.617 using the 5-fold cross validation on the training dataset. When compared with other existing methods on a benchmark dataset, the EnsemblePup provided better predictive performance, with a sensitivity of 80.00%, a specificity of 83.33%, an accuracy of 82.00%, and a Matthews correlation coefficient of 0.629. The experimental results suggested that EnsemblePup presented here might be useful to identify and annotate potential pupylation sites in proteins of interest. A web server for predicting pupylation sites was developed.

  10. Classification of genes and putative biomarker identification using distribution metrics on expression profiles.

    Directory of Open Access Journals (Sweden)

    Hung-Chung Huang

    Full Text Available BACKGROUND: Identification of genes with switch-like properties will facilitate discovery of regulatory mechanisms that underlie these properties, and will provide knowledge for the appropriate application of Boolean networks in gene regulatory models. As switch-like behavior is likely associated with tissue-specific expression, these gene products are expected to be plausible candidates as tissue-specific biomarkers. METHODOLOGY/PRINCIPAL FINDINGS: In a systematic classification of genes and search for biomarkers, gene expression profiles (GEPs of more than 16,000 genes from 2,145 mouse array samples were analyzed. Four distribution metrics (mean, standard deviation, kurtosis and skewness were used to classify GEPs into four categories: predominantly-off, predominantly-on, graded (rheostatic, and switch-like genes. The arrays under study were also grouped and examined by tissue type. For example, arrays were categorized as 'brain group' and 'non-brain group'; the Kolmogorov-Smirnov distance and Pearson correlation coefficient were then used to compare GEPs between brain and non-brain for each gene. We were thus able to identify tissue-specific biomarker candidate genes. CONCLUSIONS/SIGNIFICANCE: The methodology employed here may be used to facilitate disease-specific biomarker discovery.

  11. Genome-wide identification, characterization, and expression profile of aquaporin gene family in flax (Linum usitatissimum).

    Science.gov (United States)

    Shivaraj, S M; Deshmukh, Rupesh K; Rai, Rhitu; Bélanger, Richard; Agrawal, Pawan K; Dash, Prasanta K

    2017-04-27

    Membrane intrinsic proteins (MIPs) form transmembrane channels and facilitate transport of myriad substrates across the cell membrane in many organisms. Majority of plant MIPs have water transporting ability and are commonly referred as aquaporins (AQPs). In the present study, we identified aquaporin coding genes in flax by genome-wide analysis, their structure, function and expression pattern by pan-genome exploration. Cross-genera phylogenetic analysis with known aquaporins from rice, arabidopsis, and poplar showed five subgroups of flax aquaporins representing 16 plasma membrane intrinsic proteins (PIPs), 17 tonoplast intrinsic proteins (TIPs), 13 NOD26-like intrinsic proteins (NIPs), 2 small basic intrinsic proteins (SIPs), and 3 uncharacterized intrinsic proteins (XIPs). Amongst aquaporins, PIPs contained hydrophilic aromatic arginine (ar/R) selective filter but TIP, NIP, SIP and XIP subfamilies mostly contained hydrophobic ar/R selective filter. Analysis of RNA-seq and microarray data revealed high expression of PIPs in multiple tissues, low expression of NIPs, and seed specific expression of TIP3 in flax. Exploration of aquaporin homologs in three closely related Linum species bienne, grandiflorum and leonii revealed presence of 49, 39 and 19 AQPs, respectively. The genome-wide identification of aquaporins, first in flax, provides insight to elucidate their physiological and developmental roles in flax.

  12. Identification of circulating miRNA biomarkers based on global quantitative real-time PCR profiling

    Directory of Open Access Journals (Sweden)

    Kang Kang

    2012-02-01

    Full Text Available Abstract MicroRNAs (miRNAs are small noncoding RNAs (18-25 nucleotides that regulate gene expression at the post-transcriptional level. Recent studies have demonstrated the presence of miRNAs in the blood circulation. Deregulation of miRNAs in serum or plasma has been associated with many diseases including cancers and cardiovascular diseases, suggesting the possible use of miRNAs as diagnostic biomarkers. However, the detection of the small amount of miRNAs found in serum or plasma requires a method with high sensitivity and accuracy. Therefore, the current study describes polymerase chain reaction (PCR-based methods for measuring circulating miRNAs. Briefly, the procedure involves four major steps: (1 sample collection and preparation; (2 global miRNAs profiling using quantitative real-time PCR (qRT-PCR; (3 data normalization and analysis; and (4 selection and validation of miRNA biomarkers. In conclusion, qRT-PCR is a promising method for profiling of circulating miRNAs as biomarkers.

  13. How nonuniform contact profiles of T cell receptors modulate thymic selection outcomes

    Science.gov (United States)

    Chen, Hanrong; Chakraborty, Arup K.; Kardar, Mehran

    2018-03-01

    T cell receptors (TCRs) bind foreign or self-peptides attached to major histocompatibility complex (MHC) molecules, and the strength of this interaction determines T cell activation. Optimizing the ability of T cells to recognize a diversity of foreign peptides yet be tolerant of self-peptides is crucial for the adaptive immune system to properly function. This is achieved by selection of T cells in the thymus, where immature T cells expressing unique, stochastically generated TCRs interact with a large number of self-peptide-MHC; if a TCR does not bind strongly enough to any self-peptide-MHC, or too strongly with at least one self-peptide-MHC, the T cell dies. Past theoretical work cast thymic selection as an extreme value problem and characterized the statistical enrichment or depletion of amino acids in the postselection TCR repertoire, showing how T cells are selected to be able to specifically recognize peptides derived from diverse pathogens yet have limited self-reactivity. Here, we investigate how the diversity of the postselection TCR repertoire is modified when TCRs make nonuniform contacts with peptide-MHC. Specifically, we were motivated by recent experiments showing that amino acids at certain positions of a TCR sequence have large effects on thymic selection outcomes, and crystal structure data that reveal a nonuniform contact profile between a TCR and its peptide-MHC ligand. Using a representative TCR contact profile as an illustration, we show via simulations that the statistical enrichment or depletion of amino acids now varies by position according to the contact profile, and, importantly, it depends on the implementation of nonuniform contacts during thymic selection. We explain these nontrivial results analytically. Our study has implications for understanding the selection forces that shape the functionality of the postselection TCR repertoire.

  14. Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome

    International Nuclear Information System (INIS)

    O'Donoghue, Liza E; Ptitsyn, Andrey A; Kamstock, Debra A; Siebert, Janet; Thomas, Russell S; Duval, Dawn L

    2010-01-01

    Osteosarcoma (OSA) spontaneously arises in the appendicular skeleton of large breed dogs and shares many physiological and molecular biological characteristics with human OSA. The standard treatment for OSA in both species is amputation or limb-sparing surgery, followed by chemotherapy. Unfortunately, OSA is an aggressive cancer with a high metastatic rate. Characterization of OSA with regard to its metastatic potential and chemotherapeutic resistance will improve both prognostic capabilities and treatment modalities. We analyzed archived primary OSA tissue from dogs treated with limb amputation followed by doxorubicin or platinum-based drug chemotherapy. Samples were selected from two groups: dogs with disease free intervals (DFI) of less than 100 days (n = 8) and greater than 300 days (n = 7). Gene expression was assessed with Affymetrix Canine 2.0 microarrays and analyzed with a two-tailed t-test. A subset of genes was confirmed using qRT-PCR and used in classification analysis to predict prognosis. Systems-based gene ontology analysis was conducted on genes selected using a standard J5 metric. The genes identified using this approach were converted to their human homologues and assigned to functional pathways using the GeneGo MetaCore platform. Potential biomarkers were identified using gene expression microarray analysis and 11 differentially expressed (p < 0.05) genes were validated with qRT-PCR (n = 10/group). Statistical classification models using the qRT-PCR profiles predicted patient outcomes with 100% accuracy in the training set and up to 90% accuracy upon stratified cross validation. Pathway analysis revealed alterations in pathways associated with oxidative phosphorylation, hedgehog and parathyroid hormone signaling, cAMP/Protein Kinase A (PKA) signaling, immune responses, cytoskeletal remodeling and focal adhesion. This profiling study has identified potential new biomarkers to predict patient outcome in OSA and new pathways that may be targeted for

  15. Ageing Drosophila selected for longevity retain a young gene expression profile

    DEFF Research Database (Denmark)

    Sarup, Pernille Merete

    and longevity selected lines. Among the latter genes we found a clear overrepresentation of genes involved in immune functions supporting the hypothesis of the life shortening effect of an overactive immune system (inflammaging). Eighty-four genes were differentially expressed at the same physiological age...... between control and longevity selected lines, and the overlap between the same chronological and physiological age gene lists counted 40 candidate genes for increased longevity. Among these were genes with functions in starvation resistance, a regulator of immune responses and several genes which have......  We have investigated how the gene-expression profile of longevity selected lines of Drosophila melanogaster differed from control lines in young, middle-aged and old male flies. 530 genes were differentially expressed between selected and control flies at the same chronological age. We used...

  16. Comparison of chemical profiles of selected gaharu oils from peninsular Malaysia

    International Nuclear Information System (INIS)

    Norazah, M.A.; Chang, Y.S.; Mailina, J.; Abu, S.A.; Abdul Majid, J.; Saidatul, H.S.; Norhasnida, H.; Nik Yasmin, Y.

    2008-01-01

    Gaharu (agar wood) is a fragrant wood that is usually derived from the diseased timber of the genus Aquilaria (Thymelaeceae) and often occurs as dark coloured patches or streaks in the tree. Due to its strong, unique scent and medicinal properties, gaharu oil is greatly valued as perfumery ingredient and incense. Gaharu may be classified into various grades; Grade A, B, C and D and they are often graded according to the physical properties, gaharu formation and its unique scent. The lower grades such as Grade C are often distilled to obtain gaharu oils. As part of an on-going research on the chemical profiling of some Malaysian gaharu oils and evaluation of their potential beneficial properties; gaharu oils obtained from different sources were analysed and compared by GC and GC-MS. Identification of the chemical components was based on comparison of calculated retention indices and mass spectral data with literature values. Examination of the oils showed some variations and differences in terms of GC profiles, concentration and chemical components. Majority of the essential oil profiles were complex and made up of sesquiterpenoids and their oxygenated derivatives. However, common occurrences of chemical compounds such as 3-phenyl-butanone, α-guaiene, β-agar ofuran, α-agar ofuran, agarospirol and jinkoh-eremol were detected. (author)

  17. Talent identification and selection in elite youth football: An Australian context.

    Science.gov (United States)

    O'Connor, Donna; Larkin, Paul; Mark Williams, A

    2016-10-01

    We identified the perceptual-cognitive skills and player history variables that differentiate players selected or not selected into an elite youth football (i.e. soccer) programme in Australia. A sample of elite youth male football players (n = 127) completed an adapted participation history questionnaire and video-based assessments of perceptual-cognitive skills. Following data collection, 22 of these players were offered a full-time scholarship for enrolment at an elite player residential programme. Participants selected for the scholarship programme recorded superior performance on the combined perceptual-cognitive skills tests compared to the non-selected group. There were no significant between group differences on the player history variables. Stepwise discriminant function analysis identified four predictor variables that resulted in the best categorization of selected and non-selected players (i.e. recent match-play performance, region, number of other sports participated, combined perceptual-cognitive performance). The effectiveness of the discriminant function is reflected by 93.7% of players being correctly classified, with the four variables accounting for 57.6% of the variance. Our discriminating model for selection may provide a greater understanding of the factors that influence elite youth talent selection and identification.

  18. The energy and identification continua of burnout and work engagement: Developmental profiles over eight years

    Directory of Open Access Journals (Sweden)

    Anne Mäkikangas

    2017-06-01

    Full Text Available Understanding of the mutual developmental dynamics between burnout and work engagement is limited due to the lack of longitudinal studies with long follow-ups and multi-wave data. This study sought to identify subgroups of employees characterized by long-term exhaustion-vigor (energy continuum and cynicism-dedication (identification continuum. A further important aim was to investigate differences between the identified subgroups in their experiences of progress in their personal work goals. Five-wave, eight-year follow-up data among Finnish white-collar professionals (n = 168 were studied using Latent Profile Analysis (LPA. The analysis yielded three exhaustion-vigor subgroups: 1 “Low stable exhaustion – high stable vigor” (n = 141, 2 “Fluctuating exhaustion and vigor” (n = 19, and 3 “Stable average exhaustion – decreasing vigor” (n = 8. Three subgroups were also found for cynicism-dedication: 1 “Low stable cynicism – high stable dedication” (n = 124, 2 “Increasing cynicism – decreasing dedication” (n = 27, and 3 “Decreasing cynicism – increasing dedication” (n = 17. Exhaustion and vigor were found to be stable and mutually exclusive experiences for the great majority of the participants. However, mean changes were also detected – especially in vigor – but these were rare. A notable finding was that the levels of and changes in cynicism and dedication showed opposite trends in each subgroup: among the majority of the participants (74%, the levels of cynicism and dedication were stable and inversely related, while among one-third their levels simultaneously changed in the reverse direction. The most successful progress in personal work goals was found in the groups described by the identification continuum, i.e., in the groups of “Low stable cynicism – high stable dedication” and “Decreasing cynicism – increasing dedication”.

  19. Identification and Transcription Profiling of NDUFS8 in Aedes taeniorhynchus (Diptera: Culicidae): Developmental Regulation and Environmental Response

    Science.gov (United States)

    2014-12-18

    Identification and transcription profiling of NDUFS8 in Aedes taeniorhynchus (Diptera: Culicidae): developmental regulation and environmental response...7205 Email lmzhao@ufl.edu Abstract: The cDNA of a NADH dehydrogenase-ubiquinone Fe-S protein 8 subunit (NDUFS8) gene from Aedes (Ochlerotatus...information useful for developing dsRNA pesticide for mosquito control. Keywords: Aedes taeniorhynchus, AetNDUFS8, mRNA expression, development

  20. Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome

    Directory of Open Access Journals (Sweden)

    Thomas Russell S

    2010-09-01

    Full Text Available Abstract Background Osteosarcoma (OSA spontaneously arises in the appendicular skeleton of large breed dogs and shares many physiological and molecular biological characteristics with human OSA. The standard treatment for OSA in both species is amputation or limb-sparing surgery, followed by chemotherapy. Unfortunately, OSA is an aggressive cancer with a high metastatic rate. Characterization of OSA with regard to its metastatic potential and chemotherapeutic resistance will improve both prognostic capabilities and treatment modalities. Methods We analyzed archived primary OSA tissue from dogs treated with limb amputation followed by doxorubicin or platinum-based drug chemotherapy. Samples were selected from two groups: dogs with disease free intervals (DFI of less than 100 days (n = 8 and greater than 300 days (n = 7. Gene expression was assessed with Affymetrix Canine 2.0 microarrays and analyzed with a two-tailed t-test. A subset of genes was confirmed using qRT-PCR and used in classification analysis to predict prognosis. Systems-based gene ontology analysis was conducted on genes selected using a standard J5 metric. The genes identified using this approach were converted to their human homologues and assigned to functional pathways using the GeneGo MetaCore platform. Results Potential biomarkers were identified using gene expression microarray analysis and 11 differentially expressed (p Conclusions This profiling study has identified potential new biomarkers to predict patient outcome in OSA and new pathways that may be targeted for therapeutic intervention.

  1. Identification and real time control of current profile in Tore-supra: algorithms and simulation; Identification et controle en temps reel du profil de courant dans Tore Supra: algorithmes et simulations

    Energy Technology Data Exchange (ETDEWEB)

    Houy, P

    1999-10-15

    The aim of this work is to propose a real-time control of the current profile in order to achieve reproducible operating modes with improved energetic confinement in tokamaks. The determination of the profile is based on measurements given by interferometry and polarimetry diagnostics. Different ways to evaluate and improve the accuracy of these measurements are exposed. The position and the shape of a plasma are controlled by the poloidal system that forces them to cope with standard values. Gas or neutral ions or ice pellet or extra power injection are technical means used to control other plasma parameters. These controls are performed by servo-controlled loops. The poloidal system of Tore-supra is presented. The main obstacle to a reliable determination of the current profile is the fact that slightly different Faraday angles lead to very different profiles. The direct identification method that is exposed in this work, gives the profile that minimizes the square of the margin between measured and computed values. The different algorithms proposed to control current profiles on Tore-supra have been validated by using a plasma simulation. The code Cronos that solves the resistive diffusion equation of current has been used. (A.C.)

  2. GEPSI: A Gene Expression Profile Similarity-Based Identification Method of Bioactive Components in Traditional Chinese Medicine Formula.

    Science.gov (United States)

    Zhang, Baixia; He, Shuaibing; Lv, Chenyang; Zhang, Yanling; Wang, Yun

    2018-01-01

    The identification of bioactive components in traditional Chinese medicine (TCM) is an important part of the TCM material foundation research. Recently, molecular docking technology has been extensively used for the identification of TCM bioactive components. However, target proteins that are used in molecular docking may not be the actual TCM target. For this reason, the bioactive components would likely be omitted or incorrect. To address this problem, this study proposed the GEPSI method that identified the target proteins of TCM based on the similarity of gene expression profiles. The similarity of the gene expression profiles affected by TCM and small molecular drugs was calculated. The pharmacological action of TCM may be similar to that of small molecule drugs that have a high similarity score. Indeed, the target proteins of the small molecule drugs could be considered TCM targets. Thus, we identified the bioactive components of a TCM by molecular docking and verified the reliability of this method by a literature investigation. Using the target proteins that TCM actually affected as targets, the identification of the bioactive components was more accurate. This study provides a fast and effective method for the identification of TCM bioactive components.

  3. A Comprehensive Peptidome Profiling Technology for the Identification of Early Detection Biomarkers for Lung Adenocarcinoma

    Science.gov (United States)

    Ueda, Koji; Saichi, Naomi; Takami, Sachiko; Kang, Daechun; Toyama, Atsuhiko; Daigo, Yataro; Ishikawa, Nobuhisa; Kohno, Nobuoki; Tamura, Kenji; Shuin, Taro; Nakayama, Masato; Sato, Taka-Aki; Nakamura, Yusuke; Nakagawa, Hidewaki

    2011-01-01

    The mass spectrometry-based peptidomics approaches have proven its usefulness in several areas such as the discovery of physiologically active peptides or biomarker candidates derived from various biological fluids including blood and cerebrospinal fluid. However, to identify biomarkers that are reproducible and clinically applicable, development of a novel technology, which enables rapid, sensitive, and quantitative analysis using hundreds of clinical specimens, has been eagerly awaited. Here we report an integrative peptidomic approach for identification of lung cancer-specific serum peptide biomarkers. It is based on the one-step effective enrichment of peptidome fractions (molecular weight of 1,000–5,000) with size exclusion chromatography in combination with the precise label-free quantification analysis of nano-LC/MS/MS data set using Expressionist proteome server platform. We applied this method to 92 serum samples well-managed with our SOP (standard operating procedure) (30 healthy controls and 62 lung adenocarcinoma patients), and quantitatively assessed the detected 3,537 peptide signals. Among them, 118 peptides showed significantly altered serum levels between the control and lung cancer groups (p5.0). Subsequently we identified peptide sequences by MS/MS analysis and further assessed the reproducibility of Expressionist-based quantification results and their diagnostic powers by MRM-based relative-quantification analysis for 96 independently prepared serum samples and found that APOA4 273–283, FIBA 5–16, and LBN 306–313 should be clinically useful biomarkers for both early detection and tumor staging of lung cancer. Our peptidome profiling technology can provide simple, high-throughput, and reliable quantification of a large number of clinical samples, which is applicable for diverse peptidome-targeting biomarker discoveries using any types of biological specimens. PMID:21533267

  4. Molecular identification and distribution profile of Candida species isolated from Iranian patients.

    Science.gov (United States)

    Mohammadi, Rasoul; Mirhendi, Hossein; Rezaei-Matehkolaei, Ali; Ghahri, Mohammad; Shidfar, Mohammad Reza; Jalalizand, Nilufar; Makimura, Koichi

    2013-08-01

    A total of 855 yeast strains isolated from different clinical specimens, mainly nail (42%) and vulva-vagina (25%) were identified by a set of polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). Genomic DNA was extracted from fresh colonies using Whatman FTA Card technology. PCR assays were performed on the complete ribosomal DNA internal transcribed spacer (rDNA-ITS) region for all isolates and species identification was carried out through their specific electrophoretic profiles after digestion with the enzyme MspI. Those isolates suspected as Candida parapsilosis group were then subjected to amplification of the secondary alcohol dehydrogenase (SADH) gene and restriction digestion with NlaIII enzyme. In total, 71.1% of the strains were obtained from females and 28.9% from males. The age group of 31-40 years consisted of the highest frequency of patients with candidiasis. Candida albicans was the predominant species (58.6%) followed by C. parapsilosis (11.0%), C. glabrata (8.3%), C. tropicalis (7.0%), C. kefyr (5.8%), C. krusei (4.4%), C. orthopsilosis (2.1%), and C. guilliermondii (0.6%). A few strains of C. lusitaniae, C. rugosa, C. intermedia, C. inconspicua, C. neoformans and S. cerevisiae were isolated. We could not identify 8 (0.9%) isolates. Candida albicans remains the most frequently species isolated from Iranian patients; however, the number of non-C. albicans Candida species looks to be increasing. The simple and reliable PCR-RFLP system used in the study has the potential to identify most clinically isolated yeasts.

  5. Individual differences in selective attention predict speech identification at a cocktail party.

    Science.gov (United States)

    Oberfeld, Daniel; Klöckner-Nowotny, Felicitas

    2016-08-31

    Listeners with normal hearing show considerable individual differences in speech understanding when competing speakers are present, as in a crowded restaurant. Here, we show that one source of this variance are individual differences in the ability to focus selective attention on a target stimulus in the presence of distractors. In 50 young normal-hearing listeners, the performance in tasks measuring auditory and visual selective attention was associated with sentence identification in the presence of spatially separated competing speakers. Together, the measures of selective attention explained a similar proportion of variance as the binaural sensitivity for the acoustic temporal fine structure. Working memory span, age, and audiometric thresholds showed no significant association with speech understanding. These results suggest that a reduced ability to focus attention on a target is one reason why some listeners with normal hearing sensitivity have difficulty communicating in situations with background noise.

  6. Individual differences in selective attention predict speech identification at a cocktail party

    Science.gov (United States)

    Oberfeld, Daniel; Klöckner-Nowotny, Felicitas

    2016-01-01

    Listeners with normal hearing show considerable individual differences in speech understanding when competing speakers are present, as in a crowded restaurant. Here, we show that one source of this variance are individual differences in the ability to focus selective attention on a target stimulus in the presence of distractors. In 50 young normal-hearing listeners, the performance in tasks measuring auditory and visual selective attention was associated with sentence identification in the presence of spatially separated competing speakers. Together, the measures of selective attention explained a similar proportion of variance as the binaural sensitivity for the acoustic temporal fine structure. Working memory span, age, and audiometric thresholds showed no significant association with speech understanding. These results suggest that a reduced ability to focus attention on a target is one reason why some listeners with normal hearing sensitivity have difficulty communicating in situations with background noise. DOI: http://dx.doi.org/10.7554/eLife.16747.001 PMID:27580272

  7. Identification and expression profiling analysis of TCP family genes involved in growth and development in maize.

    Science.gov (United States)

    Chai, Wenbo; Jiang, Pengfei; Huang, Guoyu; Jiang, Haiyang; Li, Xiaoyu

    2017-10-01

    The TCP family is a group of plant-specific transcription factors. TCP genes encode proteins harboring bHLH structure, which is implicated in DNA binding and protein-protein interactions and known as the TCP domain. TCP genes play important roles in plant development and have been evolutionarily and functionally elaborated in various plants, however, no overall phylogenetic analysis or expression profiling of TCP genes in Zea mays has been reported. In the present study, a systematic analysis of molecular evolution and functional prediction of TCP family genes in maize ( Z . mays L.) has been conducted. We performed a genome-wide survey of TCP genes in maize, revealing the gene structure, chromosomal location and phylogenetic relationship of family members. Microsynteny between grass species and tissue-specific expression profiles were also investigated. In total, 29 TCP genes were identified in the maize genome, unevenly distributed on the 10 maize chromosomes. Additionally, ZmTCP genes were categorized into nine classes based on phylogeny and purifying selection may largely be responsible for maintaining the functions of maize TCP genes. What's more, microsynteny analysis suggested that TCP genes have been conserved during evolution. Finally, expression analysis revealed that most TCP genes are expressed in the stem and ear, which suggests that ZmTCP genes influence stem and ear growth. This result is consistent with the previous finding that maize TCP genes represses the growth of axillary organs and enables the formation of female inflorescences. Altogether, this study presents a thorough overview of TCP family in maize and provides a new perspective on the evolution of this gene family. The results also indicate that TCP family genes may be involved in development stage in plant growing conditions. Additionally, our results will be useful for further functional analysis of the TCP gene family in maize.

  8. Fruit Phenolic Profiling: A New Selection Criterion in Olive Breeding Programs

    Directory of Open Access Journals (Sweden)

    Ana G. Pérez

    2018-02-01

    Full Text Available Olive growing is mainly based on traditional varieties selected by the growers across the centuries. The few attempts so far reported to obtain new varieties by systematic breeding have been mainly focused on improving the olive adaptation to different growing systems, the productivity and the oil content. However, the improvement of oil quality has rarely been considered as selection criterion and only in the latter stages of the breeding programs. Due to their health promoting and organoleptic properties, phenolic compounds are one of the most important quality markers for Virgin olive oil (VOO although they are not commonly used as quality traits in olive breeding programs. This is mainly due to the difficulties for evaluating oil phenolic composition in large number of samples and the limited knowledge on the genetic and environmental factors that may influence phenolic composition. In the present work, we propose a high throughput methodology to include the phenolic composition as a selection criterion in olive breeding programs. For that purpose, the phenolic profile has been determined in fruits and oils of several breeding selections and two varieties (“Picual” and “Arbequina” used as control. The effect of three different environments, typical for olive growing in Andalusia, Southern Spain, was also evaluated. A high genetic effect was observed on both fruit and oil phenolic profile. In particular, the breeding selection UCI2-68 showed an optimum phenolic profile, which sums up to a good agronomic performance previously reported. A high correlation was found between fruit and oil total phenolic content as well as some individual phenols from the two different matrices. The environmental effect on phenolic compounds was also significant in both fruit and oil, although the low genotype × environment interaction allowed similar ranking of genotypes on the different environments. In summary, the high genotypic variance and the

  9. Small Molecule Microarrays Enable the Identification of a Selective, Quadruplex-Binding Inhibitor of MYC Expression.

    Science.gov (United States)

    Felsenstein, Kenneth M; Saunders, Lindsey B; Simmons, John K; Leon, Elena; Calabrese, David R; Zhang, Shuling; Michalowski, Aleksandra; Gareiss, Peter; Mock, Beverly A; Schneekloth, John S

    2016-01-15

    The transcription factor MYC plays a pivotal role in cancer initiation, progression, and maintenance. However, it has proven difficult to develop small molecule inhibitors of MYC. One attractive route to pharmacological inhibition of MYC has been the prevention of its expression through small molecule-mediated stabilization of the G-quadruplex (G4) present in its promoter. Although molecules that bind globally to quadruplex DNA and influence gene expression are well-known, the identification of new chemical scaffolds that selectively modulate G4-driven genes remains a challenge. Here, we report an approach for the identification of G4-binding small molecules using small molecule microarrays (SMMs). We use the SMM screening platform to identify a novel G4-binding small molecule that inhibits MYC expression in cell models, with minimal impact on the expression of other G4-associated genes. Surface plasmon resonance (SPR) and thermal melt assays demonstrated that this molecule binds reversibly to the MYC G4 with single digit micromolar affinity, and with weaker or no measurable binding to other G4s. Biochemical and cell-based assays demonstrated that the compound effectively silenced MYC transcription and translation via a G4-dependent mechanism of action. The compound induced G1 arrest and was selectively toxic to MYC-driven cancer cell lines containing the G4 in the promoter but had minimal effects in peripheral blood mononucleocytes or a cell line lacking the G4 in its MYC promoter. As a measure of selectivity, gene expression analysis and qPCR experiments demonstrated that MYC and several MYC target genes were downregulated upon treatment with this compound, while the expression of several other G4-driven genes was not affected. In addition to providing a novel chemical scaffold that modulates MYC expression through G4 binding, this work suggests that the SMM screening approach may be broadly useful as an approach for the identification of new G4-binding small

  10. A Comparison Between Jerusalem Cross and Square Patch Frequency Selective Surfaces for Low Profile Antenna Applications

    Science.gov (United States)

    Cure, David; Weller, Thomas; Miranda, Felix A.

    2011-01-01

    In this paper, a comparison between Jerusalem Cross (JC) and Square Patch (SP) based Frequency Selected Surfaces (FSS) for low profile antenna applications is presented. The comparison is aimed at understanding the performance of low profile antennas backed by high impedance surfaces. In particular, an end loaded planar open sleeve dipole (ELPOSD) antenna is examined due to the various parameters within its configuration, offering significant design flexibility and a wide operating bandwidth. Measured data of the antennas demonstrate that increasing the number of unit cells improves the fractional bandwidth. The antenna bandwidth increased from 0.8% to 1.8% and from 0.8% to 2.7% for the JC and SP structures, respectively. The number of unit cells was increased from 48 to 80 for the JC-FSS and from 24 to 48 for the SP-FSS.

  11. Assembly of tantalum porous films with graded oxidation profile from size-selected nanoparticles

    Science.gov (United States)

    Singh, Vidyadhar; Grammatikopoulos, Panagiotis; Cassidy, Cathal; Benelmekki, Maria; Bohra, Murtaza; Hawash, Zafer; Baughman, Kenneth W.; Sowwan, Mukhles

    2014-05-01

    Functionally graded materials offer a way to improve the physical and chemical properties of thin films and coatings for different applications in the nanotechnology and biomedical fields. In this work, design and assembly of nanoporous tantalum films with a graded oxidation profile perpendicular to the substrate surface are reported. These nanoporous films are composed of size-selected, amorphous tantalum nanoparticles, deposited using a gas-aggregated magnetron sputtering system, and oxidized after coalescence, as samples evolve from mono- to multi-layered structures. Molecular dynamics computer simulations shed light on atomistic mechanisms of nanoparticle coalescence, which govern the films porosity. Aberration-corrected (S) TEM, GIXRD, AFM, SEM, and XPS were employed to study the morphology, phase and oxidation profiles of the tantalum nanoparticles, and the resultant films.

  12. Mass spectrometry-based cDNA profiling as a potential tool for human body fluid identification.

    Science.gov (United States)

    Donfack, Joseph; Wiley, Anissa

    2015-05-01

    Several mRNA markers have been exhaustively evaluated for the identification of human venous blood, saliva, and semen in forensic genetics. As new candidate human body fluid specific markers are discovered, evaluated, and reported in the scientific literature, there is an increasing trend toward determining the ideal markers for cDNA profiling of body fluids of forensic interest. However, it has not been determined which molecular genetics-based technique(s) should be utilized to assess the performance of these markers. In recent years, only a few confirmatory, mRNA/cDNA-based methods have been evaluated for applications in body fluid identification. The most frequently described methods tested to date include quantitative polymerase chain reaction (qPCR) and capillary electrophoresis (CE). However these methods, in particular qPCR, often favor narrow multiplex PCR due to the availability of a limited number of fluorescent dyes/tags. In an attempt to address this technological constraint, this study explored matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for human body fluid identification via cDNA profiling of venous blood, saliva, and semen. Using cDNA samples at 20pg input phosphoglycerate kinase 1 (PGK1) amounts, body fluid specific markers for the candidate genes were amplified in their corresponding body fluid (i.e., venous blood, saliva, or semen) and absent in the remaining two (100% specificity). The results of this study provide an initial indication that MALDI-TOF MS is a potential fluorescent dye-free alternative method for body fluid identification in forensic casework. However, the inherent issues of low amounts of mRNA, and the damage caused to mRNA by environmental exposures, extraction processes, and storage conditions are important factors that significantly hinder the implementation of cDNA profiling into forensic casework. Published by Elsevier Ireland Ltd.

  13. An enhanced PSO-DEFS based feature selection with biometric authentication for identification of diabetic retinopathy

    Directory of Open Access Journals (Sweden)

    Umarani Balakrishnan

    2016-11-01

    Full Text Available Recently, automatic diagnosis of diabetic retinopathy (DR from the retinal image is the most significant research topic in the medical applications. Diabetic macular edema (DME is the major reason for the loss of vision in patients suffering from DR. Early identification of the DR enables to prevent the vision loss and encourage diabetic control activities. Many techniques are developed to diagnose the DR. The major drawbacks of the existing techniques are low accuracy and high time complexity. To overcome these issues, this paper proposes an enhanced particle swarm optimization-differential evolution feature selection (PSO-DEFS based feature selection approach with biometric authentication for the identification of DR. Initially, a hybrid median filter (HMF is used for pre-processing the input images. Then, the pre-processed images are embedded with each other by using least significant bit (LSB for authentication purpose. Simultaneously, the image features are extracted using convoluted local tetra pattern (CLTrP and Tamura features. Feature selection is performed using PSO-DEFS and PSO-gravitational search algorithm (PSO-GSA to reduce time complexity. Based on some performance metrics, the PSO-DEFS is chosen as a better choice for feature selection. The feature selection is performed based on the fitness value. A multi-relevance vector machine (M-RVM is introduced to classify the 13 normal and 62 abnormal images among 75 images from 60 patients. Finally, the DR patients are further classified by M-RVM. The experimental results exhibit that the proposed approach achieves better accuracy, sensitivity, and specificity than the existing techniques.

  14. Characterization of MicroRNA Expression Profiles and Identification of Potential Biomarkers in Leprosy.

    Science.gov (United States)

    Jorge, Karina T O S; Souza, Renan P; Assis, Marieta T A; Araújo, Marcelo G; Locati, Massimo; Jesus, Amélia M R; Dias Baptista, Ida M F; Lima, Cristiano X; Teixeira, Antônio L; Teixeira, Mauro M; Soriani, Frederico M

    2017-05-01

    Leprosy is an important cause of disability in the developing world. Early diagnosis is essential to allow for cure and to interrupt transmission of this infection. MicroRNAs (miRNAs) are important factors for host-pathogen interaction and they have been identified as biomarkers for various infectious diseases. The expression profile of 377 microRNAs were analyzed by TaqMan low-density array (TLDA) in skin lesions of tuberculoid and lepromatous leprosy patients as well as skin specimens from healthy controls. In a second step, 16 microRNAs were selected for validation experiments with reverse transcription-quantitative PCR (qRT-PCR) in skin samples from new individuals. Principal-component analysis followed by logistic regression model and receiver operating characteristic (ROC) curve analyses were performed to evaluate the diagnostic potential of selected miRNAs. Four patterns of differential expression were identified in the TLDA experiment, suggesting a diagnostic potential of miRNAs in leprosy. After validation experiments, a combination of four miRNAs (miR-101, miR-196b, miR-27b, and miR-29c) was revealed as able to discriminate between healthy control and leprosy patients with 80% sensitivity and 91% specificity. This set of miRNAs was also able to discriminate between lepromatous and tuberculoid patients with a sensitivity of 83% and 80% specificity. In this work, it was possible to identify a set of miRNAs with good diagnostic potential for leprosy. Copyright © 2017 American Society for Microbiology.

  15. Personal profile of medical students selected through a knowledge-based exam only: are we missing suitable students?

    Directory of Open Access Journals (Sweden)

    Milena Abbiati

    2016-04-01

    Full Text Available Introduction: A consistent body of literature highlights the importance of a broader approach to select medical school candidates both assessing cognitive capacity and individual characteristics. However, selection in a great number of medical schools worldwide is still based on knowledge exams, a procedure that might neglect students with needed personal characteristics for future medical practice. We investigated whether the personal profile of students selected through a knowledge-based exam differed from those not selected. Methods: Students applying for medical school (N=311 completed questionnaires assessing motivations for becoming a doctor, learning approaches, personality traits, empathy, and coping styles. Selection was based on the results of MCQ tests. Principal component analysis was used to draw a profile of the students. Differences between selected and non-selected students were examined by Multivariate ANOVAs, and their impact on selection by logistic regression analysis. Results: Students demonstrating a profile of diligence with higher conscientiousness, deep learning approach, and task-focused coping were more frequently selected (p=0.01. Other personal characteristics such as motivation, sociability, and empathy did not significantly differ, comparing selected and non-selected students. Conclusion: Selection through a knowledge-based exam privileged diligent students. It did neither advantage nor preclude candidates with a more humane profile.

  16. Atomic Layer Etching of Silicon to Solve ARDE-Selectivity-Profile-Uniformity Trade-Offs

    Science.gov (United States)

    Wang, Mingmei; Ranjan, Alok; Ventzek, Peter; Koshiishi, Akira

    2014-10-01

    With shrinking critical dimensions, dry etch faces more and more challenges. Minimizing each of aspect ratio dependent etching (ARDE), bowing, undercut, selectivity, and within die uniformly across a wafer are met by trading off one requirement against another. At the root of the problem is that roles radical flux, ion flux and ion energy play may be both good and bad. Increasing one parameter helps meeting one requirement but hinders meeting the other. Self-limiting processes like atomic layer etching (ALE) promise a way to escape the problem of balancing trade-offs. ALE was realized in the mid-1990s but the industrial implementation has been slow. In recent years interest in ALE has revived. We present how ARDE, bowing/selectivity trade-offs may be overcome by varying radical/ion ratio, byproduct re-deposition. We overcome many of the practical implementation issues associated with ALE by precise passivation process control. The Monte Carlo Feature Profile Model (MCFPM) is used to illustrate realistic scenarios built around an Ar/Cl2 chemistry driven etch of Si masked by SiO2. We demonstrate that ALE can achieve zero ARDE and infinite selectivity. Profile control depends on careful management of the ion energies and angles. For ALE to be realized in production environment, tight control of IAD is a necessary. Experimental results are compared with simulation results to provide context to the work.

  17. Identification of Eupatilin from Artemisia argyi as a Selective PPARα Agonist Using Affinity Selection Ultrafiltration LC-MS

    Directory of Open Access Journals (Sweden)

    Yongsoo Choi

    2015-07-01

    Full Text Available Peroxisome proliferator-activated receptors (PPARs are key nuclear receptors and therapeutic targets for the treatment of metabolic diseases through the regulation of insulin resistance, diabetes, and dyslipidemia. Although a few drugs that target PPARs have been approved, more diverse and novel PPAR ligands are necessary to improve the safety and efficacy of available drugs. To expedite the search for new natural agonists of PPARs, we developed a screening assay based on ultrafiltration liquid chromatography-mass spectrometry (LC-MS that is compatible with complex samples such as dietary foods or botanical extracts. The known PPARα and/or PPARγ ligands resveratrol and rosiglitazone were used as positive controls to validate the developed method. When applied to the screening of an Artemisia argyi extract, eupatilin was identified as a selective PPARα ligand. A PPAR competitive binding assay based on FRET detection also confirmed eupatilin as a selective PPARα agonist exhibiting a binding affinity of 1.18 μM (IC50. Furthermore, eupatilin activation of the transcriptional activity of PPARα was confirmed using a cell-based transactivation assay. Thus, ultrafiltration LC-MS is a suitable assay for the identification of PPAR ligands in complex matrixes such as extracts of dietary foods and botanicals.

  18. Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis.

    Science.gov (United States)

    Hanson, Erin K; Ballantyne, Jack

    2013-01-01

    Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA) profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE) or quantitative RT-PCR (qRT-PCR) platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM) assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions), IL1F7 (skin), ALAS2 (blood), MMP10 (menstrual blood), HTN3 (saliva) and TGM4 (semen).  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green). Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively inexpensive

  19. A method for crack profiles identification in eddy current testing by the multi-directional scan

    International Nuclear Information System (INIS)

    Kojima, Fumio; Ikeda, Takuya; Nguyen, Doung

    2006-01-01

    This paper is concerned with a method for identification of crack shape in conducting materials. Multi-directional scanning strategies using Eddy Current Testing is performed for sizing complex natural crackings. Two dimensional measurements by means of multi-directional scan are used in a output least square identifications. (author)

  20. Proteomic Profiling of Exosomes Leads to the Identification of Novel Biomarkers for Prostate Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Duijvesz, Diederick; Burnum-Johnson, Kristin E.; Gritsenko, Marina A.; Hoogland, Marije; Vredenbregt-van den Berg, Mirella S.; Willemsen, Rob; Luider, Theo N.; Pasa-Tolic, Ljiljana; Jenster, Guido

    2013-12-31

    Introduction: Current markers for prostate cancer, such as PSA lack specificity. Therefore, novel biomarkers are needed. Unfortunately, biomarker discovery from body fluids is often hampered by the high abundance of many proteins unrelated to disease. An attractive alternative biomarker discovery approach is the isolation of small vesicles (exosomes, ~100 nm). They contain proteins that are specific to the tissue from which they are derived and therefore can be considered as treasure chests for disease-specific marker discovery. Profiling prostate cancer-derived exosomes could reveal new markers for this malignancy. Materials and Methods: Exosomes were isolated from 2 immortalized primary prostate epithelial cells (PNT2C2 and RWPE-1) and 2 PCa cell lines (PC346C and VCaP) by ultracentrifugation. Proteomic analyses utilized a nanoLC coupled with an LTQ-Orbitrap operated in tandem MS (MS/MS) mode, followed by the Accurate Mass and Time (AMT) tag approach. Exosomal proteins were validated by Western blotting. A Tissue Micro Array, containing 481 different PCa samples (radical prostatectomy), was used to correlate candidate markers with several clinical-pathological parameters such as PSA, Gleason score, biochemical recurrence, and (PCa-related) death. Results: Proteomic characterization resulted in the identification of 263 proteins by at least 2 peptides. Specifically analysis of exosomes from PNT2C2, RWPE-1, PC346C, and VCaP identified 248, 233, 169, and 216 proteins, respectively. Statistical analyses revealed 52 proteins differently expressed between PCa and control cells, 9 of which were more abundant in PCa. Validation by Western blotting confirmed a higher abundance of FASN, XPO1 and PDCD6IP (ALIX) in PCa exosomes. The Tissue Micro 4 Array showed strong correlation of higher Gleason scores and local recurrence with increased cytoplasmic XPO1 (P<0.001). Conclusions: Differentially abundant proteins of cell line-derived exosomes make a clear subdivision between

  1. Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: a novel strategy for biomarker identification

    Directory of Open Access Journals (Sweden)

    Smolich Beverly D

    2003-02-01

    Full Text Available Abstract Background Microarray-based gene expression profiling is a powerful approach for the identification of molecular biomarkers of disease, particularly in human cancers. Utility of this approach to measure responses to therapy is less well established, in part due to challenges in obtaining serial biopsies. Identification of suitable surrogate tissues will help minimize limitations imposed by those challenges. This study describes an approach used to identify gene expression changes that might serve as surrogate biomarkers of drug activity. Methods Expression profiling using microarrays was applied to peripheral blood mononuclear cell (PBMC samples obtained from patients with advanced colorectal cancer participating in a Phase III clinical trial. The PBMC samples were harvested pre-treatment and at the end of the first 6-week cycle from patients receiving standard of care chemotherapy or standard of care plus SU5416, a vascular endothelial growth factor (VEGF receptor tyrosine kinase (RTK inhibitor. Results from matched pairs of PBMC samples from 23 patients were queried for expression changes that consistently correlated with SU5416 administration. Results Thirteen transcripts met this selection criterion; six were further tested by quantitative RT-PCR analysis of 62 additional samples from this trial and a second SU5416 Phase III trial of similar design. This method confirmed four of these transcripts (CD24, lactoferrin, lipocalin 2, and MMP-9 as potential biomarkers of drug treatment. Discriminant analysis showed that expression profiles of these 4 transcripts could be used to classify patients by treatment arm in a predictive fashion. Conclusions These results establish a foundation for the further exploration of peripheral blood cells as a surrogate system for biomarker analyses in clinical oncology studies.

  2. Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: a novel strategy for biomarker identification

    International Nuclear Information System (INIS)

    DePrimo, Samuel E; Wong, Lily M; Khatry, Deepak B; Nicholas, Susan L; Manning, William C; Smolich, Beverly D; O'Farrell, Anne-Marie; Cherrington, Julie M

    2003-01-01

    Microarray-based gene expression profiling is a powerful approach for the identification of molecular biomarkers of disease, particularly in human cancers. Utility of this approach to measure responses to therapy is less well established, in part due to challenges in obtaining serial biopsies. Identification of suitable surrogate tissues will help minimize limitations imposed by those challenges. This study describes an approach used to identify gene expression changes that might serve as surrogate biomarkers of drug activity. Expression profiling using microarrays was applied to peripheral blood mononuclear cell (PBMC) samples obtained from patients with advanced colorectal cancer participating in a Phase III clinical trial. The PBMC samples were harvested pre-treatment and at the end of the first 6-week cycle from patients receiving standard of care chemotherapy or standard of care plus SU5416, a vascular endothelial growth factor (VEGF) receptor tyrosine kinase (RTK) inhibitor. Results from matched pairs of PBMC samples from 23 patients were queried for expression changes that consistently correlated with SU5416 administration. Thirteen transcripts met this selection criterion; six were further tested by quantitative RT-PCR analysis of 62 additional samples from this trial and a second SU5416 Phase III trial of similar design. This method confirmed four of these transcripts (CD24, lactoferrin, lipocalin 2, and MMP-9) as potential biomarkers of drug treatment. Discriminant analysis showed that expression profiles of these 4 transcripts could be used to classify patients by treatment arm in a predictive fashion. These results establish a foundation for the further exploration of peripheral blood cells as a surrogate system for biomarker analyses in clinical oncology studies

  3. Spatial Scaling of the Profile of Selective Attention in the Visual Field.

    Science.gov (United States)

    Gannon, Matthew A; Knapp, Ashley A; Adams, Thomas G; Long, Stephanie M; Parks, Nathan A

    2016-01-01

    Neural mechanisms of selective attention must be capable of adapting to variation in the absolute size of an attended stimulus in the ever-changing visual environment. To date, little is known regarding how attentional selection interacts with fluctuations in the spatial expanse of an attended object. Here, we use event-related potentials (ERPs) to investigate the scaling of attentional enhancement and suppression across the visual field. We measured ERPs while participants performed a task at fixation that varied in its attentional demands (attentional load) and visual angle (1.0° or 2.5°). Observers were presented with a stream of task-relevant stimuli while foveal, parafoveal, and peripheral visual locations were probed by irrelevant distractor stimuli. We found two important effects in the N1 component of visual ERPs. First, N1 modulations to task-relevant stimuli indexed attentional selection of stimuli during the load task and further correlated with task performance. Second, with increased task size, attentional modulation of the N1 to distractor stimuli showed a differential pattern that was consistent with a scaling of attentional selection. Together, these results demonstrate that the size of an attended stimulus scales the profile of attentional selection across the visual field and provides insights into the attentional mechanisms associated with such spatial scaling.

  4. Spatial Scaling of the Profile of Selective Attention in the Visual Field.

    Directory of Open Access Journals (Sweden)

    Matthew A Gannon

    Full Text Available Neural mechanisms of selective attention must be capable of adapting to variation in the absolute size of an attended stimulus in the ever-changing visual environment. To date, little is known regarding how attentional selection interacts with fluctuations in the spatial expanse of an attended object. Here, we use event-related potentials (ERPs to investigate the scaling of attentional enhancement and suppression across the visual field. We measured ERPs while participants performed a task at fixation that varied in its attentional demands (attentional load and visual angle (1.0° or 2.5°. Observers were presented with a stream of task-relevant stimuli while foveal, parafoveal, and peripheral visual locations were probed by irrelevant distractor stimuli. We found two important effects in the N1 component of visual ERPs. First, N1 modulations to task-relevant stimuli indexed attentional selection of stimuli during the load task and further correlated with task performance. Second, with increased task size, attentional modulation of the N1 to distractor stimuli showed a differential pattern that was consistent with a scaling of attentional selection. Together, these results demonstrate that the size of an attended stimulus scales the profile of attentional selection across the visual field and provides insights into the attentional mechanisms associated with such spatial scaling.

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

    Science.gov (United States)

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

    2014-04-01

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

  6. Parameter selection for peak alignment in chromatographic sample profiling: Objective quality indicators and use of control samples

    NARCIS (Netherlands)

    Peters, S.; van Velzen, E.; Janssen, H.-G.

    2009-01-01

    In chromatographic profiling applications, peak alignment is often essential as most chromatographic systems exhibit small peak shifts over time. When using currently available alignment algorithms, there are several parameters that determine the outcome of the alignment process. Selecting the

  7. The photon identification loophole in EPRB experiments: computer models with single-wing selection

    Science.gov (United States)

    De Raedt, Hans; Michielsen, Kristel; Hess, Karl

    2017-11-01

    Recent Einstein-Podolsky-Rosen-Bohm experiments [M. Giustina et al. Phys. Rev. Lett. 115, 250401 (2015); L. K. Shalm et al. Phys. Rev. Lett. 115, 250402 (2015)] that claim to be loophole free are scrutinized. The combination of a digital computer and discrete-event simulation is used to construct a minimal but faithful model of the most perfected realization of these laboratory experiments. In contrast to prior simulations, all photon selections are strictly made, as they are in the actual experiments, at the local station and no other "post-selection" is involved. The simulation results demonstrate that a manifestly non-quantum model that identifies photons in the same local manner as in these experiments can produce correlations that are in excellent agreement with those of the quantum theoretical description of the corresponding thought experiment, in conflict with Bell's theorem which states that this is impossible. The failure of Bell's theorem is possible because of our recognition of the photon identification loophole. Such identification measurement-procedures are necessarily included in all actual experiments but are not included in the theory of Bell and his followers.

  8. RA-6 reactor's probabilistic safety evaluation. Identification and selection of starting events

    International Nuclear Information System (INIS)

    Kay, J.; Chiossi, C.; Felizia, E.; Vallerga, H.; Kalejman, G.; Navarro, R.; Caruso, G.J.

    1987-01-01

    A summary of the 'Identification and selection of starting events' stage of the previous probabilistic safety evaluation of RA-6 reactor is presented. This evaluation was performed to verify if the safety criteria required for the licensing of RA-6 are met and to promote the diffusion of its meaning and usefulness with educational purposes. At this stage the starting events of RA-6 are determined and the probability that such events occur is calculated. The identification and selection of starting events is performed in two steps: determination of proposed starting events and determination of postulated starting events. The proposed starting events are determined by means of the master logic diagram (MLD) method, while the postulated starting events are obtained by grouping the proposed starting events. The simplifying hypothesis required for the application of MLD to the reactor are also formulated. The probability that the proposed and postulated starting events occur is afterwards calculated, adopting different fault models, in accordance with the nature of events that are considered. Conservative hypothesis on the characteristics of these events and the uncertainty of parameter values of those models are also formulated. The numerical values of the above mentioned probabilities are obtained by giving the parameters suitable values that are extracted from specialized publications. (Author)

  9. Cardioprotective and Metabolomic Profiling of Selected Medicinal Plants against Oxidative Stress

    Directory of Open Access Journals (Sweden)

    Nadia Afsheen

    2018-01-01

    Full Text Available In this research work, the antioxidant and metabolomic profiling of seven selected medicinally important herbs including Rauvolfia serpentina, Terminalia arjuna, Coriandrum sativum, Elettaria cardamom, Piper nigrum, Allium sativum, and Crataegus oxyacantha was performed. The in vivo cardioprotective potential of these medicinal plants was evaluated against surgically induced oxidative stress through left anterior descending coronary artery ligation (LADCA in dogs. The antioxidant profiling of these plants was done through DPPH and DNA protection assay. The C. oxyacantha and T. arjuna showed maximum antioxidant potential, while the E. cardamom showed poor antioxidative strength even at its high concentration. Different concentrations of extracts of the said plants exhibited the protection of plasmid DNA against H2O2 damage as compared to the plasmid DNA merely treated with H2O2. The metabolomic profiling through LC-MS analysis of these antioxidants revealed the presence of active secondary metabolites responsible for their antioxidant potential. During in vivo analysis, blood samples of all treatment groups were drawn at different time intervals to analyze the cardiac and hemodynamic parameters. The results depicted that the group pretreated with HC4 significantly sustained the level of CK-MB, SGOT, and LDH as well as hemodynamic parameters near to normal. The histopathological examination also confirmed the cardioprotective potential of HC4. Thus, the HC4 being safe and inexpensive cardioprotective herbal combination could be considered as an alternate of synthetic drugs.

  10. Cardioprotective and Metabolomic Profiling of Selected Medicinal Plants against Oxidative Stress

    Science.gov (United States)

    Afsheen, Nadia; Jahan, Nazish; Ijaz, Misbah; Manzoor, Asad; Khan, Khalid Mahmood; Hina, Saman

    2018-01-01

    In this research work, the antioxidant and metabolomic profiling of seven selected medicinally important herbs including Rauvolfia serpentina, Terminalia arjuna, Coriandrum sativum, Elettaria cardamom, Piper nigrum, Allium sativum, and Crataegus oxyacantha was performed. The in vivo cardioprotective potential of these medicinal plants was evaluated against surgically induced oxidative stress through left anterior descending coronary artery ligation (LADCA) in dogs. The antioxidant profiling of these plants was done through DPPH and DNA protection assay. The C. oxyacantha and T. arjuna showed maximum antioxidant potential, while the E. cardamom showed poor antioxidative strength even at its high concentration. Different concentrations of extracts of the said plants exhibited the protection of plasmid DNA against H2O2 damage as compared to the plasmid DNA merely treated with H2O2. The metabolomic profiling through LC-MS analysis of these antioxidants revealed the presence of active secondary metabolites responsible for their antioxidant potential. During in vivo analysis, blood samples of all treatment groups were drawn at different time intervals to analyze the cardiac and hemodynamic parameters. The results depicted that the group pretreated with HC4 significantly sustained the level of CK-MB, SGOT, and LDH as well as hemodynamic parameters near to normal. The histopathological examination also confirmed the cardioprotective potential of HC4. Thus, the HC4 being safe and inexpensive cardioprotective herbal combination could be considered as an alternate of synthetic drugs. PMID:29576858

  11. Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies.

    Science.gov (United States)

    Fetterman, Christina D; Rannala, Bruce; Walter, Michael A

    2008-09-24

    refinement of domain boundaries. Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species. Overall we found that after gene duplication of forkhead family members, rapid differentiation and subsequent fixation of amino acid changes through negative selection has occurred.

  12. Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies

    Directory of Open Access Journals (Sweden)

    Rannala Bruce

    2008-09-01

    functional information allowed prediction of residue function and refinement of domain boundaries. Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species. Overall we found that after gene duplication of forkhead family members, rapid differentiation and subsequent fixation of amino acid changes through negative selection has occurred.

  13. Analysis of selected gravity profiles on the Hanford Reservation, Richland, Washington

    International Nuclear Information System (INIS)

    Little, J.T.; Richard, B.H.

    1977-07-01

    Regional gravity surveys have been conducted on the Hanford Reservation in the past. This analysis is an attempt at detailed gravity profiling over selected areas of the reservation. Over 450 gravity readings were taken during the summer of 1976. The Bouguer anomaly values of these stations, along with facies cross sections, were used to construct two-dimensional models. The models depict the buried basalt bedrock surface and the overlying sedimentary cover of the areas selected for profiling. In the eastern section of the reservation, the interpretation of the data suggests that there are three major buried valleys cut into the bedrock. These channels are most likely a combination of structural downwarping and erosion of these downwarps by an ancestral Columbia River. Along the western boundary of the reservation there are two closed depressions which are believed to be the result of the sub-fluvial vortex effect of Kolk erosion. It was found that, although two-dimensional gravity models are useful in determining the buried bedrock surface, they are ineffectual in delineating sedimentary contacts

  14. Microalgal Species Selection for Biodiesel Production Based on Fuel Properties Derived from Fatty Acid Profiles

    Directory of Open Access Journals (Sweden)

    Md. Nurun Nabi

    2013-10-01

    Full Text Available Physical and chemical properties of biodiesel are influenced by structural features of the fatty acids, such as chain length, degree of unsaturation and branching of the carbon chain. This study investigated if microalgal fatty acid profiles are suitable for biodiesel characterization and species selection through Preference Ranking Organisation Method for Enrichment Evaluation (PROMETHEE and Graphical Analysis for Interactive Assistance (GAIA analysis. Fatty acid methyl ester (FAME profiles were used to calculate the likely key chemical and physical properties of the biodiesel [cetane number (CN, iodine value (IV, cold filter plugging point, density, kinematic viscosity, higher heating value] of nine microalgal species (this study and twelve species from the literature, selected for their suitability for cultivation in subtropical climates. An equal-parameter weighted (PROMETHEE-GAIA ranked Nannochloropsis oculata, Extubocellulus sp. and Biddulphia sp. highest; the only species meeting the EN14214 and ASTM D6751-02 biodiesel standards, except for the double bond limit in the EN14214. Chlorella vulgaris outranked N. oculata when the twelve microalgae were included. Culture growth phase (stationary and, to a lesser extent, nutrient provision affected CN and IV values of N. oculata due to lower eicosapentaenoic acid (EPA contents. Application of a polyunsaturated fatty acid (PUFA weighting to saturation led to a lower ranking of species exceeding the double bond EN14214 thresholds. In summary, CN, IV, C18:3 and double bond limits were the strongest drivers in equal biodiesel parameter-weighted PROMETHEE analysis.

  15. Isolation and Fatty Acid Profile of Selected Microalgae Strains from the Red Sea for Biofuel Production

    Directory of Open Access Journals (Sweden)

    Khalid M. Abu-Salah

    2013-05-01

    Full Text Available The isolation of lipid-rich autochthonous strains of microalgae is a crucial stage for the development of a microalgae-based biofuel production plant, as these microalgae already have the necessary adaptations to withstand competition, predation and the temperatures observed at each production site. This is particularly important in extreme climates such as in Saudi Arabia. Resorting to fluorescence activated cell sorting (FACS we screened for and isolated several microalgal strains from samples collected from the Red Sea. Relying on the fluorescence of BODIPY 505/515 (4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diazasindacene and growth performance, four promising candidates were identified and the total lipid content and fatty acid profile was assessed for biofuels production. Selected isolates were classified as chlorophytes, belonging to three different genera: Picochlorum, Nannochloris and Desmochloris. The lipid contents were assessed microscopically by means of BODIPY 505/515-associated fluorescence to detect intracellular lipid bodies, which revealed several lipid drops in all selected strains. This result was confirmed by lipid gravimetric determination, which demonstrated that all strains under study presented inner cell lipid contents ranging from 20% to 25% of the biomass dry weight. Furthermore, the fatty acid methyl esters profile of all strains seems ideal for biodiesel production due to a low degree of polyunsaturated fatty acid methyl esters and high amount of palmitic and oleic acids.

  16. Total Dietary Fiber Content of Selected Traditional Beverages in Egypt: A Brief Profile

    Directory of Open Access Journals (Sweden)

    Basil H. Aboul-Enein

    2015-11-01

    Full Text Available Escalating obesity rates have become a major public health concern in North Africa and the Middle East. Culturally-congruent dietary health education and strategies continue to be warranted to address this increasing public health crisis. Knowledge and familiarity with traditional foods and their nutritive value would assist public health practitioners in becoming culturally competent when educating on healthy eating patterns. The aim of this study is to provide a brief dietary profile of the total dietary fiber (TDF contents of selected traditional beverages in Egypt. Five cookbooks for Egyptian food recipes were reviewed for traditional beverages. Beverage recipes (n = 19 were selected and reviewed for their TDF content using the United States Department of Agriculture (USDA National Nutrient Database for Standard Reference (Release 27. The published values for TDF content were tabulated and reported per 100 mL of consumable portions. The highest TDF content was found in carob juice (8.0 g and the lowest found in peppermint tea (0.0 g with an overall TDF mean content of 2.8 g. Traditional beverages could be regarded as important sources of TDF within a healthy Egyptian dietary pattern. Cultural awareness and familiarities to traditional foods and their respective dietary profiles should be encouraged as an objective towards building culturally-competent health professionals and combating obesity in Egypt. Furthermore, developments of a traditional Egyptian food nutrient database for public access should be explored.

  17. Sensitive Wavelengths Selection in Identification of Ophiopogon japonicus Based on Near-Infrared Hyperspectral Imaging Technology

    Directory of Open Access Journals (Sweden)

    Zhengyan Xia

    2017-01-01

    Full Text Available Hyperspectral imaging (HSI technology has increasingly been applied as an analytical tool in fields of agricultural, food, and Traditional Chinese Medicine over the past few years. The HSI spectrum of a sample is typically achieved by a spectroradiometer at hundreds of wavelengths. In recent years, considerable effort has been made towards identifying wavelengths (variables that contribute useful information. Wavelengths selection is a critical step in data analysis for Raman, NIRS, or HSI spectroscopy. In this study, the performances of 10 different wavelength selection methods for the discrimination of Ophiopogon japonicus of different origin were compared. The wavelength selection algorithms tested include successive projections algorithm (SPA, loading weights (LW, regression coefficients (RC, uninformative variable elimination (UVE, UVE-SPA, competitive adaptive reweighted sampling (CARS, interval partial least squares regression (iPLS, backward iPLS (BiPLS, forward iPLS (FiPLS, and genetic algorithms (GA-PLS. One linear technique (partial least squares-discriminant analysis was established for the evaluation of identification. And a nonlinear calibration model, support vector machine (SVM, was also provided for comparison. The results indicate that wavelengths selection methods are tools to identify more concise and effective spectral data and play important roles in the multivariate analysis, which can be used for subsequent modeling analysis.

  18. Identification of ligand-selective peptidic ActRIIB-antagonists using phage display technology

    Directory of Open Access Journals (Sweden)

    Kotaro Sakamoto

    2017-09-01

    Full Text Available ActRIIB (activin receptor type-2B is an activin receptor subtype constitutively expressed in the whole body, playing a role in cellular proliferation, differentiation, and metabolism. For its various physiological activities, ActRIIB interacts with activin and multiple other ligands including myostatin (MSTN, growth differentiation factor 11 (GDF11, and bone morphogenetic protein 9 (BMP9. Notably, the protein-protein interaction (PPI between ActRIIB and MSTN negatively controls muscular development. Therefore, this PPI has been targeted for effective treatment of muscle degenerative diseases such as muscular dystrophy and sarcopenia. Here, we report the identification of ligand-selective peptidic ActRIIB-antagonists by phage display technology. Our peptides bound to the extracellular domain of ActRIIB, inhibited PPIs between ActRIIB expressed on the cell surface and its ligands, and subsequently suppressed activation of Smad that serves as the downstream signal of the ActRIIB pathway. Interestingly, these peptidic antagonists displayed different ligand selectivities; the AR2mini peptide inhibited multiple ligands (activin A, MSTN, GDF11, and BMP9, AR9 inhibited MSTN and GDF11, while AR8 selectively inhibited MSTN. This is the first report of artificial peptidic ActRIIB-antagonists possessing ligand-selectivity.

  19. Profiles

    International Nuclear Information System (INIS)

    2004-01-01

    Profiles is a synthetic overview of more than 100 national energy markets in the world, providing insightful facts and key energy statistics. A Profile is structured around 6 main items and completed by key statistics: Ministries, public agencies, energy policy are concerned; main companies in the oil, gas, electricity and coal sectors, status, shareholders; reserve, production, imports and exports, electricity and refining capacities; deregulation of prices, subsidies, taxes; consumption trends by sector, energy market shares; main energy projects, production and consumption prospects. Statistical Profiles are present in about 3 pages the main data and indicators on oil, gas, coal and electricity. (A.L.B.)

  20. Identification of transcription factors potential related to brown planthopper resistance in rice via microarray expression profiling

    Directory of Open Access Journals (Sweden)

    Wang Yubing

    2012-12-01

    Full Text Available Abstract Background Brown planthopper (BPH, Nilaparvata lugens Stål, is one of the most destructive insect pests of rice. The molecular responses of plants to sucking insects resemble responses to pathogen infection. However, the molecular mechanism of BPH-resistance in rice remains unclear. Transcription factors (TF are up-stream regulators of various genes that bind to specific DNA sequences, thereby controlling the transcription from DNA to mRNA. They are key regulators for transcriptional expression in biological processes, and are probably involved in the BPH-induced pathways in resistant rice varieties. Results We conducted a microarray experiment to analyze TF genes related to BPH resistance in a Sri Lankan rice cultivar, Rathu Heenati (RHT. We compared the expression profiles of TF genes in RHT with those of the susceptible rice cultivar Taichun Native 1 (TN1. We detected 2038 TF genes showing differential expression signals between the two rice varieties. Of these, 442 TF genes were probably related to BPH-induced resistance in RHT and TN1, and 229 may be related to constitutive resistance only in RHT. These genes showed a fold change (FC of more than 2.0 (P10, there were 37 induced TF genes and 26 constitutive resistance TF genes. Of these, 13 were probably involved in BPH-induced resistance, and 8 in constitutive resistance to BPH in RHT. Conclusions We explored the molecular mechanism of resistance to BPH in rice by comparing expressions of TF genes between RHT and TN1. We speculate that the level of gene repression, especially for early TF genes, plays an important role in the defense response. The fundamental point of the resistance strategy is that plants protect themselves by reducing their metabolic level to inhibit feeding by BPH and prevent damage from water and nutrient loss. We have selected 21 TF genes related to BPH resistance for further analyses to understand the molecular responses to BPH feeding in rice.

  1. Sugarcane genes differentially expressed in response to Puccinia melanocephala infection: identification and transcript profiling.

    Science.gov (United States)

    Oloriz, María I; Gil, Víctor; Rojas, Luis; Portal, Orelvis; Izquierdo, Yovanny; Jiménez, Elio; Höfte, Monica

    2012-05-01

    Brown rust caused by the fungus Puccinia melanocephala is a major disease of sugarcane (Saccharum spp.). A sugarcane mutant, obtained by chemical mutagenesis of the susceptible variety B4362, showed a post-haustorial hypersensitive response (HR)-mediated resistance to the pathogen and was used to identify genes differentially expressed in response to P. melanocephala via suppression subtractive hybridization (SSH). Tester cDNA was derived from the brown rust-resistant mutant after inoculation with P. melanocephala, while driver cDNAs were obtained from the non-inoculated resistant mutant and the inoculated susceptible donor variety B4362. Database comparisons of the sequences of the SSH recombinant clones revealed that, of a subset of 89 non-redundant sequences, 88% had similarity to known functional genes, while 12% were of unknown function. Thirteen genes were selected for transcript profiling in the resistant mutant and the susceptible donor variety. Genes involved in glycolysis and C4 carbon fixation were up-regulated in both interactions probably due to disturbance of sugarcane carbon metabolism by the pathogen. Genes related with the nascent polypeptide associated complex, post-translational proteome modulation and autophagy were transcribed at higher levels in the compatible interaction. Up-regulation of a putative L-isoaspartyl O-methyltransferase S-adenosylmethionine gene in the compatible interaction may point to fungal manipulation of the cytoplasmatic methionine cycle. Genes coding for a putative no apical meristem protein, S-adenosylmethionine decarboxylase, non-specific lipid transfer protein, and GDP-L-galactose phosphorylase involved in ascorbic acid biosynthesis were up-regulated in the incompatible interaction at the onset of haustorium formation, and may contribute to the HR-mediated defense response in the rust-resistant mutant.

  2. Gene expression profiles in prostate cancer: identification of candidate non-invasive diagnostic markers.

    Science.gov (United States)

    Mengual, L; Ars, E; Lozano, J J; Burset, M; Izquierdo, L; Ingelmo-Torres, M; Gaya, J M; Algaba, F; Villavicencio, H; Ribal, M J; Alcaraz, A

    2014-04-01

    To analyze gene expression profiles of prostate cancer (PCa) with the aim of determining the relevant differentially expressed genes and subsequently ascertain whether this differential expression is maintained in post-prostatic massage (PPM) urine samples. Forty-six tissue specimens (36 from PCa patients and 10 controls) and 158 urine PPM-urines (113 from PCa patients and 45 controls) were collected between December 2003 and May 2007. DNA microarrays were used to identify genes differentially expressed between tumour and control samples. Ten genes were technically validated in the same tissue samples by quantitative RT-PCR (RT-qPCR). Forty two selected differentially expressed genes were validated in an independent set of PPM-urines by qRT-PCR. Multidimensional scaling plot according to the expression of all the microarray genes showed a clear distinction between control and tumour samples. A total of 1047 differentially expressed genes (FDR≤.1) were indentified between both groups of samples. We found a high correlation in the comparison of microarray and RT-qPCR gene expression levels (r=.928, P<.001). Thirteen genes maintained the same fold change direction when analyzed in PPM-urine samples and in four of them (HOXC6, PCA3, PDK4 and TMPRSS2-ERG), these differences were statistically significant (P<.05). The analysis of PCa by DNA microarrays provides new putative mRNA markers for PCa diagnosis that, with caution, can be extrapolated to PPM-urines. Copyright © 2013 AEU. Published by Elsevier Espana. All rights reserved.

  3. An Approach to Near Field Data Selection in Radio Frequency Identification

    Science.gov (United States)

    Winkworth, Robert D.

    Personal identification is needed in many civil activities, and the common identification cards, such as a driver's license, have become the standard document de facto. Radio frequency identification has complicated this matter. Unlike their printed predecessors, contemporary RFID cards lack a practical way for users to control access to their individual fields of data. This leaves them more available to unauthorized parties, and more prone to abuse. Here, then was undertaken a means to test a novel RFID card technology that allows overlays to be used for reliable, reversible data access settings. Similar to other proposed switching mechanisms, it offers advantages that may greatly improve outcomes. RFID use is increasing in identity documents such as drivers' licenses and passports, and with it concern over the theft of personal information, which can enable unauthorized tracking or fraud. Effort put into designing a strong foundation technology now may allow for widespread development on them later. In this dissertation, such a technology was designed and constructed, to drive the central thesis that selective detuning could serve as a feasible, reliable mechanism. The concept had been illustrated effective in limiting access to all fields simultaneously before, and was here effective in limiting access to specific fields selectively. A novel card was produced in familiar dimensions, with an intuitive interface by which users may conceal the visible print of the card to conceal the wireless emissions it allows. A discussion was included of similar technologies, involving capacitive switching, that could further improve the outcomes if such a product were put to large-scale commercial fabrication. The card prototype was put to a battery of laboratory tests to measure the degree of independence between data fields and the reliability of the switching mechanism when used under realistically variable coverage, demonstrating statistically consistent performance in

  4. Identification and characterization of earthquake clusters: a comparative analysis for selected sequences in Italy

    Science.gov (United States)

    Peresan, Antonella; Gentili, Stefania

    2017-04-01

    Identification and statistical characterization of seismic clusters may provide useful insights about the features of seismic energy release and their relation to physical properties of the crust within a given region. Moreover, a number of studies based on spatio-temporal analysis of main-shocks occurrence require preliminary declustering of the earthquake catalogs. Since various methods, relying on different physical/statistical assumptions, may lead to diverse classifications of earthquakes into main events and related events, we aim to investigate the classification differences among different declustering techniques. Accordingly, a formal selection and comparative analysis of earthquake clusters is carried out for the most relevant earthquakes in North-Eastern Italy, as reported in the local OGS-CRS bulletins, compiled at the National Institute of Oceanography and Experimental Geophysics since 1977. The comparison is then extended to selected earthquake sequences associated with a different seismotectonic setting, namely to events that occurred in the region struck by the recent Central Italy destructive earthquakes, making use of INGV data. Various techniques, ranging from classical space-time windows methods to ad hoc manual identification of aftershocks, are applied for detection of earthquake clusters. In particular, a statistical method based on nearest-neighbor distances of events in space-time-energy domain, is considered. Results from clusters identification by the nearest-neighbor method turn out quite robust with respect to the time span of the input catalogue, as well as to minimum magnitude cutoff. The identified clusters for the largest events reported in North-Eastern Italy since 1977 are well consistent with those reported in earlier studies, which were aimed at detailed manual aftershocks identification. The study shows that the data-driven approach, based on the nearest-neighbor distances, can be satisfactorily applied to decompose the seismic

  5. Terverticillate penicillia studied by direct electrospray mass spectrometric profiling of crude extracts II. Database and identification

    DEFF Research Database (Denmark)

    Smedsgaard, Jørn

    1997-01-01

    A mass spectral database was built using standard instrument software from 678 electrospray mass spectra (mass profiles) from crude fungal extracts of terverticillate taxa within the genus Penicillium. The match factors calculated from searching all the mass profiles stored in the database were...

  6. Long-term forecasting of hourly electricity load: Identification of consumption profiles and segmentation of customers

    DEFF Research Database (Denmark)

    Møller Andersen, Frits; Larsen, Helge V.; Boomsma, Trine Krogh

    2013-01-01

    , to model and forecast long-term changes in the aggregated electricity load profile, we identify profiles for different categories of customers and link these to projections of the aggregated annual consumption by categories of customers. Long-term projection of the aggregated load is important for future......Data for aggregated hourly electricity demand shows systematic variations over the day, week, and seasons, and forecasting of aggregated hourly electricity load has been the subject of many studies. With hourly metering of individual customers, data for individual consumption profiles is available....... Using this data and analysing the case of Denmark, we show that consumption profiles for categories of customers are equally systematic but very different for distinct categories, that is, distinct categories of customers contribute differently to the aggregated electricity load profile. Therefore...

  7. Marketing on Social Networks: Content Analysis of Facebook Profiles of Selected Czech E-shops

    Directory of Open Access Journals (Sweden)

    Jiří Čeněk

    2016-09-01

    Full Text Available Purpose of the article: The research focused on the identification of types and frequencies of posts added by e-shops and the reactions of fans to the posts. Three e-shops were analysed: Alza.cz, Czc.cz and Mironet.cz. Several categories were selected as qualitative units of analysis of communication between e-shops and fans, the frequencies of all the selected categories were measured and correlations between selected variables were calculated. Methodology/methods: The main research method was quantitative content analysis, which allows the gathering of large numbers of qualitative data and transforming them into data of quantitative nature that can be the subject of further statistical analysis. In case of interesting quantitative findings, a qualitative explanation was used. Both communication from e-shops to fans and communication from fans to e-shops (and among fans in the years 2011–2015 were analysed. Scientific aim: The objective of the research presented in this article is based on content analysis to evaluate the level of the Facebook communication of selected Czech e-shops with consumer electronics within 2011–2015 using a quantitative content analysis method. Findings: The results show that the posting frequency of all the analysed e-shops is between 1.5–4 days. The e-shops vary in the most frequent types of posts. Posts that elicited the highest numbers of reactions were characteristic with their viral nature. A strong, statistically significant correlation between the number of fans of the fan page and the frequency of their reactions to the posts was found. Conclusions: All of the analysed e-shops should increase the frequency of contact with their fans through more frequent posting and modification in the content of the posts. Based on findings, the several suggestions for effective and successful managing the Facebook activities are served.

  8. The photon identification loophole in EPRB experiments: computer models with single-wing selection

    Directory of Open Access Journals (Sweden)

    De Raedt Hans

    2017-11-01

    Full Text Available Recent Einstein-Podolsky-Rosen-Bohm experiments [M. Giustina et al. Phys. Rev. Lett. 115, 250401 (2015; L. K. Shalm et al. Phys. Rev. Lett. 115, 250402 (2015] that claim to be loophole free are scrutinized. The combination of a digital computer and discrete-event simulation is used to construct a minimal but faithful model of the most perfected realization of these laboratory experiments. In contrast to prior simulations, all photon selections are strictly made, as they are in the actual experiments, at the local station and no other “post-selection” is involved. The simulation results demonstrate that a manifestly non-quantum model that identifies photons in the same local manner as in these experiments can produce correlations that are in excellent agreement with those of the quantum theoretical description of the corresponding thought experiment, in conflict with Bell’s theorem which states that this is impossible. The failure of Bell’s theorem is possible because of our recognition of the photon identification loophole. Such identification measurement-procedures are necessarily included in all actual experiments but are not included in the theory of Bell and his followers.

  9. 4-Alkylated homoibotenic acid (HIBO) analogues: versatile pharmacological agents with diverse selectivity profiles towards metabotropic and ionotropic glutamate receptor subtypes

    DEFF Research Database (Denmark)

    Madsen, Ulf; Pickering, Darryl S; Nielsen, Birgitte

    2005-01-01

    4-Alkylated analogues of homoibotenic acid (HIBO) have previously shown high potency and selectivity at ionotropic and metabotropic glutamic acid receptor (iGluR and mGluR) subtypes. Compounds with different selectivity profiles are valuable pharmacological tools for neuropharmacological studies...

  10. Use of the "Intervention Selection Profile-Social Skills" to Identify Social Skill Acquisition Deficits: A Preliminary Validation Study

    Science.gov (United States)

    Kilgus, Stephen P.; von der Embse, Nathaniel P.; Scott, Katherine; Paxton, Sara

    2015-01-01

    The purpose of this investigation was to develop and initially validate the "Intervention Selection Profile-Social Skills" (ISP-SS), a novel brief social skills assessment method intended for use at Tier 2. Participants included 54 elementary school teachers and their 243 randomly selected students. Teachers rated students on two rating…

  11. Identification of some Fusarium species from selected crop seeds using traditional method and BIO-PCR

    Directory of Open Access Journals (Sweden)

    Tomasz Kulik

    2012-12-01

    Full Text Available We identified a species level of the fungal cultures isolated from selected crop seeds using traditional method and BIO-PCR. The use of BIO-PCR did not correspond completely to the morphological analyses. Both methods showed increased infection with F. poae in winter wheat seed sample originated from north Poland. Fungal culture No 40 (isolated from faba bean and identified with traditional method as mixed culture with F. culmorum and F. graminearum did not produce expected product after PCR reaction with species specific primers OPT18F470, OPT18R470. However, the use of additional primers Fc01F, Fc01R allowed for reliable identification of F. culmorum in the culture.

  12. Identification of transcription factors potential related to brown planthopper resistance in rice via microarray expression profiling.

    Science.gov (United States)

    Wang, Yubing; Guo, Huimin; Li, Haichao; Zhang, Hao; Miao, Xuexia

    2012-12-10

    Brown planthopper (BPH), Nilaparvata lugens Stål, is one of the most destructive insect pests of rice. The molecular responses of plants to sucking insects resemble responses to pathogen infection. However, the molecular mechanism of BPH-resistance in rice remains unclear. Transcription factors (TF) are up-stream regulators of various genes that bind to specific DNA sequences, thereby controlling the transcription from DNA to mRNA. They are key regulators for transcriptional expression in biological processes, and are probably involved in the BPH-induced pathways in resistant rice varieties. We conducted a microarray experiment to analyze TF genes related to BPH resistance in a Sri Lankan rice cultivar, Rathu Heenati (RHT). We compared the expression profiles of TF genes in RHT with those of the susceptible rice cultivar Taichun Native 1 (TN1). We detected 2038 TF genes showing differential expression signals between the two rice varieties. Of these, 442 TF genes were probably related to BPH-induced resistance in RHT and TN1, and 229 may be related to constitutive resistance only in RHT. These genes showed a fold change (FC) of more than 2.0 (Pgenes related to BPH-induced resistance, most of them were readily induced in TN1 than in RHT by BPH feeding, for instance, 154 TF genes were up-regulated in TN1, but only 31 TF genes were up-regulated in RHT at 24 hours after BPH infestation; 2-4 times more TF genes were induced in TN1 than in RHT by BPH. At an FC threshold of >10, there were 37 induced TF genes and 26 constitutive resistance TF genes. Of these, 13 were probably involved in BPH-induced resistance, and 8 in constitutive resistance to BPH in RHT. We explored the molecular mechanism of resistance to BPH in rice by comparing expressions of TF genes between RHT and TN1. We speculate that the level of gene repression, especially for early TF genes, plays an important role in the defense response. The fundamental point of the resistance strategy is that plants

  13. Maximizing Selective Cleavages at Aspartic Acid and Proline Residues for the Identification of Intact Proteins

    Science.gov (United States)

    Foreman, David J.; Dziekonski, Eric T.; McLuckey, Scott A.

    2018-04-01

    A new approach for the identification of intact proteins has been developed that relies on the generation of relatively few abundant products from specific cleavage sites. This strategy is intended to complement standard approaches that seek to generate many fragments relatively non-selectively. Specifically, this strategy seeks to maximize selective cleavage at aspartic acid and proline residues via collisional activation of precursor ions formed via electrospray ionization (ESI) under denaturing conditions. A statistical analysis of the SWISS-PROT database was used to predict the number of arginine residues for a given intact protein mass and predict a m/z range where the protein carries a similar charge to the number of arginine residues thereby enhancing cleavage at aspartic acid residues by limiting proton mobility. Cleavage at aspartic acid residues is predicted to be most favorable in the m/z range of 1500-2500, a range higher than that normally generated by ESI at low pH. Gas-phase proton transfer ion/ion reactions are therefore used for precursor ion concentration from relatively high charge states followed by ion isolation and subsequent generation of precursor ions within the optimal m/z range via a second proton transfer reaction step. It is shown that the majority of product ion abundance is concentrated into cleavages C-terminal to aspartic acid residues and N-terminal to proline residues for ions generated by this process. Implementation of a scoring system that weights both ion fragment type and ion fragment area demonstrated identification of standard proteins, ranging in mass from 8.5 to 29.0 kDa. [Figure not available: see fulltext.

  14. Comparison of behavioral profiles for anxiety-related comorbidities including ADHD and selective mutism in children.

    Science.gov (United States)

    Levin-Decanini, Tal; Connolly, Sucheta D; Simpson, David; Suarez, Liza; Jacob, Suma

    2013-09-01

    Elucidating differences in social-behavioral profiles of children with comorbid presentations, utilizing caregiver as well as teacher reports, will refine our understanding of how contextual symptoms vary across anxiety-related disorders. In our pediatric anxiety clinic, the most frequent diagnoses and comorbidities were mixed anxiety (MA; ≥ 1 anxiety disorder; N = 155), anxiety with comorbid attention-deficit hyperactivity disorder (MA/ADHD, N = 47) and selective mutism (SM, N = 48). Behavioral measures (CPRS, CTRS) were analyzed using multiple one-way multivariate analyses of covariance tests. Differences between the three diagnostic groups were examined using completed parent and teacher reports (N = 135, 46, and 48 for MA, MA/ADHD, and SM groups, respectively). Comparisons across the MA, MA/ADHD, and SM groups indicate a significant multivariate main effect of group for caregiver and teacher responses (P < 0.01). Caregivers reported that children with SM are similar in profile to those with MA, and both groups were significantly different from the MA/ADHD group. Teachers reported that children with SM had more problems with social behaviors than with the MA or MA/ADHD groups. Further comparison indicates a significant main effect of group (P < 0.001), such that children with SM have the greatest differences in behavior observed by teachers versus caregivers. Clinical profiles between MA/ADHD, MA, and SM groups varied, illustrating the importance of multi-rater assessment scales to capture subtle distinctions and to inform treatment planning given that comorbidities occur frequently in children who present with anxiety. © 2013 Wiley Periodicals, Inc.

  15. Selecting Effective Means to Any End: Futures and Ethics of Persuasion Profiling

    Science.gov (United States)

    Kaptein, Maurits; Eckles, Dean

    Interactive persuasive technologies can and do adapt to individuals. Existing systems identify and adapt to user preferences within a specific domain: e.g., a music recommender system adapts its recommended songs to user preferences. This paper is concerned with adaptive persuasive systems that adapt to individual differences in the effectiveness of particular means, rather than selecting different ends. We give special attention to systems that implement persuasion profiling - adapting to individual differences in the effects of influence strategies. We argue that these systems are worth separate consideration and raise unique ethical issues for two reasons: (1) their end-independence implies that systems trained in one context can be used in other, unexpected contexts and (2) they do not rely on - and are generally disadvantaged by - disclosing that they are adapting to individual differences. We use examples of these systems to illustrate some ethically and practically challenging futures that these characteristics make possible.

  16. Optimal Selection of Clustering Algorithm via Multi-Criteria Decision Analysis (MCDA for Load Profiling Applications

    Directory of Open Access Journals (Sweden)

    Ioannis P. Panapakidis

    2018-02-01

    Full Text Available Due to high implementation rates of smart meter systems, considerable amount of research is placed in machine learning tools for data handling and information retrieval. A key tool in load data processing is clustering. In recent years, a number of researches have proposed different clustering algorithms in the load profiling field. The present paper provides a methodology for addressing the aforementioned problem through Multi-Criteria Decision Analysis (MCDA and namely, using the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS. A comparison of the algorithms is employed. Next, a single test case on the selection of an algorithm is examined. User specific weights are applied and based on these weight values, the optimal algorithm is drawn.

  17. Children's and parent's psychological profiles in selective mutism and generalized anxiety disorder: a clinical study.

    Science.gov (United States)

    Capozzi, Flavia; Manti, Filippo; Di Trani, Michela; Romani, Maria; Vigliante, Miriam; Sogos, Carla

    2017-10-28

    Selective mutism (SM) is classified in DSM-5 as an anxiety disorder. The aim of the study was to investigate the psychological features of children with SM and their parental psychological profiles, compared to generalized anxiety disorder (GAD) children and their parents. The parents of 26 preschool children with SM and 32 with children with GAD filled out the child behavior check list for 1½-5 years (CBCL1½-5) and the symptom checklist-90-revised (SCL-90-R). Information about the children and their parents' histories was collected through clinical interviews. Children with SM scored higher than children with GAD on the CBCL1½-5 withdrawn scale and lower on the attention problems, aggressive behavior, and externalizing problems scales. Mothers of children with SM scored higher on the SCL-90-R obsessive-compulsive subscale and Global Severity Index than mothers of children with GAD, while fathers of children with SM scored higher on the SCL-90-R Phobic Anxiety subscale and on the Global Severity Index than fathers of children with GAD. Parents of children with SM displayed a greater presence of stressful life events than parents of children with GAD. Data appeared to confirm that SM and GAD share a common anxious core, though some differences in the children's psychological profiles and the parents' history and personality emerged. Future research should focus on the role of external factors, such as parent-child relationship, in the development of SM.

  18. Effect of irradiation on total chemical profiles of ten selected local herbs

    International Nuclear Information System (INIS)

    Salmah Moosa; Maizatul Akmam Mohd Nasir

    2010-01-01

    As utilisation of medicinal herbs in food and bio industry increases, mass production and the supply of high quality herbs are required. Restriction on the use of fumigants and preservatives on herbs demands safe hygienic technologies such as irradiation. The stability of the active components of ten local herbs after irradiation was studied. The herbs selected were Hempedu Bumi, Mas Cotek, Tongkat Ali, Kacip Fatimah, Misai Kucing, Dukung Anak, Jarum Tujuh Bilah, Kesom, Pegaga and Sambung Nyawa. The herbs were dried, powdered and irradiated at different doses of gamma radiation (0, 1, 3, 5, 10, 15 and 25 kGy) at room temperature prior to extraction. The herbs were then extracted either in methanol or chloroform and freeze dried. About 10.0 mg of each extract (in triplicates) were weighed into an Eppendorf vial and solubilised in 700 μl CD 3 OD using sonication in an ultrasound bath to obtain a clear solution. This solution was then transferred to a NMR vial and a 1H-NMR spectrum was acquired according to standard Total Quality Profile (TQP) protocol. The results of the statistical analysis showed clearly that all irradiated plant samples did not exhibit any significant pattern of differences. Using SIMCA analysis, we found that there is no statistical basis for separation of control, 1, 5, 10, 15 and 25 kGy irradiated samples on a 95 % confidence limit. TQP analysis for the ten selected herbal plant shows that irradiation up to 25 kGy did not cause significant changes to the total chemical profiles and thus the integrity of the herbal material in the analysed plants. (author)

  19. Identification of a putative protein-profile associating with tamoxifen therapy-resistance in breast cancer

    NARCIS (Netherlands)

    A. Umar (Arzu); J.W.M. Martens (John); J.A. Foekens (John); L. Paša-Tolić (Ljiljana); H. Kang; A.M. Timmermans (Mieke); M.P. Look (Maxime); M.E. Meijer van Gelder (Marion); N. Jaitly (Navdeep); M.A. den Bakker (Michael)

    2009-01-01

    textabstractTamoxifen-resistance is a major cause of death in patients with recurrent breast cancer. Current clinical parameters can correctly predict therapy response in only half of the treated patients. Identification of proteins that associate with tamoxifen-resistance is a first step towards

  20. Expression profile of genes during resistance reversal in a temephos selected strain of the dengue vector, Aedes aegypti.

    Directory of Open Access Journals (Sweden)

    Clare Strode

    Full Text Available BACKGROUND: The mosquito Aedes aegypti is one of the most important disease vectors because it transmits two major arboviruses, dengue and yellow fever, which cause significant global morbidity and mortality. Chemical insecticides form the cornerstone of vector control. The organophosphate temephos a larvicide recommended by WHO for controlling Ae. aegypti, however, resistance to this compound has been reported in many countries, including Brazil. METHODOLOGY/PRINCIPAL FINDINGS: The aim of this study was to identify genes implicated in metabolic resistance in an Ae. aegypti temephos resistant strain, named RecR, through microarray analysis. We utilized a custom 'Ae. aegypti detox chip' and validated microarray data through RT-PCR comparing susceptible and resistant individuals. In addition, we analyzed gene expression in 4(th instar larvae from a reversed susceptible strain (RecRev, exposed and unexposed to temephos. The results obtained revealed a set of 13 and 6 genes significantly over expressed in resistant adult mosquitoes and larvae, respectively. One of these genes, the cytochrome P450 CYP6N12, was up-regulated in both stages. RT-PCR confirmed the microarray results and, additionally, showed no difference in gene expression between temephos exposed and unexposed RecRev mosquitoes. This suggested that the differences in the transcript profiles among the strains are heritable due to a selection process and are not caused by immediate insecticide exposure. Reversal of temephos resistance was demonstrated and, importantly, there was a positive correlation between a decrease in the resistance ratio and an accompanying decrease in the expression levels of previously over expressed genes. Some of the genes identified here have also been implicated in metabolic resistance in other mosquito species and insecticide resistant populations of Ae. aegypti. CONCLUSIONS/SIGNIFICANCE: The identification of gene expression signatures associated to

  1. Identification of kin structure among Guam rail founders: a comparison of pedigrees and DNA profiles

    Science.gov (United States)

    Haig, Susan M.; Ballou, J.D.; Casna, N.J.

    1994-01-01

    Kin structure among founders can have a significant effect on subsequent population structure. Here we use the correlation between DNA profile similarity and relatedness calculated from pedigrees to test hypotheses regarding kin structure among founders to the captive Guam rail (Rallus owstoni) population. Five different pedigrees were generated under the following hypotheses: (i) founders are unrelated; (ii) founders are unrelated except for same-nest chicks; (iii) founders from the same major site are siblings; (iv) founders from the same local site are siblings; and (v) founders are related as defined by a UPGMA cluster analysis of DNA similarity data. Relatedness values from pedigrees 1, 2 and 5 had the highest correlation with DNA similarity but the correlation between relatedness and similarity were not significantly different among pedigrees. Pedigree 5 resulted in the highest correlation overall when using only relatedness values that changed as a result of different founder hypotheses. Thus, founders were assigned relatedness based on pedigree 5 because it had the highest correlations with DNA similarity, was the most conservative approach, and incorporated all field data. The analyses indicated that estimating relatedness using DNA profiles remains problematic, therefore we compared mean kinship, a measure of genetic importance, with mean DNA profile similarity to determine if genetic importance among individuals could be determined via use of DNA profiles alone. The significant correlation suggests this method may provide more information about population structure than was previously thought. Thus, DNA profiles can provide a reasonable explanation for founder relatedness and mean DNA profile similarity may be helpful in determining relative genetic importance of individuals when detailed pedigrees are absent.

  2. Preliminary Identification of Coping Profiles Relevant to Surrogate Decision Making in the ICU.

    Directory of Open Access Journals (Sweden)

    Jorie M Butler

    Full Text Available The Intensive Care Unit (ICU is a stressful environment for families of critically ill patients and these individuals are at risk to develop persistent psychological morbidity. Our study objective was to identify individual differences in coping with stress and information presentation preferences of respondents exposed to a simulated ICU experience.Participants were recruited from a university and two community populations. Participants completed questionnaires that measured demographic information and characteristics that may be relevant to an individual's ICU experience. Quality of life was measured by the EQ-5D, personality dimensions were examined with the abbreviated Big Five inventory, coping with stress was assessed with Brief COPE. Shared decision making preferences were assessed by the Degner Control Preferences Scale (CPS and information seeking style was assessed with the Miller Behavioral Style Scale (MBSS. Social support was examined using an abbreviated version of the Social Relationship Index. Participants also completed a vignette-based simulated ICU experience, in which they made a surrogate decision on behalf of a loved one in the ICU.Three hundred forty-three participants completed the study. Three distinct coping profiles were identified: adaptive copers, maladaptive copers, and disengaged copers. Profiles differed primarily on coping styles, personality, quality of their closest social relationship, and history of anxiety and depression. Responses to the simulated ICU decision making experience differed across profiles. Disengaged copers (15% were more likely to elect to refuse dialysis on behalf of an adult sibling compared to adaptive copers (7% or maladaptive copers (5% (p = 0.03. Notably, the MBSS and the CPS did not differ by coping profile.Distinct coping profiles are associated with differences in responses to a simulated ICU experience. Tailoring communication and support to specific coping profiles may represent an

  3. Identification of petroleum hydrocarbons using a reduced number of PAHs selected by Procrustes rotation.

    Science.gov (United States)

    Fernández-Varela, R; Andrade, J M; Muniategui, S; Prada, D; Ramírez-Villalobos, F

    2010-04-01

    Identifying petroleum-related products released into the environment is a complex and difficult task. To achieve this, polycyclic aromatic hydrocarbons (PAHs) are of outstanding importance nowadays. Despite traditional quantitative fingerprinting uses straightforward univariate statistical analyses to differentiate among oils and to assess their sources, a multivariate strategy based on Procrustes rotation (PR) was applied in this paper. The aim of PR is to select a reduced subset of PAHs still capable of performing a satisfactory identification of petroleum-related hydrocarbons. PR selected two subsets of three (C(2)-naphthalene, C(2)-dibenzothiophene and C(2)-phenanthrene) and five (C(1)-decahidronaphthalene, naphthalene, C(2)-phenanthrene, C(3)-phenanthrene and C(2)-fluoranthene) PAHs for each of the two datasets studied here. The classification abilities of each subset of PAHs were tested using principal components analysis, hierarchical cluster analysis and Kohonen neural networks and it was demonstrated that they unraveled the same patterns as the overall set of PAHs. (c) 2009 Elsevier Ltd. All rights reserved.

  4. Primary selection into shift work and change of cardiovascular risk profile.

    Science.gov (United States)

    Yong, Mei; Germann, Christina; Lang, Stefan; Oberlinner, Christoph

    2015-05-01

    A potential "healthy shift worker effect" may bias the studied effect of shift work on health. The observed differences among shift and day workers in health behavior and health outcomes can be caused by: (i) primary selection, (ii) the influence from the shift work-related environment, and (iii) the impact of shift work. We aimed to study these potential sources. A cohort of 4754 male trainees who had finished their professional training and started their career in production in a chemical company between 1995 and 2012 was identified. Among them, 1348 (28%) were involved in rotating shift work and 3406 (72%) in day work. Information on health behavior and risk factors for cardiovascular diseases was retrieved from the medical examinations. This information was then compared (i) at the beginning of training, (ii) at the end of training, and (iii) 3 years after the employment, in relation to the working time. At the beginning of the training, the prevalence of smokers was higher among future shift workers (26% versus 21%), from 1995 to 2012. During the training and the first three years of employment, a marginal decline of systolic blood pressure and an elevation of triglyceride were related with shift work. No difference was found with respect to other risk factors for cardiovascular diseases. Our findings do not support a primary selection in favor of shift workers. An impact of shift work on the risk profile of cardiovascular diseases was not indicated in the observation period.

  5. Transcriptome profile and unique genetic evolution of positively selected genes in yak lungs.

    Science.gov (United States)

    Lan, DaoLiang; Xiong, XianRong; Ji, WenHui; Li, Jian; Mipam, Tserang-Donko; Ai, Yi; Chai, ZhiXin

    2018-04-01

    The yak (Bos grunniens), which is a unique bovine breed that is distributed mainly in the Qinghai-Tibetan Plateau, is considered a good model for studying plateau adaptability in mammals. The lungs are important functional organs that enable animals to adapt to their external environment. However, the genetic mechanism underlying the adaptability of yak lungs to harsh plateau environments remains unknown. To explore the unique evolutionary process and genetic mechanism of yak adaptation to plateau environments, we performed transcriptome sequencing of yak and cattle (Bos taurus) lungs using RNA-Seq technology and a subsequent comparison analysis to identify the positively selected genes in the yak. After deep sequencing, a normal transcriptome profile of yak lung that containing a total of 16,815 expressed genes was obtained, and the characteristics of yak lungs transcriptome was described by functional analysis. Furthermore, Ka/Ks comparison statistics result showed that 39 strong positively selected genes are identified from yak lungs. Further GO and KEGG analysis was conducted for the functional annotation of these genes. The results of this study provide valuable data for further explorations of the unique evolutionary process of high-altitude hypoxia adaptation in yaks in the Tibetan Plateau and the genetic mechanism at the molecular level.

  6. The Energy and Identification Continua of Burnout and Work Engagement : Developmental Profiles Over Eight Years

    OpenAIRE

    Mäkikangas, Anne; Hyvönen, Katriina; Feldt, Taru

    2017-01-01

    Understanding of the mutual developmental dynamics between burnout and work engagement is limited due to the lack of longitudinal studies with long follow-ups and multi-wave data. This study sought to identify subgroups of employees characterized by long-term exhaustion-vigor (energy continuum) and cynicism-dedication (identification continuum). A further important aim was to investigate differences between the identified subgroups in their experiences of progress in their personal work goals...

  7. Identification, Typing, Antifungal Resistance Profile, and Biofilm Formation of Candida albicans Isolates from Lebanese Hospital Patients

    Directory of Open Access Journals (Sweden)

    Ibrahim Bitar

    2014-01-01

    Full Text Available As leading opportunistic fungal pathogens identification and subtyping of Candida species are crucial in recognizing outbreaks of infection, recognizing particularly virulent strains, and detecting the emergence of drug resistant strains. In this study our objective was to compare identification of Candida albicans by the hospitals through the use of conventional versus identification based on the ITS (Internal Transcribed Spacer and to assess biofilm forming capabilities, drug resistance patterns and correlate these with MLST typing. ITS typing revealed a 21.2% hospital misidentification rate. Multidrug resistance to three drugs out of four tested was detected within 25% of the isolates raising concerns about the followed treatment regimens. Drug resistant strains as well as biofilm formers were phylogenetically related, with some isolates with significant biofilm forming capabilities being correlated to those that were multidrug resistant. Such isolates were grouped closely together in a neighbor-joining tree generated by MLST typing indicating phylogenetic relatedness, microevolution, or recurrent infection. In conclusion, this pilot study gives much needed insight concerning C. albicans isolates circulating in Lebanese hospitals and is the first study of its kind correlating biofilm formation, antifungal resistance, and evolutionary relatedness.

  8. Identification of drug targets by chemogenomic and metabolomic profiling in yeast

    KAUST Repository

    Wu, Manhong

    2012-12-01

    OBJECTIVE: To advance our understanding of disease biology, the characterization of the molecular target for clinically proven or new drugs is very important. Because of its simplicity and the availability of strains with individual deletions in all of its genes, chemogenomic profiling in yeast has been used to identify drug targets. As measurement of drug-induced changes in cellular metabolites can yield considerable information about the effects of a drug, we investigated whether combining chemogenomic and metabolomic profiling in yeast could improve the characterization of drug targets. BASIC METHODS: We used chemogenomic and metabolomic profiling in yeast to characterize the target for five drugs acting on two biologically important pathways. A novel computational method that uses a curated metabolic network was also developed, and it was used to identify the genes that are likely to be responsible for the metabolomic differences found. RESULTS AND CONCLUSION: The combination of metabolomic and chemogenomic profiling, along with data analyses carried out using a novel computational method, could robustly identify the enzymes targeted by five drugs. Moreover, this novel computational method has the potential to identify genes that are causative of metabolomic differences or drug targets. © 2012 Wolters Kluwer Health | Lippincott Williams & Wilkins.

  9. Protein profile of human hepatocarcinoma cell line SMMC-7721: Identification and functional analysis

    OpenAIRE

    Feng, Yi; Tian, Zhong-Min; Wan, Ming-Xi; Zheng, Zhao-Bin

    2007-01-01

    AIM: To investigate the protein profile of human hepatocarcinoma cell line SMMC-7721, to analyze the specific functions of abundant expressed proteins in the processes of hepatocarcinoma genesis, growth and metastasis, to identify the hepatocarcinoma-specific biomarkers for the early prediction in diagnosis, and to explore the new drug targets for liver cancer therapy.

  10. Periparturient Period in Terms of Body Condition Score and Selected Parameters of Hormonal Profiles

    Directory of Open Access Journals (Sweden)

    Vargová M.

    2016-03-01

    Full Text Available The majority of all diseases in dairy cows occur during the period from three weeks before parturition to three weeks after parturition, in the periparturient or transitional period. The objective of this study was to evaluate the dynamics of selected parameters of: the hormonal profiles, the body condition score (BCS and their interrelationships. The study was carried out on 15 dairy cows of the Slovak Pied Cattle, from three weeks before to nine weeks after parturition, which were divided into six groups. The concentrations of leptin during ante partum increased from 23.08 ± 10.58 ng.ml−1 to 26.80 ± 11.47 ng.ml−1, then gradually decreased (P > 0.05, and conversely, the concentrations of ghrelin before parturition were found to be decreasing and during the postpartal period, the concentrations increased, with the highest value of 35.94 ± 16.85 pg.ml−1. In the case of insulin, we found the opposite tendency of ghrelin. We observed significantly higher values of BCS in dry cows than in cows after parturition (P < 0.001. Comparing the BCS and the parameter of the hormonal profiles, we found both positive and negative correlations: leptin and ghrelin (r = −0.235, P < 0.05, and BCS and insulin (r = 0.232, P < 0.05, and BCS and leptin (r = 0.360, P < 0.001. The interrelationships between the hormones and the body condition score, provided evidence that the variations in concentrations of leptin, ghrelin and insulin were related to variations in the BCS.

  11. Polyphenol and Microbial Profile of On-farm Cocoa Beans Fermented with Selected Microbial Consortia

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    Tochukwu Vincent Balogu

    2017-09-01

    Full Text Available Background and Objective: Quality and preference of cocoa as raw material for various mcocoa products primarily depend on fermentation techniques that modulate the resultant flavour and the phytochemical properties. This study investigated the combined effect of selected microbial consortia and bioreactors on phytochemical profiles of fermented cocoa beans.Material and Methods: Three microbial consortia labeled as Treatments (T-1, T-2, T-3 were used as starter culture (≈105cells ml-1 for on-farm cocoa fermentation on three chambers (basket, woodbox, and plastic for 7 days. These novel consortia were T-1, Staphylococcus spp + Pseudomonas spp+ Bacillus spp, T-2, Staphylococcus spp + Pseudomonas spp +L. lactis, and T-3, Bacillus spp+ Lactobacillus spp + Saccharomyces spp+ Torulopsis spp.Results and Conclusion: The microbial profile were significantly (P≤0.05 altered by all treatments (T-1, T-2, T-3 and microbial frequency was enhanced by 5 -22.5%. T-3 and T-1 significantly altered phenolic content in basket chamber. Tannin was significantly (p≤0.05 varied by T-1(basket, plastic, wood box and T-2(plastic. Tannin: polyphenol conversion ratio adopted as fermented cocoa bean quality benchmark was significantly enhanced by T-1 (basket, woodbox and T-2 (plastic, but was significantly suppressed by T-3 (basket. This study evidently concluded that the appropriate synergy of microbial flora and fermenting chambers could achieve good cocoa quality with low polyphenol content (best for cocoa beverages or high polyphenol content (best for pharmaceutical, confectionery and nutraceutical industries. These findings would avail an economic alternative to the expensive polyphenol reconstitution of cocoa butter used for various industrial products, thereby maximizing economic benefits for both cocoa farmers and industrialists.Conflict of interest: The authors declare no conflict of interest.

  12. A Profile-Based Identification of Standby and Useless Electricity Consumption in Buildings

    OpenAIRE

    De Koster, Rien; Van Roy, Juan; Driesen, Johan

    2013-01-01

    Useless electricity consumption is the electricity consumption of an electric appliance or system that is not performing its primary function or that is performing its primary function without being useful. So, useless electricity consumption does not only consist of standby losses. To identify the useless electricity consumption in a building, a profile-based approach is developed. This approach is used to investigate the useless electricity consumption in five buildings of the University of...

  13. Identification of gene expression profiling associated with erlotinib-related skin toxicity in pancreatic adenocarcinoma patients

    Energy Technology Data Exchange (ETDEWEB)

    Caba, Octavio, E-mail: ocaba@ujaen.es [Department of Health Sciences, University of Jaen, Jaen (Spain); Irigoyen, Antonio, E-mail: antonioirigoyen@yahoo.com [Department of Medical Oncology, Virgen de la Salud Hospital, Toledo (Spain); Jimenez-Luna, Cristina, E-mail: crisjilu@ugr.es [Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada (Spain); Benavides, Manuel, E-mail: manuel.benavides.sspa@juntadeandalucia.es [Department of Medical Oncology, Virgen de la Victoria Hospital, Malaga (Spain); Ortuño, Francisco M., E-mail: fortuno@ugr.es [Department of Computer Architecture and Computer Technology, Research Center for Information and Communications Technologies, University of Granada, Granada (Spain); Gallego, Javier, E-mail: j.gallegoplazas@gmail.com [Department of Medical Oncology, General Universitario de Elche Hospital, Alicante (Spain); Rojas, Ignacio, E-mail: irojas@ugr.es [Department of Computer Architecture and Computer Technology, Research Center for Information and Communications Technologies, University of Granada, Granada (Spain); Guillen-Ponce, Carmen, E-mail: carmen.guillen@salud.madrid.org [Department of Medical Oncology, Ramón y Cajal University Hospital, Madrid (Spain); Torres, Carolina, E-mail: ctorres@uic.edu [Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL (United States); Aranda, Enrique, E-mail: enrique.aranda@imibic.org [Maimonides Institute of Biomedical Research (IMIBIC), Reina Sofía Hospital, University of Córdoba, Córdoba (Spain); Prados, Jose, E-mail: jcprados@ugr.es [Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada (Spain)

    2016-11-15

    Erlotinib is an epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor that showed activity against pancreatic ductal adenocarcinoma (PDAC). The drug's most frequently reported side effect as a result of EGFR inhibition is skin rash (SR), a symptom which has been associated with a better therapeutic response to the drug. Gene expression profiling can be used as a tool to predict which patients will develop this important cutaneous manifestation. The aim of the present study was to identify which genes may influence the appearance of SR in PDAC patients. The study included 34 PDAC patients treated with erlotinib: 21 patients developed any grade of SR, while 13 patients did not (controls). Before administering any chemotherapy regimen and the development of SR, we collected RNA from peripheral blood samples of all patients and studied the differential gene expression pattern using the Illumina microarray platform HumanHT-12 v4 Expression BeadChip. Seven genes (FAM46C, IFITM3, GMPR, DENND6B, SELENBP1, NOL10, and SIAH2), involved in different pathways including regulatory, migratory, and signalling processes, were downregulated in PDAC patients with SR. Our results suggest the existence of a gene expression profiling significantly correlated with erlotinib-induced SR in PDAC that could be used as prognostic indicator in this patients. - Highlights: • Skin rash (SR) is the most characteristic side effect of erlotinib in PDAC patients. • Erlotinib-induced SR has been associated with a better clinical outcome. • Gene expression profiling was used to determine who will develop this manifestation. • 7 genes involved in different pathways were downregulated in PDAC patients with SR. • Our profile correlated with erlotinib-induced SR in PDAC could be used for prognosis.

  14. Genotypic variability and mutant identification in cicer arietinum L. by seed storage protein profiling

    International Nuclear Information System (INIS)

    Hameed, A.; Iqbal, N.; Shah, T.M.

    2012-01-01

    A collection of thirty-four chickpea genotypes, including five kabuli and twenty-nine desi, were analyzed by SDS-PAGE for seed storage protein profiling. Total soluble seed proteins were resolved on 12% gels. A low level of variability was observed in desi as compared to kabuli genotypes. Dendrogram based on electrophoretic data clustered the thirty-four genotypes in four major groups. As large number of desi genotypes illustrated identical profiles, therefore could not be differentiated on the basis of seed storage protein profiles. One kabuli genotype ILC-195 found to be the most divergent showing 86% similarity with all other genotypes. ILC-195 can be distinguished from its mutant i.e., CM-2000 and other kabuli genotypes on the basis of three peptides i.e. SSP-66, SSP-43 and SSP-39. Some proteins peptides were found to be genotype specific like SSP-26 for ICCV-92311. Uniprot and NCBI protein databases were searched for already reported and characterized seed storage proteins in chickpea. Among 33 observed peptides, only six seed storages proteins from chickpea source were available in databases. On the basis of molecular weight similarity, identified peptides were SSP-64 as Serine/Threonine dehydratase, SSP-56 as Alpha-amylase inhibitor, SSP-50 as Provicillin, SSP-39 as seed imbibition protein, SSP-35 as Isoflavane reductase and SSP-19 as lipid transport protein. Highest variability was observed in vicillin subunits and beta subunits of legumins and its polymorphic forms. In conclusion, seed storage profiling can be economically used to asses the genetic variation, phylogenetic relationship and as markers to differentiate mutants from their parents. (author)

  15. In vitro and in silico Approaches to the Identification of New Compounds with Antibacterial Profile

    Directory of Open Access Journals (Sweden)

    Carlos R. Rodrigues

    2013-06-01

    Full Text Available The emergence of multidrug-resistant bacterial strains is a world problem that increases the need for new and more effective antimicrobials. On that purpose, derivatives of cyclic systems may serve as new leads for discovering new active molecules. In this work we evaluated the antibacterial profile of 243 molecules derived from the systems thienopyridine, pyrazolopiridine, quinolone, chalcone, hydrazone and lapachone against Gram-positive and Gram-negative susceptible and multiresistant strains also comparing them with antibiotics of clinical use. Our results showed that among the 243 molecules tested, only eight derivatives were active with promissing MIC values (2-64mg/mL. Our theoretical in silico analysis showed that all active compounds fulfilled Lipinski rule of five (molecular weight = 344.37–409.24, clogP = 3.15–4.11, nHBA = 6–7, and nHBD = 2, similarly to commercial drugs as well as presented better druglikeness values (from -3.68 to 0.12 than chloramphenicol (-4.61 and linezolid (-4.08. Most of the active derivatives presented a low in silico toxicity risk profile, similar to oxacillin, ampicillin, and penicillin G, and even lower than that observed for chloramphenicol and linezolid. Theoretically HOMO and the electrostatic protential distribution may be contributing for this safer profile. This study used computacional tools and may help to deal with an important world health problem.

  16. Identification of specific gene expression profiles in fibroblasts derived from middle ear cholesteatoma.

    Science.gov (United States)

    Yoshikawa, Mamoru; Kojima, Hiromi; Wada, Kota; Tsukidate, Toshiharu; Okada, Naoko; Saito, Hirohisa; Moriyama, Hiroshi

    2006-07-01

    To investigate the role of fibroblasts in the pathogenesis of cholesteatoma. Tissue specimens were obtained from our patients. Middle ear cholesteatoma-derived fibroblasts (MECFs) and postauricular skin-derived fibroblasts (SFs) as controls were then cultured for a few weeks. These fibroblasts were stimulated with interleukin (IL) 1alpha and/or IL-1beta before gene expression assays. We used the human genome U133A probe array (GeneChip) and real-time polymerase chain reaction to examine and compare the gene expression profiles of the MECFs and SFs. Six patients who had undergone tympanoplasty. The IL-1alpha-regulated genes were classified into 4 distinct clusters on the basis of profiles differentially regulated by SF and MECF using a hierarchical clustering analysis. The messenger RNA expressions of LARC (liver and activation-regulated chemokine), GMCSF (granulocyte-macrophage colony-stimulating factor), epiregulin, ICAM1 (intercellular adhesion molecule 1), and TGFA (transforming growth factor alpha) were more strongly up-regulated by IL-1alpha and/or IL-1beta in MECF than in SF, suggesting that these fibroblasts derived from different tissues retained their typical gene expression profiles. Fibroblasts may play a role in hyperkeratosis of middle ear cholesteatoma by releasing molecules involved in inflammation and epidermal growth. These fibroblasts may retain tissue-specific characteristics presumably controlled by epigenetic mechanisms.

  17. Rapid Identification of Potential Drugs for Diabetic Nephropathy Using Whole-Genome Expression Profiles of Glomeruli

    Directory of Open Access Journals (Sweden)

    Jingsong Shi

    2016-01-01

    Full Text Available Objective. To investigate potential drugs for diabetic nephropathy (DN using whole-genome expression profiles and the Connectivity Map (CMAP. Methodology. Eighteen Chinese Han DN patients and six normal controls were included in this study. Whole-genome expression profiles of microdissected glomeruli were measured using the Affymetrix human U133 plus 2.0 chip. Differentially expressed genes (DEGs between late stage and early stage DN samples and the CMAP database were used to identify potential drugs for DN using bioinformatics methods. Results. (1 A total of 1065 DEGs (FDR 1.5 were found in late stage DN patients compared with early stage DN patients. (2 Piperlongumine, 15d-PGJ2 (15-delta prostaglandin J2, vorinostat, and trichostatin A were predicted to be the most promising potential drugs for DN, acting as NF-κB inhibitors, histone deacetylase inhibitors (HDACIs, PI3K pathway inhibitors, or PPARγ agonists, respectively. Conclusion. Using whole-genome expression profiles and the CMAP database, we rapidly predicted potential DN drugs, and therapeutic potential was confirmed by previously published studies. Animal experiments and clinical trials are needed to confirm both the safety and efficacy of these drugs in the treatment of DN.

  18. Relative profile analysis of molecular markers for identification and genetic discrimination of loaches (Pisces, Nemacheilidae).

    Science.gov (United States)

    Patil, Tejas Suresh; Tamboli, Asif Shabodin; Patil, Swapnil Mahadeo; Bhosale, Amrut Ravindra; Govindwar, Sanjay Prabhu; Muley, Dipak Vishwanathrao

    2016-01-01

    Genus Nemacheilus, Nemachilichthys and Schistura belong to the family Nemacheilidae of the order Cypriniformes. The present investigation was undertaken to observe genetic diversity, phylogenetic relationship and to develop a molecular-based tool for taxonomic identification. For this purpose, four different types of molecular markers were utilized in which 29 random amplified polymorphic DNA (RAPD), 25 inter-simple sequence repeat (ISSR) markers, and 10 amplified fragment length polymorphism (AFLP) marker sets were screened and mitochondrial COI gene was sequenced. This study added COI barcodes for the identification of Nemacheilus anguilla, Nemachilichthys rueppelli and Schistura denisoni. RAPD showed higher polymorphism (100%) than the ISSR (93.75-100%) and AFLP (93.86-98.96%). The polymorphic information content (PIC), heterozygosity, multiplex ratio, and gene diversity was observed highest for AFLP primers, whereas the major allele frequency was observed higher for RAPD (0.5556) and lowest for AFLP (0.1667). The COI region of all individuals was successfully amplified and sequenced, which gave a 100% species resolution. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  19. Identification of pummelo cultivars by using a panel of 25 selected SNPs and 12 DNA segments.

    Directory of Open Access Journals (Sweden)

    Bo Wu

    Full Text Available Pummelo cultivars are usually difficult to identify morphologically, especially when fruits are unavailable. The problem was addressed in this study with the use of two methods: high resolution melting analysis of SNPs and sequencing of DNA segments. In the first method, a set of 25 SNPs with high polymorphic information content were selected from SNPs predicted by analyzing ESTs and sequenced DNA segments. High resolution melting analysis was then used to genotype 260 accessions including 55 from Myanmar, and 178 different genotypes were thus identified. A total of 99 cultivars were assigned to 86 different genotypes since the known somatic mutants were identical to their original genotypes at the analyzed SNP loci. The Myanmar samples were genotypically different from each other and from all other samples, indicating they were derived from sexual propagation. Statistical analysis showed that the set of SNPs was powerful enough for identifying at least 1000 pummelo genotypes, though the discrimination power varied in different pummelo groups and populations. In the second method, 12 genomic DNA segments of 24 representative pummelo accessions were sequenced. Analysis of the sequences revealed the existence of a high haplotype polymorphism in pummelo, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of 1200 pummelo cultivars. The high level of haplotype diversity and an apparent population structure shown by DNA segments and by SNP genotypes, respectively, were discussed in relation to the origin and domestication of the pummelo species.

  20. [Gene Expression Profile of Apoptosis in Leukemia Cells Induced by Hsp90 Selective inhibitor 17-AAG].

    Science.gov (United States)

    Wang, Na-Na; Li, Zhi-Heng; Tao, Yan-Fang; Xu, Li-Xiao; Pan, Jian; Hu, Shao-Yan

    2016-06-01

    To investigate the apoptotic effects of Hsp90 selective inhibitor 17-AAG on human leukemia HL-60 and NB4 cells and analyse its possible mechanism. CCK-8 assay was used to quantify the growth inhibition of cells after exposure to 17-AAG for 24 hours. Flow cytometrve with annexin V/propidium iodide staining was used to detect apoptosis of leukemia cells. Then Western blot was used to detect the activation of apoptosis related protein caspase-3 and PARP level. Gene expression profile of NB4 cells treated with 17-AAG was analyzed with real-time PCR arrays. The inhibition of leukemia cell proliferation displayed a dose-dependent manner. Annexin V assay, cell cycle analysis and activation of PARP demonstrate that 17-AAG induced apoptosis leukemia cells. Real-time PCR array analysis showed that expression of 56 genes significantly up-regulated and expression of 23 genes were significantly down-regulated after 17-AAG treatment. The 17-AAG can inhibit the proliferation and induce the apoptosis of leukemia cells. After leukemia cells are treated with 17-AAG, the significant changes of apoptosis-related genes occured, and the cell apoptosis occurs via activating apoptosis related signaling pathway.

  1. Design and evaluation of multi-indicator profiles for targeted-selective treatment against gastrointestinal nematodes at housing in adult dairy cows.

    Science.gov (United States)

    Ravinet, Nadine; Lehebel, Anne; Bareille, Nathalie; Lopez, Carlos; Chartier, Christophe; Chauvin, Alain; Madouasse, Aurélien

    2017-04-15

    Targeted-selective treatments against gastrointestinal nematode (GIN) in adult dairy cows require the identification of "cows to treat", i.e. cows whose milk production (MP) would increase after treatment. This study aimed at quantifying the ability of multi-indicator profiles to identify such cows. A randomized controlled clinical trial was conducted at housing in 25 French pasturing dairy herds. In each herd, treated cows received fenbendazole orally, control cows remained untreated. Daily MP was recorded and the MP variation between the pre- and post-visit periods was calculated (ΔMP) for each cow. ΔMP was modelled with control cows data (n=412) (piecewise linear mixed model). Estimated parameters were applied to treated cows data (n=414) to predict the expected ΔMP in treated cows if they had not been treated. Treated cows with an observed ΔMP (with treatment) higher than the expected ΔMP (without treatment) were labelled as "cows to treat". Herds where at least 50% of the young cows were "cows to treat" were qualified as "herds to target". To characterize such cows and herds, the available candidate indicators were (i) at the cow-level: parity, stage of lactation and production level, faecal egg count (FEC), serum pepsinogen level and anti-Ostertagia antibody level (expressed as ODR); (ii) at the herd-level: bulk tank milk (BTM) Ostertagia ODR, Time of Effective Contact (TEC, in months) with GIN infective larvae before the first calving, and percentage of positive FEC. These indicators were tested one-by-one or in combination to assess their ability to characterize "herds to target" and "cows to treat" (Chi-square tests). 115 out of 414 treated cows (27.8%) were considered as "cows to treat", and 9 out of 22 herds were qualified as "herds to target". The indicators retained to profile such cows and herds were the parity, the production level, the BTM Ostertagia ODR and the TEC. Multi-indicator profiles were much more specific than single indicator

  2. Protein profile of human hepatocarcinoma cell line SMMC-7721: Identification and functional analysis

    Institute of Scientific and Technical Information of China (English)

    Yi Feng; Zhong-Min Tian; Ming-Xi Wan; Zhao-Bin Zheng

    2007-01-01

    AIM: To investigate the protein profile of human hepatocarcinoma cell line SMMC-7721, to analyze the specific functions of abundant expressed proteins in the processes of hepatocarcinoma genesis, growth and metastasis, to identify the hepatocarcinoma-specific biomarkers for the early prediction in diagnosis, and to explore the new drug targets for liver cancer therapy.METHODS: Total proteins from human hepatocarcinomacell line SMMC-7721 were separated by two-dimensional electrophoresis (2DE). The silver-stained gel was analyzed by 2DE software Image Master 2D Elite.Interesting protein spots were identified by peptide mass fingerprinting based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS)and database searching.RESULTS: We obtained protein profile of human hepatocarcinoma cell line SMMC-7721. Among the twenty-one successfully identified proteins, mitofilin,endoplasmic reticulum protein ERp29, ubiquinol-cytochrome C reductase complex core protein Ⅰ,peroxisomal enoyl CoA hydratase, peroxiredoxin-4 and probable 3-oxoacid CoA transferase 1 precursor were the six novel proteins identified in human hepatocarcinoma cells or tissues. Specific functions of the identified heat-shock proteins were analyzed in detail, and the results suggested that these proteins might promote tumorigenesis via inhibiting cell death induced by several cancer-related stresses or via inhibiting apoptosis at multiple points in the apoptotic signal pathway. Other identified chaperones and cancer-related proteins were also analyzed.CONCLUSION: Based on the protein profile of SMMC-7721 cells, functional analysis suggests that the identified chaperones and cancer-related proteins have their own pathways to contribute to the tumorigenesis, tumor growth and metastasis of liver cancer. Furthermore, proteomic analysis is indicated to be feasible in the cancer study.

  3. Identification and profiling of microRNAs and their target genes from developing caprine skeletal Muscle.

    Directory of Open Access Journals (Sweden)

    Yanhong Wang

    Full Text Available Goat is an important agricultural animal for meat production. Functional studies have demonstrated that microRNAs (miRNAs regulate gene expression at the post-transcriptional level and play an important role in various biological processes. Although studies on miRNAs expression profiles have been performed in various animals, relatively limited information about goat muscle miRNAs has been reported. To investigate the miRNAs involved in regulating different periods of skeletal muscle development, we herein performed a comprehensive research for expression profiles of caprine miRNAs during two developmental stages of skeletal muscles: fetal stage and six month-old stage. As a result, 15,627,457 and 15,593,721 clean reads were obtained from the fetal goat library (FC and the six month old goat library (SMC, respectively. 464 known miRNAs and 83 novel miRNA candidates were identified. Furthermore, by comparing the miRNA profile, 336 differentially expressed miRNAs were identified and then the potential targets of the differentially expressed miRNAs were predicted. To understand the regulatory network of miRNAs during muscle development, the mRNA expression profiles for the two development stages were characterized and 7322 differentially expressed genes (DEGs were identified. Then the potential targets of miRNAs were compared to the DEGs, the intersection of the two gene sets were screened out and called differentially expressed targets (DE-targets, which were involved in 231 pathways. Ten of the 231 pathways that have smallest P-value were shown as network figures. Based on the analysis of pathways and networks, we found that miR-424-5p and miR-29a might have important regulatory effect on muscle development, which needed to be further studied. This study provided the first global view of the miRNAs in caprine muscle tissues. Our results help elucidation of complex regulatory networks between miRNAs and mRNAs and for the study of muscle

  4. Identification and antimicrobial suceptibility profile of bacteria causing bovine mastitis from dairy farms in Pelotas, Rio Grande do Sul

    Directory of Open Access Journals (Sweden)

    C. H. Freitas

    2018-01-01

    Full Text Available Abstract Mastitis is an inflammatory process of the udder tissue caused mainly by the bacteria Staphylococcus aureus. The indiscriminate use of antibiotics fosters conditions that favor the selection of resistant microorganisms, suppressing at the same time susceptible forms, causing a serious problem in dairy cattle. Given the importance in performing an antibiogram to select the most adequate antimicrobial therapy, the aim of this study was to identify bacteria isolated from cow’s milk with mastitis, in dairy farms situated in the city of Pelotas, Rio Grande do Sul, and to determinate the susceptibility profile of these isolates against the antibiotics used to treat this illness. A total of 30 isolates of Staphylococcus spp., were selected from milk samples from the udder quarters with subclinical mastitis whose species were identified through the Vitek system. The susceptibility profile was performed by the disk diffusion assay, against: ampicillin, amoxicillin, bacitracin, cephalexin, ceftiofur, enrofloxacin, gentamicin, neomycin, norfloxacin, penicillin G, tetracycline and trimethoprim. In the antibiogram, 100.0% of the isolates were resistant to trimethoprim and 96.7% to tetracycline and neomycin, three strains of Staphylococcus spp., (10.0% presented resistance to the 12 antibiotics tested and 24 (80.0% to at least eight. These results showed the difficulty in treating mastitis, due to the pathogens’ resistance.

  5. Identification of Candidate B-Lymphoma Genes by Cross-Species Gene Expression Profiling

    Science.gov (United States)

    Tompkins, Van S.; Han, Seong-Su; Olivier, Alicia; Syrbu, Sergei; Bair, Thomas; Button, Anna; Jacobus, Laura; Wang, Zebin; Lifton, Samuel; Raychaudhuri, Pradip; Morse, Herbert C.; Weiner, George; Link, Brian; Smith, Brian J.; Janz, Siegfried

    2013-01-01

    Comparative genome-wide expression profiling of malignant tumor counterparts across the human-mouse species barrier has a successful track record as a gene discovery tool in liver, breast, lung, prostate and other cancers, but has been largely neglected in studies on neoplasms of mature B-lymphocytes such as diffuse large B cell lymphoma (DLBCL) and Burkitt lymphoma (BL). We used global gene expression profiles of DLBCL-like tumors that arose spontaneously in Myc-transgenic C57BL/6 mice as a phylogenetically conserved filter for analyzing the human DLBCL transcriptome. The human and mouse lymphomas were found to have 60 concordantly deregulated genes in common, including 8 genes that Cox hazard regression analysis associated with overall survival in a published landmark dataset of DLBCL. Genetic network analysis of the 60 genes followed by biological validation studies indicate FOXM1 as a candidate DLBCL and BL gene, supporting a number of studies contending that FOXM1 is a therapeutic target in mature B cell tumors. Our findings demonstrate the value of the “mouse filter” for genomic studies of human B-lineage neoplasms for which a vast knowledge base already exists. PMID:24130802

  6. Identification and developmental profiling of microRNAs in diamondback moth, Plutellaxylostella (L..

    Directory of Open Access Journals (Sweden)

    Pei Liang

    Full Text Available MicroRNAs (miRNAs are a group of small RNAs involved in various biological processes through negative regulation of mRNAs at the post-transcriptional level. Although miRNA profiles have been documented in over two dozen insect species, few are agricultural pests. In this study, both conserved and novel miRNAs in the diamondback moth, Plutella xylostella L., a devastating insect pest of cruciferous crops worldwide, were documented. High-throughput sequencing of a small RNA library constructed from a mixed life stages of P. xylostella, including eggs, 1st to 4th (last instar larvae, pupae and adults, identified 384 miRNAs, of which 174 were P. xylostella specific. In addition, temporal expressions of 234 miRNAs at various developmental stages were investigated using a customized microarray analysis. Among the 91 differentially expressed miRNAs, qRT-PCR analysis was used to validate highly expressed miRNAs at each stage. The combined results not only systematically document miRNA profiles in an agriculturally important insect pest, but also provide molecular targets for future functional analysis and, ultimately, genetic-based pest control practice.

  7. Identification of Vitis vinifera L. grape berry skin color mutants and polyphenolic profile.

    Science.gov (United States)

    Ferreira, Vanessa; Fernandes, Fátima; Pinto-Carnide, Olinda; Valentão, Patrícia; Falco, Virgílio; Martín, Juan Pedro; Ortiz, Jesús María; Arroyo-García, Rosa; Andrade, Paula B; Castro, Isaura

    2016-03-01

    A germplasm set of twenty-five grapevine accessions, forming eleven groups of possible berry skin color mutants, were genotyped with twelve microsatellite loci, being eleven of them identified as true color mutants. The polyphenolic profiling of the confirmed mutant cultivars revealed a total of twenty-four polyphenols, comprising non-colored compounds (phenolic acids, flavan-3-ols, flavonols and a stilbene) and anthocyanins. Results showed differences in the contribution of malvidin-3-O-glucoside to the characteristic Pinot Noir anthocyanins profile. Regarding the two Pique-Poul colored variants, the lighter variant was richer than the darker one in all classes of compounds, excepting anthocyanins. In Moscatel Galego Roxo the F3'H pathway seems to be more active than F3'5'H, resulting in higher amounts of cyanidin, precursor of the cyanidin derivatives. As far as we are aware, this is the first time that a relationship between the content of polyphenolic compounds is established in groups of grape berry skin color mutant cultivars. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Characterization, source identification and apportionment of selected metals in TSP in an urban atmosphere.

    Science.gov (United States)

    Shah, Munir H; Shaheen, N; Jaffar, M

    2006-03-01

    To understand the metal distribution characteristics in the atmosphere of urban Islamabad, total suspended particulate (TSP) samples were collected on daily 12 h basis, at Quaid-i-Azam University campus, using high volume sampler. The TSP samples were treated with HNO(3)/HClO(4) based wet digestion method for the quantification of eight selected metals; Fe, Zn, Pb, Mn, Cr, Co, Ni and Cd by FAAS method. The monitoring period ran from June 2001 to January 2002, with a total of 194 samples collected on cellulose filters. Effects of different meteorological conditions such as temperature, relative humidity, wind speed and wind direction on selected metal levels were interpreted by means of multivariate statistical approach. Enhanced metal levels for Fe (930 ng/m(3)), Zn (542 ng/m(3)) and Pb (210 ng/m(3)) were found on the mean scale while Mn, Cr, Co and Ni emerged as minor contributors. Statistical correlation study was also conducted and a strong correlation was observed between Pb-Cr (r=0.611). The relative humidity showed some significant influence on atmospheric metal distribution while other meteorological parameters showed weak relationship with TSP metal levels. Regarding the origin of sources of heavy metals in TSP, the statistical procedure identified three source profiles; automobile emissions, industrial/metallurgical units, and natural soil dust. The metal levels were also compared with those reported for other parts of the world which showed that the metal levels in urban atmosphere of Islamabad are in exceedence than those of European industrial and urban sites while comparable with some Asian sites.

  9. Identification of human circadian genes based on time course gene expression profiles by using a deep learning method.

    Science.gov (United States)

    Cui, Peng; Zhong, Tingyan; Wang, Zhuo; Wang, Tao; Zhao, Hongyu; Liu, Chenglin; Lu, Hui

    2018-06-01

    Circadian genes express periodically in an approximate 24-h period and the identification and study of these genes can provide deep understanding of the circadian control which plays significant roles in human health. Although many circadian gene identification algorithms have been developed, large numbers of false positives and low coverage are still major problems in this field. In this study we constructed a novel computational framework for circadian gene identification using deep neural networks (DNN) - a deep learning algorithm which can represent the raw form of data patterns without imposing assumptions on the expression distribution. Firstly, we transformed time-course gene expression data into categorical-state data to denote the changing trend of gene expression. Two distinct expression patterns emerged after clustering of the state data for circadian genes from our manually created learning dataset. DNN was then applied to discriminate the aperiodic genes and the two subtypes of periodic genes. In order to assess the performance of DNN, four commonly used machine learning methods including k-nearest neighbors, logistic regression, naïve Bayes, and support vector machines were used for comparison. The results show that the DNN model achieves the best balanced precision and recall. Next, we conducted large scale circadian gene detection using the trained DNN model for the remaining transcription profiles. Comparing with JTK_CYCLE and a study performed by Möller-Levet et al. (doi: https://doi.org/10.1073/pnas.1217154110), we identified 1132 novel periodic genes. Through the functional analysis of these novel circadian genes, we found that the GTPase superfamily exhibits distinct circadian expression patterns and may provide a molecular switch of circadian control of the functioning of the immune system in human blood. Our study provides novel insights into both the circadian gene identification field and the study of complex circadian-driven biological

  10. Application of Fourier-transform ion cyclotron resonance mass spectrometry to metabolic profiling and metabolite identification.

    Science.gov (United States)

    Ohta, Daisaku; Kanaya, Shigehiko; Suzuki, Hideyuki

    2010-02-01

    Metabolomics, as an essential part of genomics studies, intends holistic understanding of metabolic networks through simultaneous analysis of a myriad of both known and unknown metabolites occurring in living organisms. The initial stage of metabolomics was designed for the reproducible analyses of known metabolites based on their comparison to available authentic compounds. Such metabolomics platforms were mostly based on mass spectrometry (MS) technologies enabled by a combination of different ionization methods together with a variety of separation steps including LC, GC, and CE. Among these, Fourier-transform ion cyclotron resonance MS (FT-ICR/MS) is distinguished from other MS technologies by its ultrahigh resolution power in mass to charge ratio (m/z). The potential of FT-ICR/MS as a distinctive metabolomics tool has been demonstrated in nontargeted metabolic profiling and functional characterization of novel genes. Here, we discuss both the advantages and difficulties encountered in the FT-ICR/MS metabolomics studies.

  11. Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

    Science.gov (United States)

    Thompson, Vicki S; Lacey, Jeffrey A; Gentillon, Cynthia A; Apel, William A

    2015-03-03

    A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

  12. Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

    Energy Technology Data Exchange (ETDEWEB)

    Apel, William A.; Thompson, Vicki S; Lacey, Jeffrey A.; Gentillon, Cynthia A.

    2016-08-09

    A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

  13. Laser Range Profiling for Active Protection System Target Classification and Aim-Point Selection

    National Research Council Canada - National Science Library

    Jones, Michael

    2004-01-01

    .... The attractiveness of smaller, faster interceptors precipitated the investigation of a laser radar sensor augmentation for CIAPS that could quickly resolve the range profile of an incoming projectile...

  14. Identification and Expression Profiling of Chemosensory Genes in Dendrolimus punctatus Walker

    Directory of Open Access Journals (Sweden)

    Su-fang Zhang

    2017-07-01

    Full Text Available Dendrolimus punctatus Walker is a serious pest affecting conifers in southern China. As extensive pesticide spraying is currently required to control D. punctatus, new control strategies are urgently needed. Chemosensory genes represent potential molecular targets for development of alternative pest control strategies, and the expression characteristics of these genes provide an indication of their function. To date, little information is available regarding chemosensory genes in D. punctatus or their expression profiles at different development stages and in various tissues. Here, we assembled and analyzed the transcriptomes of D. punctatus collected at different developmental stages and in a range of organs, using next-generation sequencing. A total of 171 putative chemosensory genes were identified, encoding 53 odorant binding proteins, 26 chemosensory proteins, 60 odorant receptors (OR, 12 gustatory receptors (GR, 18 ionotropic receptors (IR, and 2 sensory neuron membrane proteins (SNMPs. Expression analysis indicated that the antennae possess the largest number of highly expressed olfactory genes and that olfactory gene expression patterns in the eggs, larvae, and head were similar to one another, with each having moderate numbers of highly expressed olfactory genes. Fat body, ovary, midgut, and testis tissues also had similar olfactory gene expression patterns, including few highly expressed olfactory genes. Of particular note, we identified only two pheromone binding proteins and no pheromone receptors in D. punctatus, similar to our previous findings in Dendrolimus houi and Dendrolimus kikuchii, suggesting that insects of the Dendrolimus genus have different pheromone recognition characteristics to other Lepidopteran insects. Overall, this extensive expression profile analysis provides a clear map of D. punctatus chemosensory genes, and will facilitate functional studies and the development of new pest control methods in the future.

  15. Effect of Ramadan intermittent fasting on selective fitness profile parameters in young untrained Muslim men.

    Science.gov (United States)

    Roy, Anindita Singha; Bandyopadhyay, Amit

    2015-01-01

    The present study was aimed at investigating the effects of sleep deprivation and dietary irregularities during Ramadan intermittent fasting (RIF) on selective fitness profile parameters in young untrained male Muslim individuals. 77 untrained Muslim men were recruited in the study. They were divided into the experimental group (EG; n=37, age: 22.62±1.77 years) and the control group (CG; n=40, age: 23.00±1.48 years). EG was undergoing RIF while CG abstained. Aerobic fitness, anaerobic capacity or high-intensity efforts (HIEs), agility, flexibility, vertical jump height and handgrip strength were measured on 8 separate occasions-15 days before RIF, 7 days before RIF, 1st day of RIF, 7th day of RIF, 15th day of RIF, 21st day of RIF, last day of RIF and 15 days after RIF. Aerobic fitness and HIE showed a significant difference (p<0.05) during RIF in EG. Agility and flexibility score showed a significant decrease in EG during RIF, whereas changes in the vertical jump score (VJT) and handgrip strength were statistically insignificant. Studied parameters showed an insignificant variation in CG during RIF. Aerobic fitness, HIEs, agility and flexibility showed a significant intergroup variation during different experimental trials. The present investigation revealed that RIF had adverse effects on aerobic fitness, HIEs, agility and flexibility of young untrained Muslims of Kolkata, India. VJT, waist-hip ratio and handgrip strength were not affected by RIF in the studied population. Mild but statistically insignificant reduction in body mass was also reflected after the mid-Ramadan week.

  16. Seismarmara experiment: results from reprocessing of selected multi-channel seismic reflection profiles

    Science.gov (United States)

    Cetin, S.; Voogd, B.; Carton, H.; Laigle, M.; Becel, A.; Saatcilar, R.; Singh, S.; Hirn, A.

    2003-04-01

    The North Anatolian Fault (NAF) has been responsible for the earthquakes of Izmit and Duzce in 1999. The occurrence of these earthquakes has drawn scientific attention into the Sea of Marmara since the NAF enters into the Sea of Marmara where the latest Izmit earthquake rupture stopped. The SEISMARMARA-2001 survey is a combined seismic reflection, refraction and earthquake experiment carried out in 2001 in the Marmara Region in Turkey by French-Turkish scientific cooperation. The objectives of this survey were to image the various branches of the NAF and related other fault systems. R/V Le Nadir was equipped with a 4.5 km long streamer with 360 channels and a large airgun source. During Leg 1, a grid of large regional lines encompassing the whole Marmara trough was shot. For part of them a strong 8100 cu.in. source for deepest penetration was used, with a 150 m shot interval giving a 15-fold coverage. Another part was shot for a higher resolution with a 2900 cu. in. array at a 50m or 38 m interval to give a 45 or 60-fold coverage. The latter acquisition parameters were used for Leg 2 that was devoted to a very dense grid of lines in the Cinarcik Basin Reprocessing of the multi-channel seismic data is currently being undertaken in several Institutions using different seismic processing softwares (GeoVecteur, ProMAX, Focus), to take advantage of the diverse acquisitions and cope with their limitations, for instance high fold-order for Leg 2 and strength of signal but loose spatial sampling for the bigger source. The main objectives of the reprocessing of the selected profiles are to do a detailed velocity analysis and stacking after deconvolution, filtering to remove or suppress deep sea bottom multiples and out of plane reflections, and time-migration and depth conversion and thus reveal both the shallow and deeper reflection image of the crust in the Sea of Marmara. We show that choosing an appropriate processing sequence for different sources and acquisition

  17. Identification of selected microorganisms from activated sludge capable of benzothiazole and benzotriazole transformation.

    Science.gov (United States)

    Kowalska, Katarzyna; Felis, Ewa

    2015-01-01

    Benzothiazole (BT) and benzotriazole (BTA) are present in the environment - especially in urban and industrial areas, usually as anthropogenic micropollutants. BT and BTA have been found in the municipal and industrial wastewater, rivers, soil, groundwater, sediments and sludge. The origins of those substances' presence in the environment are various industry branches (food, chemical, metallurgical, electrical), households and surface runoff from industrial areas. Increasingly strict regulations on water quality and the fact that the discussed compounds are poorly biodegradable, make them a serious problem in the environment. Considering this, it is important to look for environmentally friendly and socially acceptable ways to remove BT and BTA. The aim of this study was to identify microorganisms capable of BT and BTA transformation or/and degradation in aquatic environment. Selected microorganisms were isolated from activated sludge. The identification of microorganisms capable of BT and BTA removal was possible using molecular biology techniques (PCR, DNA sequencing). Among isolated microorganisms of activated sludge are bacteria potentially capable of BT and BTA biotransformation and/or removal. The most common bacteria capable of BT and BTA transformation were Rhodococcus sp., Enterobacter sp., Arthrobacter sp. They can grow in a medium with BT and BTA as the only carbon source. Microorganisms previously adapted to the presence of the studied substances at a concentration of 10 mg/l, showed a greater rate of growth of colonies on media than microorganisms unconditioned to the presence of such compounds. Results of the biodegradation test suggest that BT was degraded to a greater extent than BTA, 98-100% and 11-19%, respectively.

  18. Identification of cytotoxic drugs that selectively target tumor cells with MYC overexpression.

    Directory of Open Access Journals (Sweden)

    Anna Frenzel

    Full Text Available Expression of MYC is deregulated in a wide range of human cancers, and is often associated with aggressive disease and poorly differentiated tumor cells. Identification of compounds with selectivity for cells overexpressing MYC would hence be beneficial for the treatment of these tumors. For this purpose we used cell lines with conditional MYCN or c-MYC expression, to screen a library of 80 conventional cytotoxic compounds for their ability to reduce tumor cell viability and/or growth in a MYC dependent way. We found that 25% of the studied compounds induced apoptosis and/or inhibited proliferation in a MYC-specific manner. The activities of the majority of these were enhanced both by c-MYC or MYCN over-expression. Interestingly, these compounds were acting on distinct cellular targets, including microtubules (paclitaxel, podophyllotoxin, vinblastine and topoisomerases (10-hydroxycamptothecin, camptothecin, daunorubicin, doxorubicin, etoposide as well as DNA, RNA and protein synthesis and turnover (anisomycin, aphidicholin, gliotoxin, MG132, methotrexate, mitomycin C. Our data indicate that MYC overexpression sensitizes cells to disruption of specific pathways and that in most cases c-MYC and MYCN overexpression have similar effects on the responses to cytotoxic compounds. Treatment of the cells with topoisomerase I inhibitors led to down-regulation of MYC protein levels, while doxorubicin and the small molecule MYRA-A was found to disrupt MYC-Max interaction. We conclude that the MYC pathway is only targeted by a subset of conventional cytotoxic drugs currently used in the clinic. Elucidating the mechanisms underlying their specificity towards MYC may be of importance for optimizing treatment of tumors with MYC deregulation. Our data also underscores that MYC is an attractive target for novel therapies and that cellular screenings of chemical libraries can be a powerful tool for identifying compounds with a desired biological activity.

  19. Character’s Selection of Leaf Morphology in Some Families (Tree Habit In Sumatra Region for Species Identification

    Directory of Open Access Journals (Sweden)

    Saida Rasnovi

    2014-04-01

    Full Text Available Identification is a basic activity and one of primary objective on systematic. For plant biodiversity studies, it was the first steps that researcher performed before studying any topics in the research area. Unfortunately, species identification is usually a time consuming activity. One of the main objectives of this study was to obtain a set of leaf morphology characters that were useful and efficient enough for species identification, especially on the tree habits group in order to reduce time consuming for the identification species.  All of the leaf morphology characters were selected by correlation coefficient and separation coefficient values. Besides of that, the stability, simplicity and validity of the characters were also part of concern. The characters that had high value of separation coefficient and low value of correlation coefficient would be added one by one as in their rank, until the value of the combination separation coefficient was equal to 1 (100%. The result of this study suggested that 30 from 92 characters of leaf morphology were recommended as a set of characters that useful and efficient enough for species identification.

  20. Identification of Natural Frequency of Low Rise Building on Soft Ground Profile using Ambient Vibration Method

    Science.gov (United States)

    Kamarudin, A. F.; Zainal Abidin, M. H.; Mokhatar, S. N.; Daud, M. E.; Ibrahim, A.; Ibrahim, Z.; Noh, M. S. Md

    2018-04-01

    Natural frequency is the rate at which a body to vibrate or oscillate. Application of ambient vibration (AV) excitation is widely used nowadays as the input motion for building predominant frequency, fo, and ground fundamental frequency, Fo, prediction due to simple, fast, non-destructive, simple handling operation and reliable result. However, it must be emphasized and caution to isolate these frequencies (fo and Fo) from spurious frequencies of site-structure effects especially to low rise building on soft ground deposit. In this study, identification of fo and Fo by using AV measurements were performed on ground and 4-storey primary school reinforced concrete (RC) building at Sekolah Kebangsaan (SK) Sg. Tongkang, Rengit, Johor using 1 Hz of tri-axial seismometer sensor. Overlapping spectra between Fourier Amplitude Spectra (FAS) from and Horizontal to Vertical Spectra Ratio (HVSR) were used to distinguish respective frequencies of building and ground natural frequencies. Three dominant frequencies were identified from the FAS curves at 1.91 Hz, 1.98 Hz and 2.79 Hz in longitudinal (East West-EW), transverse (North South-NS) and vertical (UD) directions. It is expected the building has deformed in translational mode based on the first peak frequency by respective NS and EW components of FAS spectrum. Vertical frequency identified from the horizontal spectrums, might induces to the potential of rocking effect experienced by the school building. Meanwhile, single peak HVSR spectrum at low ground fundamental frequency concentrated at 0.93 Hz indicates to the existence deep contrast of soft deposit. Strong interaction between ground and building at similar frequency (0.93 Hz) observed from the FAS curves on the highest floor has shown the building to behave as a dependent unit against ground response as one rigid mass.

  1. Identification and characterization of angiogenesis targets through proteomic profiling of endothelial cells in human cancer tissues.

    Directory of Open Access Journals (Sweden)

    Mehdi Mesri

    Full Text Available Genomic and proteomic analysis of normal and cancer tissues has yielded abundant molecular information for potential biomarker and therapeutic targets. Considering potential advantages in accessibility to pharmacological intervention, identification of targets resident on the vascular endothelium within tumors is particularly attractive. By employing mass spectrometry (MS as a tool to identify proteins that are over-expressed in tumor-associated endothelium relative to normal cells, we aimed to discover targets that could be utilized in tumor angiogenesis cancer therapy. We developed proteomic methods that allowed us to focus our studies on the discovery of cell surface/secreted proteins, as they represent key antibody therapeutic and biomarker opportunities. First, we isolated endothelial cells (ECs from human normal and kidney cancer tissues by FACS using CD146 as a marker. Additionally, dispersed human colon and lung cancer tissues and their corresponding normal tissues were cultured ex-vivo and their endothelial content were preferentially expanded, isolated and passaged. Cell surface proteins were then preferentially captured, digested with trypsin and subjected to MS-based proteomic analysis. Peptides were first quantified, and then the sequences of differentially expressed peptides were resolved by MS analysis. A total of 127 unique non-overlapped (157 total tumor endothelial cell over-expressed proteins identified from directly isolated kidney-associated ECs and those identified from ex-vivo cultured lung and colon tissues including known EC markers such as CD146, CD31, and VWF. The expression analyses of a panel of the identified targets were confirmed by immunohistochemistry (IHC including CD146, B7H3, Thy-1 and ATP1B3. To determine if the proteins identified mediate any functional role, we performed siRNA studies which led to previously unidentified functional dependency for B7H3 and ATP1B3.

  2. Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

    Science.gov (United States)

    2011-01-01

    Background Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. Results Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. In addition, 341,984 ESTs were generated from ES and PES internodes of genotype 773 using the GS FLX Titanium platform. The first alfalfa (Medicago sativa) gene index (MSGI 1.0) was assembled using the Sanger ESTs available from GenBank, the GS FLX Titanium EST sequences, and the de novo assembled Illumina sequences. MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1,294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Out of 55 SNPs randomly selected for experimental validation, 47 (85%) were polymorphic between the two genotypes. We also identified numerous allelic variations within each genotype. Digital gene expression analysis identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. Conclusions Our results demonstrate that RNA-Seq can be

  3. Comparative Proteomic Profiling and Biomarker Identification of Traditional Chinese Medicine-Based HIV/AIDS Syndromes.

    Science.gov (United States)

    Wen, Li; Liu, Ye-Fang; Jiang, Cen; Zeng, Shao-Qian; Su, Yue; Wu, Wen-Jun; Liu, Xi-Yang; Wang, Jian; Liu, Ying; Su, Chen; Li, Bai-Xue; Feng, Quan-Sheng

    2018-03-08

    Given the challenges in exploring lifelong therapy with little side effect for human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS) cases, there is increasing interest in developing traditional Chinese medicine (TCM) treatments based on specific TCM syndrome. However, there are few objective and biological evidences for classification and diagnosis of HIV/AIDS TCM syndromes to date. In this study, iTRAQ-2DLC-MS/MS coupled with bioinformatics were firstly employed for comparative proteomic profiling of top popular TCM syndromes of HIV/AIDS: accumulation of heat-toxicity (AHT) and Yang deficiency of spleen and kidney (YDSK). It was found that for the two TCM syndromes, the identified differential expressed proteins (DEPs) as well as their biological function distributions and participation in signaling pathways were significantly different, providing biological evidence for the classification of HIV/AIDS TCM syndromes. Furthermore, the TCM syndrome-specific DEPs were confirmed as biomarkers based on western blot analyses, including FN1, GPX3, KRT10 for AHT and RBP4, ApoE, KNG1 for YDSK. These biomarkers also biologically linked with the specific TCM syndrome closely. Thus the clinical and biological basis for differentiation and diagnosis of HIV/AIDs TCM syndromes were provided for the first time, providing more opportunities for stable exertion and better application of TCM efficacy and superiority in HIV/AIDS treatment.

  4. Identification of metabolic profiling of cell culture of licorice compared with its native one.

    Science.gov (United States)

    Man, Shuli; Guo, Songbo; Gao, Wenyuan; Wang, Juan; Zhang, Liming; Li, Xinglin

    2013-04-01

    Glycyrrhiza uralensis has long been used as a flavoring and sweetening agent in food products. In the last ten years, suspensions of Glycyrhiza cells have been successfully established. However, there is no report of full metabolic profiling research on these cells. To identify their composition we used HPLC-DAD coupled with ESI(+/-)-MS (n) to compare the constituents of cultured Glycyrhiza (CG) cells with those the native cells (NG). We identified 60 compounds including flavonoids, phenols, and triterpenoids. Among these compounds, 42 occurred both in NG and CG, nine were present in NG only and nine were present in CG alone. The number of the triterpenoid aglycones without glycones in CG was smaller than that in NG. The number of flavanone, isoflavone, isoflavan, and benzenoid compounds was also smaller in CG than that in NG, whereas the number of pterocarpans was much higher. Although differences existed between CG and NG, the extract of CG was similar to that of NG. With the development of cell suspension culture-based biotransformation, cell culture of Glycyrrhiza has the potential to be more profitable than field cultivation in some areas.

  5. Source identification and apportionment of heavy metals in urban soil profiles.

    Science.gov (United States)

    Luo, Xiao-San; Xue, Yan; Wang, Yan-Ling; Cang, Long; Xu, Bo; Ding, Jing

    2015-05-01

    Because heavy metals (HMs) occurring naturally in soils accumulate continuously due to human activities, identifying and apportioning their sources becomes a challenging task for pollution prevention in urban environments. Besides the enrichment factors (EFs) and principal component analysis (PCA) for source classification, the receptor model (Absolute Principal Component Scores-Multiple Linear Regression, APCS-MLR) and Pb isotopic mixing model were also developed to quantify the source contribution for typical HMs (Cd, Co, Cr, Cu, Mn, Ni, Pb, Zn) in urban park soils of Xiamen, a representative megacity in southeast China. Furthermore, distribution patterns of their concentrations and sources in 13 soil profiles (top 20 cm) were investigated by different depths (0-5, 5-10, 10-20 cm). Currently the principal anthropogenic source for HMs in urban soil of China is atmospheric deposition from coal combustion rather than vehicle exhaust. Specifically for Pb source by isotopic model ((206)Pb/(207)Pb and (208)Pb/(207)Pb), the average contributions were natural (49%)>coal combustion (45%)≫traffic emissions (6%). Although the urban surface soils are usually more contaminated owing to recent and current human sources, leaching effects and historic vehicle emissions can also make deep soil layer contaminated by HMs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. The Guareschi Pyridine Scaffold as a Valuable Platform for the Identification of Selective PI3K Inhibitors.

    Science.gov (United States)

    Galli, Ubaldina; Ciraolo, Elisa; Massarotti, Alberto; Margaria, Jean Piero; Sorba, Giovanni; Hirsch, Emilio; Tron, Gian Cesare

    2015-09-18

    A novel series of 4-aryl-3-cyano-2-(3-hydroxyphenyl)-6-morpholino-pyridines have been designed as potential phosphatidylinositol-3-kinase (PI3K) inhibitors. The compounds have been synthesized using the Guareschi reaction to prepare the key 4-aryl-3-cyano-2,6-dihydroxypyridine intermediate. A different selectivity according to the nature of the aryl group has been observed. Compound 9b is a selective inhibitor against the PI3Kα isoform, maintaining a good inhibitory activity. Docking studies were also performed in order to rationalize its profile of selectivity.

  7. The Guareschi Pyridine Scaffold as a Valuable Platform for the Identification of Selective PI3K Inhibitors

    Directory of Open Access Journals (Sweden)

    Ubaldina Galli

    2015-09-01

    Full Text Available A novel series of 4-aryl-3-cyano-2-(3-hydroxyphenyl-6-morpholino-pyridines have been designed as potential phosphatidylinositol-3-kinase (PI3K inhibitors. The compounds have been synthesized using the Guareschi reaction to prepare the key 4-aryl-3-cyano-2,6-dihydroxypyridine intermediate. A different selectivity according to the nature of the aryl group has been observed. Compound 9b is a selective inhibitor against the PI3Kα isoform, maintaining a good inhibitory activity. Docking studies were also performed in order to rationalize its profile of selectivity.

  8. Molecular identification and antifungal susceptibility profile of Candida species isolated from patients with vulvovaginitis in Tehran, Iran.

    Science.gov (United States)

    Sharifynia, Somayeh; Falahati, Mehraban; Akhlaghi, Lame; Foroumadi, Alireza; Fateh, Roohollah

    2017-01-01

    Rapid and accurate identification and evaluation of antifungal susceptibility pattern of Candida isolates are crucial to determine suitable antifungal drugs for the treatment of patients with vulvovaginitis candidiasis. Vaginal samples were collected from 150 women with suspicious vaginal candidiasis, and then cultured on Sabouraoud's Dextrose Agar with chloramphenicol to isolate Candida species. After identification of Candida isolates using polymerase chain reaction-restriction fragment length polymorphism technique, antifungal susceptibility testing of four azolic antifungal drugs was carried out using broth microdilution method according to the CLSI M27-A3. Candida species were isolated from eighty suspected patients (61.79%). The most common pathogen was Candida albicans (63.75%). Resistance to fluconazole and ketoconazole was observed in 27.5% and 23.75% of Candida isolates, respectively, and only 2% of Candida isolates were resistant to miconazole. Interestingly, resistance to fluconazole in C. albicans was more than other Candida species. The results indicated that therapy should be selected according to the antifungal susceptibility tests for the prevention of treatment failure and miconazole therapy can be considered as the best therapeutic choice in the management of vulvovaginitis.

  9. Molecular identification and antifungal susceptibility profile of Candida species isolated from patients with vulvovaginitis in Tehran, Iran

    Directory of Open Access Journals (Sweden)

    Somayeh Sharifynia

    2017-01-01

    Full Text Available Background: Rapid and accurate identification and evaluation of antifungal susceptibility pattern of Candida isolates are crucial to determine suitable antifungal drugs for the treatment of patients with vulvovaginitis candidiasis. Materials and Methods: Vaginal samples were collected from 150 women with suspicious vaginal candidiasis, and then cultured on Sabouraoud's Dextrose Agar with chloramphenicol to isolate Candida species. After identification of Candida isolates using polymerase chain reaction-restriction fragment length polymorphism technique, antifungal susceptibility testing of four azolic antifungal drugs was carried out using broth microdilution method according to the CLSI M27-A3. Results: Candida species were isolated from eighty suspected patients (61.79%. The most common pathogen was Candida albicans (63.75%. Resistance to fluconazole and ketoconazole was observed in 27.5% and 23.75% of Candida isolates, respectively, and only 2% of Candida isolates were resistant to miconazole. Interestingly, resistance to fluconazole in C. albicans was more than other Candida species. Conclusion: The results indicated that therapy should be selected according to the antifungal susceptibility tests for the prevention of treatment failure and miconazole therapy can be considered as the best therapeutic choice in the management of vulvovaginitis.

  10. Identification of Bioactivity, Volatile and Fatty Acid Profile in Supercritical Fluid Extracts of Mexican arnica

    Directory of Open Access Journals (Sweden)

    J. Saúl García-Pérez

    2016-09-01

    Full Text Available Supercritical fluid extraction (SFE is a sustainable technique used for the extraction of lipophilic metabolites such as pigments and fatty acids. Arnica plant is considered a potential candidate material with high antioxidant and antimicrobial activities. Therefore, in this study, a locally available Heterotheca inuloides, also known as Mexican arnica, was analyzed for the extraction of high-value compounds. Based on different pressure (P, temperature (T, and co-solvent (CoS, four treatments (T were prepared. A maximum 7.13% yield was recovered from T2 (T = 60 °C, P = 10 MPa, CoS = 8 g/min, followed by 6.69% from T4 (T = 60 °C, P = 30 MPa, CoS = 4 g/min. Some bioactive sesquiterpenoids such as 7-hydroxycadalene, caryophyllene and δ-cadinene were identified in the extracts by GC/MS. The fatty acid profile revealed that the main components were palmitic acid (C16:0, followed by linoleic acid (C18:2ω6c, α-linolenic acid (C18:3ω3 and stearic acid (C18:0 differing in percent yield per treatment. Antibacterial activities were determined by the agar diffusion method, indicating that all the treatments exerted strong antibacterial activity against S. aureus, C. albicans, and E. coli strains. The antioxidant capacity of the extracts was also measured by three in vitro assays, DPPH, TEAC and FRAP, using Trolox as a standard. Results showed high antioxidant capacity enabling pharmaceutical applications of Mexican arnica.

  11. Molecular identification, antifungal susceptibility profile, and biofilm formation of clinical and environmental Rhodotorula species isolates.

    Science.gov (United States)

    Nunes, Jorge Meneses; Bizerra, Fernando César; Ferreira, Renata Carmona E; Colombo, Arnaldo Lopes

    2013-01-01

    Rhodotorula species are emergent fungal pathogens capable of causing invasive infections, primarily fungemia. They are particularly problematic in immunosuppressed patients when using a central venous catheter. In this study, we evaluated the species distribution of 51 clinical and 8 environmental Rhodotorula species isolates using the ID32C system and internal transcribed spacer (ITS) sequencing. Antifungal susceptibility testing and biofilm formation capability using a crystal violet staining assay were performed. Using ITS sequencing as the gold standard, the clinical isolates were identified as follows: 44 R. mucilaginosa isolates, 2 R. glutinis isolates, 2 R. minuta isolates, 2 R. dairenensis isolates, and 1 Rhodosporidium fluviale isolate. The environmental isolates included 7 R. mucilaginosa isolates and 1 R. slooffiae isolate. Using the ID32C system, along with a nitrate assimilation test, only 90.3% of the isolates tested were correctly identified. In the biofilm formation assay, R. mucilaginosa and R. minuta exhibited greater biofilm formation ability compared to the other Rhodotorula species; the clinical isolates of R. mucilaginosa showed greater biofilm formation compared to the environmental isolates (P = 0.04). Amphotericin B showed good in vitro activity (MIC ≤ 1 μg/ml) against planktonic cells, whereas voriconazole and posaconazole showed poor activity (MIC(50)/MIC(90), 2/4 μg/ml). Caspofungin and fluconazole MICs were consistently high for all isolates tested (≥64 μg/ml and ≥ 4 μg/ml, respectively). In this study, we emphasized the importance of molecular methods to correctly identify Rhodotorula species isolates and non-R. mucilaginosa species in particular. The antifungal susceptibility profile reinforces amphotericin B as the antifungal drug of choice for the treatment of Rhodotorula infections. To our knowledge, this is the first study evaluating putative differences in the ability of biofilm formation among different Rhodotorula

  12. Comparison of trapping profiles between d-peptides and glutathione in the identification of reactive metabolites

    Directory of Open Access Journals (Sweden)

    Jaana E. Laine

    2015-01-01

    Full Text Available Qualitative trapping profile of reactive metabolites arising from six structurally different compounds was tested with three different d-peptide isomers (Peptide 1, gly–tyr–pro–cys–pro–his-pro; Peptide 2, gly–tyr–pro–ala–pro–his–pro; Peptide 3, gly–tyr–arg–pro–cys–pro–his–lys–pro and glutathione (GSH using mouse and human liver microsomes as the biocatalyst. The test compounds were classified either as clinically “safe” (amlodipine, caffeine, ibuprofen, or clinically as “risky” (clozapine, nimesulide, ticlopidine; i.e., associated with severe clinical toxicity outcomes. Our working hypothesis was as follows: could the use of short different amino acid sequence containing d-peptides in adduct detection confer any add-on value to that obtained with GSH? All “risky” agents’ resulted in the formation of several GSH adducts in the incubation mixture and with at least one peptide adduct with both microsomal preparations. Amlodipine did not form any adducts with any of the trapping agents. No GSH and peptide 2 and 3 adducts were found with caffeine, but with peptide 1 one adduct with human liver microsomes was detected. Ibuprofen produced one Peptide 1-adduct with human and mouse liver microsomes but not with GSH. In conclusion, GSH still remains the gold trapping standard for reactive metabolites. However, targeted d-peptides could provide additional information about protein binding potential of electrophilic agents, but their clinical significance needs to be clarified using a wider spectrum of chemicals together with other safety estimates.

  13. Multiparametric Profiling for Identification of Chemosensitizers against Gram-Negative Bacteria

    Directory of Open Access Journals (Sweden)

    Vincent Lôme

    2018-02-01

    Full Text Available Antibiotic resistance is now a worldwide therapeutic problem. Since the beginning of anti-infectious treatment bacteria have rapidly shown an incredible ability to develop and transfer resistance mechanisms. In the last decades, the design variation of pioneer bioactive molecules has strongly improved their activity and the pharmaceutical companies partly won the race against the clock. Since the 1980s, the new classes of antibiotics that emerged were mainly directed to Gram-positive bacteria. Thus, we are now facing to multidrug-resistant Gram-negative bacteria, with no therapeutic options to deal with them. These bacteria are mainly resistant because of their double membrane that conjointly impairs antibiotic accumulation and extrudes these molecules when entered. The main challenge is to allow antibiotics to cross the impermeable envelope and reach their targets. One promising solution would be to associate, in a combination therapy, a usual antibiotic with a non-antibiotic chemosensitizer. Nevertheless, for effective drug discovery, there is a prominent lack of tools required to understand the rules of permeation and accumulation into Gram-negative bacteria. By the use of a multidrug-resistant enterobacteria, we introduce a high-content screening procedure for chemosensitizers discovery by quantitative assessment of drug accumulation, alteration of barriers, and deduction of their activity profile. We assembled and analyzed a control chemicals library to perform the proof of concept. The analysis was based on real-time monitoring of the efflux alteration and measure of the influx increase in the presence of studied compounds in an automatized bio-assay. Then, synergistic activity of compounds with an antibiotic was studied and kinetic data reduction was performed which led to the calculation of a score for each barrier to be altered.

  14. Identification of learning and memory genes in canine; promoter investigation and determining the selective pressure.

    Science.gov (United States)

    Seifi Moroudi, Reihane; Masoudi, Ali Akbar; Vaez Torshizi, Rasoul; Zandi, Mohammad

    2014-12-01

    One of the important behaviors of dogs is trainability which is affected by learning and memory genes. These kinds of the genes have not yet been identified in dogs. In the current research, these genes were found in animal models by mining the biological data and scientific literatures. The proteins of these genes were obtained from the UniProt database in dogs and humans. Not all homologous proteins perform similar functions, thus comparison of these proteins was studied in terms of protein families, domains, biological processes, molecular functions, and cellular location of metabolic pathways in Interpro, KEGG, Quick Go and Psort databases. The results showed that some of these proteins have the same performance in the rat or mouse, dog, and human. It is anticipated that the protein of these genes may be effective in learning and memory in dogs. Then, the expression pattern of the recognized genes was investigated in the dog hippocampus using the existing information in the GEO profile. The results showed that BDNF, TAC1 and CCK genes are expressed in the dog hippocampus, therefore, these genes could be strong candidates associated with learning and memory in dogs. Subsequently, due to the importance of the promoter regions in gene function, this region was investigated in the above genes. Analysis of the promoter indicated that the HNF-4 site of BDNF gene and the transcription start site of CCK gene is exposed to methylation. Phylogenetic analysis of protein sequences of these genes showed high similarity in each of these three genes among the studied species. The dN/dS ratio for BDNF, TAC1 and CCK genes indicates a purifying selection during the evolution of the genes.

  15. Integrated statistical learning of metabolic ion mobility spectrometry profiles for pulmonary disease identification

    DEFF Research Database (Denmark)

    Hauschild, A.C.; Baumbach, Jan; Baumbach, J.

    2012-01-01

    sophisticated statistical learning techniques for VOC-based feature selection and supervised classification into patient groups. We analyzed breath data from 84 volunteers, each of them either suffering from chronic obstructive pulmonary disease (COPD), or both COPD and bronchial carcinoma (COPD + BC), as well...... as from 35 healthy volunteers, comprising a control group (CG). We standardized and integrated several statistical learning methods to provide a broad overview of their potential for distinguishing the patient groups. We found that there is strong potential for separating MCC/IMS chromatograms of healthy...... patients from healthy controls. We conclude that these statistical learning methods have a generally high accuracy when applied to well-structured, medical MCC/IMS data....

  16. Anti-bacterial profile of some beers and their effect on some selected ...

    African Journals Online (AJOL)

    ONOS

    2010-09-06

    Sep 6, 2010 ... profile against food born diseases caused by bacteria such as Escherichia coli, Salmonella typhimurium .... technological plane, a fast, premature sporulation is .... directly used as preservative; it should be fractioned in.

  17. Role of lifestyle variables on the lipid profile of selected South Indian subjects

    Directory of Open Access Journals (Sweden)

    Uma Chitra

    2012-01-01

    Conclusion: Our results confirm that diet and exercise routines significantly affect the serum lipid profile. Obesity and overweight constitute a risk factor for the development of hypercholesterolaemia and hypertriglyceridaemia.

  18. Fatty acid profile of the fat in selected smoked marine fish.

    Science.gov (United States)

    Regulska-Ilow, Bozena; Ilow, Rafał; Konikowska, Klaudia; Kawicka, Anna; Rózańska, Dorota; Bochińska, Agnieszka

    2013-01-01

    Fish and marine animals fat is a source of unique long chain polyunsaturated fatty acids (LC-PUFA): eicosapentaenoic (EPA), docosahexaenoic (DHA) and dipicolinic (DPA). These compounds have a beneficial influence on blood lipid profile and they reduce the risk of cardiovascular diseases, atherosclerosis and disorders of central nervous system. The proper ratio of n-6/n-3 fatty acids in diet is necessary to maintain a balance between the effects of eicosanoids synthesized from these acids in the body. The aim of this study was the evaluation of total fat and cholesterol content and percentage of fatty acids in selected commercial smoked marine fish. The studied samples were smoked marine fish such as: halibut, mackerel, bloater and sprat. The percentage total fat content in edible muscles was evaluated via the Folch modified method. The fat was extracted via the Bligh-Dyer modified method. The enzymatic hydrolysis was used to assesses cholesterol content in samples. The content of fatty acids, expressed as methyl esters, was evaluated with gas chromatography. The average content of total fat in 100 g of fillet of halibut, mackerel, bloater and sprat amounted respectively to: 14.5 g, 25.7 g, 13.9 g and 13.9 g. The average content of cholesterol in 100 g of halibut, mackerel, bloater and sprat was respectively: 54.5 mg, 51.5 mg, 57.5 mg and 130.9 mg. The amount of saturated fatty acids (SFA) was about 1/4 of total fatty acids in the analyzed samples. The oleic acid (C18:1 n-9) was the major compound among monounsaturated fatty acids (MUFA) and amounted to 44% of these fatty acids. The percentage of polyunsaturated fatty acids (PUFA) in halibut, mackerel, bloater and sprat was respectively: 31.9%, 45.4%, 40.8% and 37.0%. The percentage of n-3 PUFA in mackerel and bloater was 30.1% and 30.2%, while in halibut and sprat was lower and amounted to 22.5% and 25.6%, respectively. In terms of nutritional magnitude the meat of mackerel and herring, compared to the meat of

  19. Transcriptome Profiling of Louisiana iris Root and Identification of Genes Involved in Lead-Stress Response

    Directory of Open Access Journals (Sweden)

    Songqing Tian

    2015-11-01

    Full Text Available Louisiana iris is tolerant to and accumulates the heavy metal lead (Pb. However, there is limited knowledge of the molecular mechanisms behind this feature. We describe the transcriptome of Louisiana iris using Illumina sequencing technology. The root transcriptome of Louisiana iris under control and Pb-stress conditions was sequenced. Overall, 525,498 transcripts representing 313,958 unigenes were assembled using the clean raw reads. Among them, 43,015 unigenes were annotated and their functions classified using the euKaryotic Orthologous Groups (KOG database. They were divided into 25 molecular families. In the Gene Ontology (GO database, 50,174 unigenes were categorized into three GO trees (molecular function, cellular component and biological process. After analysis of differentially expressed genes, some Pb-stress-related genes were selected, including biosynthesis genes of chelating compounds, metal transporters, transcription factors and antioxidant-related genes. This study not only lays a foundation for further studies on differential genes under Pb stress, but also facilitates the molecular breeding of Louisiana iris.

  20. Identification and Expression Profiling of the Auxin Response Factors in Dendrobium officinale under Abiotic Stresses.

    Science.gov (United States)

    Chen, Zhehao; Yuan, Ye; Fu, Di; Shen, Chenjia; Yang, Yanjun

    2017-05-04

    Auxin response factor (ARF) proteins play roles in plant responses to diverse environmental stresses by binding specifically to the auxin response element in the promoters of target genes. Using our latest public Dendrobium transcriptomes, a comprehensive characterization and analysis of 14 DnARF genes were performed. Three selected DnARFs , including DnARF1 , DnARF4 , and DnARF6 , were confirmed to be nuclear proteins according to their transient expression in epidermal cells of Nicotiana benthamiana leaves. Furthermore, the transcription activation abilities of DnARF1 , DnARF4 , and DnARF6 were tested in a yeast system. Our data showed that DnARF6 is a transcriptional activator in Dendrobium officinale . To uncover the basic information of DnARF gene responses to abiotic stresses, we analyzed their expression patterns under various hormones and abiotic treatments. Based on our data, several hormones and significant stress responsive DnARF genes have been identified. Since auxin and ARF genes have been identified in many plant species, our data is imperative to reveal the function of ARF mediated auxin signaling in the adaptation to the challenging Dendrobium environment.

  1. An unsupervised technique for optimal feature selection in attribute profiles for spectral-spatial classification of hyperspectral images

    Science.gov (United States)

    Bhardwaj, Kaushal; Patra, Swarnajyoti

    2018-04-01

    Inclusion of spatial information along with spectral features play a significant role in classification of remote sensing images. Attribute profiles have already proved their ability to represent spatial information. In order to incorporate proper spatial information, multiple attributes are required and for each attribute large profiles need to be constructed by varying the filter parameter values within a wide range. Thus, the constructed profiles that represent spectral-spatial information of an hyperspectral image have huge dimension which leads to Hughes phenomenon and increases computational burden. To mitigate these problems, this work presents an unsupervised feature selection technique that selects a subset of filtered image from the constructed high dimensional multi-attribute profile which are sufficiently informative to discriminate well among classes. In this regard the proposed technique exploits genetic algorithms (GAs). The fitness function of GAs are defined in an unsupervised way with the help of mutual information. The effectiveness of the proposed technique is assessed using one-against-all support vector machine classifier. The experiments conducted on three hyperspectral data sets show the robustness of the proposed method in terms of computation time and classification accuracy.

  2. Identification and uncertainty estimation of vertical reflectivity profiles using a Lagrangian approach to support quantitative precipitation measurements by weather radar

    Science.gov (United States)

    Hazenberg, P.; Torfs, P. J. J. F.; Leijnse, H.; Delrieu, G.; Uijlenhoet, R.

    2013-09-01

    This paper presents a novel approach to estimate the vertical profile of reflectivity (VPR) from volumetric weather radar data using both a traditional Eulerian as well as a newly proposed Lagrangian implementation. For this latter implementation, the recently developed Rotational Carpenter Square Cluster Algorithm (RoCaSCA) is used to delineate precipitation regions at different reflectivity levels. A piecewise linear VPR is estimated for either stratiform or neither stratiform/convective precipitation. As a second aspect of this paper, a novel approach is presented which is able to account for the impact of VPR uncertainty on the estimated radar rainfall variability. Results show that implementation of the VPR identification and correction procedure has a positive impact on quantitative precipitation estimates from radar. Unfortunately, visibility problems severely limit the impact of the Lagrangian implementation beyond distances of 100 km. However, by combining this procedure with the global Eulerian VPR estimation procedure for a given rainfall type (stratiform and neither stratiform/convective), the quality of the quantitative precipitation estimates increases up to a distance of 150 km. Analyses of the impact of VPR uncertainty shows that this aspect accounts for a large fraction of the differences between weather radar rainfall estimates and rain gauge measurements.

  3. Genome-wide identification of VQ motif-containing proteins and their expression profiles under abiotic stresses in maize

    Directory of Open Access Journals (Sweden)

    Weibin eSong

    2016-01-01

    Full Text Available VQ motif-containing proteins play crucial roles in abiotic stress responses in plants. Recent studies have shown that some VQ proteins physically interact with WRKY transcription factors to activate downstream genes. In the present study, we identified and characterized genes encoding VQ motif-containing proteins using the most recent version of the maize genome sequence. In total, 61VQ genes were identified. In a cluster analysis, these genes clustered into nine groups together with their homologous genes in rice and Arabidopsis. Most of the VQ genes (57 out of 61 numbers identified in maize were found to be single-copy genes. Analyses of RNA-seq data obtained using seedlings under long-term drought treatment showed that the expression levels of most ZmVQ genes (41 out of 61 members changed during the drought stress response. Quantitative real-time PCR analyses showed that most of the ZmVQ genes were responsive to NaCl treatment. Also, approximately half of the ZmVQ genes were co-expressed with ZmWRKY genes. The identification of these VQ genes in the maize genome and knowledge of their expression profiles under drought and osmotic stresses will provide a solid foundation for exploring their specific functions in the abiotic stress responses of maize.

  4. Identification of Novel and Conserved microRNAs in Homalodisca vitripennis, the Glassy-Winged Sharpshooter by Expression Profiling.

    Directory of Open Access Journals (Sweden)

    Raja Sekhar Nandety

    Full Text Available The glassy-winged sharpshooter (GWSS Homalodisca vitripennis (Hemiptera: Cicadellidae, is a xylem-feeding leafhopper and an important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce's disease of grapevines. MicroRNAs are a class of small RNAs that play an important role in the functional development of various organisms including insects. In H. vitripennis, we identified microRNAs using high-throughput deep sequencing of adults followed by computational and manual annotation. A total of 14 novel microRNAs that are not found in the miRBase were identified from adult H. vitripennis. Conserved microRNAs were also found in our datasets. By comparison to our previously determined transcriptome sequence of H. vitripennis, we identified the potential targets of the microRNAs in the transcriptome. This microRNA profile information not only provides a more nuanced understanding of the biological and physiological mechanisms that govern gene expression in H. vitripennis, but may also lead to the identification of novel mechanisms for biorationally designed management strategies through the use of microRNAs.

  5. PCI-GC-MS-MS approach for identification of non-amino organic acid and amino acid profiles.

    Science.gov (United States)

    Luan, Hemi; Yang, Lin; Ji, Fenfen; Cai, Zongwei

    2017-03-15

    Alkyl chloroformate have been wildly used for the fast derivatization of metabolites with amino and/or carboxyl groups, coupling of powerful separation and detection systems, such as GC-MS, which allows the comprehensive analysis of non-amino organic acids and amino acids. The reagents involving n-alkyl chloroformate and n-alcohol are generally employed for providing symmetric labeling terminal alkyl chain with the same length. Here, we developed an asymmetric labeling strategy and positive chemical ionization gas chromatography-tandem mass spectrometry (PCI-GC-MS-MS) approach for determination of non-amino organic acids and amino acids, as well as the short chain fatty acids. Carboxylic and amino groups could be selectively labelled by propyl and ethyl groups, respectively. The specific neutral loss of C 3 H 8 O (60Da), C 3 H 5 O 2 (74Da) and C 4 H 8 O 2 (88Da) were useful in the selective identification for qualitative analysis of organic acids and amino acid derivatives. PCI-GC-MS-MS using multiple reaction monitoring (MRM) was applied for semi-quantification of typical non-amino organic acids and amino acids. This method exhibited a wide range of linear range, good regression coefficient (R 2 ) and repeatability. The relative standard deviation (RSD) of targeted metabolites showed excellent intra- and inter-day precision (chloroformate derivatization. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. THE REDSHIFT EVOLUTION OF THE MEAN TEMPERATURE, PRESSURE, AND ENTROPY PROFILES IN 80 SPT-SELECTED GALAXY CLUSTERS

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, M.; Benson, B. A.; Vikhlinin, A.; Aird, K. A.; Allen, S. W.; Bautz, M.; Bayliss, M.; Bleem, L. E.; Bocquet, S.; Brodwin, M.; Carlstrom, J. E.; Chang, C. L.; Cho, H. M.; Clocchiatti, A.; Crawford, T. M.; Crites, A. T.; de Haan, T.; Dobbs, M. A.; Foley, R. J.; Forman, W. R.; George, E. M.; Gladders, M. D.; Gonzalez, A. H.; Halverson, N. W.; Hlavacek-Larrondo, J.; Holder, G. P.; Holzapfel, W. L.; Hrubes, J. D.; Jones, C.; Keisler, R.; Knox, L.; Lee, A. T.; Leitch, E. M.; Liu, J.; Lueker, M.; Luong-Van, D.; Mantz, A.; Marrone, D. P.; McMahon, J. J.; Meyer, S. S.; Miller, E. D.; Mocanu, L.; Mohr, J. J.; Murray, S. S.; Padin, S.; Pryke, C.; Reichardt, C. L.; Rest, A.; Ruhl, J. E.; Saliwanchik, B. R.; Saro, A.; Sayre, J. T.; Schaffer, K. K.; Shirokoff, E.; Spieler, H. G.; Stalder, B.; Stanford, S. A.; Staniszewski, Z.; Stark, A. A.; Story, K. T.; Stubbs, C. W.; Vanderlinde, K.; Vieira, J. D.; Williamson, R.; Zahn, O.; Zenteno, A.

    2014-09-24

    We present the results of an X-ray analysis of 80 galaxy clusters selected in the 2500 deg(2) South Pole Telescope survey and observed with the Chandra X-ray Observatory. We divide the full sample into subsamples of ~20 clusters based on redshift and central density, performing a joint X-ray spectral fit to all clusters in a subsample simultaneously, assuming self-similarity of the temperature profile. This approach allows us to constrain the shape of the temperature profile over 0 < r < 1.5R (500), which would be impossible on a per-cluster basis, since the observations of individual clusters have, on average, 2000 X-ray counts. The results presented here represent the first constraints on the evolution of the average temperature profile from z = 0 to z = 1.2. We find that high-z (0.6 < z < 1.2) clusters are slightly (~30%) cooler both in the inner (r < 0.1R (500)) and outer (r > R (500)) regions than their low-z (0.3 < z < 0.6) counterparts. Combining the average temperature profile with measured gas density profiles from our earlier work, we infer the average pressure and entropy profiles for each subsample. Confirming earlier results from this data set, we find an absence of strong cool cores at high z, manifested in this analysis as a significantly lower observed pressure in the central 0.1R (500) of the high-z cool-core subset of clusters compared to the low-z cool-core subset. Overall, our observed pressure profiles agree well with earlier lower-redshift measurements, suggesting minimal redshift evolution in the pressure profile outside of the core. We find no measurable redshift evolution in the entropy profile at r lsim 0.7R (500)—this may reflect a long-standing balance between cooling and feedback over long timescales and large physical scales. We observe a slight flattening of the entropy profile at r gsim R (500) in our high-z subsample. This flattening is consistent with a temperature bias due to the enhanced (~3×) rate at which group-mass (~2

  7. Initial identification & selection bias versus the eventual confirmation of talent: evidence for the benefits of a rocky road?

    Science.gov (United States)

    McCarthy, Neil; Collins, Dave

    2014-01-01

    The relative age effect (RAE), whereby earlier birthdate children within a selection year are more commonly selected as talented, has been highlighted in the literature. As a consequence, these young athletes get into specialised training earlier and in greater numbers, leading (it is suggested) to a disproportionate opportunity for success. However, this disproportionality seems not to be manifest in senior teams. Accordingly, we examine the identification and conversion rates for academy rugby players, examining a sample of all players passing into and either graduating, or being dismissed from, a major English rugby academy. Data demonstrated a reversal of the RAE "benefit", whereby late-birth players were less likely to be selected, but more likely to achieve senior professional status. Possible reasons are explored and, on the basis of our data, we propose a psychologically based explanation of greater "growth" due to additional challenge experienced by these initially disadvantaged younger players.

  8. High-resolution bacterial growth inhibition profiling combined with HPLC-HRMS-SPE-NMR for identification of antibacterial constituents in Chinese plants used to treat snakebites

    DEFF Research Database (Denmark)

    Liu, Yueqiu; Nielsen, Mia; Stærk, Dan

    2014-01-01

    Bacillus subtilis, Staphylococcus aureus, Escherichia coli or Pseudomonas aeruginosa. The biochromatograms demonstrated that tannins play a main role for the bacterial growth inhibition observed for all above-mentioned plants except for Polygonum cuspidatum. Furthermore, the high-resolution bacterial...... growth inhibition profiling combined with HPLC–HRMS–SPE–NMR allowed fast identification of three non-tannin active compounds, i.e., piceid, resveratrol and emodin from ethanol extract of Polygonum cuspidatum. Conclusion The high-resolution bacterial growth inhibition profiling allowed fast pinpointing...... of constituents responsible for the bioactivity, e.g., either showing tannins being the main bacterial growth inhibitors as observed for the majority of the active plants, or combined with HPLC–HRMS–SPE–NMR for fast structural identification of non-tannin constituents correlated with antibacterial activity....

  9. mRMR-ABC: A Hybrid Gene Selection Algorithm for Cancer Classification Using Microarray Gene Expression Profiling

    Directory of Open Access Journals (Sweden)

    Hala Alshamlan

    2015-01-01

    Full Text Available An artificial bee colony (ABC is a relatively recent swarm intelligence optimization approach. In this paper, we propose the first attempt at applying ABC algorithm in analyzing a microarray gene expression profile. In addition, we propose an innovative feature selection algorithm, minimum redundancy maximum relevance (mRMR, and combine it with an ABC algorithm, mRMR-ABC, to select informative genes from microarray profile. The new approach is based on a support vector machine (SVM algorithm to measure the classification accuracy for selected genes. We evaluate the performance of the proposed mRMR-ABC algorithm by conducting extensive experiments on six binary and multiclass gene expression microarray datasets. Furthermore, we compare our proposed mRMR-ABC algorithm with previously known techniques. We reimplemented two of these techniques for the sake of a fair comparison using the same parameters. These two techniques are mRMR when combined with a genetic algorithm (mRMR-GA and mRMR when combined with a particle swarm optimization algorithm (mRMR-PSO. The experimental results prove that the proposed mRMR-ABC algorithm achieves accurate classification performance using small number of predictive genes when tested using both datasets and compared to previously suggested methods. This shows that mRMR-ABC is a promising approach for solving gene selection and cancer classification problems.

  10. mRMR-ABC: A Hybrid Gene Selection Algorithm for Cancer Classification Using Microarray Gene Expression Profiling.

    Science.gov (United States)

    Alshamlan, Hala; Badr, Ghada; Alohali, Yousef

    2015-01-01

    An artificial bee colony (ABC) is a relatively recent swarm intelligence optimization approach. In this paper, we propose the first attempt at applying ABC algorithm in analyzing a microarray gene expression profile. In addition, we propose an innovative feature selection algorithm, minimum redundancy maximum relevance (mRMR), and combine it with an ABC algorithm, mRMR-ABC, to select informative genes from microarray profile. The new approach is based on a support vector machine (SVM) algorithm to measure the classification accuracy for selected genes. We evaluate the performance of the proposed mRMR-ABC algorithm by conducting extensive experiments on six binary and multiclass gene expression microarray datasets. Furthermore, we compare our proposed mRMR-ABC algorithm with previously known techniques. We reimplemented two of these techniques for the sake of a fair comparison using the same parameters. These two techniques are mRMR when combined with a genetic algorithm (mRMR-GA) and mRMR when combined with a particle swarm optimization algorithm (mRMR-PSO). The experimental results prove that the proposed mRMR-ABC algorithm achieves accurate classification performance using small number of predictive genes when tested using both datasets and compared to previously suggested methods. This shows that mRMR-ABC is a promising approach for solving gene selection and cancer classification problems.

  11. Aging and mechanisms of visual selective attention : effects on word localization and identification

    NARCIS (Netherlands)

    Mccalley, L.T.

    1995-01-01

    The present study investigated age differences in attentional allocation in a word localization and identification task. Response times for valid and invalid spatial cue conditions were compared for each of two age groups under two SOA conditions: 500 msec and 1000 msec. Very high benefits for valid

  12. Muon Identification performance: hadron mis-Id measurements and RPC Muon selections

    CERN Document Server

    CMS Collaboration

    2014-01-01

    Pion, kaon, proton mis-identification probabilities as muons have been measured for different Muon ID algorithms. Results from two independent analyses are presented. The performance of a new muon ID algorithm based on matching of inner tracks with hits in muon RPC chambers is also presented.

  13. Selectivity Profiling and Biological Activity of Novel β-Carbolines as Potent and Selective DYRK1 Kinase Inhibitors.

    Directory of Open Access Journals (Sweden)

    Katharina Rüben

    Full Text Available DYRK1A is a pleiotropic protein kinase with diverse functions in cellular regulation, including cell cycle control, neuronal differentiation, and synaptic transmission. Enhanced activity and overexpression of DYRK1A have been linked to altered brain development and function in Down syndrome and neurodegenerative diseases such as Alzheimer's disease. The β-carboline alkaloid harmine is a high affinity inhibitor of DYRK1A but suffers from the drawback of inhibiting monoamine oxidase A (MAO-A with even higher potency. Here we characterized a series of novel harmine analogs with minimal or absent MAO-A inhibitory activity. We identified several inhibitors with submicromolar potencies for DYRK1A and selectivity for DYRK1A and DYRK1B over the related kinases DYRK2 and HIPK2. An optimized inhibitor, AnnH75, inhibited CLK1, CLK4, and haspin/GSG2 as the only off-targets in a panel of 300 protein kinases. In cellular assays, AnnH75 dose-dependently reduced the phosphorylation of three known DYRK1A substrates (SF3B1, SEPT4, and tau without negative effects on cell viability. AnnH75 inhibited the cotranslational tyrosine autophosphorylation of DYRK1A and threonine phosphorylation of an exogenous substrate protein with similar potency. In conclusion, we have characterized an optimized β-carboline inhibitor as a highly selective chemical probe that complies with desirable properties of drug-like molecules and is suitable to interrogate the function of DYRK1A in biological studies.

  14. Building America Top Innovations 2014 Profile: California Energy Standards Recognize the Importance of Filter Selection

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2014-11-01

    This 2014 Top Innovation profile describes Building America research on HVAC air filter sizing that prompted a change in the California “Title 24” Energy Code requiring filter manufacturers, HVAC designers, and HERS raters to make changes that will encourage the use of higher MERV filters without degrading HVAC performance.

  15. SPSP Phase III Recruiting, Selecting, and Developing Secure Power Systems Professionals. Job Profiles

    Energy Technology Data Exchange (ETDEWEB)

    O' Neil, Lori Ross [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Conway, T. J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Tobey, D. H. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Greitzer, Frank L. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Dalton, Angela C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Pusey, Portia K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-03-01

    The Secure Power Systems Professional Phase III final report was released last year which an appendix of Job Profiles. This new report is that appendix broken out as a standalone document to assist utilities in recruiting and developing Secure Power Systems Professionals at their site.

  16. Carotenoid profiling of leaves of selected eggplant accessions subjected to drought stress

    Science.gov (United States)

    This study focused on the quantification of carotenoids of the leaves of African eggplants commonly consumed as leafy and fruit vegetables. The results gave comparative profiles of carotenoids at different growth and developmental stages and under drought stress. Stress was achieved by limiting irri...

  17. SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera).

    Science.gov (United States)

    Muñoz, Irene; Henriques, Dora; Jara, Laura; Johnston, J Spencer; Chávez-Galarza, Julio; De La Rúa, Pilar; Pinto, M Alice

    2017-07-01

    The honeybee (Apis mellifera) has been threatened by multiple factors including pests and pathogens, pesticides and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A. m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify pure-bred A. m. mellifera colonies. Microsatellites have been preferred for identification of A. m. mellifera stocks across conservation centres. However, owing to high throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite set to detect structure and introgression with that of different sets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellite loci. Contrary to every SNP data set, microsatellites did not discriminate between the two lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level, microsatellites' performance was relatively poor at the upper range of Q-values, a result reflected by their lower precision. Our results suggest that SNPs are more accurate and powerful than microsatellites for identification of A. m. mellifera colonies, especially when they are selected by information content. © 2016 John Wiley & Sons Ltd.

  18. Identification of lipid profile on γ-irradiated primary cultured human diploid fibroblasts by UPLC-ESI-QTOF-MS

    International Nuclear Information System (INIS)

    Lee, Eun Kyeong; Yun, Hyun Jin; Kim, Sun Young; Kim, So Ra; Kim, Eun Ju; Kang, Chang Mo; Hwang, Geum Sook

    2013-01-01

    The study of biomarkers in normal-tissue radiobiology is of great importance to people subjected to non-destructive testing, to nuclear power industry, and to radiological terrorism. Cytogenetics has remained the 'gold standard' for the detection of chromosomal changes, but this method is cumbersome and time consuming. Therefore, it is necessary to establish a rapid, high-throughput biological monitoring protocol to determine the exposure radiation dose in order to rapidly triage mass casualties. Metabolomics studies is an effective platform for identification and quantification of the complete set of metabolites in a biological system, and it has been successfully provides important insights into physiological and disease states and facilitate in depth understanding of underlying biochemical pathways. Radiation metabolomics has been used to identify radiation effects at the metabolite levels in cells and in urine or serum collected from laboratory animals such as mouse, rat and monkey. Recently, a few radiation metabolomics studies showed that multiple metabolites related to the purine, inositol or pyrimidine metabolism, fatty acid biosynthesis and glycolysis/gluconeogenesis could be potential minimal-invasive markers for radiation exposure. However, there is little consistency in these studies due to differences in analyzed sample (cells, urine, serum), animal models (mouse, rat and monkey). Furthermore, the biological effects of ionizing radiation (IR) were differently regulated in the different absorbed doses, dose-rates and type of IR. Thus, it is necessary to explore the entire biosphere profiling of metabolic markers to make reasonable biological explanation under radiation exposure. We hypothesized that the variations in lipid expression in IR-induced cells would result in a unique lipid profile in human diploid fibroblasts (HDF), which can be detected with the targeted and quantitative metabolomics approach. Irradiated HDF cells showed the dose

  19. Identification of lipid profile on γ-irradiated primary cultured human diploid fibroblasts by UPLC-ESI-QTOF-MS

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Eun Kyeong; Yun, Hyun Jin; Kim, Sun Young; Kim, So Ra; Kim, Eun Ju; Kang, Chang Mo [Division of Radiation Effect, Korea Institute of Radiological and Medical Sciences, Seoul (Korea, Republic of); Hwang, Geum Sook [Integrated Metabolomics Research Group, Korea Basic Science Institute, Sejong (Korea, Republic of)

    2013-11-15

    The study of biomarkers in normal-tissue radiobiology is of great importance to people subjected to non-destructive testing, to nuclear power industry, and to radiological terrorism. Cytogenetics has remained the 'gold standard' for the detection of chromosomal changes, but this method is cumbersome and time consuming. Therefore, it is necessary to establish a rapid, high-throughput biological monitoring protocol to determine the exposure radiation dose in order to rapidly triage mass casualties. Metabolomics studies is an effective platform for identification and quantification of the complete set of metabolites in a biological system, and it has been successfully provides important insights into physiological and disease states and facilitate in depth understanding of underlying biochemical pathways. Radiation metabolomics has been used to identify radiation effects at the metabolite levels in cells and in urine or serum collected from laboratory animals such as mouse, rat and monkey. Recently, a few radiation metabolomics studies showed that multiple metabolites related to the purine, inositol or pyrimidine metabolism, fatty acid biosynthesis and glycolysis/gluconeogenesis could be potential minimal-invasive markers for radiation exposure. However, there is little consistency in these studies due to differences in analyzed sample (cells, urine, serum), animal models (mouse, rat and monkey). Furthermore, the biological effects of ionizing radiation (IR) were differently regulated in the different absorbed doses, dose-rates and type of IR. Thus, it is necessary to explore the entire biosphere profiling of metabolic markers to make reasonable biological explanation under radiation exposure. We hypothesized that the variations in lipid expression in IR-induced cells would result in a unique lipid profile in human diploid fibroblasts (HDF), which can be detected with the targeted and quantitative metabolomics approach. Irradiated HDF cells showed the dose

  20. Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum.

    Science.gov (United States)

    Steindorff, Andrei Stecca; Ramada, Marcelo Henrique Soller; Coelho, Alexandre Siqueira Guedes; Miller, Robert Neil Gerard; Pappas, Georgios Joannis; Ulhoa, Cirano José; Noronha, Eliane Ferreira

    2014-03-18

    The species of T. harzianum are well known for their biocontrol activity against plant pathogens. However, few studies have been conducted to further our understanding of its role as a biological control agent against S. sclerotiorum, a pathogen involved in several crop diseases around the world. In this study, we have used RNA-seq and quantitative real-time PCR (RT-qPCR) techniques in order to explore changes in T. harzianum gene expression during growth on cell wall of S. sclerotiorum (SSCW) or glucose. RT-qPCR was also used to examine genes potentially involved in biocontrol, during confrontation between T. harzianum and S. sclerotiorum. Data obtained from six RNA-seq libraries were aligned onto the T. harzianum CBS 226.95 reference genome and compared after annotation using the Blast2GO suite. A total of 297 differentially expressed genes were found in mycelia grown for 12, 24 and 36 h under the two different conditions: supplemented with glucose or SSCW. Functional annotation of these genes identified diverse biological processes and molecular functions required during T. harzianum growth on SSCW or glucose. We identified various genes of biotechnological value encoding proteins with functions such as transporters, hydrolytic activity, adherence, appressorium development and pathogenesis. To validate the expression profile, RT-qPCR was performed using 20 randomly chosen genes. RT-qPCR expression profiles were in complete agreement with the RNA-Seq data for 17 of the genes evaluated. The other three showed differences at one or two growth times. During the confrontation assay, some genes were up-regulated during and after contact, as shown in the presence of SSCW which is commonly used as a model to mimic this interaction. The present study is the first initiative to use RNA-seq for identification of differentially expressed genes in T. harzianum strain TR274, in response to the phytopathogenic fungus S. sclerotiorum. It provides insights into the mechanisms of

  1. Behavioral profiles of genetically selected aggressive and nonaggressive male wild house mice in two anxiety tests

    NARCIS (Netherlands)

    Hogg, S; Wurbel, H; Steimer, T; de Ruiter, A; Koolhaas, J; Sluyter, F; Driscoll, Peter

    2000-01-01

    Artificially selected aggressive (SAL) and non-aggressive (LAL) male house mice were tested in a hexagonal tunnel maze and light-dark preference (LD) box to determine if the bidirectional selection for aggressive behavior leads to a coselection for different levels of trait anxiety. The tunnel maze

  2. Feature selection and recognition from nonspecific volatile profiles for discrimination of apple juices according to variety and geographical origin.

    Science.gov (United States)

    Guo, Jing; Yue, Tianli; Yuan, Yahong

    2012-10-01

    Apple juice is a complex mixture of volatile and nonvolatile components. To develop discrimination models on the basis of the volatile composition for an efficient classification of apple juices according to apple variety and geographical origin, chromatography volatile profiles of 50 apple juice samples belonging to 6 varieties and from 5 counties of Shaanxi (China) were obtained by headspace solid-phase microextraction coupled with gas chromatography. The volatile profiles were processed as continuous and nonspecific signals through multivariate analysis techniques. Different preprocessing methods were applied to raw chromatographic data. The blind chemometric analysis of the preprocessed chromatographic profiles was carried out. Stepwise linear discriminant analysis (SLDA) revealed satisfactory discriminations of apple juices according to variety and geographical origin, provided respectively 100% and 89.8% success rate in terms of prediction ability. Finally, the discriminant volatile compounds selected by SLDA were identified by gas chromatography-mass spectrometry. The proposed strategy was able to verify the variety and geographical origin of apple juices involving only a reduced number of discriminate retention times selected by the stepwise procedure. This result encourages the similar procedures to be considered in quality control of apple juices. This work presented a method for an efficient discrimination of apple juices according to apple variety and geographical origin using HS-SPME-GC-MS together with chemometric tools. Discrimination models developed could help to achieve greater control over the quality of the juice and to detect possible adulteration of the product. © 2012 Institute of Food Technologists®

  3. Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray.

    Science.gov (United States)

    Colombo, Ana Paula V; Boches, Susan K; Cotton, Sean L; Goodson, J Max; Kent, Ralph; Haffajee, Anne D; Socransky, Sigmund S; Hasturk, Hatice; Van Dyke, Thomas E; Dewhirst, Floyd; Paster, Bruce J

    2009-09-01

    This study compared the subgingival microbiota of subjects with refractory periodontitis (RP) to those in subjects with treatable periodontitis (GRs = good responders) or periodontal health (PH) using the Human Oral Microbe Identification Microarray (HOMIM). At baseline, subgingival plaque samples were taken from 47 subjects with periodontitis and 20 individuals with PH and analyzed for the presence of 300 species by HOMIM. The subjects with periodontitis were classified as having RP (n = 17) based on mean attachment loss (AL) and/or more than three sites with AL >or=2.5 mm after scaling and root planing, surgery, and systemically administered amoxicillin and metronidazole or as GRs (n = 30) based on mean attachment gain and no sites with AL >or=2.5 mm after treatment. Significant differences in taxa among the groups were sought using the Kruskal-Wallis and chi(2) tests. More species were detected in patients with disease (GR or RP) than in those without disease (PH). Subjects with RP were distinguished from GRs or those with PH by a significantly higher frequency of putative periodontal pathogens, such as Parvimonas micra (previously Peptostreptococcus micros or Micromonas micros), Campylobacter gracilis, Eubacterium nodatum, Selenomonas noxia, Tannerella forsythia (previously T. forsythensis), Porphyromonas gingivalis, Prevotella spp., Treponema spp., and Eikenella corrodens, as well as unusual species (Pseudoramibacter alactolyticus, TM7 spp. oral taxon [OT] 346/356, Bacteroidetes sp. OT 272/274, Solobacterium moorei, Desulfobulbus sp. OT 041, Brevundimonas diminuta, Sphaerocytophaga sp. OT 337, Shuttleworthia satelles, Filifactor alocis, Dialister invisus/pneumosintes, Granulicatella adiacens, Mogibacterium timidum, Veillonella atypica, Mycoplasma salivarium, Synergistes sp. cluster II, and Acidaminococcaceae [G-1] sp. OT 132/150/155/148/135) (P spp. cluster I, Capnocytophaga sputigena, Cardiobacterium hominis, Haemophilus parainfluenzae, Lautropia mirabilis

  4. [Identification of anaerobic gram-negative bacilli isolated from various clinical specimens and determination of antibiotic resistance profiles with E-test methods].

    Science.gov (United States)

    Demir, Cengiz; Keşli, Recep

    2018-01-01

    The aim of this study was to identify gram-negative anaerobic bacilli isolated from various clinical specimens that were obtained from patients with suspected anaerobic infections and to determine the antibiotic resistance profiles by using the antibiotic concentration gradient method. The study was performed in Afyon Kocatepe University Ahmet Necdet Sezer Research and Practice Hospital, Medical Microbiology Laboratory between 1 November 2014 and 30 October 2015. Two hundred and seventyeight clinical specimens accepted for anaerobic culture were enrolled in the study. All the samples were cultivated anaerobically by using Schaedler agar with 5% defibrinated sheep blood and Schaedler broth. The isolated anaerobic gram-negative bacilli were identified by using both the conventional methods and automated identification system (VITEK 2, bioMerieux, France). Antibiotic susceptibility tests were performed with antibiotic concentration gradient method (E-test, bioMerieux, France); against penicillin G, clindamycin, cefoxitin, metronidazole, moxifloxacin, imipenem, meropenem, ertapenem and doripenem for each isolate. Of the 28 isolated anaerobic gram-negative bacilli; 14 were identified as Bacteroides fragilis group, 9 were Prevotella spp., and 5 were Fusobacterium spp. The highest resistance rate was found against penicillin (78.5%) and resistance rates against clindamycin and cefoxitin were found as 17.8% and 21.4%, respectively. No resistance was found against metronidazole, moxifloxacin, imipenem, meropenem, ertapenem and doripenem. As a result, isolation and identification of anaerobic bacteria are difficult, time-consuming and more expensive when compared with the cost of aerobic culture. The rate of anaerobic bacteria isolation may be increased by obtaining the appropriate clinical specimen and appropriate transportation of these specimens. We believe that the data obtained from the study in our center may offer benefits for the follow up and treatment of infections

  5. Tree resin composition, collection behavior and selective filters shape chemical profiles of tropical bees (Apidae: Meliponini.

    Directory of Open Access Journals (Sweden)

    Sara D Leonhardt

    Full Text Available The diversity of species is striking, but can be far exceeded by the chemical diversity of compounds collected, produced or used by them. Here, we relate the specificity of plant-consumer interactions to chemical diversity applying a comparative network analysis to both levels. Chemical diversity was explored for interactions between tropical stingless bees and plant resins, which bees collect for nest construction and to deter predators and microbes. Resins also function as an environmental source for terpenes that serve as appeasement allomones and protection against predators when accumulated on the bees' body surfaces. To unravel the origin of the bees' complex chemical profiles, we investigated resin collection and the processing of resin-derived terpenes. We therefore analyzed chemical networks of tree resins, foraging networks of resin collecting bees, and their acquired chemical networks. We revealed that 113 terpenes in nests of six bee species and 83 on their body surfaces comprised a subset of the 1,117 compounds found in resins from seven tree species. Sesquiterpenes were the most variable class of terpenes. Albeit widely present in tree resins, they were only found on the body surface of some species, but entirely lacking in others. Moreover, whereas the nest profile of Tetragonula melanocephala contained sesquiterpenes, its surface profile did not. Stingless bees showed a generalized collecting behavior among resin sources, and only a hitherto undescribed species-specific "filtering" of resin-derived terpenes can explain the variation in chemical profiles of nests and body surfaces from different species. The tight relationship between bees and tree resins of a large variety of species elucidates why the bees' surfaces contain a much higher chemodiversity than other hymenopterans.

  6. Informing the Selection of Screening Hit Series with in Silico Absorption, Distribution, Metabolism, Excretion, and Toxicity Profiles.

    Science.gov (United States)

    Sanders, John M; Beshore, Douglas C; Culberson, J Christopher; Fells, James I; Imbriglio, Jason E; Gunaydin, Hakan; Haidle, Andrew M; Labroli, Marc; Mattioni, Brian E; Sciammetta, Nunzio; Shipe, William D; Sheridan, Robert P; Suen, Linda M; Verras, Andreas; Walji, Abbas; Joshi, Elizabeth M; Bueters, Tjerk

    2017-08-24

    High-throughput screening (HTS) has enabled millions of compounds to be assessed for biological activity, but challenges remain in the prioritization of hit series. While biological, absorption, distribution, metabolism, excretion, and toxicity (ADMET), purity, and structural data are routinely used to select chemical matter for further follow-up, the scarcity of historical ADMET data for screening hits limits our understanding of early hit compounds. Herein, we describe a process that utilizes a battery of in-house quantitative structure-activity relationship (QSAR) models to generate in silico ADMET profiles for hit series to enable more complete characterizations of HTS chemical matter. These profiles allow teams to quickly assess hit series for desirable ADMET properties or suspected liabilities that may require significant optimization. Accordingly, these in silico data can direct ADMET experimentation and profoundly impact the progression of hit series. Several prospective examples are presented to substantiate the value of this approach.

  7. Identification of biomarkers for radiation-induced acute intestinal symptoms (RIAISs) in cervical cancer patients by serum protein profiling

    International Nuclear Information System (INIS)

    Chai Yanlan; Wang Juan; Gao Ying

    2015-01-01

    Radiation-induced acute intestinal symptoms (RIAISs) are the most frequent complication of radiotherapy that causes great pain and limits the treatment efficacy. The aim of this study was to identify serum biomarkers of RIAISs in cervical cancer patients by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). Serum samples were collected from 66 cervical cancer patients prior to pelvic radiotherapy. In our study, RIAISs occurred in 11 patients. An additional 11 patients without RIAISs were selected as controls, whose age, stage, histological type and treatment methods were matched to RIAISs patients. The 22 sera were subsequently analyzed by SELDI-TOF MS, and the resulting protein profiles were evaluated to identify biomarkers using appropriate bioinformatics tools. Comparing the protein profiles of serum samples from the RIAIS group and the control group, it was found that 22 protein peaks were significantly different (P < 0.05), and six of these peaks with mass-to-charge (m/z) ratios of 7514.9, 4603.94, 6887.41, 2769.21, 3839.72 and 4215.7 were successfully identified. A decision tree model of biomarkers was constructed based on three biomarkers (m/z 1270.88, 1503.23 and 7514.90), which separated RIAIS-affected patients from the control group with an accuracy of 81%. This study suggests that serum proteomic analysis by SELDI-TOF MS can identify cervical cancer patients that are susceptible to RIAISs prior to pelvic radiotherapy. (author)

  8. Lipase genes in Mucor circinelloides: identification, sub-cellular location, phylogenetic analysis and expression profiling during growth and lipid accumulation.

    Science.gov (United States)

    Zan, Xinyi; Tang, Xin; Chu, Linfang; Zhao, Lina; Chen, Haiqin; Chen, Yong Q; Chen, Wei; Song, Yuanda

    2016-10-01

    Lipases or triacylglycerol hydrolases are widely spread in nature and are particularly common in the microbial world. The filamentous fungus Mucor circinelloides is a potential lipase producer, as it grows well in triacylglycerol-contained culture media. So far only one lipase from M. circinelloides has been characterized, while the majority of lipases remain unknown in this fungus. In the present study, 47 potential lipase genes in M. circinelloides WJ11 and 30 potential lipase genes in M. circinelloides CBS 277.49 were identified by extensive bioinformatics analysis. An overview of these lipases is presented, including several characteristics, sub-cellular location, phylogenetic analysis and expression profiling of the lipase genes during growth and lipid accumulation. All of these proteins contained the consensus sequence for a classical lipase (GXSXG motif) and were divided into four types including α/β-hydrolase_1, α/β-hydrolase_3, class_3 and GDSL lipase (GDSL) based on gene annotations. Phylogenetic analyses revealed that class_3 family and α/β-hydrolase_3 family were the conserved lipase family in M. circinelloides. Additionally, some lipases also contained a typical acyltransferase motif of H-(X) 4-D, and these lipases may play a dual role in lipid metabolism, catalyzing both lipid hydrolysis and transacylation reactions. The differential expression of all lipase genes were confirmed by quantitative real-time PCR, and the expression profiling were analyzed to predict the possible biological roles of these lipase genes in lipid metabolism in M. circinelloides. We preliminarily hypothesized that lipases may be involved in triacylglycerol degradation, phospholipid synthesis and beta-oxidation. Moreover, the results of sub-cellular localization, the presence of signal peptide and transcriptional analyses of lipase genes indicated that four lipase in WJ11 most likely belong to extracellular lipases with a signal peptide. These findings provide a platform

  9. Identification of Site Selection Factors in the U.S. Franchise Restaurant Industry: An Exploratory Study

    OpenAIRE

    Park, Kunsoon

    2002-01-01

    The purpose of this study was to identify and rank the importance of the site selection factors that influence the U.S. franchise restaurant industry as well as rank the confidence level of the experts. To identify the site selection factors, this study sought assistance and support from restaurant professionals. The Delphi technique was used to elicit the opinions of a panel of experts regarding the site selection factors. The panel was composed of restaurant professionals of restaurant c...

  10. On the selection of user-defined parameters in data-driven stochastic subspace identification

    Science.gov (United States)

    Priori, C.; De Angelis, M.; Betti, R.

    2018-02-01

    The paper focuses on the time domain output-only technique called Data-Driven Stochastic Subspace Identification (DD-SSI); in order to identify modal models (frequencies, damping ratios and mode shapes), the role of its user-defined parameters is studied, and rules to determine their minimum values are proposed. Such investigation is carried out using, first, the time histories of structural responses to stationary excitations, with a large number of samples, satisfying the hypothesis on the input imposed by DD-SSI. Then, the case of non-stationary seismic excitations with a reduced number of samples is considered. In this paper, partitions of the data matrix different from the one proposed in the SSI literature are investigated, together with the influence of different choices of the weighting matrices. The study is carried out considering two different applications: (1) data obtained from vibration tests on a scaled structure and (2) in-situ tests on a reinforced concrete building. Referring to the former, the identification of a steel frame structure tested on a shaking table is performed using its responses in terms of absolute accelerations to a stationary (white noise) base excitation and to non-stationary seismic excitations of low intensity. Black-box and modal models are identified in both cases and the results are compared with those from an input-output subspace technique. With regards to the latter, the identification of a complex hospital building is conducted using data obtained from ambient vibration tests.

  11. Free DICOM de-identification tools in clinical research : functioning and safety of patient privacy

    NARCIS (Netherlands)

    Aryanto, K. Y. E.; Oudkerk, M.; van Ooijen, P. M. A.

    2015-01-01

    To compare non-commercial DICOM toolkits for their de-identification ability in removing a patient's personal health information (PHI) from a DICOM header. Ten DICOM toolkits were selected for de-identification tests. Tests were performed by using the system's default de-identification profile and,

  12. Identification of landscape features influencing gene flow: How useful are habitat selection models?

    Science.gov (United States)

    Gretchen H. Roffler; Michael K. Schwartz; Kristine Pilgrim; Sandra L. Talbot; George K. Sage; Layne G. Adams; Gordon Luikart

    2016-01-01

    Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is...

  13. Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping

    DEFF Research Database (Denmark)

    Vaysse, Amaury; Ratnakumar, Abhirami; Derrien, Thomas

    2011-01-01

    The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse br...

  14. PSP: rapid identification of orthologous coding genes under positive selection across multiple closely related prokaryotic genomes.

    Science.gov (United States)

    Su, Fei; Ou, Hong-Yu; Tao, Fei; Tang, Hongzhi; Xu, Ping

    2013-12-27

    With genomic sequences of many closely related bacterial strains made available by deep sequencing, it is now possible to investigate trends in prokaryotic microevolution. Positive selection is a sub-process of microevolution, in which a particular mutation is favored, causing the allele frequency to continuously shift in one direction. Wide scanning of prokaryotic genomes has shown that positive selection at the molecular level is much more frequent than expected. Genes with significant positive selection may play key roles in bacterial adaption to different environmental pressures. However, selection pressure analyses are computationally intensive and awkward to configure. Here we describe an open access web server, which is designated as PSP (Positive Selection analysis for Prokaryotic genomes) for performing evolutionary analysis on orthologous coding genes, specially designed for rapid comparison of dozens of closely related prokaryotic genomes. Remarkably, PSP facilitates functional exploration at the multiple levels by assignments and enrichments of KO, GO or COG terms. To illustrate this user-friendly tool, we analyzed Escherichia coli and Bacillus cereus genomes and found that several genes, which play key roles in human infection and antibiotic resistance, show significant evidence of positive selection. PSP is freely available to all users without any login requirement at: http://db-mml.sjtu.edu.cn/PSP/. PSP ultimately allows researchers to do genome-scale analysis for evolutionary selection across multiple prokaryotic genomes rapidly and easily, and identify the genes undergoing positive selection, which may play key roles in the interactions of host-pathogen and/or environmental adaptation.

  15. South African medical schools: Current state of selection criteria and medical students' demographic profile.

    Science.gov (United States)

    van der Merwe, L J; van Zyl, G J; St Clair Gibson, A; Viljoen, M; Iputo, J E; Mammen, M; Chitha, W; Perez, A M; Hartman, N; Fonn, S; Green-Thompson, L; Ayo-Ysuf, O A; Botha, G C; Manning, D; Botha, S J; Hift, R; Retief, P; van Heerden, B B; Volmink, J

    2015-12-16

    Selection of medical students at South African (SA) medical schools must promote equitable and fair access to students from all population groups, while ensuring optimal student throughput and success, and training future healthcare practitioners who will fulfil the needs of the local society. In keeping with international practices, a variety of academic and non-academic measures are used to select applicants for medical training programmes in SA medical schools. To provide an overview of the selection procedures used by all eight medical schools in SA, and the student demographics (race and gender) at these medical schools, and to determine to what extent collective practices are achieving the goals of student diversity and inclusivity. A retrospective, quantitative, descriptive study design was used. All eight medical schools in SA provided information regarding selection criteria, selection procedures, and student demographics (race and gender). Descriptive analysis of data was done by calculating frequencies and percentages of the variables measured. Medical schools in SA make use of academic and non-academic criteria in their selection processes. The latter include indices of socioeconomic disadvantage. Most undergraduate medical students in SA are black (38.7%), followed by white (33.0%), coloured (13.4%) and Indian/Asian (13.6%). The majority of students are female (62.2%). The number of black students is still proportionately lower than in the general population, while other groups are overrepresented. Selection policies for undergraduate medical programmes aimed at redress should be continued and further refined, along with the provision of support to ensure student success.

  16. Combining metal oxide affinity chromatography (MOAC and selective mass spectrometry for robust identification of in vivo protein phosphorylation sites

    Directory of Open Access Journals (Sweden)

    Weckwerth Wolfram

    2005-11-01

    Full Text Available Abstract Background Protein phosphorylation is accepted as a major regulatory pathway in plants. More than 1000 protein kinases are predicted in the Arabidopsis proteome, however, only a few studies look systematically for in vivo protein phosphorylation sites. Owing to the low stoichiometry and low abundance of phosphorylated proteins, phosphorylation site identification using mass spectrometry imposes difficulties. Moreover, the often observed poor quality of mass spectra derived from phosphopeptides results frequently in uncertain database hits. Thus, several lines of evidence have to be combined for a precise phosphorylation site identification strategy. Results Here, a strategy is presented that combines enrichment of phosphoproteins using a technique termed metaloxide affinity chromatography (MOAC and selective ion trap mass spectrometry. The complete approach involves (i enrichment of proteins with low phosphorylation stoichiometry out of complex mixtures using MOAC, (ii gel separation and detection of phosphorylation using specific fluorescence staining (confirmation of enrichment, (iii identification of phosphoprotein candidates out of the SDS-PAGE using liquid chromatography coupled to mass spectrometry, and (iv identification of phosphorylation sites of these enriched proteins using automatic detection of H3PO4 neutral loss peaks and data-dependent MS3-fragmentation of the corresponding MS2-fragment. The utility of this approach is demonstrated by the identification of phosphorylation sites in Arabidopsis thaliana seed proteins. Regulatory importance of the identified sites is indicated by conservation of the detected sites in gene families such as ribosomal proteins and sterol dehydrogenases. To demonstrate further the wide applicability of MOAC, phosphoproteins were enriched from Chlamydomonas reinhardtii cell cultures. Conclusion A novel phosphoprotein enrichment procedure MOAC was applied to seed proteins of A. thaliana and to

  17. Temperature, salinity, species identification, nutrient profiles and meteorological data collected by bottle and net in the Northwest Pacific Ocean from 6/10/1975 - 8/5/1975 (NODC Accession 0000194)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile, nutrients, species identification, and other data were collected using net and bottle casts from the RYOFU MARU in the Northwest Pacific Ocean....

  18. Strain profiles in ion implanted ceramic polycrystals: An approach based on reciprocal-space crystal selection

    Energy Technology Data Exchange (ETDEWEB)

    Palancher, H., E-mail: herve.palancher@cea.fr; Martin, G.; Fouet, J. [CEA, DEN, DEC, F-13108 Saint Paul lez Durance (France); Goudeau, P. [Institut Pprime, CNRS-Université de Poitiers–ENSMA, SP2MI, F-86360 Chasseneuil (France); Boulle, A. [Science des Procédés Céramiques et Traitements de Surface (SPCTS), CNRS UMR 7315, Centre Européen de la Céramique, 12 rue Atlantis, 87068 Limoges (France); Rieutord, F. [CEA, DSM, INAC, F-38054 Grenoble Cedex 9 (France); Favre-Nicolin, V. [Université Grenoble-Alpes, F-38041 Grenoble, France, Institut Universitaire de France, F-75005 Paris (France); Blanc, N. [Institut NEEL, CNRS-Univ Grenoble Alpes, F-38042 Grenoble (France); Onofri, C. [CEA, DEN, DEC, F-13108 Saint Paul lez Durance (France); CEMES, CNRS UPR 8011, 29 rue Jeanne Marvig, BP 94347, 31055 Toulouse Cedex 4 (France)

    2016-01-18

    The determination of the state of strain in implanted materials is a key issue in the study of their mechanical stability. Whereas this question is nowadays relatively easily solved in the case of single crystals, it remains a challenging task in the case of polycrystalline materials. In this paper, we take benefit of the intense and parallel beams provided by third generation synchrotron sources combined with a two-dimensional detection system to analyze individual grains in polycrystals, hence obtaining “single crystal-like” data. The feasibility of the approach is demonstrated with implanted UO{sub 2} polycrystals where the in-depth strain profile is extracted for individual grains using numerical simulations of the diffracted signal. The influence of the implantation dose is precisely analyzed for several diffracting planes and grains. This work suggests that, at low fluences, the development of strain is mainly due to ballistic effects with little effect from He ions, independently from the crystallographic orientation. At higher fluences, the evolution of the strain profiles suggests a partial and anisotropic plastic relaxation. With the present approach, robust and reliable structural information can be obtained, even from complex polycrystalline ceramic materials.

  19. Selected metabolic and hormonal profiles during maintenance of spontaneous ovarian cysts in dairy cows.

    Science.gov (United States)

    Probo, M; Comin, A; Cairoli, F; Faustini, M; Kindahl, H; De Amicis, I; Veronesi, M C

    2011-06-01

    Information is lacking regarding the relationship between metabolic and hormonal profiles and the maintenance of spontaneous ovarian cyst disease in dairy cows. For this reason, the concentrations of non-esterified fatty acids (NEFA), insulin-like growth factor I (IGF-I) and cortisol (C) were investigated during the spontaneous course of ovarian cyst disease in dairy cows (n=6) between the 7th and 16th weeks post-partum (PP). The control group consisted of normally cycling cows (n=6). Blood samples were collected twice a day, and plasma was analysed using different techniques. Progesterone and 15-ketodihydro-PGF(2α) plasma profiles were investigated to confirm the ovulatory or anovulatory conditions of the cows. Cortisol plasma levels were not significantly different among sampling times within each group or between the two groups. NEFA plasma levels were significantly higher in cycling cows compared to cystic cows at the 16th week PP (pcows during the 8th, 10th, 11th (pdisease in cattle. © 2010 Blackwell Verlag GmbH.

  20. Evaluation of selected agricultural solid wastes on biochemical profile and liver histology of Albino rats

    Directory of Open Access Journals (Sweden)

    Isaac Oluseun Adejumo

    2017-01-01

    Full Text Available Wheat bran, groundnut shell, watermelon peel and corn bran were analyzed for chemical composition and amino acid profile. A feeding trial was conducted to assess their effect on biochemical profile and liver histology of rats. Watermelon peel obtained the highest dry matter content (91.93±0.03 g/100g, followed by groundnut shell meal (89.57±0.31 g/100g. Carbohydrate content ranged between 35.28±0.08 g/100g and 65.19±0.13 g/100g. Crude protein content ranged between 6.53±0.06 g/100g (groundnut shell meal and 10.88±0.02 g/100g (wheat bran. Liver histopathology revealed normal architecture. The nutritional analyses of the wastes revealed rich nutritional content which may be explored for feed ingredient in livestock production. Further processing of these wastes may further enhance their nutritional composition; thereby providing alternative cheap animal feed for improved animal production and consequently improved animal protein consumption in developing countries.

  1. Identification of a selective small molecule inhibitor of breast cancer stem cells.

    Science.gov (United States)

    Germain, Andrew R; Carmody, Leigh C; Morgan, Barbara; Fernandez, Cristina; Forbeck, Erin; Lewis, Timothy A; Nag, Partha P; Ting, Amal; VerPlank, Lynn; Feng, Yuxiong; Perez, Jose R; Dandapani, Sivaraman; Palmer, Michelle; Lander, Eric S; Gupta, Piyush B; Schreiber, Stuart L; Munoz, Benito

    2012-05-15

    A high-throughput screen (HTS) with the National Institute of Health-Molecular Libraries Small Molecule Repository (NIH-MLSMR) compound collection identified a class of acyl hydrazones to be selectively lethal to breast cancer stem cell (CSC) enriched populations. Medicinal chemistry efforts were undertaken to optimize potency and selectivity of this class of compounds. The optimized compound was declared as a probe (ML239) with the NIH Molecular Libraries Program and displayed greater than 20-fold selective inhibition of the breast CSC-like cell line (HMLE_sh_Ecad) over the isogenic control line (HMLE_sh_GFP). Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Profiling antibody responses to infections by Chlamydia abortus enables identification of potential virulence factors and candidates for serodiagnosis.

    Science.gov (United States)

    Forsbach-Birk, Vera; Foddis, Corinna; Simnacher, Ulrike; Wilkat, Max; Longbottom, David; Walder, Gernot; Benesch, Christiane; Ganter, Martin; Sachse, Konrad; Essig, Andreas

    2013-01-01

    Enzootic abortion of ewes (EAE) due to infection with the obligate intracellular pathogen Chlamydia (C.) abortus is an important zoonosis leading to considerable economic loss to agriculture worldwide. The pathogen can be transmitted to humans and may lead to serious infection in pregnant women. Knowledge about epidemiology, clinical course and transmission to humans is hampered by the lack of reliable diagnostic tools. Immunoreactive proteins, which are expressed in infected animals and humans, may serve as novel candidates for diagnostic marker proteins and represent putative virulence factors. In order to broaden the spectrum of immunogenic C. abortus proteins we applied 2D immunoblot analysis and screening of an expression library using human and animal sera. We have identified 48 immunoreactive proteins representing potential diagnostic markers and also putative virulence factors, such as CAB080 (homologue of the "macrophage infectivity potentiator", MIP), CAB167 (homologue of the "translocated actin recruitment protein", TARP), CAB712 (homologue of the "chlamydial protease-like activity factor", CPAF), CAB776 (homologue of the "Polymorphic membrane protein D", PmpD), and the "hypothetical proteins" CAB063, CAB408 and CAB821, which are predicted to be type III secreted. We selected two putative virulence factors for further characterization, i.e. CAB080 (cMIP) and CAB063, and studied their expression profiles at transcript and protein levels. Analysis of the subcellular localization of both proteins throughout the developmental cycle revealed CAB063 being the first C. abortus protein shown to be translocated to the host cell nucleus.

  3. Profiling antibody responses to infections by Chlamydia abortus enables identification of potential virulence factors and candidates for serodiagnosis.

    Directory of Open Access Journals (Sweden)

    Vera Forsbach-Birk

    Full Text Available Enzootic abortion of ewes (EAE due to infection with the obligate intracellular pathogen Chlamydia (C. abortus is an important zoonosis leading to considerable economic loss to agriculture worldwide. The pathogen can be transmitted to humans and may lead to serious infection in pregnant women. Knowledge about epidemiology, clinical course and transmission to humans is hampered by the lack of reliable diagnostic tools. Immunoreactive proteins, which are expressed in infected animals and humans, may serve as novel candidates for diagnostic marker proteins and represent putative virulence factors. In order to broaden the spectrum of immunogenic C. abortus proteins we applied 2D immunoblot analysis and screening of an expression library using human and animal sera. We have identified 48 immunoreactive proteins representing potential diagnostic markers and also putative virulence factors, such as CAB080 (homologue of the "macrophage infectivity potentiator", MIP, CAB167 (homologue of the "translocated actin recruitment protein", TARP, CAB712 (homologue of the "chlamydial protease-like activity factor", CPAF, CAB776 (homologue of the "Polymorphic membrane protein D", PmpD, and the "hypothetical proteins" CAB063, CAB408 and CAB821, which are predicted to be type III secreted. We selected two putative virulence factors for further characterization, i.e. CAB080 (cMIP and CAB063, and studied their expression profiles at transcript and protein levels. Analysis of the subcellular localization of both proteins throughout the developmental cycle revealed CAB063 being the first C. abortus protein shown to be translocated to the host cell nucleus.

  4. Long-term effect of dexfenfluramine on amino acid profiles and food selection in obese patients during weight loss

    DEFF Research Database (Denmark)

    Breum, L.; Møller, S.-E.; Andersen, T.

    1996-01-01

    In depressive disorders an association between basal pre-treatment plasma ratios of tryptophan (Trp) and tyrosine (Tyr) to other large neutral amino acids (LNAA) and the clinical efficacy of serotonergic acting drugs have been established. In order to clarify whether a similar relation exists...... in obesity and to elucidate the long-term effect of dexfenfluramine (dF) on plasma amino acid profiles and macronutrient selection, we examined 29 obese patients participating in a 12 months double-blind weight loss trial with either dexfenfluramine (dF) (30 mg/day) or placebo (PL) in conjunction with 4...... groups. Macronutrient selection was not affected by the dF treatment. In the placebo group weight loss was associated with a high pre-treatment energy intake and a high carbohydrate-protein ratio (p

  5. Identification and evaluation of influential criteria for the selection of an environmental shipping carrier using DEMATEL

    DEFF Research Database (Denmark)

    Jia, Peng; Govindan, Kannan; Kannan, Devika

    2015-01-01

    The current environmental pollution is a major factor in economic development and vehicle pollution is ranked next to industrial emissions in total emissions worldwide. This study focuses on the selection of a suitable shipping carrier from an economic and environmental perspective. In practice......, there are many criteria's available to select a suitable shipping container. But, shipping container companies are struggling to identify the most influential criteria to select a shipping container as it requires in-depth analysis. So, the objective of this paper is to analyse the criteria and identify the most...... influential criteria from an environmental practices perspective. In this study, seventeen factors are identified from literature aimed at locating the most influential criteria to select a suitable shipping carrier using the decision making trial and evaluation laboratory (DEMATEL). This procedure helps...

  6. A profile analysis of some selected health risk indicators in South ...

    African Journals Online (AJOL)

    The respondents were selected in two age groups (≤ 49 and ≥ 50 year) primarily representing the pre and postmenopausal life stages of women. From the descriptive data it appears that the younger group (≤ 49) tends to be physically less active than the older group (≥ 50). In all the other parameters the older group ...

  7. SELECTIVITY PROFILE OF SOME RECENT MUSCARINIC ANTAGONISTS IN BOVINE AND GUINEA-PIG TRACHEA AND HEART

    NARCIS (Netherlands)

    ROFFEL, AF; HAMSTRA, JJ; ELZINGA, CRS; ZAAGSMA, J

    1994-01-01

    The functional affinities of some recently developed subtype-selective muscarinic antagonists towards bovine tracheal smooth muscle muscarinic M(3) receptors were established and compared to binding affinities for bovine cardiac M(2) and functional affinities for guinea-pig tracheal smooth muscle

  8. The effect of addition of selected vegetables on the microbiological, textural and flavour profile properties of yoghurts.

    Science.gov (United States)

    Najgebauer-Lejko, Dorota; Tabaszewska, Małgorzata; Grega, Tadeusz

    2015-01-01

    Vegetables, apart from having high nutritional value, also contain considerable amounts of dietary fibre and other components, which may affect physico-chemical properties of fermented milks, e.g. viscosity, texture, susceptibility to syneresis, flavour profile etc. The present work was established to study the effect of selected vegetables addition on the rheological, textural, microbiological and flavour profile parameters of yoghurts. The vegetable preparations (carrot, pumpkin, broccoli and red sweet pepper) were added (10% w/w) to the processed cow's milk fermented with DVS yoghurt culture. Texture profile analysis, determination of viscosity, susceptibility to syneresis and descriptive flavour evaluation were conducted at the 1st, 7th and 14th day after production. Additionally, microbiological studies were performed for 28 days, at 7-day intervals. The highest apparent viscosity and adhesiveness were obtained for the carrot yoghurt, whereas yoghurt with pumpkin was the least susceptible to syneresis. The other texture parameters were not affected by the addition of vegetables. Broccoli and red sweet pepper flavours were dominating in the fermented milks fortified with these vegetables, whereas carrot and pumpkin flavours were less distinctive. Yoghurt supplemented with red sweet pepper got the highest sensoric acceptability. The number of starter bacteria was not influenced by the vegetable additives, except for pumpkin yoghurt, which contained lower population of lactobacilli. Among all tested vegetables, carrot additive had the greatest potential to improve yoghurt structure, whereas red sweet pepper imparted the most acceptable flavour.

  9. Identification of novel candidate target genes in amplicons of Glioblastoma multiforme tumors detected by expression and CGH microarray profiling

    Directory of Open Access Journals (Sweden)

    Hernández-Moneo Jose-Luis

    2006-09-01

    Full Text Available Abstract Background Conventional cytogenetic and comparative genomic hybridization (CGH studies in brain malignancies have shown that glioblastoma multiforme (GBM is characterized by complex structural and numerical alterations. However, the limited resolution of these techniques has precluded the precise identification of detailed specific gene copy number alterations. Results We performed a genome-wide survey of gene copy number changes in 20 primary GBMs by CGH on cDNA microarrays. A novel amplicon at 4p15, and previously uncharacterized amplicons at 13q32-34 and 1q32 were detected and are analyzed here. These amplicons contained amplified genes not previously reported. Other amplified regions containg well-known oncogenes in GBMs were also detected at 7p12 (EGFR, 7q21 (CDK6, 4q12 (PDGFRA, and 12q13-15 (MDM2 and CDK4. In order to identify the putative target genes of the amplifications, and to determine the changes in gene expression levels associated with copy number change events, we carried out parallel gene expression profiling analyses using the same cDNA microarrays. We detected overexpression of the novel amplified genes SLA/LP and STIM2 (4p15, and TNFSF13B and COL4A2 (13q32-34. Some of the candidate target genes of amplification (EGFR, CDK6, MDM2, CDK4, and TNFSF13B were tested in an independent set of 111 primary GBMs by using FISH and immunohistological assays. The novel candidate 13q-amplification target TNFSF13B was amplified in 8% of the tumors, and showed protein expression in 20% of the GBMs. Conclusion This high-resolution analysis allowed us to propose novel candidate target genes such as STIM2 at 4p15, and TNFSF13B or COL4A2 at 13q32-34 that could potentially contribute to the pathogenesis of these tumors and which would require futher investigations. We showed that overexpression of the amplified genes could be attributable to gene dosage and speculate that deregulation of those genes could be important in the development

  10. Chronic Voluntary Ethanol Consumption Induces Favorable Ceramide Profiles in Selectively Bred Alcohol-Preferring (P Rats.

    Directory of Open Access Journals (Sweden)

    Jessica Godfrey

    Full Text Available Heavy alcohol consumption has detrimental neurologic effects, inducing widespread neuronal loss in both fetuses and adults. One proposed mechanism of ethanol-induced cell loss with sufficient exposure is an elevation in concentrations of bioactive lipids that mediate apoptosis, including the membrane sphingolipid metabolites ceramide and sphingosine. While these naturally-occurring lipids serve as important modulators of normal neuronal development, elevated levels resulting from various extracellular insults have been implicated in pathological apoptosis of neurons and oligodendrocytes in several neuroinflammatory and neurodegenerative disorders. Prior work has shown that acute administration of ethanol to developing mice increases levels of ceramide in multiple brain regions, hypothesized to be a mediator of fetal alcohol-induced neuronal loss. Elevated ceramide levels have also been implicated in ethanol-mediated neurodegeneration in adult animals and humans. Here, we determined the effect of chronic voluntary ethanol consumption on lipid profiles in brain and peripheral tissues from adult alcohol-preferring (P rats to further examine alterations in lipid composition as a potential contributor to ethanol-induced cellular damage. P rats were exposed for 13 weeks to a 20% ethanol intermittent-access drinking paradigm (45 ethanol sessions total or were given access only to water (control. Following the final session, tissues were collected for subsequent chromatographic analysis of lipid content and enzymatic gene expression. Contrary to expectations, ethanol-exposed rats displayed substantial reductions in concentrations of ceramides in forebrain and heart relative to non-exposed controls, and modest but significant decreases in liver cholesterol. qRT-PCR analysis showed a reduction in the expression of sphingolipid delta(4-desaturase (Degs2, an enzyme involved in de novo ceramide synthesis. These findings indicate that ethanol intake levels

  11. Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.

    Directory of Open Access Journals (Sweden)

    Amaury Vaysse

    2011-10-01

    Full Text Available The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease.

  12. A 100-Year Review: Identification and genetic selection of economically important traits in dairy cattle.

    Science.gov (United States)

    Miglior, Filippo; Fleming, Allison; Malchiodi, Francesca; Brito, Luiz F; Martin, Pauline; Baes, Christine F

    2017-12-01

    Over the past 100 yr, the range of traits considered for genetic selection in dairy cattle populations has progressed to meet the demands of both industry and society. At the turn of the 20th century, dairy farmers were interested in increasing milk production; however, a systematic strategy for selection was not available. Organized milk performance recording took shape, followed quickly by conformation scoring. Methodological advances in both genetic theory and statistics around the middle of the century, together with technological innovations in computing, paved the way for powerful multitrait analyses. As more sophisticated analytical techniques for traits were developed and incorporated into selection programs, production began to increase rapidly, and the wheels of genetic progress began to turn. By the end of the century, the focus of selection had moved away from being purely production oriented toward a more balanced breeding goal. This shift occurred partly due to increasing health and fertility issues and partly due to societal pressure and welfare concerns. Traits encompassing longevity, fertility, calving, health, and workability have now been integrated into selection indices. Current research focuses on fitness, health, welfare, milk quality, and environmental sustainability, underlying the concentrated emphasis on a more comprehensive breeding goal. In the future, on-farm sensors, data loggers, precision measurement techniques, and other technological aids will provide even more data for use in selection, and the difficulty will lie not in measuring phenotypes but rather in choosing which traits to select for. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  13. Identification and characterization of the novel reversible and selective cathepsin X inhibitors.

    Science.gov (United States)

    Fonović, Urša Pečar; Mitrović, Ana; Knez, Damijan; Jakoš, Tanja; Pišlar, Anja; Brus, Boris; Doljak, Bojan; Stojan, Jure; Žakelj, Simon; Trontelj, Jurij; Gobec, Stanislav; Kos, Janko

    2017-09-13

    Cathepsin X is a cysteine peptidase involved in the progression of cancer and neurodegenerative diseases. Targeting this enzyme with selective inhibitors opens a new possibility for intervention in several therapeutic areas. In this study triazole-based reversible and selective inhibitors of cathepsin X have been identified. Their selectivity and binding is enhanced when the 2,3-dihydrobenzo[b][1,4]dioxine moiety is present as the R 1 substituent. Of a series of selected triazole-benzodioxine derivatives, compound 22 is the most potent inhibitor of cathepsin X carboxypeptidase activity (K i  = 2.45 ± 0.05 μM) with at least 100-fold greater selectivity in comparison to cathepsin B or other related cysteine peptidases. Compound 22 is not cytotoxic to prostate cancer cells PC-3 or pheochromocytoma PC-12 cells at concentrations up to 10 μM. It significantly inhibits the migration of tumor cells and increases the outgrowth of neurites, both processes being under the control of cathepsin X carboxypeptidase activity. Compound 22 and other characterized triazole-based inhibitors thus possess a great potential for further development resulting in several in vivo applications.

  14. Talent identification in Hungary: From identification to investigation

    Directory of Open Access Journals (Sweden)

    Szilvia Péter-Szarka

    2015-03-01

    Full Text Available This article provides an outline of talent identification practices and challenges in Hungary. First, it gives a summary of gifted education in the country; then the general challenges of talent identification are introduced: difficulties of defining talent, talent as potential, environmental factors, the role of perseverance and motivation, and individual variety. Later, recent Hungarian identification practices are shown, followed by a summary and a conclusion about how our identification practice should be developed into an investigation of individual characetristics. We propose stronger focus on the use of cognitive profile tests, investigation of interest-based characteristics, the use of observation and dynamic assessment methods, teacher nomination and emphasizing the need for effort. The focus from identification toward investigation exploring individual needs and characteristics to provide the most appropriate pathway for development in the 21st century seems to be a more effective way of talent support than mere selection.

  15. Minimal gene selection for classification and diagnosis prediction based on gene expression profile

    Directory of Open Access Journals (Sweden)

    Alireza Mehridehnavi

    2013-01-01

    Conclusion: We have shown that the use of two most significant genes based on their S/N ratios and selection of suitable training samples can lead to classify DLBCL patients with a rather good result. Actually with the aid of mentioned methods we could compensate lack of enough number of patients, improve accuracy of classifying and reduce complication of computations and so running time.

  16. Typeability of PowerPlex Y (Promega) profiles in selected tissue samples incubated in various environments.

    Science.gov (United States)

    Niemcunowicz-Janica, Anna; Pepiński, Witold; Janica, Jacek Robert; Janica, Jerzy; Skawrońska, Małgorzata; Koc-Zórawska, Ewa

    2007-01-01

    In cases of decomposed bodies, Y chromosomal STR markers may be useful in identification of a male relative. The authors assessed typeability of PowerPlex Y (Promega) loci in post mortem tissue material stored in various environments. Kidney, spleen and pancreas specimens were collected during autopsies of five persons aged 20-30 years, whose time of death was determined within the limit of 14 hours. Tissue material was incubated at 21 degrees C and 4 degrees C in various environmental conditions. DNA was extracted by the organic method from tissue samples collected in 7-day intervals and subsequently typed using the PowerPlexY-STR kit and ABI 310. A fast decrease in the typeability rate was seen in specimens incubated in peat soil and in sand. Kidney tissue samples were typeable in all PowerPlexY-STR loci within 63 days of incubation at 4 degrees C. Faster DNA degradation was recorded in spleen and pancreas specimens. In samples with negative genotyping results, no DNA was found by fluorometric quantitation. Decomposed soft tissues are a potential material for DNA typing.

  17. Identification of hemoglobin variants by top-down mass spectrometry using selected diagnostic product ions.

    Science.gov (United States)

    Coelho Graça, Didia; Hartmer, Ralf; Jabs, Wolfgang; Beris, Photis; Clerici, Lorella; Stoermer, Carsten; Samii, Kaveh; Hochstrasser, Denis; Tsybin, Yury O; Scherl, Alexander; Lescuyer, Pierre

    2015-04-01

    Hemoglobin disorder diagnosis is a complex procedure combining several analytical steps. Due to the lack of specificity of the currently used protein analysis methods, the identification of uncommon hemoglobin variants (proteoforms) can become a hard task to accomplish. The aim of this work was to develop a mass spectrometry-based approach to quickly identify mutated protein sequences within globin chain variants. To reach this goal, a top-down electron transfer dissociation mass spectrometry method was developed for hemoglobin β chain analysis. A diagnostic product ion list was established with a color code strategy allowing to quickly and specifically localize a mutation in the hemoglobin β chain sequence. The method was applied to the analysis of rare hemoglobin β chain variants and an (A)γ-β fusion protein. The results showed that the developed data analysis process allows fast and reliable interpretation of top-down electron transfer dissociation mass spectra by nonexpert users in the clinical area.

  18. Identification of multi-criteria for supplier selection in IT project outsourcing

    Science.gov (United States)

    Fusiripong, Prashaya; Baharom, Fauziah; Yusof, Yuhanis

    2017-10-01

    In the increasing global business competitiveness, most organizations have attempted to determine the suitable external parties to support their core and non-core competency, particularly, in IT project outsourcing. The IT supplier selection is required to apply multi-criteria which comprised tangible criteria and intangible criteria in consider optimal IT supplier. Most researches attempted to identify optimal criteria for selecting IT supplier, however, the criteria cannot be the considered common criteria support the variety of IT outsourcing. Therefore, the study aimed to identify a common set of criteria being used in the various types of IT outsourcing. The common criteria are constructed by multi-criteria and success criteria, which were collected by literature review with comprehensive and comparative approach. Consequently, the researchers are able to identify a common set of criteria adopted in the variety of selection problem IT outsourcing supplier.

  19. Biochemical profiling of histone binding selectivity of the yeast bromodomain family.

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    2010-01-01

    Full Text Available It has been shown that molecular interactions between site-specific chemical modifications such as acetylation and methylation on DNA-packing histones and conserved structural modules present in transcriptional proteins are closely associated with chromatin structural changes and gene activation. Unlike methyl-lysine that can interact with different protein modules including chromodomains, Tudor and MBT domains, as well as PHD fingers, acetyl-lysine (Kac is known thus far to be recognized only by bromodomains. While histone lysine acetylation plays a crucial role in regulation of chromatin-mediated gene transcription, a high degree of sequence variation of the acetyl-lysine binding site in the bromodomains has limited our understanding of histone binding selectivity of the bromodomain family. Here, we report a systematic family-wide analysis of 14 yeast bromodomains binding to 32 lysine-acetylated peptides derived from known major acetylation sites in four core histones that are conserved in eukaryotes.The histone binding selectivity of purified recombinant yeast bromodomains was assessed by using the native core histones in an overlay assay, as well as N-terminally biotinylated lysine-acetylated histone peptides spotted on streptavidin-coated nitrocellulose membrane in a dot blot assay. NMR binding analysis further validated the interactions between histones and selected bromodomain. Structural models of all yeast bromodomains were built using comparative modeling to provide insights into the molecular basis of their histone binding selectivity.Our study reveals that while not all members of the bromodomain family are privileged to interact with acetylated-lysine, identifiable sequence features from those that bind histone emerge. These include an asparagine residue at the C-terminus of the third helix in the 4-helix bundle, negatively charged residues around the ZA loop, and preponderance of aromatic amino acid residues in the binding pocket

  20. Identification and Structure-Function Analysis of Subfamily Selective G Protein-Coupled Receptor Kinase Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Homan, Kristoff T.; Larimore, Kelly M.; Elkins, Jonathan M.; Szklarz, Marta; Knapp, Stefan; Tesmer, John J.G. [Michigan; (Oxford)

    2015-02-13

    Selective inhibitors of individual subfamilies of G protein-coupled receptor kinases (GRKs) would serve as useful chemical probes as well as leads for therapeutic applications ranging from heart failure to Parkinson’s disease. To identify such inhibitors, differential scanning fluorimetry was used to screen a collection of known protein kinase inhibitors that could increase the melting points of the two most ubiquitously expressed GRKs: GRK2 and GRK5. Enzymatic assays on 14 of the most stabilizing hits revealed that three exhibit nanomolar potency of inhibition for individual GRKs, some of which exhibiting orders of magnitude selectivity. Most of the identified compounds can be clustered into two chemical classes: indazole/dihydropyrimidine-containing compounds that are selective for GRK2 and pyrrolopyrimidine-containing compounds that potently inhibit GRK1 and GRK5 but with more modest selectivity. The two most potent inhibitors representing each class, GSK180736A and GSK2163632A, were cocrystallized with GRK2 and GRK1, and their atomic structures were determined to 2.6 and 1.85 Å spacings, respectively. GSK180736A, developed as a Rho-associated, coiled-coil-containing protein kinase inhibitor, binds to GRK2 in a manner analogous to that of paroxetine, whereas GSK2163632A, developed as an insulin-like growth factor 1 receptor inhibitor, occupies a novel region of the GRK active site cleft that could likely be exploited to achieve more selectivity. However, neither compound inhibits GRKs more potently than their initial targets. This data provides the foundation for future efforts to rationally design even more potent and selective GRK inhibitors.

  1. Selecting Sensitive Parameter Subsets in Dynamical Models With Application to Biomechanical System Identification.

    Science.gov (United States)

    Ramadan, Ahmed; Boss, Connor; Choi, Jongeun; Peter Reeves, N; Cholewicki, Jacek; Popovich, John M; Radcliffe, Clark J

    2018-07-01

    Estimating many parameters of biomechanical systems with limited data may achieve good fit but may also increase 95% confidence intervals in parameter estimates. This results in poor identifiability in the estimation problem. Therefore, we propose a novel method to select sensitive biomechanical model parameters that should be estimated, while fixing the remaining parameters to values obtained from preliminary estimation. Our method relies on identifying the parameters to which the measurement output is most sensitive. The proposed method is based on the Fisher information matrix (FIM). It was compared against the nonlinear least absolute shrinkage and selection operator (LASSO) method to guide modelers on the pros and cons of our FIM method. We present an application identifying a biomechanical parametric model of a head position-tracking task for ten human subjects. Using measured data, our method (1) reduced model complexity by only requiring five out of twelve parameters to be estimated, (2) significantly reduced parameter 95% confidence intervals by up to 89% of the original confidence interval, (3) maintained goodness of fit measured by variance accounted for (VAF) at 82%, (4) reduced computation time, where our FIM method was 164 times faster than the LASSO method, and (5) selected similar sensitive parameters to the LASSO method, where three out of five selected sensitive parameters were shared by FIM and LASSO methods.

  2. Identification of novel selective V2 receptor non-peptide agonists.

    Science.gov (United States)

    Del Tredici, Andria L; Vanover, Kim E; Knapp, Anne E; Bertozzi, Sine M; Nash, Norman R; Burstein, Ethan S; Lameh, Jelveh; Currier, Erika A; Davis, Robert E; Brann, Mark R; Mohell, Nina; Olsson, Roger; Piu, Fabrice

    2008-10-30

    Peptides with agonist activity at the vasopressin V(2) receptor are used clinically to treat fluid homeostasis disorders such as polyuria and central diabetes insipidus. Of these peptides, the most commonly used is desmopressin, which displays poor bioavailability as well as potent activity at the V(1b) receptor, with possible stress-related adverse effects. Thus, there is a strong need for the development of small molecule chemistries with selective V(2) receptor agonist activity. Using the functional cell-based assay Receptor Selection and Amplification Technology (R-SAT((R))), a screening effort identified three small molecule chemotypes (AC-94544, AC-88324, and AC-110484) with selective agonist activity at the V(2) receptor. One of these compounds, AC-94544, displayed over 180-fold selectivity at the V(2) receptor compared to related vasopressin and oxytocin receptors and no activity at 28 other G protein-coupled receptors (GPCRs). All three compounds also showed partial agonist activity at the V(2) receptor in a cAMP accumulation assay. In addition, in a rat model of central diabetes insipidus, AC-94544 was able to significantly reduce urine output in a dose-dependent manner. Thus, AC-94544, AC-88324, and AC-110484 represent novel opportunities for the treatment of disorders associated with V(2) receptor agonist deficiency.

  3. Identification of Early Intermediates of Caspase Activation Using Selective Inhibitors and Activity-Based Probes

    NARCIS (Netherlands)

    Berger, Alicia B.; Witte, Martin D.; Denault, Jean-Bernard; Sadaghiani, Amir Masoud; Sexton, Kelly M.B.; Salvesen, Guy S.; Bogyo, Matthew

    2006-01-01

    Caspases are cysteine proteases that are key effectors in apoptotic cell death. Currently, there is a lack of tools that can be used to monitor the regulation of specific caspases in the context of distinct apoptotic programs. We describe the development of highly selective inhibitors and active

  4. Identification of solid state fermentation degree with FT-NIR spectroscopy: Comparison of wavelength variable selection methods of CARS and SCARS

    Science.gov (United States)

    Jiang, Hui; Zhang, Hang; Chen, Quansheng; Mei, Congli; Liu, Guohai

    2015-10-01

    The use of wavelength variable selection before partial least squares discriminant analysis (PLS-DA) for qualitative identification of solid state fermentation degree by FT-NIR spectroscopy technique was investigated in this study. Two wavelength variable selection methods including competitive adaptive reweighted sampling (CARS) and stability competitive adaptive reweighted sampling (SCARS) were employed to select the important wavelengths. PLS-DA was applied to calibrate identified model using selected wavelength variables by CARS and SCARS for identification of solid state fermentation degree. Experimental results showed that the number of selected wavelength variables by CARS and SCARS were 58 and 47, respectively, from the 1557 original wavelength variables. Compared with the results of full-spectrum PLS-DA, the two wavelength variable selection methods both could enhance the performance of identified models. Meanwhile, compared with CARS-PLS-DA model, the SCARS-PLS-DA model achieved better results with the identification rate of 91.43% in the validation process. The overall results sufficiently demonstrate the PLS-DA model constructed using selected wavelength variables by a proper wavelength variable method can be more accurate identification of solid state fermentation degree.

  5. Neuropsychological profile of Parkinson's disease patients selected for deep brain stimulation surgery

    Directory of Open Access Journals (Sweden)

    Flavia Amaral Machado

    Full Text Available ABSTRACT Background: Parkinson's disease (PD shows symptoms involving motor and non-motor complications, including cognitive and behavioral changes, such changes might to contraindicate deep brain stimulation surgery (DBS. Objective: The aim of study was to investigate the neuropsychological profile of patients with PD in a waiting list for DBS. Methods: The neuropsychological evaluation was held in 30 patients of the ISCMPA Movement Disorders Clinic, with surgical indication based on the criteria of the responsible neurologists, in the period of 12 months. Instruments used: MMSE, FAB, MoCA, BDI, Semantic Verbal Fluency, PDQ-39, PDSS; and the UPDRS and Hoehn-Yahr scale. Results: The patients were mostly male (66.7% with a mean age of 59.37 (SD 10.60 and disease duration 9.33 (SD 4.08. There was cognitive impairment in 56.7% of patients by FAB and 76.7% by MoCA. Conclusion: Even in the earliest stages of the disease, there is the incidence of non-motor symptoms, especially in those subjects who had an early onset of the disease.

  6. Profile of Trace Elements in Selected Medicinal Plants Used for the Treatment of Diabetes in Eritrea.

    Science.gov (United States)

    Sium, Mussie; Kareru, Patrick; Keriko, Joseph; Girmay, Berhane; Medhanie, Ghebrehiwet; Debretsion, Semere

    This study was designed to investigate the profile of certain trace elements having therapeutic properties related to diabetes mellitus. The investigated plants were Aloe camperi , Meriandra dianthera , Lepidium sativum , Brassica nigra, and Nigella sativa . These plants are traditionally used in the management of diabetes in Eritrea. The elemental analysis was conducted using inductively coupled plasma optical emission spectrometry (ICP-OES) and flame atomic absorption spectroscopy (FAAS) techniques. The accuracy of the methods was verified using in-house reference materials (CRMs) and no significant differences were observed between the measured and certified values. The analysis displayed variable concentrations of the different trace elements including Zn, Cr, V, Mn, and Se in the plants. Moreover, the levels of major elements, such as Mg, Ca, K, Na, and Ba, and heavy metals, such as Fe, Cu, Ni, Co, As, and Pb, were determined and found to be in the permissible limit defined by WHO. Among the plants, Meriandra dianthera showed the highest levels of Mn, Cr, V, and other elements and the values were significantly different ( P < 0.05).

  7. Variability in HOMA-IR, lipoprotein profile and selected hormones in young active men.

    Science.gov (United States)

    Keska, Anna; Lutoslawska, Grazyna; Czajkowska, Anna; Tkaczyk, Joanna; Mazurek, Krzysztof

    2013-01-01

    Resistance to insulin actions is contributing to many metabolic disturbances. Such factors as age, sex, nutrition, body fat, and physical activity determine body insulin resistance. Present study attempted to asses insulin resistance and its metabolic effects with respect to energy intake in young, lean, and active men. A total of 87 men aged 18-23 participated in the study. Plasma levels of glucose, insulin, lipoproteins, cortisol, and TSH were determined. Insulin resistance was expressed as Homeostasis Model Assessment for Insulin Resistance (HOMA-IR) and calculated using homeostatic model. The median value of HOMA-IR (1.344) was used to divide subjects into two groups. Men did not differ in anthropometric parameters, daily physical activity, and plasma TSH and cortisol levels. However, in men with higher HOMA-IR significantly lower daily energy intake was observed concomitantly with higher TG, TC, and HDL-C concentrations in plasma versus their counterparts with lower HOMA-IR. Exclusively in subjects with higher HOMA-IR significant and positive correlation was noted between HOMA-IR and TC and LDL-C. We concluded that despite a normal body weight and physical activity, a subset of young men displayed unfavorable changes in insulin sensitivity and lipid profile, probably due to insufficient energy intake.

  8. Flavour profiles of dry sausages fermented by selected novel meat starter cultures.

    Science.gov (United States)

    Erkkilä, S; Petäjä, E; Eerola, S; Lilleberg, L; Mattila-Sandholm, T; Suihko, M L

    2001-06-01

    Probiotic or bioprotective Lactobacillus rhamnosus strains GG, LC-705 and E-97800 as well as Pediococcus pentosaceus E-90390 and Lactobacillus plantarum E-98098 were studied for their ability to act as main fermenting organisms in the manufacturing process of dry sausages. In the preliminary tests, their abilities to produce lactic acid and biogenic amines, histamine or tyramine, were studied in MRS broth and analysed by high-performance liquid chromatography. The strains produced higher or equal amounts of lactic acid compared to control and were amine negative. During the actual fermentation process of dry sausages the numbers of inoculated bacteria increased from the level 6.5-7.0 log cfu/g to 8.0-9.0 log cfu/g. The most fast growing strains were P. pentosaceus E-90390 and the control while the growth of L. plantarum E-98098 and L. rhamnosus LC-705 were the slowest. The pH value of the sausages decreased from 5.6 to 4.9-5.0. The presence of these experimental strains as major organisms in the sausages after fermentation and ripening was confirmed on the bases of their genetic fingerprints. The flavour profiles of the experimental sausages produced by these probiotic or protective strains were similar with that produced by the commercial meat starter culture and commercial North European dry sausage recipe.

  9. Integration K-Means Clustering Method and Elbow Method For Identification of The Best Customer Profile Cluster

    Science.gov (United States)

    Syakur, M. A.; Khotimah, B. K.; Rochman, E. M. S.; Satoto, B. D.

    2018-04-01

    Clustering is a data mining technique used to analyse data that has variations and the number of lots. Clustering was process of grouping data into a cluster, so they contained data that is as similar as possible and different from other cluster objects. SMEs Indonesia has a variety of customers, but SMEs do not have the mapping of these customers so they did not know which customers are loyal or otherwise. Customer mapping is a grouping of customer profiling to facilitate analysis and policy of SMEs in the production of goods, especially batik sales. Researchers will use a combination of K-Means method with elbow to improve efficient and effective k-means performance in processing large amounts of data. K-Means Clustering is a localized optimization method that is sensitive to the selection of the starting position from the midpoint of the cluster. So choosing the starting position from the midpoint of a bad cluster will result in K-Means Clustering algorithm resulting in high errors and poor cluster results. The K-means algorithm has problems in determining the best number of clusters. So Elbow looks for the best number of clusters on the K-means method. Based on the results obtained from the process in determining the best number of clusters with elbow method can produce the same number of clusters K on the amount of different data. The result of determining the best number of clusters with elbow method will be the default for characteristic process based on case study. Measurement of k-means value of k-means has resulted in the best clusters based on SSE values on 500 clusters of batik visitors. The result shows the cluster has a sharp decrease is at K = 3, so K as the cut-off point as the best cluster.

  10. Profiling Antibody Responses to Infections by Chlamydia abortus Enables Identification of Potential Virulence Factors and Candidates for Serodiagnosis

    Science.gov (United States)

    Forsbach-Birk, Vera; Foddis, Corinna; Simnacher, Ulrike; Wilkat, Max; Longbottom, David; Walder, Gernot; Benesch, Christiane; Ganter, Martin; Sachse, Konrad; Essig, Andreas

    2013-01-01

    Enzootic abortion of ewes (EAE) due to infection with the obligate intracellular pathogen Chlamydia (C.) abortus is an important zoonosis leading to considerable economic loss to agriculture worldwide. The pathogen can be transmitted to humans and may lead to serious infection in pregnant women. Knowledge about epidemiology, clinical course and transmission to humans is hampered by the lack of reliable diagnostic tools. Immunoreactive proteins, which are expressed in infected animals and humans, may serve as novel candidates for diagnostic marker proteins and represent putative virulence factors. In order to broaden the spectrum of immunogenic C. abortus proteins we applied 2D immunoblot analysis and screening of an expression library using human and animal sera. We have identified 48 immunoreactive proteins representing potential diagnostic markers and also putative virulence factors, such as CAB080 (homologue of the “macrophage infectivity potentiator”, MIP), CAB167 (homologue of the “translocated actin recruitment protein”, TARP), CAB712 (homologue of the “chlamydial protease-like activity factor”, CPAF), CAB776 (homologue of the “Polymorphic membrane protein D”, PmpD), and the “hypothetical proteins” CAB063, CAB408 and CAB821, which are predicted to be type III secreted. We selected two putative virulence factors for further characterization, i.e. CAB080 (cMIP) and CAB063, and studied their expression profiles at transcript and protein levels. Analysis of the subcellular localization of both proteins throughout the developmental cycle revealed CAB063 being the first C. abortus protein shown to be translocated to the host cell nucleus. PMID:24260366

  11. A Rough Guide to Metabolite Identification Using High Resolution Liquid Chromatography Mass Spectrometry in Metabolomic Profiling in Metazoans

    Directory of Open Access Journals (Sweden)

    David G Watson

    2013-01-01

    Full Text Available Compound identification in mass spectrometry based metabolomics can be a problem but sometimes the problem seems to be presented in an over complicated way. The current review focuses on metazoans where the range of metabolites is more restricted than for example in plants. The focus is on liquid chromatography with high resolution mass spectrometry where it is proposed that most of the problems in compound identification relate to structural isomers rather than to isobaric compounds. Thus many of the problems faced relate to separation of isomers, which is usually required even if fragmentation is used to support structural identification. Many papers report the use of MS/MS or MS2 as an adjunct to the identification of known metabolites but there a few examples in metabolomics studies of metazoans of complete structure elucidation of novel metabolites or metabolites where no authentic standards are available for comparison.

  12. Selection and identification of fungi isolated from sugarcane bagasse and their application for phenanthrene removal from soil.

    Science.gov (United States)

    Cortés-Espinosa, D V; Fernández-Perrino, F J; Arana-Cuenca, A; Esparza-García, F; Loera, O; Rodríguez-Vázquez, R

    2006-01-01

    This work investigated the identification and selection of fungi isolated from sugarcane bagasse and their application for phenanthrene (Phe) removal from soil. Fungi were identified by PCR amplification of ITS regions as Aspergillus terrus, Aspergillus fumigatus and Aspergillus niger, Penicillium glabrum and Cladosporium cladosporioides. A primary selection of fungi was accomplished in plate, considering Phe tolerance of every strain in two different media: potato dextrose agar (PDA) and mineral medium (MM). The radial extension rate (r(r)) in PDA exhibited significant differences (p<0.05) at 200 and 400 ppm of Phe. A secondary selection of A. niger, C. cladosporoides, and P. glabrum sp. was achieved based on their tolerance to 200, 400, 600 and 800 ppm of Phe, in solid culture at a sugarcane bagasse/contaminated soil ratio of 95:5, in Toyamas, Czapeck and Wunder media. Under these conditions, a maximum (70%) Phe removal by A. niger was obtained. In addition C. cladosporioides and A. niger were able to remove high (800 ppm) Phe concentrations.

  13. Profile of rheumatology patients willing to report adverse drug reactions: bias from selective reporting

    Directory of Open Access Journals (Sweden)

    Protić D

    2016-02-01

    Full Text Available Dragana Protić,1 Nada Vujasinović-Stupar,2 Zoran Bukumirić,3 Slavica Pavlov-Dolijanović,4 Snežana Baltić,5 Slavica Mutavdžin,6 Ljiljana Markovic-Denić,7 Marija Zdravković,8 Zoran Todorović1 1Department of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia; 2Department 2, Institute of Rheumatology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia; 3Institute for Medical Statistics and Informatics, Faculty of Medicine, University of Belgrade, Belgrade, Serbia; 4Department 5, Institute of Rheumatology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia; 5Department 5, Institute of Rheumatology, Belgrade, Serbia; 6Institute of Physiology “Rihard Burjan”, Faculty of Medicine, University of Belgrade, Belgrade, Serbia; 7Institute of Epidemiology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia; 8Department of Cardiology, Medical Center “Bežanijska kosa”, Faculty of Medicine, University of Belgrade, Belgrade, Serbia Background: Adverse drug reactions (ADRs have a significant impact on human health and health care costs. The aims of our study were to determine the profile of rheumatology patients willing to report ADRs and to identify bias in such a reporting system. Methods: Semi-intensive ADRs reporting system was used in our study. Patients willing to participate (N=261 completed the questionnaire designed for the purpose of the study at the hospital admission. They were subsequently classified into two groups according to their ability to identify whether they had experienced ADRs during the previous month. Group 1 included 214 out of 261 patients who were able to identify ADRs, and group 2 consisted of 43 out of 261 patients who were not able to identify ADRs in their recent medical history. Results: Group 1 patients were more significantly aware of their diagnosis than the patients from group 2. Marginal significance was found

  14. Identification of epigallocatechin-3-O-(3-O-methyl)-gallate (EGCG3''Me) and amino acid profiles in various tea (Camellia sinensis L.) cultivars.

    Science.gov (United States)

    Ji, Hyang-Gi; Lee, Yeong-Ran; Lee, Min-Seuk; Hwang, Kyeng Hwan; Kim, Eun-Hee; Park, Jun Seong; Hong, Young-Shick

    2017-10-01

    This article includes experimental data on the identification of epigallocatechin-3-O-(3-O-methyl)-gallate (EGCG3''Me) by 2-dimensional (2D) proton ( 1 H) NMR analysis and on the information of amino acid and catechin compound profiles by HPLC analysis in leaf extracts of various tea cultivars. These data are related to the research article " Metabolic phenotyping of various tea (Camellia sinensis L.) cultivars and understanding of their intrinsic metabolism " (Ji et al., 2017) [1]. The assignment for EGCG3x''Me by 1 H NMR analysis was also confirmed with spiking experiment of its pure chemical.

  15. High-resolution α-glucosidase inhibition profiling combined with HPLC-HRMS-SPE-NMR for identification of anti-diabetic compounds in Eremanthus crotonoides (Asteraceae)

    DEFF Research Database (Denmark)

    Lana e Silva, Eder; Felipe Revoredo Lobo, Jonathas; Vinther, Joachim Møllesøe

    2016-01-01

    with an inhibitory concentration (IC50) of 34.5 μg/mL towards α-glucosidase was investigated by high-resolution α-glucosidase inhibition profiling combined with HPLC-HRMS-SPE-NMR. This led to identification of six α-glucosidase inhibitors, namely quercetin (16), trans-tiliroside (17), luteolin (19), quercetin-3.......93 and 5.20 μM, respectively. This is the first report of the α-glucosidase inhibitory activity of compounds 20, 26, and 29, and the findings support the important role of Eremanthus species as novel sources of new drugs and/or herbal remedies for treatment of type 2 diabetes....

  16. Influence of High-Pressure Processing on the Profile of Polyglutamyl 5-Methyltetrahydrofolate in Selected Vegetables

    Science.gov (United States)

    Wang, Chao; Riedl, Ken M.; Somerville, Jeremy; Balasubramaniam, V. M.; Schwartz, Steven J.

    2013-01-01

    In plants, folate occurs predominantly as 5-methyltetrahydrofolate (5MTHF) polyglutamyl forms. Differences in stability and bioavailability of food folate compared to synthetic folic acid have been attributed to the presence of the polyglutamyl chain. High-pressure processing (HPP) was tested for whether it might shorten polyglutamyl chains of 5MTHF species in fresh vegetables by enabling action of native γ-glutamylhydrolase (GGH). A validated ultrahigh-performance reversed-phase liquid chromatography–tandem mass spectrometry method using stable isotope as internal standard was applied for characterizing 5MTHF polyglutamyl profiles. HPP conditions included 300, 450, and 600 MPa at 30 °C for 0 or 5 min, and vegetables were vacuum-packed before treatment. Investigated vegetables included cauliflower (Brassica oleracea), baby carrots (Daucus carota), and carrot greens (D. carota). HPP treatment caused conversion of polyglutamyl 5MTHF species to short-chain and monoglutamyl forms. Maximal conversion of polyglutamyl folate to monoglutamyl folate occurred at the highest pressure/time combination investigated, 600 MPa/30 °C/5 min. Under this condition, cauliflower monoglutamyl folate increased nearly 4-fold, diglutamyl folate 32-fold, and triglutamyl folate 8-fold; carrot monoglutamyl increased 23-fold and diglutamyl 32-fold; and carrot greens monoglutamyl increased 2.5-fold and the diglutamyl form 19-fold. Although some folate degradation was observed at certain intermediate HPP conditions, total 5MTHF folate was largely preserved at 600 MPa/5 min. Thus, HPP of raw vegetables is a feasible strategy for enhancing vegetable monoglutamate 5MTHF. PMID:21770413

  17. Nutritional profile of selected expectant mothers and the cost of pregnancy.

    Science.gov (United States)

    Purushothaman, V; Kupputhai, U; Meenakshi, N D

    1988-08-01

    The nutritional profile during pregnancy, pregnancy-related expenditures, and pregnancy wastage were analyzed in 316 women attending a maternity or general hospital in Coimbatore, India. The sample included 195 low-income women (under Rs 600/month), 76 middle-income women (Rs 601-1500/month), and 45 high-income women (above Rs 1500/month). 51% of study participants had 3 fewer children; 71% were literate. The pregnancy diet of low-income women was starchy and inadequate in terms of all nutrients except vitamin C. Middle- and high-income women reported a satisfactory intake of all essential nutrients. The mean weight gain during pregnancy for low-, middle-, and high-income women was 6.41 kg, 7.37 kg, and 8.33 kg, respectively, while the mean hemoglobin level was 10.52, 10.74, and 10.96 gm/100 ml, respectively. No study participant was found to be anemic. The rate of pregnancy wastage was 11.8% among low-income women, 7.9% in the middle-income group, and 4.4% among high-income women; mean birthweight was 2.9 kg for low-income mothers and 3.1 kg for the offspring of both middle- and upper-income women. Regardless of income group, all pregnant women spent a substantial amount of extra money during pregnancy on food, clothing, medical examinations, transportation, ceremonies, servants, and delivery charges. These extra expenditures totalled Rs 1295.20 for low-income women, Rs 2913.68 for middle-income women, and Rs 4595.01 for high-income women. Given the fact that Indian women are investing substantial amounts in their pregnancies, increased attention must be given to prenatal care to prevent pregnancy wastage and the waste of scarce financial resources.

  18. Profile of sacubitril/valsartan in the treatment of heart failure: patient selection and perspectives.

    Science.gov (United States)

    Yandrapalli, Srikanth; Andries, Gabriela; Biswas, Medha; Khera, Sahil

    2017-01-01

    the profile of sacubitril/valsartan in the management of HF.

  19. The profile of general practitioners (GPs who publish in selected family practice journals

    Directory of Open Access Journals (Sweden)

    Serna C

    2011-05-01

    Full Text Available Abstract Background Providing support for research is one of the key issues in the ongoing attempts to improve Primary Care. However, when patient care takes up a significant part of a GP's time, conducting research is difficult. In this study we examine the working conditions and profile of GPs who publish in three leading medical journals and propose possible remedial policy actions. Findings The authors of all articles published in 2006 and 2007 in three international Family Medicine journals - Annals of Family Medicine, Family Practice, and Journal of Family Practice - were contacted by E-mail. They were asked to complete a questionnaire investigating the following variables: availability of specific time for research, time devoted to research, number of patients attended, and university affiliation. Only GPs were included in the study. Three hundred and ten relevant articles published between 2006 and 2007 were identified and the authors contacted using a survey tool. 124 researchers responded to our questionnaire; 45% of respondents who were not GPs were excluded. On average GPs spent 2.52 days per week and 6.9 hours per day on patient care, seeing 45 patients per week. Seventy-five per cent of GPs had specific time assigned to research, on average 13 hours per week; 79% were affiliated to a university and 69% held teaching positions. Conclusions Most GPs who publish original articles in leading journals have time specifically assigned to research as part of their normal working schedule. They see a relatively small number of patients. Improving the working conditions of family physicians who intend to investigate is likely to lead to better research results.

  20. PCR-based identification of selected pathogens associated with endodontic infections in deciduous and permanent teeth.

    Science.gov (United States)

    Cogulu, Dilsah; Uzel, Atac; Oncag, Ozant; Eronat, Cemal

    2008-09-01

    The aim of the present study was to evaluate the presence of the selected pathogens in samples from deciduous and permanent tooth root canals by using PCR method and to determine the association of these organisms with clinical symptoms. A total of 145 children, 5 to 13 years old, were involved in this study. The presence of selected pathogens (Actinomyces israelii, Candida albicans, Enterococcus faecalis, Fusobacterium nucleatum, Porphyromonas endodontalis, Porphyromonas gingivalis, Prevotella intermedia, Streptococcus intermedius, Treponema denticola, Parvimonas micra, Tannerella forsythensis, Enterococcus faecium, Prevotella melaninogenica) in infected root canals was studied using PCR. T. denticola (P = .012, .02) and E. faecalis (P = .012, .04) were highly associated with periapical radiolucency and previous pain, while P. gingivalis was associated with tenderness to percussion in both deciduous and permanent teeth (P = .01, .015). The results of the present study confirm that certain species of microorganisms are associated with clinical signs and symptoms of endodontic disease in both deciduous and permanent teeth.

  1. Identification of temperature changes dynamics in selected castings as a contribution to performance life improvement

    Directory of Open Access Journals (Sweden)

    A. Pytel

    2010-07-01

    Full Text Available Parameters describing boundary conditions and dynamics of temperature changes during casting cooling in foundry moulds and thesuccessive performance, especially as regards the massive cast elements, were discussed. Considering the specific nature of castingoperation, non-standard methods of examination of the isotherms of temperature fields on the casting surface were described to determinelocal overheating resulting from the technological process, chemical composition, properties of the currently applied insulation materials,casting defects and/or design. Identification of these parameters can be interpolated to laboratory conditions and to the validation of virtual models subject to computer simulation. The use in simulation of genetic algorithms combined with the results of measurements under real conditions enables more precise determination of the performance parameters, including critical states of stresses present in a structure. This should allow further optimisation of the massive castings design, considering the specific nature of a manufacturing process (alloy composition included, combined with performance parameters. Measures described here are expected to contribute to the reduced casting weight and longer time of operation.

  2. Profile of selected bacterial counts and Salmonella prevalence on raw poultry in a poultry slaughter establishment.

    Science.gov (United States)

    James, W O; Williams, W O; Prucha, J C; Johnston, R; Christensen, W

    1992-01-01

    The USDA Food Safety and Inspection Service determined populations of bacteria on poultry during processing at a slaughter plant in Puerto Rico in November and December 1987. The plant was selected because of its management's willingness to support important changes in equipment and processing procedures. The plant was representative of modern slaughter facilities. Eight-hundred samples were collected over 20 consecutive 8-hour days of operation from 5 sites in the processing plant. Results indicated that slaughter, dressing, and chilling practices significantly decreased the bacterial contamination on poultry carcasses, as determined by counts of aerobic bacteria, Enterobacteriaceae, and Escherichia coli. Salmonella was not enumerated; rather, it was determined to be present or absent by culturing almost the entire rinse. The prevalence of Salmonella in the study decreased during evisceration, then increased during immersion chilling.

  3. Identification of genomic variants putatively targeted by selection during dog domestication.

    Science.gov (United States)

    Cagan, Alex; Blass, Torsten

    2016-01-12

    Dogs [Canis lupus familiaris] were the first animal species to be domesticated and continue to occupy an important place in human societies. Recent studies have begun to reveal when and where dog domestication occurred. While much progress has been made in identifying the genetic basis of phenotypic differences between dog breeds we still know relatively little about the genetic changes underlying the phenotypes that differentiate all dogs from their wild progenitors, wolves [Canis lupus]. In particular, dogs generally show reduced aggression and fear towards humans compared to wolves. Therefore, selection for tameness was likely a necessary prerequisite for dog domestication. With the increasing availability of whole-genome sequence data it is possible to try and directly identify the genetic variants contributing to the phenotypic differences between dogs and wolves. We analyse the largest available database of genome-wide polymorphism data in a global sample of dogs 69 and wolves 7. We perform a scan to identify regions of the genome that are highly differentiated between dogs and wolves. We identify putatively functional genomic variants that are segregating or at high frequency [> = 0.75 Fst] for alternative alleles between dogs and wolves. A biological pathways analysis of the genes containing these variants suggests that there has been selection on the 'adrenaline and noradrenaline biosynthesis pathway', well known for its involvement in the fight-or-flight response. We identify 11 genes with putatively functional variants fixed for alternative alleles between dogs and wolves. The segregating variants in these genes are strong candidates for having been targets of selection during early dog domestication. We present the first genome-wide analysis of the different categories of putatively functional variants that are fixed or segregating at high frequency between a global sampling of dogs and wolves. We find evidence that selection has been strongest

  4. Profile of sacubitril/valsartan in the treatment of heart failure: patient selection and perspectives

    Directory of Open Access Journals (Sweden)

    Yandrapalli S

    2017-10-01

    guideline recommendations might lead to this medication being used in a larger population than it was studied in. In this review, we will discuss the current role of sacubitril/valsartan in the management of HF, concerns related to PARADIGM-HF and answers, shortcomings of this novel drug, effects on patient characteristics, real-world eligibility, and the role of ongoing and further investigations to clarify the profile of sacubitril/valsartan in the management of HF. Keywords: sacubitril/valsartan, Entresto, HFrEF, systolic heart failure, LCZ696, angiotensin receptor neprilysin inhibitor

  5. Morbidity profile of elderly outpatients attending selected sub-district Siddha health facilities in Tamil Nadu, India

    Science.gov (United States)

    Selvaraj, Kalaiselvi; Srinivasan, Manikandan; Duraisamy, Venkatachalam; Ramaswamy, Gomathi; Venugopal, Vinayagamurthy; Chinnakali, Palanivel

    2016-01-01

    Background: Recently, under National Health Mission alternate systems of Medicine are mainstreamed in public health care system. Effective action plan generation, logistic arrangement and roll out of these alternate systems of Medicine needs understanding on profile of morbidities among attendees who come to these facilities. Objectives: This study was planned to report profile of morbidities, age and sex differentials in specific morbidities among geriatric attendees in secondary level siddha health facilities. Materials and Methods: A facility based cross sectional study was conducted among elderly person (60 years and above) attending Siddha outpatient department (OPD) from two of the randomly selected sub district level siddha facilities in Erode district, Tamil Nadu, India. Information on socio-demographic variables like age, gender, education and clinical profile (diagnosis) were collected from records already maintained in the siddha OPD. Morbidities were summarized in terms of proportions based on age and gender. Age and sex specific differentials on specific morbidities were compared using ‘z’ test. Results: Of 2710 patients who visited these two siddha facilities during the reference period, 763 (28.1%) patients were elderly. Arthritis (45.2%), neuritis (8.8%), diabetes (6.6%), bronchial asthma (5.2%), hemiplegia (3.7%) were the top five morbidities diagnosed and treated among elderly attending the siddha OPD. There was a predilection towards elderly male for morbidities such as bronchial asthma and hemiplegia compared to elderly female. Similarly, higher proportions of lumbar spondylosis, hypertension and fungal skin diseases were reported among aged 80 years or more compared to elderly aged 60-79 years. Conclusion: Elderly constitute more than one fourth of outpatients load from siddha health facilities. Degenerative diseases like arthritis and non-communicable diseases were the common morbidities in this age group. Geriatric clinics and mobile

  6. Hydrostatic Chandra X-ray analysis of SPT-selected galaxy clusters - I. Evolution of profiles and core properties

    Science.gov (United States)

    Sanders, J. S.; Fabian, A. C.; Russell, H. R.; Walker, S. A.

    2018-02-01

    We analyse Chandra X-ray Observatory observations of a set of galaxy clusters selected by the South Pole Telescope using a new publicly available forward-modelling projection code, MBPROJ2, assuming hydrostatic equilibrium. By fitting a power law plus constant entropy model we find no evidence for a central entropy floor in the lowest entropy systems. A model of the underlying central entropy distribution shows a narrow peak close to zero entropy which accounts for 60 per cent of the systems, and a second broader peak around 130 keV cm2. We look for evolution over the 0.28-1.2 redshift range of the sample in density, pressure, entropy and cooling time at 0.015R500 and at 10 kpc radius. By modelling the evolution of the central quantities with a simple model, we find no evidence for a non-zero slope with redshift. In addition, a non-parametric sliding median shows no significant change. The fraction of cool-core clusters with central cooling times below 2 Gyr is consistent above and below z = 0.6 (˜30-40 per cent). Both by comparing the median thermodynamic profiles, centrally biased towards cool cores, in two redshift bins, and by modelling the evolution of the unbiased average profile as a function of redshift, we find no significant evolution beyond self-similar scaling in any of our examined quantities. Our average modelled radial density, entropy and cooling-time profiles appear as power laws with breaks around 0.2R500. The dispersion in these quantities rises inwards of this radius to around 0.4 dex, although some of this scatter can be fitted by a bimodal model.

  7. Diacetyl levels and volatile profiles of commercial starter distillates and selected dairy foods.

    Science.gov (United States)

    Rincon-Delgadillo, M I; Lopez-Hernandez, A; Wijaya, I; Rankin, S A

    2012-03-01

    Starter distillates (SDL) are used as ingredients in the formulation of many food products such as cottage cheese, margarine, vegetable oil spreads, processed cheese, and sour cream to increase the levels of naturally occurring buttery aroma associated with fermentation. This buttery aroma results, in part, from the presence of the vicinal dicarbonyl, diacetyl, which imparts a high level of buttery flavor notes and is a key component of SDL. Diacetyl (2,3-butanedione) is a volatile product of citrate metabolism produced by certain bacteria, including Lactococcus lactis ssp. diacetylactis and Leuconostoc citrovorum. In the United States, SDL are regarded as generally recognized as safe ingredients, whereby usage in food products is limited by good manufacturing practices. Recently, diacetyl has been implicated as a causative agent in certain lung ailments in plant workers; however, little is published about the volatile composition of SDL and the levels of diacetyl or other flavoring components in finished dairy products. The objective of this work was to characterize the volatile compounds of commercial SDL and to quantitate levels of diacetyl and other Flavor and Extract Manufacturers Association-designated high-priority flavoring components found in 18 SDL samples and 24 selected dairy products. Headspace volatiles were assessed using a solid-phase microextraction and analyzed by gas chromatography-mass spectrometry. In addition to diacetyl (ranging from 1.2 to 22,000 μg/g), 40 compounds including 8 organic acids, 4 alcohols, 3 aldehydes, 7 esters, 3 furans, 10 ketones, 2 lactones, 2 sulfur-containing compounds, and 1 terpene were detected in the SDL. A total of 22 food samples were found to contain diacetyl ranging from 4.5 to 2,700 μg/100g. Other volatile compounds, including acetaldehyde, acetic acid, acetoin, benzaldehyde, butyric acid, formic acid, furfural, 2,3-heptanedione, 2,3-pentanedione, and propanoic acid, were also identified and quantified in SDL

  8. Profiles of Reservoir Properties of Oil-Bearing Plays for Selected Petroleum Provinces in the United States

    Science.gov (United States)

    Freeman, P.A.; Attanasi, E.D.

    2015-11-05

    Profiles of reservoir properties of oil-bearing plays for selected petroleum provinces in the United States were developed to characterize the database to be used for a potential assessment by the U.S. Geological Survey (USGS) of oil that would be technically recoverable by the application of enhanced oil recovery methods using injection of carbon dioxide (CO2-EOR). The USGS assessment methodology may require reservoir-level data for the purposes of screening conventional oil reservoirs and projecting CO2-EOR performance in terms of the incremental recoverable oil. The information used in this report is based on reservoir properties from the “Significant Oil and Gas Fields of the United States Database” prepared by Nehring Associates, Inc. (2012). As described by Nehring Associates, Inc., the database “covers all producing provinces (basins) in the United States except the Appalachian Basin and the Cincinnati Arch.”

  9. Improvement of Depth Profiling into Biotissues Using Micro Electrical Impedance Spectroscopy on a Needle with Selective Passivation.

    Science.gov (United States)

    Yun, Joho; Kim, Hyeon Woo; Lee, Jong-Hyun

    2016-12-21

    A micro electrical impedance spectroscopy (EIS)-on-a-needle for depth profiling (μEoN-DP) with a selective passivation layer (SPL) on a hypodermic needle was recently fabricated to measure the electrical impedance of biotissues along with the penetration depths. The SPL of the μEoN-DP enabled the sensing interdigitated electrodes (IDEs) to contribute predominantly to the measurement by reducing the relative influence of the connection lines on the sensor output. The discrimination capability of the μEoN-DP was verified using phosphate-buffered saline (PBS) at various concentration levels. The resistance and capacitance extracted through curve fitting were similar to those theoretically estimated based on the mixing ratio of PBS and deionized water; the maximum discrepancies were 8.02% and 1.85%, respectively. Depth profiling was conducted using four-layered porcine tissue to verify the effectiveness of the discrimination capability of the μEoN-DP. The magnitude and phase between dissimilar porcine tissues (fat and muscle) were clearly discriminated at the optimal frequency of 1 MHz. Two kinds of simulations, one with SPL and the other with complete passivation layer (CPL), were performed, and it was verified that the SPL was advantageous over CPL in the discrimination of biotissues in terms of sensor output.

  10. Improvement of Depth Profiling into Biotissues Using Micro Electrical Impedance Spectroscopy on a Needle with Selective Passivation

    Directory of Open Access Journals (Sweden)

    Joho Yun

    2016-12-01

    Full Text Available A micro electrical impedance spectroscopy (EIS-on-a-needle for depth profiling (μEoN-DP with a selective passivation layer (SPL on a hypodermic needle was recently fabricated to measure the electrical impedance of biotissues along with the penetration depths. The SPL of the μEoN-DP enabled the sensing interdigitated electrodes (IDEs to contribute predominantly to the measurement by reducing the relative influence of the connection lines on the sensor output. The discrimination capability of the μEoN-DP was verified using phosphate-buffered saline (PBS at various concentration levels. The resistance and capacitance extracted through curve fitting were similar to those theoretically estimated based on the mixing ratio of PBS and deionized water; the maximum discrepancies were 8.02% and 1.85%, respectively. Depth profiling was conducted using four-layered porcine tissue to verify the effectiveness of the discrimination capability of the μEoN-DP. The magnitude and phase between dissimilar porcine tissues (fat and muscle were clearly discriminated at the optimal frequency of 1 MHz. Two kinds of simulations, one with SPL and the other with complete passivation layer (CPL, were performed, and it was verified that the SPL was advantageous over CPL in the discrimination of biotissues in terms of sensor output.

  11. Expression profiling of selected glutathione transferase genes in Zea mays (L.) seedlings infested with cereal aphids.

    Science.gov (United States)

    Sytykiewicz, Hubert; Chrzanowski, Grzegorz; Czerniewicz, Paweł; Sprawka, Iwona; Łukasik, Iwona; Goławska, Sylwia; Sempruch, Cezary

    2014-01-01

    The purpose of this report was to evaluate the expression patterns of selected glutathione transferase genes (gst1, gst18, gst23 and gst24) in the tissues of two maize (Zea mays L.) varieties (relatively resistant Ambrozja and susceptible Tasty Sweet) that were colonized with oligophagous bird cherry-oat aphid (Rhopalosiphum padi L.) or monophagous grain aphid (Sitobion avenae L.). Simultaneously, insect-triggered generation of superoxide anion radicals (O2•-) in infested Z. mays plants was monitored. Quantified parameters were measured at 1, 2, 4, 8, 24, 48 and 72 h post-initial aphid infestation (hpi) in relation to the non-infested control seedlings. Significant increases in gst transcript amounts were recorded in aphid-stressed plants in comparison to the control seedlings. Maximal enhancement in the expression of the gst genes in aphid-attacked maize plants was found at 8 hpi (gst23) or 24 hpi (gst1, gst18 and gst24) compared to the control. Investigated Z. mays cultivars formed excessive superoxide anion radicals in response to insect treatments, and the highest overproduction of O2•- was noted 4 or 8 h after infestation, depending on the aphid treatment and maize genotype. Importantly, the Ambrozja variety could be characterized as having more profound increments in the levels of gst transcript abundance and O2•- generation in comparison with the Tasty Sweet genotype.

  12. Expression Profiling of Selected Glutathione Transferase Genes in Zea mays (L.) Seedlings Infested with Cereal Aphids

    Science.gov (United States)

    Sytykiewicz, Hubert; Chrzanowski, Grzegorz; Czerniewicz, Paweł; Sprawka, Iwona; Łukasik, Iwona; Goławska, Sylwia; Sempruch, Cezary

    2014-01-01

    The purpose of this report was to evaluate the expression patterns of selected glutathione transferase genes (gst1, gst18, gst23 and gst24) in the tissues of two maize (Zea mays L.) varieties (relatively resistant Ambrozja and susceptible Tasty Sweet) that were colonized with oligophagous bird cherry-oat aphid (Rhopalosiphum padi L.) or monophagous grain aphid (Sitobion avenae L.). Simultaneously, insect-triggered generation of superoxide anion radicals (O2 •−) in infested Z. mays plants was monitored. Quantified parameters were measured at 1, 2, 4, 8, 24, 48 and 72 h post-initial aphid infestation (hpi) in relation to the non-infested control seedlings. Significant increases in gst transcript amounts were recorded in aphid-stressed plants in comparison to the control seedlings. Maximal enhancement in the expression of the gst genes in aphid-attacked maize plants was found at 8 hpi (gst23) or 24 hpi (gst1, gst18 and gst24) compared to the control. Investigated Z. mays cultivars formed excessive superoxide anion radicals in response to insect treatments, and the highest overproduction of O2 •− was noted 4 or 8 h after infestation, depending on the aphid treatment and maize genotype. Importantly, the Ambrozja variety could be characterized as having more profound increments in the levels of gst transcript abundance and O2 •− generation in comparison with the Tasty Sweet genotype. PMID:25365518

  13. Plasma cytokine profiles in depressed patients who fail to respond to selective serotonin reuptake inhibitor therapy.

    LENUS (Irish Health Repository)

    O'Brien, Sinead M

    2012-02-03

    OBJECTIVE: Approximately 30% of patients with depression fail to respond to a selective serotonin reuptake inhibitor (SSRI). Few studies have attempted to define these patients from a biological perspective. Studies suggest that overall patients with depression show increased production of proinflammatory cytokines. We examined pro- and anti-inflammatory cytokine levels in patients who were SSRI resistant. METHODS: Plasma concentrations of IL-6, IL-8, IL-10, TNF-alpha and sIL-6R were measured with enzyme linked immunosorbent assays (ELISA) in DSM-1V major depressives who were SSRI resistant, in formerly SSRI resistant patients currently euthymic and in healthy controls. RESULTS: Patients with SSRI-resistant depression had significantly higher production of the pro-inflammatory cytokines IL-6 (p=0.01) and TNF-alpha (p=0.004) compared to normal controls. Euthymic patients who were formerly SSRI resistant had proinflammatory cytokine levels which were similar to the healthy subject group. Anti-inflammatory cytokine levels did not differ across the 3 groups. CONCLUSION: Suppression of proinflammatory cytokines does not occur in depressed patients who fail to respond to SSRIs and is necessary for clinical recovery.

  14. Analytical profiling of selected antioxidants and total antioxidant capacity of goji (Lycium spp.) berries.

    Science.gov (United States)

    Protti, Michele; Gualandi, Isacco; Mandrioli, Roberto; Zappoli, Sergio; Tonelli, Domenica; Mercolini, Laura

    2017-09-05

    Goji berries and derived products represent a relevant source of micronutrients, most of which are natural antioxidants and contribute to the high nutritional quality of these fruits. Three brands of dried goji berries have been analysed by a multidisciplinary approach to get an insight into both their content of selected antioxidants and their antioxidant capacity (AC). The former goal has been achieved by developing a liquid chromatographic method coupled to mass spectrometry and combined to a fast solid phase extraction. Several significant representative antioxidant compounds belonging to the following classes: flavonoids, flavan-3-ols, phenolic acids, amino acids and derivatives, and carotenoids have been taken into account. Quercetin and rutin were found to be the predominant flavonoids, chlorogenic acid was the most abundant phenolic acid and zeaxanthin was the major carotenoid. The AC of the goji berries has been evaluated by four analytical methods in order to estimate the contributions of different reactions involved in radicals scavenging. In particular, AC has been determined using 3 standardised methods (DPPH, ABTS, ORAC) and a recently proposed electrochemical method, which measures the scavenging activity of antioxidants towards OH radicals generated both by hydrogen peroxide photolysis and the Fenton reaction. The results obtained from chemical composition and antioxidant capacity assays confirm the high nutritional and commercial value of goji berries and highlight that the three brands do not exhibit significant differences. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Selection for growth rate and body size have altered the expression profiles of somatotropic axis genes in chickens

    Science.gov (United States)

    Liu, Yong; Xu, Zhiqiang; Duan, Xiaohua; Li, Qihua; Dou, Tengfei; Gu, Dahai; Rong, Hua; Wang, Kun; Li, Zhengtian; Talpur, Mir Zulqarnain; Huang, Ying; Wang, Shanrong; Yan, Shixiong; Tong, Huiquan; Zhao, Sumei; Zhao, Guiping; Su, Zhengchang; Ge, Changrong

    2018-01-01

    The growth hormone / insulin-like growth factor-1 (GH/IGF-1) pathway of the somatotropic axis is the major controller for growth rate and body size in vertebrates, but the effect of selection on the expression of GH/IGF-1 somatotropic axis genes and their association with body size and growth performance in farm animals is not fully understood. We analyzed a time series of expression profiles of GH/IGF-1 somatotropic axis genes in two chicken breeds, the Daweishan mini chickens and Wuding chickens, and the commercial Avian broilers hybrid exhibiting markedly different body sizes and growth rates. We found that growth rate and feed conversion efficiency in Daweishan mini chickens were significantly lower than those in Wuding chickens and Avian broilers. The Wuding and Daweishan mini chickens showed higher levels of plasma GH, pituitary GH mRNA but lower levels of hepatic growth hormone receptor (GHR) mRNA than in Avian broilers. Daweishan mini chickens showed significantly lower levels of plasma IGF-1, thigh muscle and hepatic IGF-1 mRNA than did Avian broilers and Wuding chickens. These results suggest that the GH part of the somatotropic axis is the main regulator of growth rate, while IGF-1 may regulate both growth rate and body weight. Selection for growth performance and body size have altered the expression profiles of somatotropic axis genes in a breed-, age-, and tissue-specific manner, and manner, and alteration of regulatory mechanisms of these genes might play an important role in the developmental characteristics of chickens. PMID:29630644

  16. Fluoride Uptake Profiles of Selected European Toothpastes into Hard Tissues and Plaque.

    Science.gov (United States)

    Moore, Joel; Schneiderman, Eva; Farmer, Teresa; Zsiska, Marianne

    2017-09-01

    To compare the fluoridating potential of selected European toothpastes using a combination of enamel, dentin, and plaque in vitromodels. Four in vitromodels were included: 1) Enamel Fluoride (F) Uptake (EFU); 2) Dentin F Uptake (DFU); 3) Enamel Solubility Reduction (ESR); and 4) Plaque F Uptake (PFU). A core set of marketed products was included in all studies, plus a standard toothpaste (1100 ppm F as NaF/silica) and placebo control (the PFU study did not include a placebo control). Test dentifrices: [A] Fluocaril® Bi-Fluoré 250 (1500 ppm F as NaF+1000 ppm F as SMFP); [B] LacerAnticaries (2500 ppm F as SMFP); [C] Elmex® Caries Professional™ (1450 ppm F as SMFP+1.5% arginine); [D] Colgate® Triple Action (1450 ppm F as SMFP); [E] Placebo (0 ppm F); and [F] standard toothpaste (1100 ppm as NaF/silica). In all studies (EFU, DFU, ESR, and PFU), assessments were compared for each pair using the Tukey-Kramer HSD test (p F = B = C = D > E; DFU: A > F = B = C = D = E; PFU: A = B > F = C = D). In demineralization prevention, the Fluocaril dentifrice [A] also provided the greatest benefit (ESR: A = F = C = B = D > E). In all studies that included a placebo control, all of the F-containing dentifrices performed better than the placebo control. While these results demonstrate that all of the marketed products tested provide effective anticaries benefits, the Fluocaril Bi-Fluoré 250 dentifrice consistently delivered unsurpassed performance. It delivered the highest level of F to plaque, provided greater measures of efficacy in both remineralization and inhibition of demineralization, and delivered substantial improvement in fluoridation of dentin, suggesting the potential for delivering both coronal and root caries benefits.

  17. IDENTIFICATION OF KCN IN IRC+10216: EVIDENCE FOR SELECTIVE CYANIDE CHEMISTRY

    International Nuclear Information System (INIS)

    Pulliam, R. L.; Ziurys, L. M.; Savage, C.; Agundez, M.; Cernicharo, J.; Guelin, M.

    2010-01-01

    A new interstellar molecule, KCN, has been identified toward the circumstellar envelope of the carbon-rich asymptotic giant branch star, IRC+10216-the fifth metal cyanide species to be detected in space. Fourteen rotational transitions of this T-shaped, asymmetric top were searched for in the frequency range of 83-250 GHz using the Arizona Radio Observatory (ARO) 12 m Kitt Peak antenna, the IRAM 30 m telescope, and the ARO Submillimeter Telescope. Distinct lines were measured for 10 of these transitions, including the K a = 1 and 2 asymmetry components of the J = 11 → 10 and J = 10 → 9 transitions, i.e., the K-ladder structure distinct to an asymmetric top. These data are some of the most sensitive astronomical spectra at λ ∼ 1 and 3 mm obtained to date, with 3σ noise levels ∼0.3 mK, made possible by new ALMA technology. The line profiles from the ARO and IRAM telescopes are consistent with a shell-like distribution for KCN with r outer ∼ 15'', but with an inner shell radius that extends into warmer gas. The column density for KCN in IRC+10216 was found to be N tot ∼ 1.0 x 10 12 cm -2 with a rotational temperature of T rot ∼ 53 K. The fractional abundance was calculated to be f(KCN/H 2 ) ∼ 6 x 10 -10 , comparable to that of KCl. The presence of KCN in IRC+10216, along with MgNC, MgCN, NaCN, and AlNC, suggests that cyanide/isocyanide species are the most common metal-containing molecules in carbon-rich circumstellar gas.

  18. Global gene expression profiling in PAI-1 knockout murine heart and kidney: molecular basis of cardiac-selective fibrosis.

    Directory of Open Access Journals (Sweden)

    Asish K Ghosh

    Full Text Available Fibrosis is defined as an abnormal matrix remodeling due to excessive synthesis and accumulation of extracellular matrix proteins in tissues during wound healing or in response to chemical, mechanical and immunological stresses. At present, there is no effective therapy for organ fibrosis. Previous studies demonstrated that aged plasminogen activator inhibitor-1 (PAI-1 knockout mice develop spontaneously cardiac-selective fibrosis without affecting any other organs. We hypothesized that differential expressions of profibrotic and antifibrotic genes in PAI-1 knockout hearts and unaffected organs lead to cardiac selective fibrosis. In order to address this prediction, we have used a genome-wide gene expression profiling of transcripts derived from aged PAI-1 knockout hearts and kidneys. The variations of global gene expression profiling were compared within four groups: wildtype heart vs. knockout heart; wildtype kidney vs. knockout kidney; knockout heart vs. knockout kidney and wildtype heart vs. wildtype kidney. Analysis of illumina-based microarray data revealed that several genes involved in different biological processes such as immune system processing, response to stress, cytokine signaling, cell proliferation, adhesion, migration, matrix organization and transcriptional regulation were affected in hearts and kidneys by the absence of PAI-1, a potent inhibitor of urokinase and tissue-type plasminogen activator. Importantly, the expressions of a number of genes, involved in profibrotic pathways including Ankrd1, Pi16, Egr1, Scx, Timp1, Timp2, Klf6, Loxl1 and Klotho, were deregulated in PAI-1 knockout hearts compared to wildtype hearts and PAI-1 knockout kidneys. While the levels of Ankrd1, Pi16 and Timp1 proteins were elevated during EndMT, the level of Timp4 protein was decreased. To our knowledge, this is the first comprehensive report on the influence of PAI-1 on global gene expression profiling in the heart and kidney and its implication

  19. Radio-guided sentinel lymph node identification by lymphoscintigraphy fused with an anatomical vector profile: clinical applications.

    Science.gov (United States)

    Niccoli Asabella, A; Antonica, F; Renna, M A; Rubini, D; Notaristefano, A; Nicoletti, A; Rubini, G

    2013-12-01

    To develop a method to fuse lymphoscintigraphic images with an adaptable anatomical vector profile and to evaluate its role in the clinical practice. We used Adobe Illustrator CS6 to create different vector profiles, we fused those profiles, using Adobe Photoshop CS6, with lymphoscintigraphic images of the patient. We processed 197 lymphoscintigraphies performed in patients with cutaneous melanomas, breast cancer or delayed lymph drainage. Our models can be adapted to every patient attitude or position and contain different levels of anatomical details ranging from external body profiles to the internal anatomical structures like bones, muscles, vessels, and lymph nodes. If needed, more new anatomical details can be added and embedded in the profile without redrawing them, saving a lot of time. Details can also be easily hidden, allowing the physician to view only relevant information and structures. Fusion times are about 85 s. The diagnostic confidence of the observers increased significantly. The validation process showed a slight shift (mean 4.9 mm). We have created a new, practical, inexpensive digital technique based on commercial software for fusing lymphoscintigraphic images with built-in anatomical reference profiles. It is easily reproducible and does not alter the original scintigraphic image. Our method allows a more meaningful interpretation of lymphoscintigraphies, an easier recognition of the anatomical site and better lymph node dissection planning.

  20. Identification Of Inequalities In The Selection Of Liver Surgery For Colorectal Liver Metastases In Sweden.

    Science.gov (United States)

    Norén, A; Sandström, P; Gunnarsdottir, K; Ardnor, B; Isaksson, B; Lindell, G; Rizell, M

    2018-04-01

    Liver resection for colorectal liver metastases offers a 5-year survival rate of 25%-58%. This study aimed to analyze whether patients with colorectal liver metastases undergo resection to an equal extent and whether selection factors play a role in the selection process. Data were retrieved from the Swedish Colorectal Cancer Registry (2007-2011) for colorectal cancer and colorectal liver metastases. The patients identified were linked to the Swedish Registry of Liver and Bile surgery and the National Patient Registry to identify whether liver surgery or ablative treatment was performed. Analyses for age, sex, type of primary tumor and treating hospital (university, county, or district), American Society of Anesthesiologists class, and radiology for detection of metastatic disease were performed. Of 28,355 patients with colorectal cancer, 21.6% (6127/28,355) presented with liver metastases. Of the patients with liver metastases, 18.5% (1134/6127) underwent liver resection or ablation. The cumulative proportion of liver resection/ablation was 4% (1134/28,355) of all colorectal cancer. If "not bowel resected" were excluded, the proportion slightly increased to 4.7% (1134/24,262). Around 15% of the patients with metastases were registered as referrals for liver surgery. In a multivariable analysis patients treated at a university hospital for primary tumor were more frequently surgically treated for liver metastases (p 70 years and those with American Society of Anesthesiologists class >2 underwent liver resection less frequently. Magnetic resonance imaging of the liver was more often used in diagnostic work-up in men. Patients with colorectal liver metastases are unequally treated in Sweden, as indicated by the low referral rate. The proximity to a hepatobiliary unit seems important to enhance the patient's chances of being offered liver surgery.

  1. Structure-selective hot-spot Raman enhancement for direct identification and detection of trace penicilloic acid allergen in penicillin.

    Science.gov (United States)

    Zhang, Liying; Jin, Yang; Mao, Hui; Zheng, Lei; Zhao, Jiawei; Peng, Yan; Du, Shuhu; Zhang, Zhongping

    2014-08-15

    Trace penicilloic acid allergen frequently leads to various fatal immune responses to many patients, but it is still a challenge to directly discriminate and detect its residue in penicillin by a chemosensing way. Here, we report that silver-coated gold nanoparticles (Au@Ag NPs) exhibit a structure-selective hot-spot Raman enhancement capability for direct identification and detection of trace penicilloic acid in penicillin. It has been demonstrated that penicilloic acid can very easily link Au@Ag NPs together by its two carboxyl groups, locating itself spontaneously at the interparticle of Au@Ag NPs to form strong Raman hot-spot. At the critical concentration inducing the nanoparticle aggregation, Raman-enhanced effect of penicilloic acid is ~60,000 folds higher than that of penicillin. In particular, the selective Raman enhancement to the two carboxyl groups makes the peak of carboxyl group at C6 of penicilloic acid appear as a new Raman signal due to the opening of β-lactam ring of penicillin. The surface-enhanced Raman scattering (SERS) nanoparticle sensor reaches a sensitive limit lower than the prescribed 1.0‰ penicilloic acid residue in penicillin. The novel strategy to examine allergen is more rapid, convenient and inexpensive than the conventional separation-based assay methods. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. The cognitive profile of occipital lobe epilepsy and the selective association of left temporal lobe hypometabolism with verbal memory impairment.

    Science.gov (United States)

    Knopman, Alex A; Wong, Chong H; Stevenson, Richard J; Homewood, Judi; Mohamed, Armin; Somerville, Ernest; Eberl, Stefan; Wen, Lingfeng; Fulham, Michael; Bleasel, Andrew F

    2014-08-01

    We investigated the cognitive profile of structural occipital lobe epilepsy (OLE) and whether verbal memory impairment is selectively associated with left temporal lobe hypometabolism on [18F]-fluorodeoxyglucose positron emission tomography (FDG-PET). Nine patients with OLE, ages 8-29 years, completed presurgical neuropsychological assessment. Composite measures were calculated for intelligence quotient (IQ), speed, attention, verbal memory, nonverbal memory, and executive functioning. In addition, the Wisconsin Card Sorting Test (WCST) was used as a specific measure of frontal lobe functioning. Presurgical FDG-PET was analyzed with statistical parametric mapping in 8 patients relative to 16 healthy volunteers. Mild impairments were evident for IQ, speed, attention, and executive functioning. Four patients demonstrated moderate or severe verbal memory impairment. Temporal lobe hypometabolism was found in seven of eight patients. Poorer verbal memory was associated with left temporal lobe hypometabolism (p = 0.002), which was stronger (p = 0.03 and p = 0.005, respectively) than the association of left temporal lobe hypometabolism with executive functioning or with performance on the WCST. OLE is associated with widespread cognitive comorbidity, suggesting cortical dysfunction beyond the occipital lobe. Verbal memory impairment is selectively associated with left temporal lobe hypometabolism in OLE, supporting a link between neuropsychological dysfunction and remote hypometabolism in focal epilepsy. Wiley Periodicals, Inc. © 2014 International League Against Epilepsy.

  3. Identifying Pre-High School Students' Science Class Motivation Profiles to Increase Their Science Identification and Persistence

    Science.gov (United States)

    Chittum, Jessica R.; Jones, Brett D.

    2017-01-01

    One purpose of this study was to determine whether patterns existed in pre-high school students' motivation-related perceptions of their science classes. Another purpose was to examine the extent to which these patterns were related to their science identification, gender, grade level, class effort, and intentions to persist in science. We…

  4. Allosteric Inhibition of SHP2: Identification of a Potent, Selective, and Orally Efficacious Phosphatase Inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Fortanet, Jorge Garcia; Chen, Christine Hiu-Tung; Chen, Ying-Nan P.; Chen, Zhouliang; Deng, Zhan; Firestone, Brant; Fekkes, Peter; Fodor, Michelle; Fortin, Pascal D.; Fridrich, Cary; Grunenfelder, Denise; Ho, Samuel; Kang, Zhao B.; Karki, Rajesh; Kato, Mitsunori; Keen, Nick; LaBonte, Laura R.; Larrow, Jay; Lenoir, Francois; Liu, Gang; Liu, Shumei; Lombardo, Franco; Majumdar, Dyuti; Meyer, Matthew J.; Palermo, Mark; Perez, Lawrence; Pu, Minying; Ramsey, Timothy; Sellers, William R.; Shultz, Michael D.; Stams, Travis; Towler, Christopher; Wang, Ping; Williams, Sarah L.; Zhang, Ji-Hu; LaMarche, Matthew J. (Novartis)

    2016-09-08

    SHP2 is a nonreceptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also purportedly plays an important role in the programmed cell death pathway (PD-1/PD-L1). Because it is an oncoprotein associated with multiple cancer-related diseases, as well as a potential immunomodulator, controlling SHP2 activity is of significant therapeutic interest. Recently in our laboratories, a small molecule inhibitor of SHP2 was identified as an allosteric modulator that stabilizes the autoinhibited conformation of SHP2. A high throughput screen was performed to identify progressable chemical matter, and X-ray crystallography revealed the location of binding in a previously undisclosed allosteric binding pocket. Structure-based drug design was employed to optimize for SHP2 inhibition, and several new protein–ligand interactions were characterized. These studies culminated in the discovery of 6-(4-amino-4-methylpiperidin-1-yl)-3-(2,3-dichlorophenyl)pyrazin-2-amine (SHP099, 1), a potent, selective, orally bioavailable, and efficacious SHP2 inhibitor.

  5. Voltammetric electronic tongue and support vector machines for identification of selected features in Mexican coffee.

    Science.gov (United States)

    Domínguez, Rocio Berenice; Moreno-Barón, Laura; Muñoz, Roberto; Gutiérrez, Juan Manuel

    2014-09-24

    This paper describes a new method based on a voltammetric electronic tongue (ET) for the recognition of distinctive features in coffee samples. An ET was directly applied to different samples from the main Mexican coffee regions without any pretreatment before the analysis. The resulting electrochemical information was modeled with two different mathematical tools, namely Linear Discriminant Analysis (LDA) and Support Vector Machines (SVM). Growing conditions (i.e., organic or non-organic practices and altitude of crops) were considered for a first classification. LDA results showed an average discrimination rate of 88% ± 6.53% while SVM successfully accomplished an overall accuracy of 96.4% ± 3.50% for the same task. A second classification based on geographical origin of samples was carried out. Results showed an overall accuracy of 87.5% ± 7.79% for LDA and a superior performance of 97.5% ± 3.22% for SVM. Given the complexity of coffee samples, the high accuracy percentages achieved by ET coupled with SVM in both classification problems suggested a potential applicability of ET in the assessment of selected coffee features with a simpler and faster methodology along with a null sample pretreatment. In addition, the proposed method can be applied to authentication assessment while improving cost, time and accuracy of the general procedure.

  6. Comprehensive examination of conventional and innovative body fluid identification approaches and DNA profiling of laundered blood- and saliva-stained pieces of cloths.

    Science.gov (United States)

    Kulstein, G; Wiegand, P

    2018-01-01

    Body fluids like blood and saliva are commonly encountered during investigations of high volume crimes like homicides. The identification of the cellular origin and the composition of the trace can link suspects or victims to a certain crime scene and provide a probative value for criminal investigations. To erase all traces from the crime scene, perpetrators often wash away their traces. Characteristically, items that show exposed stains like blood are commonly cleaned or laundered to free them from potential visible leftovers. Mostly, investigators do not delegate the DNA analysis of laundered items. However, some studies have already revealed that items can still be used for DNA analysis even after they have been laundered. Nonetheless, a systematical evaluation of laundered blood and saliva traces that provides a comparison of different established and newly developed methods for body fluid identification (BFI) is still missing. Herein, we present the results of a comprehensive study of laundered blood- and saliva-stained pieces of cloths that were applied to a broad range of methods for BFI including conventional approaches as well as molecular mRNA profiling. The study included the evaluation of cellular origin as well as DNA profiling of blood- and saliva-stained (synthetic fiber and cotton) pieces of cloths, which have been washed at various washing temperatures for one or multiple times. Our experiments demonstrate that, while STR profiling seems to be sufficiently sensitive for the individualization of laundered items, there is a lack of approaches for BFI with the same sensitivity and specificity allowing to characterize the cellular origin of challenging, particularly laundered, blood and saliva samples.

  7. Prospective evaluation of the chromogenic medium CandiSelect 4 for differentiation and presumptive identification of non-Candida albicans Candida species

    NARCIS (Netherlands)

    Zhao, Liang; de Hoog, G Sybren; Cornelissen, Akke; Lyu, Qian; Mou, Lili; Liu, Taohua; Cao, Yu; Vatanshenassan, Mansoureh; Kang, Yingqian

    Rapid identification of pathogenic yeasts is a crucial step in timely and appropriate antifungal therapy. For diagnostics in the clinical laboratory, simplified alternatives to barcoding are needed. CandiSelect 4 (CS4) medium, a chromogenic medium for isolation of clinical yeasts, allows routine

  8. The Relationship between 4-H Division Leaders' Propensity toward Delegation and Involvement in and Major Responsibility for Leader Identification and Selection.

    Science.gov (United States)

    Dunbar, Mary Elizabeth

    This research was to determine the relationship between New York State Cooperative Extension 4-H Division Leaders' propensity toward delegation of work responsibility and (1) their degree of involvement in the performance of leader identification and selection tasks, (2) assignment of major responsibility for these tasks, and (3) other selected…

  9. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies

    Science.gov (United States)

    Lehmann, Brian D.; Bauer, Joshua A.; Chen, Xi; Sanders, Melinda E.; Chakravarthy, A. Bapsi; Shyr, Yu; Pietenpol, Jennifer A.

    2011-01-01

    Triple-negative breast cancer (TNBC) is a highly diverse group of cancers, and subtyping is necessary to better identify molecular-based therapies. In this study, we analyzed gene expression (GE) profiles from 21 breast cancer data sets and identified 587 TNBC cases. Cluster analysis identified 6 TNBC subtypes displaying unique GE and ontologies, including 2 basal-like (BL1 and BL2), an immunomodulatory (IM), a mesenchymal (M), a mesenchymal stem–like (MSL), and a luminal androgen receptor (LAR) subtype. Further, GE analysis allowed us to identify TNBC cell line models representative of these subtypes. Predicted “driver” signaling pathways were pharmacologically targeted in these cell line models as proof of concept that analysis of distinct GE signatures can inform therapy selection. BL1 and BL2 subtypes had higher expression of cell cycle and DNA damage response genes, and representative cell lines preferentially responded to cisplatin. M and MSL subtypes were enriched in GE for epithelial-mesenchymal transition, and growth factor pathways and cell models responded to NVP-BEZ235 (a PI3K/mTOR inhibitor) and dasatinib (an abl/src inhibitor). The LAR subtype includes patients with decreased relapse-free survival and was characterized by androgen receptor (AR) signaling. LAR cell lines were uniquely sensitive to bicalutamide (an AR antagonist). These data may be useful in biomarker selection, drug discovery, and clinical trial design that will enable alignment of TNBC patients to appropriate targeted therapies. PMID:21633166

  10. Characterization and Profiling of Liver microRNAs by RNA-sequencing in Cattle Divergently Selected for Residual Feed Intake

    Directory of Open Access Journals (Sweden)

    Wijdan Al-Husseini

    2016-10-01

    Full Text Available MicroRNAs (miRNAs are short non-coding RNAs that post-transcriptionally regulate expression of mRNAs in many biological pathways. Liver plays an important role in the feed efficiency of animals and high and low efficient cattle demonstrated different gene expression profiles by microarray. Here we report comprehensive miRNAs profiles by next-gen deep sequencing in Angus cattle divergently selected for residual feed intake (RFI and identify miRNAs related to feed efficiency in beef cattle. Two microRNA libraries were constructed from pooled RNA extracted from livers of low and high RFI cattle, and sequenced by Illumina genome analyser. In total, 23,628,103 high quality short sequence reads were obtained and more than half of these reads were matched to the bovine genome (UMD 3.1. We identified 305 known bovine miRNAs. Bta-miR-143, bta-miR-30, bta-miR-122, bta-miR-378, and bta-let-7 were the top five most abundant miRNAs families expressed in liver, representing more than 63% of expressed miRNAs. We also identified 52 homologous miRNAs and 10 novel putative bovine-specific miRNAs, based on precursor sequence and the secondary structure and utilizing the miRBase (v. 21. We compared the miRNAs profile between high and low RFI animals and ranked the most differentially expressed bovine known miRNAs. Bovine miR-143 was the most abundant miRNA in the bovine liver and comprised 20% of total expressed mapped miRNAs. The most highly expressed miRNA in liver of mice and humans, miR-122, was the third most abundant in our cattle liver samples. We also identified 10 putative novel bovine-specific miRNA candidates. Differentially expressed miRNAs between high and low RFI cattle were identified with 18 miRNAs being up-regulated and 7 other miRNAs down-regulated in low RFI cattle. Our study has identified comprehensive miRNAs expressed in bovine liver. Some of the expressed miRNAs are novel in cattle. The differentially expressed miRNAs between high and low RFI

  11. NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children

    OpenAIRE

    Vignali, Marissa; Armour, Christopher D.; Chen, Jingyang; Morrison, Robert; Castle, John C.; Biery, Matthew C.; Bouzek, Heather; Moon, Wonjong; Babak, Tomas; Fried, Michal; Raymond, Christopher K.; Duffy, Patrick E.

    2011-01-01

    Malaria caused by Plasmodium falciparum results in approximately 1 million annual deaths worldwide, with young children and pregnant mothers at highest risk. Disease severity might be related to parasite virulence factors, but expression profiling studies of parasites to test this hypothesis have been hindered by extensive sequence variation in putative virulence genes and a prep...

  12. Actin gene identification from selected medicinal plants for their use as internal controls for gene expression studies

    International Nuclear Information System (INIS)

    Mufti, F.U.D.; Banaras, S.

    2015-01-01

    Internal control genes are the constitutive genes which maintain the basic cellular functions and regularly express in both normal and stressed conditions in living organisms. They are used in normalization of gene expression studies in comparative analysis of target genes, as their expression remains comparatively unchanged in all varied conditions. Among internal control genes, actin is considered as a candidate gene for expression studies due to its vital role in shaping cytoskeleton and plant physiology. Unfortunately most of such knowledge is limited to only model plants or crops, not much is known about important medicinal plants. Therefore, we selected seven important medicinal wild plants for molecular identification of actin gene. We used gene specific primers designed from the conserved regions of several known orthologues or homologues of actin genes from other plants. The amplified products of 370-380 bp were sequenced and submitted to GeneBank after their confirmation using different bioinformatics tools. All the novel partial sequences of putative actin genes were submitted to GeneBank (Parthenium hysterophorus (KJ774023), Fagonia indica (KJ774024), Rhazya stricta (KJ774025), Whithania coagulans (KJ774026), Capparis decidua (KJ774027), Verbena officinalis (KJ774028) and Aerva javanica (KJ774029)). The comparisons of these partial sequences by Basic Local Alignment Search Tool (BLAST) and phylogenetic trees demonstrated high similarity with known actin genes of other plants. Our findings illustrated highly conserved nature of actin gene among these selected plants. These novel partial fragments of actin genes from these wild medicinal plants can be used as internal controls for future gene expression studies of these important plants after precise validations of their stable expression in such plants. (author)

  13. Modification of Sunlight Radiation through Colored Photo-Selective Nets Affects Anthocyanin Profile in Vaccinium spp. Berries.

    Directory of Open Access Journals (Sweden)

    Laura Zoratti

    Full Text Available In recent years, the interest on the effects of the specific wavelengths of the light spectrum on growth and metabolism of plants has been increasing markedly. The present study covers the effect of modified sunlight conditions on the accumulation of anthocyanin pigments in two Vaccinium species: the European wild bilberry (V. myrtillus L. and the cultivated highbush blueberry (V. corymbosum L..The two Vaccinium species were grown in the same test field in the Alps of Trentino (Northern Italy under modified light environment. The modification of sunlight radiation was carried out in field, through the use of colored photo-selective nets throughout the berry ripening during two consecutive growing seasons. The anthocyanin profile was then assessed in berries at ripeness.The results indicated that the light responses of the two Vaccinium species studied were different. Although both studied species are shade-adapted plants, 90% shading of sunlight radiation was beneficial only for bilberry plants, which accumulated the highest content of anthocyanins in both seasons. The same condition, instead, was not favorable for blueberries, whose maturation was delayed for at least two weeks, and anthocyanin accumulation was significantly decreased compared to berries grown under sunlight conditions. Moreover, the growing season had strong influence on the anthocyanin accumulation in both species, in relation to temperature flow and sunlight spectra composition during the berry ripening period.Our results suggest that the use of colored photo-selective nets may be a complementary agricultural practice for cultivation of Vaccinium species. However, further studies are needed to analyze the effect of the light spectra modifications to other nutritional properties, and to elucidate the molecular mechanisms behind the detected differences between the two relative Vaccinium species.

  14. Modification of Sunlight Radiation through Colored Photo-Selective Nets Affects Anthocyanin Profile in Vaccinium spp. Berries.

    Science.gov (United States)

    Zoratti, Laura; Jaakola, Laura; Häggman, Hely; Giongo, Lara

    2015-01-01

    In recent years, the interest on the effects of the specific wavelengths of the light spectrum on growth and metabolism of plants has been increasing markedly. The present study covers the effect of modified sunlight conditions on the accumulation of anthocyanin pigments in two Vaccinium species: the European wild bilberry (V. myrtillus L.) and the cultivated highbush blueberry (V. corymbosum L.). The two Vaccinium species were grown in the same test field in the Alps of Trentino (Northern Italy) under modified light environment. The modification of sunlight radiation was carried out in field, through the use of colored photo-selective nets throughout the berry ripening during two consecutive growing seasons. The anthocyanin profile was then assessed in berries at ripeness. The results indicated that the light responses of the two Vaccinium species studied were different. Although both studied species are shade-adapted plants, 90% shading of sunlight radiation was beneficial only for bilberry plants, which accumulated the highest content of anthocyanins in both seasons. The same condition, instead, was not favorable for blueberries, whose maturation was delayed for at least two weeks, and anthocyanin accumulation was significantly decreased compared to berries grown under sunlight conditions. Moreover, the growing season had strong influence on the anthocyanin accumulation in both species, in relation to temperature flow and sunlight spectra composition during the berry ripening period. Our results suggest that the use of colored photo-selective nets may be a complementary agricultural practice for cultivation of Vaccinium species. However, further studies are needed to analyze the effect of the light spectra modifications to other nutritional properties, and to elucidate the molecular mechanisms behind the detected differences between the two relative Vaccinium species.

  15. A stochastic analysis approach on the cost-time profile for selecting the best future state MA

    Directory of Open Access Journals (Sweden)

    Seyedhosseini, Seyed Mohammad

    2015-05-01

    Full Text Available In the literature on value stream mapping (VSM, the only basis for choosing the best future state map (FSM among the proposed alternatives is the time factor. As a result, the FSM is selected as the best option because it has the least amount of total production lead time (TPLT. In this paper, the cost factor is considered in the FSM selection process, in addition to the time factor. Thus, for each of the proposed FSMs, the cost-time profile (CTP is used. Two factors that are of particular importance for the customer and the manufacturer – the TPLT and the direct cost of the product – are reviewed and analysed by calculating the sub-area of the CTP curve, called the cost-time investment (CTI. In addition, variability in the generated data has been studied in each of the CTPs in order to choose the best FSM more precisely and accurately. Based on a proposed step-by-step stochastic analysis method, and also by using non-parametric Kernel estimation methods for estimating the probability density function of CTIs, the process of choosing the best FSM has been carried out, based not only on the minimum expected CTI, but also on the minimum expected variability amount in CTIs among proposed alternatives. By implementing this method during the process of choosing the best FSM, the manufacturing organisations will consider both the cost factor and the variability in the generated data, in addition to the time factor. Accordingly, the decision-making process proceeds more easily and logically than do traditional methods. Finally, to describe the effectiveness and applicability of the proposed method in this paper, it is applied to a case study on an industrial parts manufacturing company in Iran.

  16. Pharmacological profile of CS-3150, a novel, highly potent and selective non-steroidal mineralocorticoid receptor antagonist.

    Science.gov (United States)

    Arai, Kiyoshi; Homma, Tsuyoshi; Morikawa, Yuka; Ubukata, Naoko; Tsuruoka, Hiyoyuki; Aoki, Kazumasa; Ishikawa, Hirokazu; Mizuno, Makoto; Sada, Toshio

    2015-08-15

    The present study was designed to characterize the pharmacological profile of CS-3150, a novel non-steroidal mineralocorticoid receptor antagonist. In the radioligand-binding assay, CS-3150 inhibited (3)H-aldosterone binding to mineralocorticoid receptor with an IC50 value of 9.4nM, and its potency was superior to that of spironolactone and eplerenone, whose IC50s were 36 and 713nM, respectively. CS-3150 also showed at least 1000-fold higher selectivity for mineralocorticoid receptor over other steroid hormone receptors, glucocorticoid receptor, androgen receptor and progesterone receptor. In the reporter gene assay, CS-3150 inhibited aldosterone-induced transcriptional activation of human mineralocorticoid receptor with an IC50 value of 3.7nM, and its potency was superior to that of spironolactone and eplerenone, whose IC50s were 66 and 970nM, respectively. CS-3150 had no agonistic effect on mineralocorticoid receptor and did not show any antagonistic or agonistic effect on glucocorticoid receptor, androgen receptor and progesterone receptor even at the high concentration of 5μM. In adrenalectomized rats, single oral administration of CS-3150 suppressed aldosterone-induced decrease in urinary Na(+)/K(+) ratio, an index of in vivo mineralocorticoid receptor activation, and this suppressive effect was more potent and longer-lasting than that of spironolactone and eplerenone. Chronic treatment with CS-3150 inhibited blood pressure elevation induced by deoxycorticosterone acetate (DOCA)/salt-loading to rats, and this antihypertensive effect was more potent than that of spironolactone and eplerenone. These findings indicate that CS-3150 is a selective and highly potent mineralocorticoid receptor antagonist with long-lasting oral activity. This agent could be useful for the treatment of hypertension, cardiovascular and renal disorders. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Effects of Selected Egyptian Honeys on the Cellular Ultrastructure and the Gene Expression Profile of Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Reham Wasfi

    Full Text Available The purpose of this study was to: (i evaluate the antibacterial activities of three Egyptian honeys collected from different floral sources (namely, citrus, clover, and marjoram against Escherichia coli; (ii investigate the effects of these honeys on bacterial ultrastructure; and (iii assess the anti-virulence potential of these honeys, by examining their impacts on the expression of eight selected genes (involved in biofilm formation, quorum sensing, and stress survival in the test organism. The minimum inhibitory concentration (MIC of the honey samples against E. coli ATCC 8739 were assessed by the broth microdilution assay in the presence and absence of catalase enzyme. Impacts of the honeys on the cellular ultrastructure and the expression profiles of the selected genes of E. coli were examined using transmission electron microscopy (TEM and quantitative real-time polymerase chain reaction (qPCR analysis, respectively. The susceptibility tests showed promising antibacterial activities of all the tested honeys against E. coli. This was supported by the TEM observations, which revealed "ghost" cells lacking DNA, in addition to cells with increased vacuoles, and/or with irregular shrunken cytoplasm. Among the tested honeys, marjoram exhibited the highest total antibacterial activity and the highest levels of peroxide-dependent activity. The qPCR analysis showed that all honey-treated cells share a similar overall pattern of gene expression, with a trend toward reduced expression of the virulence genes of interest. Our results indicate that some varieties of the Egyptian honey have the potential to be effective inhibitor and virulence modulator of E. coli via multiple molecular targets.

  18. Strategy for Comprehensive Profiling and Identification of Acidic Glycosphingolipids Using Ultra-High-Performance Liquid Chromatography Coupled with Quadrupole Time-of-Flight Mass Spectrometry.

    Science.gov (United States)

    Hu, Ting; Jia, Zhixin; Zhang, Jin-Lan

    2017-07-18

    Acidic glycosphingolipids (AGSLs), which mainly consist of ganglioside and sulfatide moieties, are highly concentrated in the central nervous system. Comprehensive profiling of AGSLs has historically been challenging because of their high complexity and the lack of standards. In this study, a novel strategy was developed to comprehensively profile AGSLs using ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Ganglioside isomers with different glycan chains such as GD1a/GD1b were completely separated on a C18 column for the first time to our knowledge, facilitated by the addition of formic acid in the mobile phase. A mathematical model was established to predict the retention times (RTs) of all theoretically possible AGSLs on the basis of the good logarithmic relationship between the ceramide carbon numbers of the AGSLs in the reference material and their RTs. A data set was created of 571 theoretically possible AGSLs, including the ceramide carbon numbers, RTs, and high-resolution quasi-molecular ions. A novel fast identification strategy was established for global AGSL profiling by comparing the high-resolution quasi-molecular ions and RTs of the tested peaks to those in the data set of 571 AGSLs. Using this strategy, 199 AGSL candidates were identified in rat brain tissue. MS/MS fragments were further collected for these 199 candidates to confirm their identity as AGSLs. This novel strategy was employed to profile AGSLs in brain tissue samples from control rats and model rats with bilateral common carotid artery (2-VO) cerebral ischemia. Forty AGSLs were significantly different between the control and model groups, and these differences were further interpreted.

  19. Profiling cancer

    DEFF Research Database (Denmark)

    Ciro, Marco; Bracken, Adrian P; Helin, Kristian

    2003-01-01

    In the past couple of years, several very exciting studies have demonstrated the enormous power of gene-expression profiling for cancer classification and prediction of patient survival. In addition to promising a more accurate classification of cancer and therefore better treatment of patients......, gene-expression profiling can result in the identification of novel potential targets for cancer therapy and a better understanding of the molecular mechanisms leading to cancer....

  20. Selection and use of microsatellite markers for individual identification and meat traceability of six swine breeds in the Chinese market.

    Science.gov (United States)

    Zhao, Jie; Li, Tingting; Zhu, Chao; Jiang, Xiaoling; Zhao, Yan; Xu, Zhenzhen; Yang, Shuming; Chen, Ailiang

    2018-06-01

    Meat traceability based on molecular markers is exerting a great influence on food safety and will enhance its key role in the future. This study aimed to investigate and verify the polymorphism of 23 microsatellite markers and select the most suitable markers for individual identification and meat traceability of six swine breeds in the Chinese market. The mean polymorphism information content value of these 23 loci was 0.7851, and each locus exhibited high polymorphism in the pooled population. There were 10 loci showing good polymorphism in each breed, namely, Sw632, S0155, Sw2406, Sw830, Sw2525, Sw72, Sw2448, Sw911, Sw122 and CGA. When six highly polymorphic loci were combined, the match probability value for two random individual genotypes among the pig breeds (Beijing Black, Sanyuan and Taihu) was lower than 1.151 E-06. An increasing number of loci indicated a gradually decreasing match probability value and therefore enhanced traceability accuracy. The validation results of tracing 18 blood and corresponding meat samples based on five highly polymorphic loci (Sw2525, S0005, Sw0107, Sw911 and Sw857) were successful, with 100% conformation probability, which provided a foundation for establishing a traceability system for pork in the Chinese market.

  1. Accurate and precise measurement of oxygen isotopic fractions and diffusion profiles by selective attenuation of secondary ions (SASI).

    Science.gov (United States)

    Téllez, Helena; Druce, John; Hong, Jong-Eun; Ishihara, Tatsumi; Kilner, John A

    2015-03-03

    The accuracy and precision of isotopic analysis in Time-of-Flight secondary ion mass spectrometry (ToF-SIMS) relies on the appropriate reduction of the dead-time and detector saturation effects, especially when analyzing species with high ion yields or present in high concentrations. Conventional approaches to avoid these problems are based on Poisson dead-time correction and/or an overall decrease of the total secondary ion intensity by reducing the target current. This ultimately leads to poor detection limits for the minor isotopes and high uncertainties of the measured isotopic ratios. An alternative strategy consists of the attenuation of those specific secondary ions that saturate the detector, providing an effective extension of the linear dynamic range. In this work, the selective attenuation of secondary ion signals (SASI) approach is applied to the study of oxygen transport properties in electroceramic materials by isotopic labeling with stable (18)O tracer and ToF-SIMS depth profiling. The better analytical performance in terms of accuracy and precision allowed a more reliable determination of the oxygen surface exchange and diffusion coefficients while maintaining good mass resolution and limits of detection for other minor secondary ion species. This improvement is especially relevant to understand the ionic transport mechanisms and properties of solid materials, such as the parallel diffusion pathways (e.g., oxygen diffusion through bulk, grain boundary, or dislocations) in electroceramic materials with relevant applications in energy storage and conversion devices.

  2. Chloroform-assisted phenol extraction improving proteome profiling of maize embryos through selective depletion of high-abundance storage proteins.

    Directory of Open Access Journals (Sweden)

    Erhui Xiong

    Full Text Available The presence of abundant storage proteins in plant embryos greatly impedes seed proteomics analysis. Vicilin (or globulin-1 is the most abundant storage protein in maize embryo. There is a need to deplete the vicilins from maize embryo extracts for enhanced proteomics analysis. We here reported a chloroform-assisted phenol extraction (CAPE method for vicilin depletion. By CAPE, maize embryo proteins were first extracted in an aqueous buffer, denatured by chloroform and then subjected to phenol extraction. We found that CAPE can effectively deplete the vicilins from maize embryo extract, allowing the detection of low-abundance proteins that were masked by vicilins in 2-DE gel. The novelty of CAPE is that it selectively depletes abundant storage proteins from embryo extracts of both monocot (maize and dicot (soybean and pea seeds, whereas other embryo proteins were not depleted. CAPE can significantly improve proteome profiling of embryos and extends the application of chloroform and phenol extraction in plant proteomics. In addition, the rationale behind CAPE depletion of abundant storage proteins was explored.

  3. Real-world exhaust temperature profiles of on-road heavy-duty diesel vehicles equipped with selective catalytic reduction.

    Science.gov (United States)

    Boriboonsomsin, Kanok; Durbin, Thomas; Scora, George; Johnson, Kent; Sandez, Daniel; Vu, Alexander; Jiang, Yu; Burnette, Andrew; Yoon, Seungju; Collins, John; Dai, Zhen; Fulper, Carl; Kishan, Sandeep; Sabisch, Michael; Jackson, Doug

    2018-09-01

    On-road heavy-duty diesel vehicles are a major contributor of oxides of nitrogen (NO x ) emissions. In the US, many heavy-duty diesel vehicles employ selective catalytic reduction (SCR) technology to meet the 2010 emission standard for NO x . Typically, SCR needs to be at least 200°C before a significant level of NO x reduction is achieved. However, this SCR temperature requirement may not be met under some real-world operating conditions, such as during cold starts, long idling, or low speed/low engine load driving activities. The frequency of vehicle operation with low SCR temperature varies partly by the vehicle's vocational use. In this study, detailed vehicle and engine activity data were collected from 90 heavy-duty vehicles involved in a range of vocations, including line haul, drayage, construction, agricultural, food distribution, beverage distribution, refuse, public work, and utility repair. The data were used to create real-world SCR temperature and engine load profiles and identify the fraction of vehicle operating time that SCR may not be as effective for NO x control. It is found that the vehicles participated in this study operate with SCR temperature lower than 200°C for 11-70% of the time depending on their vocation type. This implies that real-world NO x control efficiency could deviate from the control efficiency observed during engine certification. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Chemical Profiling and Evaluation of Antioxidant and Anti-Microbial Properties of Selected Commercial Essential Oils: A Comparative Study

    Directory of Open Access Journals (Sweden)

    Ângelo Luís

    2017-06-01

    Full Text Available Background: The last decades have seen an increased awareness by the scientific community of the extent of resistance to conventional antibiotics, particularly with respect to the emerging multidrug-resistant pathogenic microbes. Additionally, natural antioxidants have received significant attention among food professionals and consumers because of their assumed safety and potential therapeutic value. The aim of this work was to assess the antioxidant activities of eight selected commercial essential oils (EOs, together with the evaluation of their antibacterial and anti-quorum sensing properties. Methods: The chemical profiling of the EOs was performed using gas chromatography-mass spectrometry (GC-MS analysis. The antioxidant properties of the EOs were evaluated using the 2,2-diphenyl-1-picrylhydrazyl (DPPH free radical scavenging assay and by β-carotene bleaching test. Disc diffusion assays were employed to evaluate the anti-bacterial and anti-quorum sensing activities of the EOs. Results: It was observed that EOs from three Eucalyptus species are rich in eucalyptol. Generally, linalool is abundant in EOs from four Lavandula species. The oil of Cymbopogon citratus is the one with the best capacity to scavenge the DPPH free radicals and presented great antibacterial activity. Conclusions: The geographical origins of the plant species are determinant factors in the EO composition and in the corresponding biological activities.

  5. Classifications within molecular subtypes enables identification of BRCA1/BRCA2 mutation carriers by RNA tumor profiling

    DEFF Research Database (Denmark)

    Larsen, Martin J; Kruse, Torben A; Tan, Qihua

    2013-01-01

    Pathogenic germline mutations in BRCA1 or BRCA2 are detected in less than one third of families with a strong history of breast cancer. It is therefore expected that mutations still remain undetected by currently used screening methods. In addition, a growing number of BRCA1/2 sequence variants...... of unclear pathogen significance are found in the families, constituting an increasing clinical challenge. New methods are therefore needed to improve the detection rate and aid the interpretation of the clinically uncertain variants. In this study we analyzed a series of 33 BRCA1, 22 BRCA2, and 128 sporadic...... tumors by RNA profiling to investigate the classification potential of RNA profiles to predict BRCA1/2 mutation status. We found that breast tumors from BRCA1 and BRCA2 mutation carriers display characteristic RNA expression patterns, allowing them to be distinguished from sporadic tumors. The majority...

  6. Novel biomarker identification using metabolomic profiling to differentiate radiation necrosis and recurrent tumor following Gamma Knife radiosurgery.

    Science.gov (United States)

    Lu, Alex Y; Turban, Jack L; Damisah, Eyiyemisi C; Li, Jie; Alomari, Ahmed K; Eid, Tore; Vortmeyer, Alexander O; Chiang, Veronica L

    2017-08-01

    OBJECTIVE Following an initial response of brain metastases to Gamma Knife radiosurgery, regrowth of the enhancing lesion as detected on MRI may represent either radiation necrosis (a treatment-related inflammatory change) or recurrent tumor. Differentiation of radiation necrosis from tumor is vital for management decision making but remains difficult by imaging alone. In this study, gas chromatography with time-of-flight mass spectrometry (GC-TOF) was used to identify differential metabolite profiles of the 2 tissue types obtained by surgical biopsy to find potential targets for noninvasive imaging. METHODS Specimens of pure radiation necrosis and pure tumor obtained from patient brain biopsies were flash-frozen and validated histologically. These formalin-free tissue samples were then analyzed using GC-TOF. The metabolite profiles of radiation necrosis and tumor samples were compared using multivariate and univariate statistical analysis. Statistical significance was defined as p ≤ 0.05. RESULTS For the metabolic profiling, GC-TOF was performed on 7 samples of radiation necrosis and 7 samples of tumor. Of the 141 metabolites identified, 17 (12.1%) were found to be statistically significantly different between comparison groups. Of these metabolites, 6 were increased in tumor, and 11 were increased in radiation necrosis. An unsupervised hierarchical clustering analysis found that tumor had elevated levels of metabolites associated with energy metabolism, whereas radiation necrosis had elevated levels of metabolites that were fatty acids and antioxidants/cofactors. CONCLUSIONS To the authors' knowledge, this is the first tissue-based metabolomics study of radiation necrosis and tumor. Radiation necrosis and recurrent tumor following Gamma Knife radiosurgery for brain metastases have unique metabolite profiles that may be targeted in the future to develop noninvasive metabolic imaging techniques.

  7. Proteomic and transcriptomic profiling of in vitro established radiation resistant oral cancer cells for identification of radioresistance related biomarkers

    International Nuclear Information System (INIS)

    Mohd Yasser; Pawar, Sagar; Teni, Tanuja

    2016-01-01

    Radiotherapy is an integral part of oral cancer treatment, either alone or in combination with surgery. But, during radiotherapy, oral tumours of a subset of patients develop radioresistance that creates major obstruction towards its efficacy. The aim of our study was to establish radioresistant cell lines from different oral subsites using clinically admissible low dose radiation and profile them by proteomic and transcriptomic approaches to identify proteins associated with radioresistance in oral cancer

  8. Integrated identification, qualification and quantification strategy for pharmacokinetic profile study of Guizhi Fuling capsule in healthy volunteers

    OpenAIRE

    Yun-Xi Zhong; Xiao-Liang Jin; Shi-Yin Gu; Ying Peng; Ke-Rong Zhang; Bing-Chen Ou-Yang; Yu Wang; Wei Xiao; Zhen-Zhong Wang; Ji-Ye Aa; Guang-Ji Wang; Jian-Guo Sun

    2016-01-01

    Guizhi Fuling capsule (GZFL), a traditional Chinese medicine formulation, is widely used in China to relieve pain from dysmenorrhea and is now in a Phase II clinical trial in the USA. Due to the low exposure of the five main medicative ingredients (amygdalin, cinnamic acid, gallic acid, paeoniflorin and paeonol) of GZFL in human, a strategy was built to qualitatively and quantitatively identify the possible metabolites of GZFL and to describe the pharmacokinetic profiles of GZFL in human. In ...

  9. Chemical Profiling and Identification of Alkaloids and Flavonoids in Uncaria lanosa var. ferrea Via UHPLC-Orbitrap MS

    International Nuclear Information System (INIS)

    Nursyaza Husna Shaharuddin; Nor Hadiani Ismail; Nurhuda Manshoor; Fatimah Salim; Rohaya Ahmad; Nursyaza Husna Shaharuddin; Nor Hadiani Ismail; Fatimah Salim; Rohaya Ahmad; Nurhuda Manshoor

    2016-01-01

    Our previous studies on Malaysian Uncaria (Rubiaceae) have yielded over 20 compounds including alkaloids and flavonoids with some compounds showing interesting biological activities. In the search of new bioactive compounds from the genus, a phytochemicals investigation on Uncaria lanosa (Wall.) locally known as gegambir paya or gegambir hitam was carried out via metabolite profiling. The plant is reported to be used as an infusion for intestine inflammation and a decoction for cleaning wounds and ulcers. Metabolite profiling was carried out using ultrahigh-performance liquid chromatography coupled with orbitrap mass spectrometry detectors (UHPLC-Orbitrap MS). Ten alkaloids and six flavonoids previously isolated from other Uncaria species were used as reference compounds. Phytochemicals analysis of the stem extracts of the plant found the presence of a flavonoid and three alkaloids whose identities were obtained through the comparison of their mass and fragmentation pattern as well as the retention times of the reference compounds. The developed LC-MS method is expected to lead to a more rapid and reliable approach in discovery of new or novel compounds in Uncaria genus. The development of the MS database will also aid in the metabolite profiling of other medicinal plants in natural product research. (author)

  10. Identification of ballast water discharge profiles of a port to enable effective ballast water management and environmental studies

    Science.gov (United States)

    David, Matej; Gollasch, Stephan; Penko, Ludvik

    2018-03-01

    Information about the profile of ballast water discharges in a port is one of the basic elements of the decision making process in ballast water risk assessment and management, and supports the evaluation of dimensions and processes of aquatic species invasions with vessels ballast water. In the lack of ballast water reporting, ballast water discharge assessments need to be conducted. In this study we have assessed and compared ballast water discharge profiles of two ports with different maritime traffic and cargo profiles, the Port of Hamburg (Germany) and the Muuga Harbour, Port of Tallinn (Estonia). This study shows methods and approaches which can be used to assess volumes and donor ports of ballast water discharges for a port at the level of each vessel call. These methods and approaches can be applied to any port to support the implementation of feasible and efficient ballast water management measures and to enable environmental studies including long-term accumulation risks of disinfection by-products from ballast water management systems making use of active substances, as well as for discharges of other chemical compounds.

  11. Identification of the chemical constituents of Chinese medicine Yi-Xin-Shu capsule by molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation.

    Science.gov (United States)

    Wang, Hong-ping; Chen, Chang; Liu, Yan; Yang, Hong-Jun; Wu, Hong-Wei; Xiao, Hong-Bin

    2015-11-01

    The incomplete identification of the chemical components of traditional Chinese medicinal formula has been one of the bottlenecks in the modernization of traditional Chinese medicine. Tandem mass spectrometry has been widely used for the identification of chemical substances. Current automatic tandem mass spectrometry acquisition, where precursor ions were selected according to their signal intensity, encounters a drawback in chemical substances identification when samples contain many overlapping signals. Compounds in minor or trace amounts could not be identified because most tandem mass spectrometry information was lost. Herein, a molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation method for complex Chinese medicine chemical constituent analysis was developed. The precursor ions were selected according to their two-dimensional characteristics of retention times and mass-to-charge ratio ranges from herbal compounds, so that all precursor ions from herbal compounds were included and more minor chemical constituents in Chinese medicine were identified. Compared to the conventional automatic tandem mass spectrometry setups, the approach is novel and can overcome the drawback for chemical substances identification. As an example, 276 compounds from the Chinese Medicine of Yi-Xin-Shu capsule were identified. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects.

    Science.gov (United States)

    Buelow, Elena; Bello González, Teresita D J; Fuentes, Susana; de Steenhuijsen Piters, Wouter A A; Lahti, Leo; Bayjanov, Jumamurat R; Majoor, Eline A M; Braat, Johanna C; van Mourik, Maaike S M; Oostdijk, Evelien A N; Willems, Rob J L; Bonten, Marc J M; van Passel, Mark W J; Smidt, Hauke; van Schaik, Willem

    2017-08-14

    The gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed "selective decontamination of the digestive tract" (SDD), is used in some countries where it improves clinical outcome in ICU patients. Yet, the impact of ICU hospitalization and SDD on the gut microbiota remains largely unknown. Here, we characterize the composition of the gut microbiota and its antimicrobial resistance genes ("the resistome") of ICU patients during SDD and of healthy subjects. From ten patients that were acutely admitted to the ICU, 30 fecal samples were collected during ICU stay. Additionally, feces were collected from five of these patients after transfer to a medium-care ward and cessation of SDD. Feces from ten healthy subjects were collected twice, with a 1-year interval. Gut microbiota and resistome composition were determined using 16S rRNA gene phylogenetic profiling and nanolitre-scale quantitative PCRs. The microbiota of the ICU patients differed from the microbiota of healthy subjects and was characterized by lower microbial diversity, decreased levels of Escherichia coli and of anaerobic Gram-positive, butyrate-producing bacteria of the Clostridium clusters IV and XIVa, and an increased abundance of Bacteroidetes and enterococci. Four resistance genes (aac(6')-Ii, ermC, qacA, tetQ), providing resistance to aminoglycosides, macrolides, disinfectants, and tetracyclines, respectively, were significantly more abundant among ICU patients than in healthy subjects, while a chloramphenicol resistance gene (catA) and a tetracycline resistance gene (tetW) were more abundant in healthy subjects. The gut microbiota of SDD-treated ICU patients deviated strongly from the gut microbiota of healthy subjects. The negative effects on the resistome were limited to selection

  13. The importance of the selection of appropriate reference genes for gene expression profiling in adrenal medulla or sympathetic ganglia of spontaneously hypertensive rat

    Czech Academy of Sciences Publication Activity Database

    Vavřínová, Anna; Behuliak, Michal; Zicha, Josef

    2016-01-01

    Roč. 65, č. 3 (2016), s. 401-411 ISSN 0862-8408 R&D Projects: GA ČR(CZ) GP14-16225P Institutional support: RVO:67985823 Keywords : adrenal medulla * gene expression profiling * reference gene selection * sympathetic nervous system Subject RIV: FA - Cardiovascular Diseases incl. Cardiotharic Surgery Impact factor: 1.461, year: 2016

  14. Identification of intestinal loss of a drug through physiologically based pharmacokinetic simulation of plasma concentration-time profiles.

    Science.gov (United States)

    Peters, Sheila Annie

    2008-01-01

    Despite recent advances in understanding of the role of the gut as a metabolizing organ, recognition of gut wall metabolism and/or other factors contributing to intestinal loss of a compound has been a challenging task due to the lack of well characterized methods to distinguish it from first-pass hepatic extraction. The implications of identifying intestinal loss of a compound in drug discovery and development can be enormous. Physiologically based pharmacokinetic (PBPK) simulations of pharmacokinetic profiles provide a simple, reliable and cost-effective way to understand the mechanisms underlying pharmacokinetic processes. The purpose of this article is to demonstrate the application of PBPK simulations in bringing to light intestinal loss of orally administered drugs, using two example compounds: verapamil and an in-house compound that is no longer in development (referred to as compound A in this article). A generic PBPK model, built in-house using MATLAB software and incorporating absorption, metabolism, distribution, biliary and renal elimination models, was employed for simulation of concentration-time profiles. Modulation of intrinsic hepatic clearance and tissue distribution parameters in the generic PBPK model was done to achieve a good fit to the observed intravenous pharmacokinetic profiles of the compounds studied. These optimized clearance and distribution parameters are expected to be invariant across different routes of administration, as long as the kinetics are linear, and were therefore employed to simulate the oral profiles of the compounds. For compounds with reasonably good solubility and permeability, an area under the concentration-time curve for the simulated oral profile that far exceeded the observed would indicate some kind of loss in the intestine. PBPK simulations applied to compound A showed substantial loss of the compound in the gastrointestinal tract in humans but not in rats. This accounted for the lower bioavailability of the

  15. Temporal Texture Profile and Identification of Glass Transition Temperature as an Instrumental Predictor of Stickiness in a Caramel System.

    Science.gov (United States)

    Mayhew, Emily J; Schmidt, Shelly J; Schlich, Pascal; Lee, Soo-Yeun

    2017-09-01

    Stickiness is an important texture attribute in many food systems, but its meaning can vary by person, product, and throughout mastication. This variability and complexity makes it difficult to devise analytical tests that accurately and consistently predict sensory stickiness. Glass transition temperature (T g ) is a promising candidate for texture prediction. Our objective is to elucidate the temporal profile of stickiness in order to probe the relationship between T g and dynamic stickiness perception. Nine caramel samples with diverse texture and thermal profiles were produced for sensory testing and differential scanning calorimetry. Sixteen trained panelists generated stickiness-relevant terms to be used in a subsequent temporal dominance of sensation (TDS) test with the same panelists. Following the TDS study, these panelists also rated samples for overall tactile and oral stickiness. Stickiness ratings were then correlated to TDS dominance parameters across the full evaluation period and within the first, middle, and final thirds of the evaluation period. Samples with temporal texture profiles dominated by tacky, stringy, and enveloping attributes consistently received the highest stickiness scores, although the correlation strength varied by time period. T g was found to correlate well with trained panelist and consumer ratings of oral (R 2 trained = 0.85; R 2 consumer = 0.96) and tactile (R 2 trained = 0.78; R 2 consumer = 0.79) stickiness intensity, and stickiness intensity ratings decreased with T g of completely amorphous samples. Further, glassy samples followed a different texture trajectory (brittle-cohesive-toothpacking) than rubbery samples (deformable-tacky-enveloping). These results illuminate the dynamic perception of stickiness and support the potential of T g to predict both stickiness intensity and texture trajectory in caramel systems. © 2017 Institute of Food Technologists®.

  16. Mexican Americans, Chicanos, and Others: Ethnic Self-Identification and Selected Social Attributes of Rural Texas Youth

    Science.gov (United States)

    Miller, Michael V.

    1976-01-01

    Following the thesis that variations in ethnic identification reflect social differentiation within the Mexican American population, this paper sought to: (1) delineate primary terms for ethnic self-identification among youths residing in a relatively homogeneous area of South Texas, (2) test the generalizability of past findings, and (3) examine…

  17. Identification and profiling of conserved and novel microRNAs in Laodelphax striatellus in response to rice black-streaked dwarf virus (RBSDV infection

    Directory of Open Access Journals (Sweden)

    Jun-Min Li

    2015-03-01

    Full Text Available MicroRNAs (miRNAs are small non-coding endogenous RNA molecules that play important roles in various biological processes. This study examined microRNA profiles of Laodelphax striatellus using the small RNA libraries derived from virus free (VF and rice black-streaked dwarf virus (RBSDV infected (RB insects. A total of 59 mature miRNAs (46 miRNA families were identified as conserved insect miRNAs in both VF and RB libraries. Among these conserved miRNAs, 24 were derived from the two arms of 12 miRNA precursors. Nine conserved L. striatellus miRNAs were up-regulated and 12 were down-regulated in response to RBSDV infection. In addition, a total of 20 potential novel miRNA candidates were predicted in the VF and RB libraries. The miRNA transcriptome profiles and the identification of L. striatellus miRNAs differentially expressed in response to RBSDV infection will contribute to future studies to elucidate the complex miRNA-mediated regulatory network activated by pathogen challenge in insect vectors.

  18. Signal transduction profile of chemical sensitisers in dendritic cells: An endpoint to be included in a cell-based in vitro alternative approach to hazard identification?

    International Nuclear Information System (INIS)

    Neves, Bruno Miguel; Goncalo, Margarida; Figueiredo, Americo; Duarte, Carlos B.; Lopes, Maria Celeste; Cruz, Maria Teresa

    2011-01-01

    The development of non-animal testing methods for the assessment of skin sensitisation potential is an urgent challenge within the framework of existing and forthcoming legislation. Efforts have been made to replace current animal tests, but so far no alternative methods have been developed. It is widely recognised that alternatives to animal testing cannot be accomplished with a single approach, but rather will require the integration of results obtained from different in vitro and in silico assays. The argument subjacent to the development of in vitro dendritic cell (DC)-based assays is that sensitiser-induced changes in the DC phenotype can be differentiated from those induced by irritants. This assumption is derived from the unique capacity of DC to convert environmental signals encountered at the skin into a receptor expression pattern (MHC class II molecules, co-stimulatory molecules, chemokine receptors) and a soluble mediator release profile that will stimulate T lymphocytes. Since signal transduction cascades precede changes in surface marker expression and cytokine/chemokine secretion, these phenotypic modifications are a consequence of a signal transduction profile that is specifically triggered by sensitisers and not by irritants. A limited number of studies have addressed this subject and the present review attempts to summarise and highlight all of the signalling pathways modulated by skin sensitisers and irritants. Furthermore, we conclude this review by focusing on the most promising strategies suitable for inclusion into a cell-based in vitro alternative approach to hazard identification.

  19. Identification of non-streptococcal organisms from human dental plaque grown on the Streptococcus-selective medium mitis-salivarius agar.

    Science.gov (United States)

    Kim, Yeon-Hee; Lee, Si Young

    2015-02-01

    Mitis-salivarius (MS) agar has been used widely in microbial epidemiological studies because oral viridans streptococci can be selectively grown on this medium. Even though the previous findings reported the limited selecting power of MS agar for streptococcus strains, the identities of non-streptococcal strains from human oral samples which can grow on this medium are not clear yet. In this study, we identified non-streptococcal organisms grown on MS agar plates by polymerase chain reaction (PCR) amplification and sequencing of the 16S ribosomal RNA (rRNA) gene. Eighty bacterial colonies on MS plates were isolated from plaque samples, and bacterial identification was achieved with the rapid ID 32 Strep system and mini API reader. The bacterial colonies identified as non-streptococci by the API system were selected for further identification. The 16S rRNA gene was amplified by PCR and verified using DNA sequencing analysis for identification. Sequences were compared with those of reference organisms in the genome database of the National Center for Biotechnology Information using the Basic Local Alignment Search Tool (BLAST). Among the 11 isolated non-streptococcal strains on MS plates, 3 strains were identified as Actinomyces naeslundii, 7 strains were identified as Actinomyces oris and 1 strain were identified as Actinomyces sp. using Blastn. In this study, we showed that some oral Actinomyces species can grow on Streptococcus-selective MS agar plates. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Identification of Plasma Metabolomic Profiling for Diagnosis of Esophageal Squamous-Cell Carcinoma Using an UPLC/TOF/MS Platform

    Directory of Open Access Journals (Sweden)

    Lihong Yin

    2013-04-01

    Full Text Available Epidemiological studies indicated that esophageal squamous-cell carcinoma (ESCC is still one of the most common causes of cancer incidence in the world. Searching for valuable markers including circulating endogenous metabolites associated with the risk of esophageal cancer, is extremely important A comparative metabolomics study was performed by using ultraperformance liquid chromatography-electrospray ionization-accurate mass time-of-flight mass spectrometry to analyze 53 pairs of plasma samples from ESCC patients and healthy controls recruited in Huaian, China. The result identified a metabolomic profiling of plasma including 25 upregulated metabolites and five downregulated metabolites, for early diagnosis of ESCC. With a database-based verification protocol, 11 molecules were identified, and six upregulated molecules of interest in ESCC were found to belong to phospholipids as follows: phosphatidylserine, phosphatidic acid, phosphatidyl choline, phosphatidylinositol, phosphatidyl ethanolamine, and sphinganine 1-phosphate. Clinical estimation of metabolic biomarkers through hierarchical cluster analysis in plasma samples from 17 ESCC patients and 29 healthy volunteers indicated that the present metabolite profile could distinguish ESCC patients from healthy individuals. The cluster of aberrant expression of these metabolites in ESCC indicates the critical role of phospholipid metabolism in the oncogenesis of ESCC and suggests its potential ability to assess the risk of ESCC development in addition to currently used risk factors.

  1. Selection, Identification and Optimization of the Growth Water Probiotic Consortium of Mangrove Ecosystems as Bioremediation and Biocontrol in Shrimp Ponds

    Directory of Open Access Journals (Sweden)

    Wilis Ari Setyati

    2015-01-01

    Full Text Available Shrimp aquaculture is an activity that potentially generates organic waste. The accumulation of organic matter is becoming one of the main factors causing the emergence of disease. Problem-solving approach that is most effective is through bioremediation. The aims of this study were to select, identify and cultivate bacteria from mangrove sediments from Cilacap, Rembang and Banyuwangi which potentially as probiotic consortium of bioremediation activity and biocontrol. The results showed that total of 45 isolates (proteolytic, 35 isolates (amylolytic, 35 isolates (lipolytic, and 18 isolates (cellulolytic. There were 59 bacterial isolates had antibacterial activity of vibrio (V. harveyi, V. alginolyticus, V. vulnificus and V. anguilarum. Based on the identification of 16 S-rRNA genes, 4 isolates showed that the C2 isolate was identified as Bacillus subtilis, C11 isolate was identified as Bacillus firmus, C13 and C14 isolates were identified as B. Flexus. This study concluded that cultivation of Bacillus subtilis C2 optimum at 2% molase and yeast extract 0.5% at pH 8 and 30 0C. Bacillus firmus C11 optimum at 2% molase and yeast extract 0.5% at pH 8 and 30 0C. Bacillus flexus C13 optimum at 2% glucose and yeast extract 0.5% at pH 8 and 30 0C. Bacillus flexus C14 optimum at 4% molase and yeast extract 0.25% at pH 8 and 30 0C. The result of culture applications of 4 isolates showed an effect of increasing shrimp weight by 141, 9% compared by the control.Keywords: sediment, mangrove, bioremediation, biocontrol

  2. Screening and identification of phytotoxic volatile compounds in medicinal plants and characterizations of a selected compound, eucarvone.

    Science.gov (United States)

    Sunohara, Yukari; Baba, Yohei; Matsuyama, Shigeru; Fujimura, Kaori; Matsumoto, Hiroshi

    2015-07-01

    Screening and identification of phytotoxic volatile compounds were performed using 71 medicinal plant species to find new natural compounds, and the characterization of the promising compound was investigated to understand the mode of action. The volatile compounds from Asarum sieboldii Miq. showed the strongest inhibitory effect on the hypocotyl growth of lettuce seedlings (Lactuca sativa L.cv. Great Lakes 366), followed by those from Schizonepeta tenuifolia Briquet and Zanthoxylum piperitum (L.) DC.. Gas chromatography-mass spectrometry (GC/MS) identified four volatile compounds, α-pinene (2,6,6-trimethylbicyclo[3.1.1]hept-2-ene), β-pinene (6,6-dimethyl-2-methylenebicyclo[3.1.1]heptane), 3-carene (3,7,7-trimethylbicyclo[4.1.0]hept-3-ene), and eucarvone (2,6,6-trimethy-2,4-cycloheptadien-1-one), from A. sieboldii, and three volatile compounds, limonene (1-methyl-4-(1-methylethenyl)-cyclohexene), menthone (5-methyl-2-(propan-2-yl)cyclohexan-1-one), and pulegone (5-methyl-2-propan-2-ylidenecyclohexan-1-one), from S. tenuifolia. Among these volatile compounds, eucarvone, menthone, and pulegone exhibited strong inhibitory effects on both the root and shoot growth of lettuce seedlings. Eucarvone-induced growth inhibition was species-selective. Cell death, the generation of reactive oxygen species (ROS), and lipid peroxidation were induced in susceptible finger millet seedlings by eucarvone treatment, whereas this compound (≤158 μM) did not cause the increase of lipid peroxidation and ROS production in tolerant maize. The results of the present study show that eucarvone can have strong phytotoxic activity, which may be due to ROS overproduction and subsequent oxidative damage in finger millet seedlings.

  3. Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence.

    Directory of Open Access Journals (Sweden)

    Juliana Bernardes

    2016-07-01

    Full Text Available Traditional protein annotation methods describe known domains with probabilistic models representing consensus among homologous domain sequences. However, when relevant signals become too weak to be identified by a global consensus, attempts for annotation fail. Here we address the fundamental question of domain identification for highly divergent proteins. By using high performance computing, we demonstrate that the limits of state-of-the-art annotation methods can be bypassed. We design a new strategy based on the observation that many structural and functional protein constraints are not globally conserved through all species but might be locally conserved in separate clades. We propose a novel exploitation of the large amount of data available: 1. for each known protein domain, several probabilistic clade-centered models are constructed from a large and differentiated panel of homologous sequences, 2. a decision-making protocol combines outcomes obtained from multiple models, 3. a multi-criteria optimization algorithm finds the most likely protein architecture. The method is evaluated for domain and architecture prediction over several datasets and statistical testing hypotheses. Its performance is compared against HMMScan and HHblits, two widely used search methods based on sequence-profile and profile-profile comparison. Due to their closeness to actual protein sequences, clade-centered models are shown to be more specific and functionally predictive than the broadly used consensus models. Based on them, we improved annotation of Plasmodium falciparum protein sequences on a scale not previously possible. We successfully predict at least one domain for 72% of P. falciparum proteins against 63% achieved previously, corresponding to 30% of improvement over the total number of Pfam domain predictions on the whole genome. The method is applicable to any genome and opens new avenues to tackle evolutionary questions such as the reconstruction of

  4. Rain cell-based identification of the vertical profile of reflectivity as observed by weather radar and its use for precipitation uncertainty estimation

    Science.gov (United States)

    Hazenberg, P.; Torfs, P. J. J. F.; Leijnse, H.; Uijlenhoet, R.

    2012-04-01

    The wide scale implementation of weather radar systems over the last couple of decades has increased our understanding concerning spatio-temporal precipitation dynamics. However, the quantitative estimation of precipitation by these devices is affected by many sources of error. A very dominant source of error results from vertical variations in the hydrometeor size distribution known as the vertical profile of reflectivity (VPR). Since the height of the measurement as well as the beam volume increases with distance from the radar, for stratiform precipitation this results in a serious underestimation (overestimation) of the surface reflectivity while sampling within the snow (bright band) region. This research presents a precipitation cell-based implementation to correct volumetric weather radar measurements for VPR effects. Using the properties of a flipping carpenter square, a contour-based identification technique was developed, which is able to identify and track precipitation cells in real time, distinguishing between convective, stratiform and undefined precipitation. For the latter two types of systems, for each individual cell, a physically plausible vertical profile of reflectivity is estimated using a Monte Carlo optimization method. Since it can be expected that the VPR will vary within a given precipitation cell, a method was developed to take the uncertainty of the VPR estimate into account. As a result, we are able to estimate the amount of precipitation uncertainty as observed by weather radar due to VPR for a given precipitation type and storm cell. We demonstrate the possibilities of this technique for a number of winter precipitation systems observed within the Belgian Ardennes. For these systems, in general, the precipitation uncertainty estimate due to vertical reflectivity profile variations varies between 10-40%.

  5. Exploring the physicochemical profile and the binding patterns of selected novel anticancer Himalayan plant derived active compounds with macromolecular targets

    Directory of Open Access Journals (Sweden)

    Arun Bahadur Gurung

    Full Text Available Plants are vital source of compounds offering plethora of therapeutic effects against various ailments without much side effects. Due to wide spread prevalence and drug resistance in cancer; there is an urgent need for discovery of new anti-cancer drugs. In the present study, selected novel anti-cancer plants derived compounds (cmpd1 to cmpd15 from Himalayan region were docked with defined molecular targets that regulate cell proliferation and apoptosis. The binding energies of best docked compounds ranged between −8.0 kcal/mol and −11.71 kcal/mol. Further analysis revealed critical hydrogen bonds and hydrophobic interactions between compounds and targets. The best docked compounds viz., cmpd15 against cyclin-dependent kinase-2 (CDK-2, cmpd8 against CDK-6 and cmpd9 against Topoisomerase I and II showed higher binding affinities than the native co-crystal ligands. The root mean square deviation (RMSD and potential energy plot clearly indicates the stability of the complexes during 20 ns molecular dynamics (MD simulation. The Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA binding energy analysis revealed Van der Waals energy component which is the principal stabilizing energy for their interactions except CDK-2/cmpd15 complex. The polar solvation energy did not have favorable contribution to their stabilization. The binding energy decomposition analysis revealed per residue contribution for each docked complexes. Physicochemical profile studies showed that majority of the compounds conform to Lipinski's rule of five (ROF having low to high blood brain barrier (BBB penetration, human intestinal absorption, plasma binding protein inhibition and P glycoprotein inhibition. Keywords: ADMET, Anticancer, MM/PBSA, Molecular docking, Molecular dynamics simulation and plant derived compounds

  6. Identification of sixteen peptides reflecting heat and/or storage induced processes by profiling of commercial milk samples.

    Science.gov (United States)

    Ebner, Jennifer; Baum, Florian; Pischetsrieder, Monika

    2016-09-16

    Peptide profiles of different drinking milk samples were examined to study how the peptide fingerprint of milk reflects processing conditions. The combination of a simple and fast method for peptide extraction using stage tips and MALDI-TOF-MS enabled the fast and easy generation and relative quantification of peptide fingerprints for high-temperature short-time (HTST), extended shelf life (ESL) and ultra-high temperature (UHT) milk of the same dairies. The relative quantity of 16 peptides changed as a function of increasing heat load. Additional heating experiments showed that among those, the intensity of peptide β-casein 196-209 (m/z 1460.9Da) was most heavily influenced by heat treatment indicating a putative marker peptide for milk processing conditions. Storage experiments with HTST- and UHT milk revealed that the differences between different types of milk samples were not only caused by the heating process. Relevant was also the proteolytic activity of enzymes during storage, which were differently influenced by the heat treatment. These results indicate that the peptide profile may be suitable to monitor processing as well as storage conditions of milk. In the present study, peptide profiling of different types of milk was carried out by MALDI-TOF-MS after stage-tip extraction and relative quantification using an internal reference peptide. Although MALDI-TOF-MS covers only part of the peptidome, the method is easy and quick and is, therefore, suited for routine analysis to address several aspects of food authenticity. Using this method, 16 native peptides were detected in milk that could be modulated by different industrial processes. Subsequent heating and storage experiments with pasteurized and UHT milk confirmed that these peptides are indeed related to the production or storage conditions of the respective products. Furthermore, the heating experiments revealed one peptide, namely the β-casein-derived sequence β-casein 196-209, which underwent

  7. Identification of wild soybean (Glycine soja) TIFY family genes and their expression profiling analysis under bicarbonate stress.

    Science.gov (United States)

    Zhu, Dan; Bai, Xi; Luo, Xiao; Chen, Qin; Cai, Hua; Ji, Wei; Zhu, Yanming

    2013-02-01

    Wild soybean (Glycine soja L. G07256) exhibits a greater adaptability to soil bicarbonate stress than cultivated soybean, and recent discoveries show that TIFY family genes are involved in the response to several abiotic stresses. A genomic and transcriptomic analysis of all TIFY genes in G. soja, compared with G. max, will provide insight into the function of this gene family in plant bicarbonate stress response. This article identified and characterized 34 TIFY genes in G. soja. Sequence analyses indicated that most GsTIFY proteins had two conserved domains: TIFY and Jas. Phylogenetic analyses suggested that these GsTIFY genes could be classified into two groups. A clustering analysis of all GsTIFY transcript expression profiles from bicarbonate stress treated G. soja showed that there were five different transcript patterns in leaves and six different transcript patterns in roots when the GsTIFY family responds to bicarbonate stress. Moreover, the expression level changes of all TIFY genes in cultivated soybean, treated with bicarbonate stress, were also verified. The expression comparison analysis of TIFYs between wild and cultivated soybeans confirmed that, different from the cultivated soybean, GsTIFY (10a, 10b, 10c, 10d, 10e, 10f, 11a, and 11b) were dramatically up-regulated at the early stage of stress, while GsTIFY 1c and 2b were significantly up-regulated at the later period of stress. The frequently stress responsive and diverse expression profiles of the GsTIFY gene family suggests that this family may play important roles in plant environmental stress responses and adaptation.

  8. Genome-wide identification and expression profiling of serine proteases and homologs in the diamondback moth, Plutella xylostella (L.).

    Science.gov (United States)

    Lin, Hailan; Xia, Xiaofeng; Yu, Liying; Vasseur, Liette; Gurr, Geoff M; Yao, Fengluan; Yang, Guang; You, Minsheng

    2015-12-10

    Serine proteases (SPs) are crucial proteolytic enzymes responsible for digestion and other processes including signal transduction and immune responses in insects. Serine protease homologs (SPHs) lack catalytic activity but are involved in innate immunity. This study presents a genome-wide investigation of SPs and SPHs in the diamondback moth, Plutella xylostella (L.), a globally-distributed destructive pest of cruciferous crops. A total of 120 putative SPs and 101 putative SPHs were identified in the P. xylostella genome by bioinformatics analysis. Based on the features of trypsin, 38 SPs were putatively designated as trypsin genes. The distribution, transcription orientation, exon-intron structure and sequence alignments suggested that the majority of trypsin genes evolved from tandem duplications. Among the 221 SP/SPH genes, ten SP and three SPH genes with one or more clip domains were predicted and designated as PxCLIPs. Phylogenetic analysis of CLIPs in P. xylostella, two other Lepidoptera species (Bombyx mori and Manduca sexta), and two more distantly related insects (Drosophila melanogaster and Apis mellifera) showed that seven of the 13 PxCLIPs were clustered with homologs of the Lepidoptera rather than other species. Expression profiling of the P. xylostella SP and SPH genes in different developmental stages and tissues showed diverse expression patterns, suggesting high functional diversity with roles in digestion and development. This is the first genome-wide investigation on the SP and SPH genes in P. xylostella. The characterized features and profiled expression patterns of the P. xylostella SPs and SPHs suggest their involvement in digestion, development and immunity of this species. Our findings provide a foundation for further research on the functions of this gene family in P. xylostella, and a better understanding of its capacity to rapidly adapt to a wide range of environmental variables including host plants and insecticides.

  9. Napping-Ultra Flash Profile as a Tool for Category Identification and Subsequent Model System Formulation of Caramel Corn Products.

    Science.gov (United States)

    Mayhew, Emily; Schmidt, Shelly; Lee, Soo-Yeun

    2016-07-01

    In a novel approach to formulation, the flash descriptive profiling technique Napping-Ultra Flash Profile (Napping-UFP) was used to characterize a wide range of commercial caramel corn products. The objectives were to identify product categories, develop model systems based on product categories, and correlate analytical parameters with sensory terms generated through the Napping-UFP exercise. In one 2 h session, 12 panelists participated in 4 Napping-UFP exercises, describing and grouping, on a 43×56 cm paper sheet, 12 commercial caramel corn samples by degree of similarity, globally and in terms of aroma-by-mouth, texture, and taste. The coordinates of each sample's placement on the paper sheet and descriptive terms generated by the panelists were used to conduct Multiple Factor Analysis (MFA) and hierarchical clustering of the samples. Strong trends in the clustering of samples across the 4 Napping-UFP exercises resulted in the determination of 3 overarching types of commercial caramel corn: "small-scale dark" (typified by burnt, rich caramel corn), "large-scale light" (typified by light and buttery caramel corn), and "large-scale dark" (typified by sweet and molasses-like caramel corn). Representative samples that best exemplified the properties of each category were used as guides in the formulation of 3 model systems that represent the spread of commercial caramel corn products. Analytical testing of the commercial products, including aw measurement, moisture content determination, and thermal characterization via differential scanning calorimetry, were conducted and results related to sensory descriptors using Spearman's correlation. © 2016 Institute of Food Technologists®

  10. Identification and in Vivo Evaluation of Liver X Receptor β-Selective Agonists for the Potential Treatment of Alzheimer’s Disease

    Energy Technology Data Exchange (ETDEWEB)

    Stachel, Shawn J.; Zerbinatti, Celina; Rudd, Michael T.; Cosden, Mali; Suon, Sokreine; Nanda, Kausik K.; Wessner, Keith; DiMuzio, Jillian; Maxwell, Jill; Wu, Zhenhua; Uslaner, Jason M.; Michener, Maria S.; Szczerba, Peter; Brnardic, Edward; Rada, Vanessa; Kim, Yuntae; Meissner, Robert; Wuelfing, Peter; Yuan, Yang; Ballard, Jeanine; Holahan, Marie; Klein, Daniel J.; Lu, Jun; Fradera, Xavier; Parthasarathy, Gopal; Uebele, Victor N.; Chen, Zhongguo; Li, Yingjie; Li, Jian; Cooke, Andrew J.; Bennett, D. Jonathan; Bilodeau, Mark T.; Renger, John (Merck); (WuXi App Tec)

    2016-04-14

    Herein, we describe the development of a functionally selective liver X receptor β (LXRβ) agonist series optimized for Emax selectivity, solubility, and physical properties to allow efficacy and safety studies in vivo. Compound 9 showed central pharmacodynamic effects in rodent models, evidenced by statistically significant increases in apolipoprotein E (apoE) and ATP-binding cassette transporter levels in the brain, along with a greatly improved peripheral lipid safety profile when compared to those of full dual agonists. These findings were replicated by subchronic dosing studies in non-human primates, where cerebrospinal fluid levels of apoE and amyloid-β peptides were increased concomitantly with an improved peripheral lipid profile relative to that of nonselective compounds. These results suggest that optimization of LXR agonists for Emax selectivity may have the potential to circumvent the adverse lipid-related effects of hepatic LXR activity.

  11. Representation of a Method for Identification of the Best Safe Contractors by Fuzzy Input Efficiency Profiling and AHP

    Directory of Open Access Journals (Sweden)

    F. Taheri

    2011-04-01

    Full Text Available Background and Aims Health, Safety and Environment (HSE performance measurement of the contractors and identification of the best ones can make a perception of the past changes in their HSE performance. Consequently, this may motivate them and provide an opportunity to improve their quality of services. The aim of this study is to rank the contractor-companies of one of the Iranian steel manufacturing companies considering their safety behavior and also to determine the best combination of contractors-companies.   Methods safety behavior sampling method used to determine the status of unsafe acts. The fuzzy efficiency numbers of each input were ranked by Chen & Klein method. To obtain a final ranking AHP was applied. The obtained rankings by FIEP-AHP were compared to the ranking of DEA.   Results Results indicated that the most frequent unsafe behaviors were related to not-using or miss-using the PPE, using broken tools and inappropriate working condition respectively. A significant relationship between experience, education and age with safety behaviors was obtained (p<0.05. Results showed that companies’ number 2 and 6 had respectively the best and worst ranks.   Conclusion Because FIEP increases the power of recognition especially when the number of DMUs is lower than inputs and outputs, it can be suggested as an appropriate model for determining the best contractor companies.

  12. Variations in fatty acid composition, glucosinolate profile and some phytochemical contents in selected oil seed rape (Brassica napus L. cultivars

    Directory of Open Access Journals (Sweden)

    Amin Mohamed, Amal

    2010-06-01

    Full Text Available Rapeseed (Brassica napus L. is now the third most important source of edible oil in the world after soybean and palm oil. In this study seeds of five different rapeseed cultivars namely; pactol, silvo, topas, serw 4 and serw 6 were evaluated for their fatty acid composition, glucosinolate profile, amino acids, total tocopherols and phenolic content. Among all cultivars significant variability in fatty acids were observed. The oleic acid (C18:1 ranged from 56.31% to 58.67%, linoleic acid (C18:2 from 10.52% to 13.74%, α-linolenic acid (C18:3 from 8.83% to 10.32% and erucic acid (22:1 from 0.15% to 0.91%. The glucosinolate profile of rapeseed was also separated and identified using high-performance liquid chromatography. Small variations in the glucosinolate profile were observed among all tested cultivars; however, progoitrin and gluconapin were the major glucosinolate found. Additionally, silvo cultivar showed the highest total glucosinolate c ontents (5.97 μmol/g dw. Generally, the contents of aspartic, glutamic, arginine and leucine were high, while the contents of tyrosine and isoleucine were low among all cultivars. For total tocopherols, the results indicated that both serw 6 and pactol cultivars had the highest total tocopherol contents (138.3 and 102.8 mg/100 g oil, respectively. Total phenolic contents varied from 28.0 to 35.4 mg/g dw. The highest total phenolic content was found in topas while the lowest value was detected in serw 6. These parameters; fatty acid contents, glucosinolate profile and amino acids together with total tocopherols and phenolic contents, could be taken into consideration by oilseed rape breeders as selection criteria for developing genotypes with modified seed quality traits in Brassica napus L.La colza (Brassica napus L. es hoy en día el tercer cultivo más importante de aceites comestibles en el mundo tras el aceite de soja y de palma. En este estudio semillas de cinco cultivos diferentes de colza

  13. Krebs cycle metabolite profiling for identification and stratification of pheochromocytomas/paragangliomas due to succinate dehydrogenase deficiency.

    Science.gov (United States)

    Richter, Susan; Peitzsch, Mirko; Rapizzi, Elena; Lenders, Jacques W; Qin, Nan; de Cubas, Aguirre A; Schiavi, Francesca; Rao, Jyotsna U; Beuschlein, Felix; Quinkler, Marcus; Timmers, Henri J; Opocher, Giuseppe; Mannelli, Massimo; Pacak, Karel; Robledo, Mercedes; Eisenhofer, Graeme

    2014-10-01

    Mutations of succinate dehydrogenase A/B/C/D genes (SDHx) increase susceptibility to development of pheochromocytomas and paragangliomas (PPGLs), with particularly high rates of malignancy associated with SDHB mutations. We assessed whether altered succinate dehydrogenase product-precursor relationships, manifested by differences in tumor ratios of succinate to fumarate or other metabolites, might aid in identifying and stratifying patients with SDHx mutations. PPGL tumor specimens from 233 patients, including 45 with SDHx mutations, were provided from eight tertiary referral centers for mass spectrometric analyses of Krebs cycle metabolites. Diagnostic performance of the succinate:fumarate ratio for identification of pathogenic SDHx mutations. SDH-deficient PPGLs were characterized by 25-fold higher succinate and 80% lower fumarate, cis-aconitate, and isocitrate tissue levels than PPGLs without SDHx mutations. Receiver-operating characteristic curves for use of ratios of succinate to fumarate or to cis-aconitate and isocitrate to identify SDHx mutations indicated areas under curves of 0.94 to 0.96; an optimal cut-off of 97.7 for the succinate:fumarate ratio provided a diagnostic sensitivity of 93% at a specificity of 97% to identify SDHX-mutated PPGLs. Succinate:fumarate ratios were higher in both SDHB-mutated and metastatic tumors than in those due to SDHD/C mutations or without metastases. Mass spectrometric-based measurements of ratios of succinate:fumarate and other metabolites in PPGLs offer a useful method to identify patients for testing of SDHx mutations, with additional utility to quantitatively assess functionality of mutations and metabolic factors responsible for malignant risk.

  14. Identification of the full-length β-actin sequence and expression profiles in the tree shrew (Tupaia belangeri).

    Science.gov (United States)

    Zheng, Yu; Yun, Chenxia; Wang, Qihui; Smith, Wanli W; Leng, Jing

    2015-02-01

    The tree shrew (Tupaia belangeri) diverges from the primate order (Primates) and is classified as a separate taxonomic group of mammals - Scandentia. It has been suggested that the tree shrew can be used as an animal model for studying human diseases; however, the genomic sequence of the tree shrew is largely unidentified. In the present study, we reported the full-length cDNA sequence of the housekeeping gene, β-actin, in the tree shrew. The amino acid sequence of β-actin in the tree shrew was compared to that of humans and other species; a simple phylogenetic relationship was discovered. Quantitative polymerase chain reaction (qPCR) and western blot analysis further demonstrated that the expression profiles of β-actin, as a general conservative housekeeping gene, in the tree shrew were similar to those in humans, although the expression levels varied among different types of tissue in the tree shrew. Our data provide evidence that the tree shrew has a close phylogenetic association with humans. These findings further enhance the potential that the tree shrew, as a species, may be used as an animal model for studying human disorders.

  15. NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children

    Science.gov (United States)

    Vignali, Marissa; Armour, Christopher D.; Chen, Jingyang; Morrison, Robert; Castle, John C.; Biery, Matthew C.; Bouzek, Heather; Moon, Wonjong; Babak, Tomas; Fried, Michal; Raymond, Christopher K.; Duffy, Patrick E.

    2011-01-01

    Malaria caused by Plasmodium falciparum results in approximately 1 million annual deaths worldwide, with young children and pregnant mothers at highest risk. Disease severity might be related to parasite virulence factors, but expression profiling studies of parasites to test this hypothesis have been hindered by extensive sequence variation in putative virulence genes and a preponderance of host RNA in clinical samples. We report here the application of RNA sequencing to clinical isolates of P. falciparum, using not-so-random (NSR) primers to successfully exclude human ribosomal RNA and globin transcripts and enrich for parasite transcripts. Using NSR-seq, we confirmed earlier microarray studies showing upregulation of a distinct subset of genes in parasites infecting pregnant women, including that encoding the well-established pregnancy malaria vaccine candidate var2csa. We also describe a subset of parasite transcripts that distinguished parasites infecting children from those infecting pregnant women and confirmed this observation using quantitative real-time PCR and mass spectrometry proteomic analyses. Based on their putative functional properties, we propose that these proteins could have a role in childhood malaria pathogenesis. Our study provides proof of principle that NSR-seq represents an approach that can be used to study clinical isolates of parasites causing severe malaria syndromes as well other blood-borne pathogens and blood-related diseases. PMID:21317536

  16. Gene Expression Profiling and Identification of Resistance Genes to Aspergillus flavus Infection in Peanut through EST and Microarray Strategies

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    Baozhu Guo

    2011-06-01

    Full Text Available Aspergillus flavus and A. parasiticus infect peanut seeds and produce aflatoxins, which are associated with various diseases in domestic animals and humans throughout the world. The most cost-effective strategy to minimize aflatoxin contamination involves the development of peanut cultivars that are resistant to fungal infection and/or aflatoxin production. To identify peanut Aspergillus-interactive and peanut Aspergillus-resistance genes, we carried out a large scale peanut Expressed Sequence Tag (EST project which we used to construct a peanut glass slide oligonucleotide microarray. The fabricated microarray represents over 40% of the protein coding genes in the peanut genome. For expression profiling, resistant and susceptible peanut cultivars were infected with a mixture of Aspergillus flavus and parasiticus spores. The subsequent microarray analysis identified 62 genes in resistant cultivars that were up-expressed in response to Aspergillus infection. In addition, we identified 22 putative Aspergillus-resistance genes that were constitutively up-expressed in the resistant cultivar in comparison to the susceptible cultivar. Some of these genes were homologous to peanut, corn, and soybean genes that were previously shown to confer resistance to fungal infection. This study is a first step towards a comprehensive genome-scale platform for developing Aspergillus-resistant peanut cultivars through targeted marker-assisted breeding and genetic engineering.

  17. NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children.

    Science.gov (United States)

    Vignali, Marissa; Armour, Christopher D; Chen, Jingyang; Morrison, Robert; Castle, John C; Biery, Matthew C; Bouzek, Heather; Moon, Wonjong; Babak, Tomas; Fried, Michal; Raymond, Christopher K; Duffy, Patrick E

    2011-03-01

    Malaria caused by Plasmodium falciparum results in approximately 1 million annual deaths worldwide, with young children and pregnant mothers at highest risk. Disease severity might be related to parasite virulence factors, but expression profiling studies of parasites to test this hypothesis have been hindered by extensive sequence variation in putative virulence genes and a preponderance of host RNA in clinical samples. We report here the application of RNA sequencing to clinical isolates of P. falciparum, using not-so-random (NSR) primers to successfully exclude human ribosomal RNA and globin transcripts and enrich for parasite transcripts. Using NSR-seq, we confirmed earlier microarray studies showing upregulation of a distinct subset of genes in parasites infecting pregnant women, including that encoding the well-established pregnancy malaria vaccine candidate var2csa. We also describe a subset of parasite transcripts that distinguished parasites infecting children from those infecting pregnant women and confirmed this observation using quantitative real-time PCR and mass spectrometry proteomic analyses. Based on their putative functional properties, we propose that these proteins could have a role in childhood malaria pathogenesis. Our study provides proof of principle that NSR-seq represents an approach that can be used to study clinical isolates of parasites causing severe malaria syndromes as well other blood-borne pathogens and blood-related diseases.

  18. Comprehensive profiling and marker identification in non-volatile citrus oil residues by mass spectrometry and nuclear magnetic resonance.

    Science.gov (United States)

    Marti, Guillaume; Boccard, Julien; Mehl, Florence; Debrus, Benjamin; Marcourt, Laurence; Merle, Philippe; Delort, Estelle; Baroux, Lucie; Sommer, Horst; Rudaz, Serge; Wolfender, Jean-Luc

    2014-05-01

    The detailed characterization of cold-pressed lemon oils (CPLOs) is of great importance for the flavor and fragrance (F&F) industry. Since a control of authenticity by standard analytical techniques can be bypassed using elaborated adulterated oils to pretend a higher quality, a combination of advanced orthogonal methods has been developed. The present study describes a combined metabolomic approach based on UHPLC-TOF-MS profiling and (1)H NMR fingerprinting to highlight metabolite differences on a set of representative samples used in the F&F industry. A new protocol was set up and adapted to the use of CPLO residues. Multivariate analysis based on both fingerprinting methods showed significant chemical variations between Argentinian and Italian samples. Discriminating markers identified in mixtures belong to furocoumarins, flavonoids, terpenoids and fatty acids. Quantitative NMR revealed low citropten and high bergamottin content in Italian samples. The developed metabolomic approach applied to CPLO residues gives some new perspectives for authenticity assessment. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Identification and Expression Profiling of the Auxin Response Factors in Capsicum annuum L. under Abiotic Stress and Hormone Treatments

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    Chenliang Yu

    2017-12-01

    Full Text Available Auxin response factors (ARFs play important roles in regulating plant growth and development and response to environmental stress. An exhaustive analysis of the CaARF family was performed using the latest publicly available genome for pepper (Capsicum annuum L.. In total, 22 non-redundant CaARF gene family members in six classes were analyzed, including chromosome locations, gene structures, conserved motifs of proteins, phylogenetic relationships and Subcellular localization. Phylogenetic analysis of the ARFs from pepper (Capsicum annuum L., tomato (Solanum lycopersicum L., Arabidopsis and rice (Oryza sativa L. revealed both similarity and divergence between the four ARF families, and aided in predicting biological functions of the CaARFs. Furthermore, expression profiling of CaARFs was obtained in various organs and tissues using quantitative real-time RT-PCR (qRT-PCR. Expression analysis of these genes was also conducted with various hormones and abiotic treatments using qRT-PCR. Most CaARF genes were regulated by exogenous hormone treatments at the transcriptional level, and many CaARF genes were altered by abiotic stress. Systematic analysis of CaARF genes is imperative to elucidate the roles of CaARF family members in mediating auxin signaling in the adaptation of pepper to a challenging environment.

  20. Integrated identification, qualification and quantification strategy for pharmacokinetic profile study of Guizhi Fuling capsule in healthy volunteers.

    Science.gov (United States)

    Zhong, Yun-Xi; Jin, Xiao-Liang; Gu, Shi-Yin; Peng, Ying; Zhang, Ke-Rong; Ou-Yang, Bing-Chen; Wang, Yu; Xiao, Wei; Wang, Zhen-Zhong; Aa, Ji-Ye; Wang, Guang-Ji; Sun, Jian-Guo

    2016-08-16

    Guizhi Fuling capsule (GZFL), a traditional Chinese medicine formulation, is widely used in China to relieve pain from dysmenorrhea and is now in a Phase II clinical trial in the USA. Due to the low exposure of the five main medicative ingredients (amygdalin, cinnamic acid, gallic acid, paeoniflorin and paeonol) of GZFL in human, a strategy was built to qualitatively and quantitatively identify the possible metabolites of GZFL and to describe the pharmacokinetic profiles of GZFL in human. In this strategy, LC-Q-TOF/MS was used to identify and structurally elucidate the possible metabolites of GZFL in vivo; and a time-based metabolite-confirming step (TBMCs) was used to confirm uncertain metabolites. The simultaneously quantitation results by LC-MS/MS showed low exposure of the five medicative ingredients. According to the strategy we built, a total of 36 metabolites were found and structurally elucidated. The simultaneously semi-quantitative analysis by LC-MS/MS showed that obvious time-concentration curves could be established for 12 of the metabolites, and most of them showed a relatively higher exposure. This study provides a better understanding of the metabolic processes of GZFL in human.

  1. Molecular cloning, sequence identification and expression profile of domestic guinea pig (Cavia porcellus UGT1A1 gene

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    Yang Deming

    2016-01-01

    Full Text Available Domestic guinea pig is a model animal for human disease research. Uridine diphosphate glucuronosyltransferase 1 family, polypeptide A1 (UGT1A1 is an important human disease-related gene. In this study, the complete coding sequence of domestic guinea pig gene UGT1A1 was amplified by reverse transcription-polymerase chain reaction. The open reading frame of the domestic guinea pig UGT1A1 gene is 1602 bp in length and was found to encode a protein of 533 amino acids. Sequence analysis revealed that the UGT1A1 protein of domestic guinea pig shared high homology with the UGT1A1 proteins of degu (84%, damara mole-rat (84%, human (80%, northern white-cheeked gibbon (80%, Colobus angolensis palliatus (80% and golden snub-nosed monkey (79%. This gene contains five exons and four introns, as revealed by the computer-assisted analysis. The results also showed that the domestic guinea pig UGT1A1 gene had a close genetic relationship with the UGT1A1 gene of degu. The prediction of transmembrane helices showed that domestic guinea pig UGT1A1 might be a transmembrane protein. Expression profile analysis indicated that the domestic guinea pig UGT1A1 gene was differentially expressed in detected domestic guinea pig tissues. Our experiment laid a primary foundation for using the domestic guinea pig as a model animal to study the UGT1A1-related human diseases.

  2. Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs.

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    Md Mehedi Hasan

    Full Text Available Prokaryotic proteins are regulated by pupylation, a type of post-translational modification that contributes to cellular function in bacterial organisms. In pupylation process, the prokaryotic ubiquitin-like protein (Pup tagging is functionally analogous to ubiquitination in order to tag target proteins for proteasomal degradation. To date, several experimental methods have been developed to identify pupylated proteins and their pupylation sites, but these experimental methods are generally laborious and costly. Therefore, computational methods that can accurately predict potential pupylation sites based on protein sequence information are highly desirable. In this paper, a novel predictor termed as pbPUP has been developed for accurate prediction of pupylation sites. In particular, a sophisticated sequence encoding scheme [i.e. the profile-based composition of k-spaced amino acid pairs (pbCKSAAP] is used to represent the sequence patterns and evolutionary information of the sequence fragments surrounding pupylation sites. Then, a Support Vector Machine (SVM classifier is trained using the pbCKSAAP encoding scheme. The final pbPUP predictor achieves an AUC value of 0.849 in 10-fold cross-validation tests and outperforms other existing predictors on a comprehensive independent test dataset. The proposed method is anticipated to be a helpful computational resource for the prediction of pupylation sites. The web server and curated datasets in this study are freely available at http://protein.cau.edu.cn/pbPUP/.

  3. Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile.

    Science.gov (United States)

    Qi, Xiao-Hua; Xu, Xue-Wen; Lin, Xiao-Jian; Zhang, Wen-Jie; Chen, Xue-Hao

    2012-03-01

    High-throughput tag-sequencing (Tag-seq) analysis based on the Solexa Genome Analyzer platform was applied to analyze the gene expression profiling of cucumber plant at 5 time points over a 24h period of waterlogging treatment. Approximately 5.8 million total clean sequence tags per library were obtained with 143013 distinct clean tag sequences. Approximately 23.69%-29.61% of the distinct clean tags were mapped unambiguously to the unigene database, and 53.78%-60.66% of the distinct clean tags were mapped to the cucumber genome database. Analysis of the differentially expressed genes revealed that most of the genes were down-regulated in the waterlogging stages, and the differentially expressed genes mainly linked to carbon metabolism, photosynthesis, reactive oxygen species generation/scavenging, and hormone synthesis/signaling. Finally, quantitative real-time polymerase chain reaction using nine genes independently verified the tag-mapped results. This present study reveals the comprehensive mechanisms of waterlogging-responsive transcription in cucumber. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. Identification of pathogenic genes related to rheumatoid arthritis through integrated analysis of DNA methylation and gene expression profiling.

    Science.gov (United States)

    Zhang, Lei; Ma, Shiyun; Wang, Huailiang; Su, Hang; Su, Ke; Li, Longjie

    2017-11-15

    The purpose of our study was to identify new pathogenic genes used for exploring the pathogenesis of rheumatoid arthritis (RA). To screen pathogenic genes of RA, an integrated analysis was performed by using the microarray datasets in RA derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Afterwards, the integrated analysis of DNA methylation and gene expression profiling was used to screen crucial genes. In addition, we used RT-PCR and MSP to verify the expression levels and methylation status of these crucial genes in 20 synovial biopsy samples obtained from 10 RA model mice and 10 normal mice. BCL11B, CCDC88C, FCRLA and APOL6 were both up-regulated and hypomethylated in RA according to integrated analysis, RT-PCR and MSP verification. Four crucial genes (BCL11B, CCDC88C, FCRLA and APOL6) identified and analyzed in this study might be closely connected with the pathogenesis of RA. Copyright © 2017. Published by Elsevier B.V.

  5. Identification of novel candidate genes involved in mineralization of dental enamel by genome-wide transcript profiling.

    Science.gov (United States)

    Lacruz, Rodrigo S; Smith, Charles E; Bringas, Pablo; Chen, Yi-Bu; Smith, Susan M; Snead, Malcolm L; Kurtz, Ira; Hacia, Joseph G; Hubbard, Michael J; Paine, Michael L

    2012-05-01

    The gene repertoire regulating vertebrate biomineralization is poorly understood. Dental enamel, the most highly mineralized tissue in mammals, differs from other calcifying systems in that the formative cells (ameloblasts) lack remodeling activity and largely degrade and resorb the initial extracellular matrix. Enamel mineralization requires that ameloblasts undergo a profound functional switch from matrix-secreting to maturational (calcium transport, protein resorption) roles as mineralization progresses. During the maturation stage, extracellular pH decreases markedly, placing high demands on ameloblasts to regulate acidic environments present around the growing hydroxyapatite crystals. To identify the genetic events driving enamel mineralization, we conducted genome-wide transcript profiling of the developing enamel organ from rat incisors and highlight over 300 genes differentially expressed during maturation. Using multiple bioinformatics analyses, we identified groups of maturation-associated genes whose functions are linked to key mineralization processes including pH regulation, calcium handling, and matrix turnover. Subsequent qPCR and Western blot analyses revealed that a number of solute carrier (SLC) gene family members were up-regulated during maturation, including the novel protein Slc24a4 involved in calcium handling as well as other proteins of similar function (Stim1). By providing the first global overview of the cellular machinery required for enamel maturation, this study provide a strong foundation for improving basic understanding of biomineralization and its practical applications in healthcare. Copyright © 2011 Wiley Periodicals, Inc.

  6. Identification of genes and pathways associated with aluminum stress and tolerance using transcriptome profiling of wheat near-isogenic lines.

    Science.gov (United States)

    Houde, Mario; Diallo, Amadou Oury

    2008-08-27

    Aluminum is considered the most limiting factor for plant productivity in acidic soils, which cover large areas of the world's potential arable lands. The inhibition of root growth is recognized as the primary effect of Al toxicity. To identify genes associated with Al stress and tolerance, transcriptome analyses of four different wheat lines (2 Al-tolerant and 2 Al sensitive) that differ in their response to Al were performed. Microarray expression profiling revealed that 83 candidate genes are associated with Al stress and 25 are associated with tolerance. The stress-associated genes include important enzymes such as pyruvate dehydrogenase, alternative oxidase, and galactonolactone oxidase, ABC transporter and ascorbate oxido-reducatase. The Al tolerance-associated genes include the ALMT-1 malate transporter, glutathione S-transferase, germin/oxalate oxidase, fructose 1,6-bisphosphatase, cysteine-rich proteins, cytochrome P450 monooxygenase, cellulose synthase, zinc finger transcription factor, disease resistance response protein and F-box containing domain protein. In this survey, we identified stress- and tolerance-associated genes that may be involved in the detoxification of Al and reactive oxygen species. Alternative pathways could help maintain the supply of important metabolites (H2O2, ascorbate, NADH, and phosphate) needed for Al tolerance and root growth. The Al tolerance-associated genes may be key factors that regulate these pathways.

  7. Identification of genes and pathways associated with aluminum stress and tolerance using transcriptome profiling of wheat near-isogenic lines

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    Diallo Amadou

    2008-08-01

    Full Text Available Abstract Background Aluminum is considered the most limiting factor for plant productivity in acidic soils, which cover large areas of the world's potential arable lands. The inhibition of root growth is recognized as the primary effect of Al toxicity. To identify genes associated with Al stress and tolerance, transcriptome analyses of four different wheat lines (2 Al-tolerant and 2 Al sensitive that differ in their response to Al were performed. Results Microarray expression profiling revealed that 83 candidate genes are associated with Al stress and 25 are associated with tolerance. The stress-associated genes include important enzymes such as pyruvate dehydrogenase, alternative oxidase, and galactonolactone oxidase, ABC transporter and ascorbate oxido-reducatase. The Al tolerance-associated genes include the ALMT-1 malate transporter, glutathione S-transferase, germin/oxalate oxidase, fructose 1,6-bisphosphatase, cysteine-rich proteins, cytochrome P450 monooxygenase, cellulose synthase, zinc finger transcription factor, disease resistance response protein and F-box containing domain protein. Conclusion In this survey, we identified stress- and tolerance-associated genes that may be involved in the detoxification of Al and reactive oxygen species. Alternative pathways could help maintain the supply of important metabolites (H2O2, ascorbate, NADH, and phosphate needed for Al tolerance and root growth. The Al tolerance-associated genes may be key factors that regulate these pathways.

  8. IDENTIFICATION AND ANTIBIOTIC RESISTANCE PROFILE OFENTEROBACTERIACEAE SPECIES AND LACTOBACILLUS SPP. ISOLATED FROM HONEY BEES (APIS MELLIFERA DIGESTIVE TRACT

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    Lukáš Hleba

    2014-02-01

    Full Text Available Honey bees play important role in agricultural environment as main pollinators. Its important for many agricultural and wild plants. Also honey bee are producers of honey, which is consumed directly and it should be not a heat treatment. Many bacteria can be survive in honey for long time. Some of these bacteria are human and animal facultative pathogens, including Enterobactericaeae genera. If these bacteria contain antibiotic resistant genes than it can to leads to troubles in healing of some of bacterial infections. Lactobacillus spp. can be a reservoir of resistant genes for pathogenic bacterial strains. In this study we isolated Enterobacteriaceae strains from digestive tracts of honey bees. These strains was tested to the eight selected antibiotics by disc diffusion method and strains were indentified by MALDI TOF MS Biotyper. From this study we determined resistance to piperacillin in the highest level. Equally, we determined that Citrobacter gillenii was resistant to three antibiotics (piperacillin, chloramphenicol and levofloxacin from eight. Resistance to other antibiotics were determined in low levels and other indentified bacteria were resistant to one antibiotic, if any. Also we detected resistance in Lactobacillus spp. and determined MICs distribution for some selected antibiotics. For absence of similar studies we could not to discuss our results and we think that further experiments and studies are needed.

  9. Reactor protection system software test-case selection based on input-profile considering concurrent events and uncertainties

    International Nuclear Information System (INIS)

    Khalaquzzaman, M.; Lee, Seung Jun; Cho, Jaehyun; Jung, Wondea

    2016-01-01

    Recently, the input-profile-based testing for safety critical software has been proposed for determining the number of test cases and quantifying the failure probability of the software. Input-profile of a reactor protection system (RPS) software is the input which causes activation of the system for emergency shutdown of a reactor. This paper presents a method to determine the input-profile of a RPS software which considers concurrent events/transients. A deviation of a process parameter value begins through an event and increases owing to the concurrent multi-events depending on the correlation of process parameters and severity of incidents. A case of reactor trip caused by feedwater loss and main steam line break is simulated and analyzed to determine the RPS software input-profile and estimate the number of test cases. The different sizes of the main steam line breaks (e.g., small, medium, large break) with total loss of feedwater supply are considered in constructing the input-profile. The uncertainties of the simulation related to the input-profile-based software testing are also included. Our study is expected to provide an option to determine test cases and quantification of RPS software failure probability. (author)

  10. The DnaJ Gene Family in Pepper (Capsicum annuum L.: Comprehensive Identification, Characterization and Expression Profiles

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    Yunyan Kang

    2017-05-01

    Full Text Available The DnaJ proteins which function as molecular chaperone played critical roles in plant growth and development and response to heat stress (HS and also called heat shock protein 40 based on molecular weight. However, little was reported on this gene family in pepper. Recently, the release of the whole pepper genome provided an opportunity for identifying putative DnaJ homologous. In this study, a total of 76 putative pepper DnaJ genes (CaDnaJ01 to CaDnaJ76 were identified using bioinformatics methods and classified into five groups by the presence of the complete three domains (J-domain, zinc finger domain, and C-terminal domain. Chromosome mapping suggested that segmental duplication and tandem duplication were occurred in evolution. The multiple stress-related cis-elements were found in the promoter region of these CaDnaJ genes, which indicated that the CaDnaJs might be involved in the process of responding to complex stress conditions. In addition, expression profiles based on RNA-seq showed that the 47 CaDnaJs were expressed in at least one tissue tested. The result implied that they could be involved in the process of pepper growth and development. qRT-PCR analysis found that 80.60% (54/67 CaDnaJs were induced by HS, indicated that they could participated in pepper response to high temperature treatments. In conclusion, all these results would provide a comprehensive basis for further analyzing the function of CaDnaJ members and be also significant for elucidating the evolutionary relationship in pepper.

  11. Identification of potential crucial genes associated with steroid-induced necrosis of femoral head based on gene expression profile.

    Science.gov (United States)

    Lin, Zhe; Lin, Yongsheng

    2017-09-05

    The aim of this study was to explore potential crucial genes associated with the steroid-induced necrosis of femoral head (SINFH) and to provide valid biological information for further investigation of SINFH. Gene expression profile of GSE26316, generated from 3 SINFH rat samples and 3 normal rat samples were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using LIMMA package. After functional enrichment analyses of DEGs, protein-protein interaction (PPI) network and sub-PPI network analyses were conducted based on the STRING database and cytoscape. In total, 59 up-regulated DEGs and 156 downregulated DEGs were identified. The up-regulated DEGs were mainly involved in functions about immunity (e.g. Fcer1A and Il7R), and the downregulated DEGs were mainly enriched in muscle system process (e.g. Tnni2, Mylpf and Myl1). The PPI network of DEGs consisted of 123 nodes and 300 interactions. Tnni2, Mylpf, and Myl1 were the top 3 outstanding genes based on both subgraph centrality and degree centrality evaluation. These three genes interacted with each other in the network. Furthermore, the significant network module was composed of 22 downregulated genes (e.g. Tnni2, Mylpf and Myl1). These genes were mainly enriched in functions like muscle system process. The DEGs related to the regulation of immune system process (e.g. Fcer1A and Il7R), and DEGs correlated with muscle system process (e.g. Tnni2, Mylpf and Myl1) may be closely associated with the progress of SINFH, which is still needed to be confirmed by experiments. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Identification of distinct genes associated with seawater aspiration-induced acute lung injury by gene expression profile analysis

    Science.gov (United States)

    Liu, Wei; Pan, Lei; Zhang, Minlong; Bo, Liyan; Li, Congcong; Liu, Qingqing; Wang, Li; Jin, Faguang

    2016-01-01

    Seawater aspiration-induced acute lung injury (ALI) is a syndrome associated with a high mortality rate, which is characterized by severe hypoxemia, pulmonary edema and inflammation. The present study is the first, to the best of our knowledge, to analyze gene expression profiles from a rat model of seawater aspiration-induced ALI. Adult male Sprague-Dawley rats were instilled with seawater (4 ml/kg) in the seawater aspiration-induced ALI group (S group) or with distilled water (4 ml/kg) in the distilled water negative control group (D group). In the blank control group (C group) the rats' tracheae were exposed without instillation. Subsequently, lung samples were examined by histopathology; total protein concentration was detected in bronchoalveolar lavage fluid (BALF); lung wet/dry weight ratios were determined; and transcript expression was detected by gene sequencing analysis. The results demonstrated that histopathological alterations, pulmonary edema and total protein concentrations in BALF were increased in the S group compared with in the D group. Analysis of differential gene expression identified up and downregulated genes in the S group compared with in the D and C groups. A gene ontology analysis of the differential gene expression revealed enrichment of genes in the functional pathways associated with neutrophil chemotaxis, immune and defense responses, and cytokine activity. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the cytokine-cytokine receptor interaction pathway was one of the most important pathways involved in seawater aspiration-induced ALI. In conclusion, activation of the cytokine-cytokine receptor interaction pathway may have an essential role in the progression of seawater aspiration-induced ALI, and the downregulation of tumor necrosis factor superfamily member 10 may enhance inflammation. Furthermore, IL-6 may be considered a biomarker in seawater aspiration-induced ALI. PMID:27509884

  13. Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.).

    Science.gov (United States)

    Pandit, Awadhesh; Rai, Vandna; Bal, Subhashis; Sinha, Shikha; Kumar, Vinod; Chauhan, Mahesh; Gautam, Raj K; Singh, Rakesh; Sharma, Prakash C; Singh, Ashok K; Gaikwad, Kishor; Sharma, Tilak R; Mohapatra, Trilochan; Singh, Nagendra K

    2010-08-01

    Identification of genes for quantitative traits is difficult using any single approach due to complex inheritance of the traits and limited resolving power of the individual techniques. Here a combination of genetic mapping and bulked transcriptome profiling was used to narrow down the number of differentially expressed salt-responsive genes in rice in order to identify functional polymorphism of genes underlying the quantitative trait loci (QTL). A population of recombinant inbred lines (RILs) derived from cross between salt-tolerant variety CSR 27 and salt-sensitive variety MI 48 was used to map QTL for salt ion concentrations in different tissues and salt stress susceptibility index (SSI) for spikelet fertility, grain weight, and grain yield. Eight significant QTL intervals were mapped on chromosomes 1, 8, and 12 for the salt ion concentrations and a QTL controlling SSI for spikelet fertility was co-located in one of these intervals on chromosome 8. However, there were total 2,681 genes in these QTL intervals, making it difficult to pinpoint the genes responsible for the functional differences for the traits. Similarly, transcriptome profiling of the seedlings of tolerant and sensitive parents grown under control and salt-stress conditions showed 798 and 2,407 differentially expressed gene probes, respectively. By analyzing pools of RNA extracted from ten each of extremely tolerant and extremely sensitive RILs to normalize the background noise, the number of differentially expressed genes under salt stress was drastically reduced to 30 only. Two of these genes, an integral transmembrane protein DUF6 and a cation chloride cotransporter, were not only co-located in the QTL intervals but also showed the expected distortion of allele frequencies in the extreme tolerant and sensitive RILs, and therefore are suitable for future validation studies and development of functional markers for salt tolerance in rice to facilitate marker-assisted breeding.

  14. Genome-wide identification and expression profiling of tomato Hsp20 gene family in response to biotic and abiotic stresses

    Directory of Open Access Journals (Sweden)

    jiahong yu

    2016-08-01

    Full Text Available The Hsp20 genes are involved in the response of plants to environment stresses including heat shock and also play a vital role in plant growth and development. They represent the most abundant small heat shock proteins (sHsps in plants, but little is known about this family in tomato (Solanum lycopersicum, an important vegetable crop in the world. Here, we characterized heat shock protein 20 (SlHsp20 gene family in tomato through integration of gene structure, chromosome location, phylogenetic relationship and expression profile. Using bioinformatics-based methods, we identified at least 42 putative SlHsp20 genes in tomato. Sequence analysis revealed that most of SlHsp20 genes possessed no intron or a relatively short intron in length. Chromosome mapping indicated that inter-arm and intra-chromosome duplication events contributed remarkably to the expansion of SlHsp20 genes. Phylogentic tree of Hsp20 genes from tomato and other plant species revealed that SlHsp20 genes were grouped into 13 subfamilies, indicating that these genes may have a common ancestor that generated diverse subfamilies prior to the mono-dicot split. In addition, expression analysis using RNA-seq in various tissues and developmental stages of cultivated tomato and the wild relative Solanum pimpinellifolium revealed that most of these genes (83% were expressed in at least one stage from at least one genotype. Out of 42 genes, 4 genes were expressed constitutively in almost all the tissues analyzed, implying that these genes might have specific housekeeping function in tomato cell under normal growth conditions. Two SlHsp20 genes displayed differential expression levels between cultivated tomato and S. pimpinellifolium in vegetative (leaf and root and reproductive organs (floral bud and flower, suggesting inter-species diversification for functional specialization during the process of domestication. Based on genome-wide microarray analysis, we showed that the transcript

  15. Genome-Wide Identification and Expression Profiling of Tomato Hsp20 Gene Family in Response to Biotic and Abiotic Stresses.

    Science.gov (United States)

    Yu, Jiahong; Cheng, Yuan; Feng, Kun; Ruan, Meiying; Ye, Qingjing; Wang, Rongqing; Li, Zhimiao; Zhou, Guozhi; Yao, Zhuping; Yang, Yuejian; Wan, Hongjian

    2016-01-01

    The Hsp20 genes are involved in the response of plants to environment stresses including heat shock and also play a vital role in plant growth and development. They represent the most abundant small heat shock proteins (sHsps) in plants, but little is known about this family in tomato (Solanum lycopersicum), an important vegetable crop in the world. Here, we characterized heat shock protein 20 (SlHsp20) gene family in tomato through integration of gene structure, chromosome location, phylogenetic relationship, and expression profile. Using bioinformatics-based methods, we identified at least 42 putative SlHsp20 genes in tomato. Sequence analysis revealed that most of SlHsp20 genes possessed no intron or a relatively short intron in length. Chromosome mapping indicated that inter-arm and intra-chromosome duplication events contributed remarkably to the expansion of SlHsp20 genes. Phylogentic tree of Hsp20 genes from tomato and other plant species revealed that SlHsp20 genes were grouped into 13 subfamilies, indicating that these genes may have a common ancestor that generated diverse subfamilies prior to the mono-dicot split. In addition, expression analysis using RNA-seq in various tissues and developmental stages of cultivated tomato and the wild relative Solanum pimpinellifolium revealed that most of these genes (83%) were expressed in at least one stage from at least one genotype. Out of 42 genes, 4 genes were expressed constitutively in almost all the tissues analyzed, implying that these genes might have specific housekeeping function in tomato cell under normal growth conditions. Two SlHsp20 genes displayed differential expression levels between cultivated tomato and S. pimpinellifolium in vegetative (leaf and root) and reproductive organs (floral bud and flower), suggesting inter-species diversification for functional specialization during the process of domestication. Based on genome-wide microarray analysis, we showed that the transcript levels of SlHsp20

  16. Identification of stable endogenous control genes for transcriptional profiling of photon, proton and carbon-ion irradiated cells

    International Nuclear Information System (INIS)

    Sharungbam, Geeta D; Schwager, Christian; Chiblak, Sara; Brons, Stephan; Hlatky, Lynn; Haberer, Thomas; Debus, Jürgen; Abdollahi, Amir

    2012-01-01

    Quantitative analysis of transcriptional regulation of genes is a prerequisite for a better understanding of the molecular mechanisms of action of different radiation qualities such as photon, proton or carbon ion irradiation. Microarrays and real-time quantitative RT-PCR (qRT-PCR) are considered the two cornerstones of gene expression analysis. In interpreting these results it is critical to normalize the expression levels of the target genes by that of appropriately selected endogenous control genes (ECGs) or housekeeping genes. We sought to systematically investigate common ECG candidates for their stability after different radiation modalities in different human cell lines by qRT-PCR. We aimed to identify the most robust set of ECGs or housekeeping genes for transcriptional analysis in irradiation studies. We tested the expression stability of 32 ECGs in three human cancer cell lines. The epidermoid carcinoma cells (A431), the non small cell lung carcinoma cells (A549) and the pancreatic adenocarincoma cells (BxPC3) were irradiated with photon, proton and carbon ions. Expression Heat maps, clustering and statistic algorithms were employed using SUMO software package. The expression stability was evaluated by computing: mean, standard deviation, ANOVA, coefficient of variation and the stability measure (M) given by the geNorm algorithm. Expression analysis revealed significant cell type specific regulation of 18 out of 32 ECGs (p < 0.05). A549 and A431 cells shared a similar pattern of ECG expression as the function of different radiation qualities as compared to BxPC3. Of note, the ribosomal protein 18S, one of the most frequently used ECG, was differentially regulated as the function of different radiation qualities (p ≤ 0.01). A comprehensive search for the most stable ECGs using the geNorm algorithm identified 3 ECGs for A431 and BxPC3 to be sufficient for normalization. In contrast, 6 ECGs were required to properly normalize expression data in the more

  17. Genome-Wide Identification, Molecular Evolution, and Expression Profiling Analysis of Pectin Methylesterase Inhibitor Genes in Brassica campestris ssp. chinensis

    Directory of Open Access Journals (Sweden)

    Tingting Liu

    2018-05-01

    Full Text Available Pectin methylesterase inhibitor genes (PMEIs are a large multigene family and play crucial roles in cell wall modifications in plant growth and development. Here, a comprehensive analysis of the PMEI gene family in Brassica campestris, an important leaf vegetable, was performed. We identified 100 Brassica campestris PMEI genes (BcPMEIs, among which 96 BcPMEIs were unevenly distributed on 10 chromosomes and nine tandem arrays containing 20 BcPMEIs were found. We also detected 80 pairs of syntenic PMEI orthologs. These findings indicated that whole-genome triplication (WGT and tandem duplication (TD were the main mechanisms accounting for the current number of BcPMEIs. In evolution, BcPMEIs were retained preferentially and biasedly, consistent with the gene balance hypothesis and two-step theory, respectively. The molecular evolution analysis of BcPMEIs manifested that they evolved through purifying selection and the divergence time is in accordance with the WGT data of B. campestris. To obtain the functional information of BcPMEIs, the expression patterns in five tissues and the cis-elements distributed in promoter regions were investigated. This work can provide a better understanding of the molecular evolution and biological function of PMEIs in B. campestris.

  18. High-resolution H-band spectroscopy of Be stars with SDSS-III/apogee. I. New Be stars, line identifications, and line profiles

    International Nuclear Information System (INIS)

    Chojnowski, S. Drew; Majewski, Steven R.; Hall, Matthew; Beaton, Rachael; Burton, Adam; Damke, Guillermo; Wilson, John; Whelan, David G.; Wisniewski, John P.; Shetrone, Matthew; Eikenberry, Steve; Hasselquist, Sten; Holtzman, Jon A.; Brewington, Howard; Brinkmann, J.; Mészáros, Szabolcs; Nidever, David; Schneider, Donald P.; Zasowski, Gail; Bizyaev, Dmitry

    2015-01-01

    The Apache Point Observatory Galactic Evolution Experiment (APOGEE) has amassed the largest ever collection of multi-epoch, high-resolution (R∼22,500), H-band spectra for B-type emission line (Be) stars. These stars were targeted by APOGEE as telluric standard stars and subsequently identified via visual inspection as Be stars based on H i Brackett series emission or shell absorption in addition to otherwise smooth continua and occasionally non-hydrogen emission features. The 128/238 APOGEE Be stars for which emission had never previously been reported serve to increase the total number of known Be stars by ∼6%. Because the H band is relatively unexplored compared to other wavelength regimes, we focus here on identification of the H-band lines and analysis of the emission peak velocity separations (Δv p ) and emission peak intensity ratios (V/R) of the usually double-peaked H i and non-hydrogen emission lines. H i Br11 emission is found to preferentially form in the circumstellar disks at an average distance of ∼2.2 stellar radii. Increasing Δv p toward the weaker Br12–Br20 lines suggests these lines are formed interior to Br11. By contrast, the observed IR Fe ii emission lines present evidence of having significantly larger formation radii; distinctive phase lags between IR Fe ii and H i Brackett emission lines further supports that these species arise from different radii in Be disks. Several emission lines have been identified for the first time including C i 16895, a prominent feature in the spectra for almost a fifth of the sample and, as inferred from relatively large Δv p compared to the Br11–Br20, a tracer of the inner regions of Be disks. Emission lines at 15760 Å and 16781 Å remain unidentified, but usually appear along with and always have similar line profile morphology to Fe ii 16878. Unlike the typical metallic lines observed for Be stars in the optical, the H-band metallic lines, such as Fe ii 16878, never exhibit any evidence of

  19. High-Resolution Inhibition Profiling Combined with HPLC-HRMS-SPE-NMR for Identification of PTP1B Inhibitors from Vietnamese Plants.

    Science.gov (United States)

    Trinh, Binh Thi Dieu; Jäger, Anna K; Staerk, Dan

    2017-07-20

    Protein tyrosine phosphatase 1B (PTP1B) plays a key role as a negative regulator in insulin signal transduction by deactivating the insulin receptor. Thus, PTP1B inhibition has emerged as a potential therapeutic strategy for curing insulin resistance. In this study, 40 extracts from 18 different plant species were investigated for PTP1B inhibitory activity in vitro. The most promising one, the EtOAc extract of Ficus racemosa , was investigated by high-resolution PTP1B inhibition profiling combined with HPLC-HRMS-SPE-NMR analysis. This led to the identification of isoderrone ( 1 ), derrone ( 2 ), alpinumisoflavone ( 3 ) and mucusisoflavone B ( 4 ) as PTP1B inhibitors. IC 50 of these compounds were 22.7 ± 1.7, 12.6 ± 1.6, 21.2 ± 3.8 and 2.5 ± 0.2 µM, respectively. Kinetics analysis revealed that these compounds inhibited PTP1B non-competitively with K i values of 21.3 ± 2.8, 7.9 ± 1.9, 14.3 ± 2.0, and 3.0 ± 0.5 µM, respectively. These findings support the important role of F. racemosa as a novel source of new drugs and/or as a herbal remedy for treatment of type 2 diabetes.

  20. High-Resolution Inhibition Profiling Combined with HPLC-HRMS-SPE-NMR for Identification of PTP1B Inhibitors from Vietnamese Plants

    Directory of Open Access Journals (Sweden)

    Binh Thi Dieu Trinh

    2017-07-01

    Full Text Available Protein tyrosine phosphatase 1B (PTP1B plays a key role as a negative regulator in insulin signal transduction by deactivating the insulin receptor. Thus, PTP1B inhibition has emerged as a potential therapeutic strategy for curing insulin resistance. In this study, 40 extracts from 18 different plant species were investigated for PTP1B inhibitory activity in vitro. The most promising one, the EtOAc extract of Ficus racemosa, was investigated by high-resolution PTP1B inhibition profiling combined with HPLC-HRMS-SPE-NMR analysis. This led to the identification of isoderrone (1, derrone (2, alpinumisoflavone (3 and mucusisoflavone B (4 as PTP1B inhibitors. IC50 of these compounds were 22.7 ± 1.7, 12.6 ± 1.6, 21.2 ± 3.8 and 2.5 ± 0.2 µM, respectively. Kinetics analysis revealed that these compounds inhibited PTP1B non-competitively with Ki values of 21.3 ± 2.8, 7.9 ± 1.9, 14.3 ± 2.0, and 3.0 ± 0.5 µM, respectively. These findings support the important role of F. racemosa as a novel source of new drugs and/or as a herbal remedy for treatment of type 2 diabetes.

  1. Selective orthosteric free fatty acid receptor 2 (FFA2) agonists: identification of the structural and chemical requirements for selective activation of FFA2 versus FFA3

    DEFF Research Database (Denmark)

    Schmidt, Johannes; Smith, Nicola J; Christiansen, Elisabeth

    2011-01-01

    given its size. Propionate, however, does not discriminate between FFA2 and the closely related receptor FFA3 (GPR41). To identify FFA2 selective ligands and understand the molecular basis for FFA2 selectivity, a targeted library of small carboxylic acids (SCAs) was examined using holistic, label...

  2. Who Should They Relate To? A Study For the Identification and Analysis of Criteria to the Partners’ Selection in Inter-Organizational Networks

    Directory of Open Access Journals (Sweden)

    Denise Rossato Quatrin

    2017-01-01

    Full Text Available The selection of partners is strategic in inter-organizational networks. One of the most important aspects is the definition of criteria for selection, that are the minimal characteristics required from those prospected. This study aimed to identify the most important criteria for the selection of members in horizontal inter-organizational networks, also describing their influence on network activities. First, we applied 120 questionnaires to managers of inter-organizational networks to identify the degree of importance of criteria previously treated in the literature. After, we interviewed 16 managers enabling us to identify other criteria, as well as understanding their influence on network activities. All of the 20 criteria from the literature were considered with significant importance by managers and the following criteria were added: trustworthiness, entrepreneur’s profile and company lifetime. The results aim to contribute to the selection of partners and provide information for the construction of the inter-organizational networks literature.

  3. Proteotranscriptomic Profiling of 231-BR Breast Cancer Cells: Identification of Potential Biomarkers and Therapeutic Targets for Brain Metastasis*

    Science.gov (United States)

    Dun, Matthew D.; Chalkley, Robert J.; Faulkner, Sam; Keene, Sheridan; Avery-Kiejda, Kelly A.; Scott, Rodney J.; Falkenby, Lasse G.; Cairns, Murray J.; Larsen, Martin R.; Bradshaw, Ralph A.; Hondermarck, Hubert

    2015-01-01

    Brain metastases are a devastating consequence of cancer and currently there are no specific biomarkers or therapeutic targets for risk prediction, diagnosis, and treatment. Here the proteome of the brain metastatic breast cancer cell line 231-BR has been compared with that of the parental cell line MDA-MB-231, which is also metastatic but has no organ selectivity. Using SILAC and nanoLC-MS/MS, 1957 proteins were identified in reciprocal labeling experiments and 1584 were quantified in the two cell lines. A total of 152 proteins were confidently determined to be up- or down-regulated by more than twofold in 231-BR. Of note, 112/152 proteins were decreased as compared with only 40/152 that were increased, suggesting that down-regulation of specific proteins is an important part of the mechanism underlying the ability of breast cancer cells to metastasize to the brain. When matched against transcriptomic data, 43% of individual protein changes were associated with corresponding changes in mRNA, indicating that the transcript level is a limited predictor of protein level. In addition, differential miRNA analyses showed that most miRNA changes in 231-BR were up- (36/45) as compared with down-regulations (9/45). Pathway analysis revealed that proteome changes were mostly related to cell signaling and cell cycle, metabolism and extracellular matrix remodeling. The major protein changes in 231-BR were confirmed by parallel reaction monitoring mass spectrometry and consisted in increases (by more than fivefold) in the matrix metalloproteinase-1, ephrin-B1, stomatin, myc target-1, and decreases (by more than 10-fold) in transglutaminase-2, the S100 calcium-binding protein A4, and l-plastin. The clinicopathological significance of these major proteomic changes to predict the occurrence of brain metastases, and their potential value as therapeutic targets, warrants further investigation. PMID:26041846

  4. MYB Transcription Factors in Chinese Pear (Pyrus bretschneideri Rehd.: Genome-Wide Identification, Classification and Expression Profiling during Fruit Development

    Directory of Open Access Journals (Sweden)

    Yun Peng eCao

    2016-04-01

    Full Text Available The MYB family is one of the largest families of transcription factors in plants. Although some MYBs have been reported to play roles in secondary metabolism, no comprehensive study of the MYB family in Chinese pear (Pyrus bretschneideri Rehd. has been reported. In the present study, we performed genome-wide analysis of MYB genes in Chinese pear, designated as PbMYBs, including analyses of their phylogenic relationships, structures, chromosomal locations, promoter regions, GO annotations and collinearity. A total of 129 PbMYB genes were identified in the pear genome and were divided into 31 subgroups based on phylogenetic analysis. These PbMYBs were unevenly distributed among 16 chromosomes (total of 17 chromosomes. The occurrence of gene duplication events indicated that whole-genome duplication and segmental duplication likely played key roles in expansion of the PbMYB gene family. Ka/Ks analysis suggested that the duplicated PbMYBs mainly experienced purifying selection with restrictive functional divergence after the duplication events. Interspecies microsynteny analysis revealed maximum orthology between pear and peach, followed by plum and strawberry. Subsequently, the expression patterns of 20 PbMYB genes that may be involved in lignin biosynthesis according to their phylogenetic relationships were examined throughout fruit development. Among the twenty genes examined, PbMYB25 and PbMYB52 exhibited expression patterns consistent with the typical variations in the lignin content previously reported. Moreover, sub-cellular localization analysis revealed that two proteins PbMYB25 and PbMYB52 were localized to the nucleus. All together, PbMYB25 and PbMYB52 were inferred to be candidate genes involved in the regulation of lignin biosynthesis during the development of pear fruit. This study provides useful information for further functional analysis of the MYB gene family in pear.

  5. Identification of a potent and selective free fatty acid receptor 1 (FFA1/GPR40) agonist with favorable physicochemical and in vitro ADME properties

    DEFF Research Database (Denmark)

    Christiansen, Elisabeth; Urban, Christian; Grundmann, Manuel

    2011-01-01

    The free fatty acid receptor 1 (FFA1, also known as GPR40) enhances glucose-stimulated insulin secretion from pancreatic ß-cells and is recognized as an interesting new target for treatment of type 2 diabetes. Several series of selective FFA1 agonists are already known. Most of these are derived...... from free fatty acids (FFAs) or glitazones, and are relatively lipophilic. Aiming at the development of potent, selective and less lipophilic FFA1 agonists, the terminal phenyl of a known compound series was replaced by nitrogen containing heterocycles. This resulted in the identification of 37......, a selective FFA1 agonist with potent activity on recombinant human FFA1 receptors and on the rat insulinoma cell line INS-1E, optimal lipophilicity and excellent in vitro permeability and metabolic stability....

  6. Inter-laboratory variation in in vitro gas production profiles of some selected feeds, using both manual and automated methods

    NARCIS (Netherlands)

    Rymer, C.; Williams, B.A.; Brooks, A.E.; Davies, D.R.; Givens, D.I.

    2005-01-01

    A study was conducted to estimate variation among laboratories and between manual and automated techniques of measuring pressure on the resulting gas production profiles (GPP). Eight feeds (molassed sugarbeet feed, grass silage, maize silage, soyabean hulls, maize gluten feed, whole crop wheat

  7. Sliding window analyses for optimal selection of mini-barcodes, and application to 454-pyrosequencing for specimen identification from degraded DNA.

    Science.gov (United States)

    Boyer, Stephane; Brown, Samuel D J; Collins, Rupert A; Cruickshank, Robert H; Lefort, Marie-Caroline; Malumbres-Olarte, Jagoba; Wratten, Stephen D

    2012-01-01

    DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI) is over 600 base pairs (bp), amplification fails when the DNA molecule is degraded into smaller fragments. However, relevant information for specimen identification may not be evenly distributed along the barcoding region, and a shorter target can be sufficient for identification purposes. This study proposes a new, widely applicable, method to compare the performance of all potential 'mini-barcodes' for a given molecular marker and to objectively select the shortest and most informative one. Our method is based on a sliding window analysis implemented in the new R package SPIDER (Species IDentity and Evolution in R). This method is applicable to any taxon and any molecular marker. Here, it was tested on earthworm DNA that had been degraded through digestion by carnivorous landsnails. A 100 bp region of 16 S rDNA was selected as the shortest informative fragment (mini-barcode) required for accurate specimen identification. Corresponding primers were designed and used to amplify degraded earthworm (prey) DNA from 46 landsnail (predator) faeces using 454-pyrosequencing. This led to the detection of 18 earthworm species in the diet of the snail. We encourage molecular ecologists to use this method to objectively select the most informative region of the gene they aim to amplify from degraded DNA. The method and tools provided here, can be particularly useful (1) when dealing with degraded DNA for which only small fragments can be amplified, (2) for cases where no consensus has yet been reached on the appropriate barcode gene, or (3) to allow direct analysis of short reads derived from massively parallel sequencing without the need for bioinformatic consolidation.

  8. Sliding window analyses for optimal selection of mini-barcodes, and application to 454-pyrosequencing for specimen identification from degraded DNA.

    Directory of Open Access Journals (Sweden)

    Stephane Boyer

    Full Text Available DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI is over 600 base pairs (bp, amplification fails when the DNA molecule is degraded into smaller fragments. However, relevant information for specimen identification may not be evenly distributed along the barcoding region, and a shorter target can be sufficient for identification purposes. This study proposes a new, widely applicable, method to compare the performance of all potential 'mini-barcodes' for a given molecular marker and to objectively select the shortest and most informative one. Our method is based on a sliding window analysis implemented in the new R package SPIDER (Species IDentity and Evolution in R. This method is applicable to any taxon and any molecular marker. Here, it was tested on earthworm DNA that had been degraded through digestion by carnivorous landsnails. A 100 bp region of 16 S rDNA was selected as the shortest informative fragment (mini-barcode required for accurate specimen identification. Corresponding primers were designed and used to amplify degraded earthworm (prey DNA from 46 landsnail (predator faeces using 454-pyrosequencing. This led to the detection of 18 earthworm species in the diet of the snail. We encourage molecular ecologists to use this method to objectively select the most informative region of the gene they aim to amplify from degraded DNA. The method and tools provided here, can be particularly useful (1 when dealing with degraded DNA for which only small fragments can be amplified, (2 for cases where no consensus has yet been reached on the appropriate barcode gene, or (3 to allow direct analysis of short reads derived from massively parallel sequencing without the need for bioinformatic consolidation.

  9. ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research.

    Science.gov (United States)

    Wang, Nanyi; Wang, Lirong; Xie, Xiang-Qun

    2017-11-27

    Molecular docking is widely applied to computer-aided drug design and has become relatively mature in the recent decades. Application of docking in modeling varies from single lead compound optimization to large-scale virtual screening. The performance of molecular docking is highly dependent on the protein structures selected. It is especially challenging for large-scale target prediction research when multiple structures are available for a single target. Therefore, we have established ProSelection, a docking preferred-protein selection algorithm, in order to generate the proper structure subset(s). By the ProSelection algorithm, protein structures of "weak selectors" are filtered out whereas structures of "strong selectors" are kept. Specifically, the structure which has a good statistical performance of distinguishing active ligands from inactive ligands is defined as a strong selector. In this study, 249 protein structures of 14 autophagy-related targets are investigated. Surflex-dock was used as the docking engine to distinguish active and inactive compounds against these protein structures. Both t test and Mann-Whitney U test were used to distinguish the strong from the weak selectors based on the normality of the docking score distribution. The suggested docking score threshold for active ligands (SDA) was generated for each strong selector structure according to the receiver operating characteristic (ROC) curve. The performance of ProSelection was further validated by predicting the potential off-targets of 43 U.S. Federal Drug Administration approved small molecule antineoplastic drugs. Overall, ProSelection will accelerate the computational work in protein structure selection and could be a useful tool for molecular docking, target prediction, and protein-chemical database establishment research.

  10. Comparison and Description o f Fitness Level ، Physiological a nd Anthropometric Profiles o f Selected Versus Non Selected Iranian National Team Table Tennis Players

    Directory of Open Access Journals (Sweden)

    Reza BEHDARİ

    2015-08-01

    Full Text Available Objectives: The aims of this study were to comparison and describe the anthropometric characteristics physical fitness and physiological profile of the f irst 5 and the lower ranked elite male Iranian national table tennis players, who participated in table tennis championship, to compare the anthropometric data, physical fitness and physiological profile of the first 5elite tennis players on the ranking wi th the lower ranked players, and to establish an anthropometric and physiological profile chart for elite tennis players. Methods: On the direction of this aim 16 male National table tennis Players' participated in this study. According to ranked some phy sical fitness, physiological and anthropometric variables were recorded of each subject. In this research; Physical fitness was determined using the following test: 1 speed; 36m sprint, 2 shoulder, back and hamstring flexibility; sit and reach, 3 lower limb power; side jump, 4 Anaerobic power; wingate test, 5 Aerobic power; 1600 m running, 6 reaction time; visual reaction time, 7 mussel endurance; sit - ups. In addition to anthropometric analysis (height, weight, siting height, arm length, body com position and somatotype of participants have been assessed. The kolmogorof - smirnov test was applied to determine the nature of data distribution. Since a normal distribution was confirmed, a t - test for independent samples was performed to examine statisti cal differences between groups and p value < 0.05 was considered to be significant. Results: There were no significant differences in height, jump, shoulder, back and hamstring flexibility, speed, visual reaction time, anaerobic power and BMI between th e first 5 and the lower ranked table tennis players, while there were significant differences in weight, side jump, aerobic power, present body fat and somatotype component. A mesomorph – endomorph somatotype was registered for the lower ranked and somat otype of first 5 table tennis players

  11. Site-selective dopant profiling of p-n junction specimens in the dual-beam FIB/SEM system

    International Nuclear Information System (INIS)

    Chee, K W A; Beanland, R; Midgley, P A; Humphreys, C J

    2010-01-01

    Results from site-specific dopant profiling in a dual-beam FIB/SEM system are reported. Si specimens containing p-n junctions were milled using Ga + ion beam energies ranging from 30 keV to 2 keV, and analysed in situin the vacuum chamber. We compare the dopant contrast observed when milling a cleaved surface to that obtained from a side-wall of a trench cut using 30 kV Ga + ions, and using successively lower ion beam energies. The latter technique is suitable for site-specific dopant profiling. We find that lower energy ion beam milling significantly improves contrast, but only achieves 50 % of that observed on a freshly-cleaved surface. Furthermore, the contrast on a side-wall previously milled using high energy Ga + ions is less than that of a cleaved surface subjected to the same ion beam energy.

  12. Genome-Wide Characterization of Major Intrinsic Proteins in Four Grass Plants and Their Non-Aqua Transport Selectivity Profiles with Comparative Perspective.

    Directory of Open Access Journals (Sweden)

    Abul Kalam Azad

    Full Text Available Major intrinsic proteins (MIPs, commonly known as aquaporins, transport not only water in plants but also other substrates of physiological significance and heavy metals. In most of the higher plants, MIPs are divided into five subfamilies (PIPs, TIPs, NIPs, SIPs and XIPs. Herein, we identified 68, 42, 38 and 28 full-length MIPs, respectively in the genomes of four monocot grass plants, specifically Panicum virgatum, Setaria italica, Sorghum bicolor and Brachypodium distachyon. Phylogenetic analysis showed that the grass plants had only four MIP subfamilies including PIPs, TIPs, NIPs and SIPs without XIPs. Based on structural analysis of the homology models and comparing the primary selectivity-related motifs [two NPA regions, aromatic/arginine (ar/R selectivity filter and Froger's positions (FPs] of all plant MIPs that have been experimentally proven to transport non-aqua substrates, we predicted the transport profiles of all MIPs in the four grass plants and also in eight other plants. Groups of MIP subfamilies based on ar/R selectivity filter and FPs were linked to the non-aqua transport profiles. We further deciphered the substrate selectivity profiles of the MIPs in the four grass plants and compared them with their counterparts in rice, maize, soybean, poplar, cotton, Arabidopsis thaliana, Physcomitrella patens and Selaginella moellendorffii. In addition to two NPA regions, ar/R filter and FPs, certain residues, especially in loops B and C, contribute to the functional distinctiveness of MIP groups. Expression analysis of transcripts in different organs indicated that non-aqua transport was related to expression of MIPs since most of the unexpressed MIPs were not predicted to facilitate the transport of non-aqua molecules. Among all MIPs in every plant, TIP (BdTIP1;1, SiTIP1;2, SbTIP2;1 and PvTIP1;2 had the overall highest mean expression. Our study generates significant information for understanding the diversity, evolution, non

  13. Global gene expression in larval zebrafish (Danio rerio) exposed to selective serotonin reuptake inhibitors (fluoxetine and sertraline) reveals unique expression profiles and potential biomarkers of exposure

    International Nuclear Information System (INIS)

    Park, June-Woo; Heah, Tze Ping; Gouffon, Julia S.; Henry, Theodore B.; Sayler, Gary S.

    2012-01-01

    Larval zebrafish (Danio rerio) were exposed (96 h) to selective serotonin reuptake inhibitors (SSRIs) fluoxetine and sertraline and changes in transcriptomes analyzed by Affymetrix GeneChip ® Zebrafish Array were evaluated to enhance understanding of biochemical pathways and differences between these SSRIs. The number of genes differentially expressed after fluoxetine exposure was 288 at 25 μg/L and 131 at 250 μg/L; and after sertraline exposure was 33 at 25 μg/L and 52 at 250 μg/L. Same five genes were differentially regulated in both SSRIs indicating shared molecular pathways. Among these, the gene coding for FK506 binding protein 5, annotated to stress response regulation, was highly down-regulated in all treatments (results confirmed by qRT-PCR). Gene ontology analysis indicated at the gene expression level that regulation of stress response and cholinesterase activities were influenced by these SSRIs, and suggested that changes in transcription of these genes could be used as biomarkers of SSRI exposure. - Highlights: ► Exposure of zebrafish to selective serotonin reuptake inhibitors (SSRIs). ► Fluoxetine and sertraline generate different global gene expression profiles. ► Genes linked to stress response and acetylcholine esterase affected by both SSRIs. - Global gene expression profiles in zebrafish exposed to selective serotonin reuptake inhibitors.

  14. Genome-Wide Identification, Characterization, and Expression Profiling of Glutathione S-Transferase (GST) Family in Pumpkin Reveals Likely Role in Cold-Stress Tolerance

    Science.gov (United States)

    Abdul Kayum, Md.; Nath, Ujjal Kumar; Park, Jong-In; Choi, Eung Kyoo; Song, Jae-Young; Kim, Hoy-Taek; Nou, Ill-Sup

    2018-01-01

    Plant growth and development can be adversely affected by cold stress, limiting productivity. The glutathione S-transferase (GST) family comprises important detoxifying enzymes, which play major roles in biotic and abiotic stress responses by reducing the oxidative damage caused by reactive oxygen species. Pumpkins (Cucurbita maxima) are widely grown, economically important, and nutritious; however, their yield can be severely affected by cold stress. The identification of putative candidate genes responsible for cold-stress tolerance, including the GST family genes, is therefore vital. For the first time, we identified 32 C. maxima GST (CmaGST) genes using a combination of bioinformatics approaches and characterized them by expression profiling. These CmaGST genes represent seven of the 14 known classes of plant GSTs, with 18 CmaGSTs categorized into the tau class. The CmaGSTs were distributed across 13 of pumpkin’s 20 chromosomes, with the highest numbers found on chromosomes 4 and 6. The large number of CmaGST genes resulted from gene duplication; 11 and 5 pairs of CmaGST genes were segmental- and tandem-duplicated, respectively. In addition, all CmaGST genes showed organ-specific expression. The expression of the putative GST genes in pumpkin was examined under cold stress in two lines with contrasting cold tolerance: cold-tolerant CP-1 (C. maxima) and cold-susceptible EP-1 (Cucurbita moschata). Seven genes (CmaGSTU3, CmaGSTU7, CmaGSTU8, CmaGSTU9, CmaGSTU11, CmaGSTU12, and CmaGSTU14) were highly expressed in the cold-tolerant line and are putative candidates for use in breeding cold-tolerant crop varieties. These results increase our understanding of the cold-stress-related functions of the GST family, as well as potentially enhancing pumpkin breeding programs. PMID:29439434

  15. Comparisons of Subgingival Microbial Profiles of Refractory Periodontitis, Severe Periodontitis and Periodontal Health using the Human Oral Microbe Identification Microarray (HOMIM)

    Science.gov (United States)

    Colombo, Ana Paula V.; Boches, Susan K.; Cotton, Sean L.; Goodson, J. Max; Kent, Ralph; Haffajee, Anne D.; Socransky, Sigmund S.; Hasturk, Hatice; Van Dyke, Thomas E.; Paster, Bruce J.

    2013-01-01

    Aim This study compared the subgingival microbiota of subjects with refractory periodontitis (RP) to those in subjects with treatable periodontitis (GR) or periodontal health (PH) using the Human Oral Microbe Identification Microarray (HOMIM). Methods At baseline, subgingival plaque samples were taken from 47 periodontitis and 20 PH individuals, and analyzed for the presence of 300 species by HOMIM. The periodontitis subjects were classified as RP (n=17) based on mean attachment loss (AL) and/or >3 sites with AL ≥2.5 mm after SRP, surgery and systemically administered amoxicillin and metronidazole or as GR (n=30) based on mean attachment gain and no sites with AL ≥2.5 mm after treatment. Significant differences in taxa among groups were sought using the Kruskal Wallis and Chi-square tests. Results More species were detected in diseased patients (GR or RP) than those without disease (PH). RP subjects were distinguished from GR and PH by a significantly high frequency of putative periodontal pathogens such as, Parvimonas micra, Campylobacter gracilis, Eubacterium nodatum, Selenomonas noxia, Tannerella forsythia, Porphyromonas gingivalis, Prevotella spp., Treponema spp., Eikenella corrodens, as well as “unusual” species (Pseudoramibacter alactolyticus, TM7 spp. oral taxon (OT) 346/356, Bacteroidetes spp. OT 272/274, Solobacterium moorei, Desulfobulbus sp. OT 041, Brevundimonas diminuta, Sphaerocytophaga sp. OT 337, Shuttleworthia satelles, Filifactor alocis, Dialister invisus/pneumosintes, Granulicatella adiacens, Mogibacterium tidmidum, Veillonella atypica, Mycoplasma salivarium, Synergistes sp. cluster II, Acidaminococcaceae [G-1] sp. OT 132/150/155/148/135) [pspp. cluster I, Capnocytophaga sputigena, Cardiobacterium hominis, Haemophilus parainfluenzae, Lautropia mirabilis, Propionibacterium propionicum, Rothia dentocariosa/mucilagenosa, Streptococcus sanguinis (p<0.05). Conclusion RP patients present a distinct microbial profile compared to patients in the

  16. Identification of an imidazopyridine scaffold to generate potent and selective TYK2 inhibitors that demonstrate activity in an in vivo psoriasis model.

    Science.gov (United States)

    Liang, Jun; Van Abbema, Anne; Balazs, Mercedesz; Barrett, Kathy; Berezhkovsky, Leo; Blair, Wade S; Chang, Christine; Delarosa, Donnie; DeVoss, Jason; Driscoll, Jim; Eigenbrot, Charles; Goodacre, Simon; Ghilardi, Nico; MacLeod, Calum; Johnson, Adam; Bir Kohli, Pawan; Lai, Yingjie; Lin, Zhonghua; Mantik, Priscilla; Menghrajani, Kapil; Nguyen, Hieu; Peng, Ivan; Sambrone, Amy; Shia, Steven; Smith, Jan; Sohn, Sue; Tsui, Vickie; Ultsch, Mark; Williams, Karen; Wu, Lawren C; Yang, Wenqian; Zhang, Birong; Magnuson, Steven

    2017-09-15

    Herein we report identification of an imidazopyridine class of potent and selective TYK2 inhibitors, exemplified by prototype 6, through constraint of the rotatable amide bond connecting the pyridine and aryl rings of compound 1. Further optimization led to generation of compound 30 that potently inhibits the TYK2 enzyme and the IL-23 pathway in cells, exhibits selectivity against cellular JAK2 activity, and has good pharmacokinetic properties. In mice, compound 30 demonstrated dose-dependent reduction of IL-17 production in a PK/PD model as well as in an imiquimod-induced psoriasis model. In this efficacy model, the IL-17 decrease was accompanied by a reduction of ear thickness indicating the potential of TYK2 inhibition as a therapeutic approach for psoriasis patients. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. The Malus domestica sugar transporter gene family: identifications based on genome and expression profiling related to the accumulation of fruit sugars.

    Science.gov (United States)

    Wei, Xiaoyu; Liu, Fengli; Chen, Cheng; Ma, Fengwang; Li, Mingjun

    2014-01-01

    In plants, sugar transporters are involved not only in long-distance transport, but also in sugar accumulations in sink cells. To identify members of sugar transporter gene families and to analyze their function in fruit sugar accumulation, we conducted a phylogenetic analysis of the Malus domestica genome. Expression profiling was performed with shoot tips, mature leaves, and developed fruit of "Gala" apple. Genes for sugar alcohol [including 17 sorbitol transporters (SOTs)], sucrose, and monosaccharide transporters, plus SWEET genes, were selected as candidates in 31, 9, 50, and 27 loci, respectively, of the genome. The monosaccharide transporter family appears to include five subfamilies (30 MdHTs, 8 MdEDR6s, 5 MdTMTs, 3 MdvGTs, and 4 MdpGLTs). Phylogenetic analysis of the protein sequences indicated that orthologs exist among Malus, Vitis, and Arabidopsis. Investigations of transcripts revealed that 68 candidate transporters are expressed in apple, albeit to different extents. Here, we discuss their possible roles based on the relationship between their levels of expression and sugar concentrations. The high accumulation of fructose in apple fruit is possibly linked to the coordination and cooperation between MdTMT1/2 and MdEDR6. By contrast, these fruits show low MdSWEET4.1 expression and a high flux of fructose produced from sorbitol. Our study provides an exhaustive survey of sugar transporter genes and demonstrates that sugar transporter gene families in M. domestica are comparable to those in other species. Expression profiling of these transporters will likely contribute to improving our understanding of their physiological functions in fruit formation and the development of sweetness properties.

  18. The Malus domestica sugar transporter gene family: identifications based on genome and expression profiling related to the accumulation of fruit sugars

    Directory of Open Access Journals (Sweden)

    Xiaoyu eWei

    2014-11-01

    Full Text Available In plants, sugar transporters are involved not only in long-distance transport, but also in sugar accumulations in sink cells. To identify members of sugar transporter gene families and to analyze their function in fruit sugar accumulation, we conducted a phylogenetic analysis of the Malus domestica genome. Expression profiling was performed with shoot tips, mature leaves, and developed fruit of ‘Gala’ apple. Genes for sugar alcohol (including 17 sorbitol transporters, sucrose, and monosaccharide transporters, plus SWEET genes, were selected as candidates in 31, 9, 50, and 27 loci, respectively, of the genome. The monosaccharide transporter family appears to include five subfamilies (30 MdHTs, 8 MdEDR6s, 5 MdTMTs, 3 MdvGTs, and 4 MdpGLTs. Phylogenetic analysis of the protein sequences indicated that orthologs exist among Malus, Vitis, and Arabidopsis. Investigations of transcripts revealed that 68 candidate transporters are expressed in apple, albeit to different extents. Here, we discuss their possible roles based on the relationship between their levels of expression and sugar concentrations. The high accumulation of fructose in apple fruit is possibly linked to the coordination and cooperation between MdTMT1/2 and MdEDR6. By contrast, these fruits show low MdSWEET4.1 expression and a high flux of fructose produced from sorbitol. Our study provides an exhaustive survey of sugar transporter genes and demonstrates that sugar transporter gene families in M. domestica are comparable to those in other species. Expression profiling of these transporters will likely contribute to improving our understanding of their physiological functions in fruit formation and the development of sweetness properties.

  19. Inactivation and changes in metabolic profile of selected foodborne bacteria by 460 nm LED illumination.

    Science.gov (United States)

    Kumar, Amit; Ghate, Vinayak; Kim, Min-Jeong; Zhou, Weibiao; Khoo, Gek Hoon; Yuk, Hyun-Gyun

    2017-05-01

    The objective of this study was to investigate the effect of 460 nm light-emitting diode (LED) on the inactivation of foodborne bacteria. Additionally, the change in the endogenous metabolic profile of LED illuminated cells was analyzed to understand the bacterial response to the LED illumination. Six different species of bacteria (Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7, Pseudomonas aeruginosa and Salmonella Typhimurium) were illuminated with 460 nm LED to a maximum dose of 4080 J/cm 2 at 4, 10 and 25 °C. Inactivation curves were modeled using Hom model. Metabolic profiling of the non-illuminated and illuminated cells was performed using a Liquid chromatography-mass spectrometry system. Results indicate that the 460 nm LED significantly (p illuminated cells indicated that several metabolites e.g. 11-deoxycortisol, actinonin, coformycin, tyramine, chitobiose etc. were regulated during LED illumination. These results elucidate the effectiveness of 460 nm LED against foodborne bacteria and hence, its suitability as a novel antimicrobial control method to ensure food safety. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Dual High-Resolution α-Glucosidase and Radical Scavenging Profiling Combined with HPLC-HRMS-SPE-NMR for Identification of Minor and Major Constituents Directly from the Crude Extract of Pueraria lobata

    DEFF Research Database (Denmark)

    Liu, Bingrui; Kongstad, Kenneth Thermann; Qinglei, Sun

    2015-01-01

    The crude methanol extract of Pueraria lobata was investigated by dual high-resolution α-glucosidase inhibition and radical scavenging profiling combined with hyphenated HPLC-HRMS-SPE-NMR. Direct analysis of the crude extract without preceding purification was facilitated by combining chromatograms...... from two analytical-scale HPLC separations of 120 and 600 μg on-column, respectively. High-resolution α-glucosidase and radical scavenging profiles were obtained after microfractionation of the eluate in 96-well microplates. This allowed full bioactivity profiling of individual peaks in the HPLC...... chromatogram of the crude methanol extract. Subsequent HPLC-HRMS-SPE-NMR analysis allowed identification of 21 known compounds in addition to two new compounds, i.e., 3′-methoxydaidzein 8-C-[α-d-apiofuranosyl-(1→6)]-β-d-glucopyranoside and 6″-O-malonyl-3′-methoxydaidzin, as well as an unstable compound...

  1. Effect of participatory selection of varieties on the identification of outstanding common bean genotypes (Phaseolus vulgaris L.

    Directory of Open Access Journals (Sweden)

    Alexis Lamz Piedra

    2017-10-01

    Full Text Available Among the main factors affecting bean production is poor distribution of varieties for different environmental conditions in which its are grown. The aim of this work was to evaluate the impact of participatory selection of foreign genetic materials and national commercial and pre-commercial common bean in identifying genotypes for their outstanding performance and resistance to common bacteriosis (Xanthomonas campestris pv. phaseoli (Smith Dye (Xcp. In the "El Mulato" farm belonging to the Empowered Cooperative of Credit and Services (CCSF "Orlando Cuellar" in the municipality San José de las Lajas, Mayabeque, two experiments were conducted. In the first one, 15 genotypes were planted in 13 September 2014 (early season in experimental plots to develop a diversity Fair and evaluate the natural incidence of common bean bacteriosis. In the second experiment, they were sown on 25 December (late season the materials selected by farmers with superior agronomic performance (7 genotypes to validate the stability of its performance. Among the results, an effective range of 93,33 % between the selected materials and selective criteria that this diversity was identified were high performance, resistance to common bacteriosis and color of beans. It was found that the selection of the diversity of beans by farmers is not influenced by the origin of materials and participatory selection identified common bean genotypes with high yield potential and stability between planting seasons.

  2. Identification of contemporary selection signatures using composite log likelihood and their associations with marbling score in Korean cattle.

    Science.gov (United States)

    Ryu, Jihye; Lee, Chaeyoung

    2014-12-01

    Positive selection not only increases beneficial allele frequency but also causes augmentation of allele frequencies of sequence variants in close proximity. Signals for positive selection were detected by the statistical differences in subsequent allele frequencies. To identify selection signatures in Korean cattle, we applied a composite log-likelihood (CLL)-based method, which calculates a composite likelihood of the allelic frequencies observed across sliding windows of five adjacent loci and compares the value with the critical statistic estimated by 50,000 permutations. Data for a total of 11,799 nucleotide polymorphisms were used with 71 Korean cattle and 209 foreign beef cattle. As a result, 147 signals were identified for Korean cattle based on CLL estimates (P selected. Further genetic association analysis with 41 intragenic variants in the selection signatures with the greatest CLL for each chromosome revealed that marbling score was associated with five variants. Intensive association studies with all the selection signatures identified in this study are required to exclude signals associated with other phenotypes or signals falsely detected and thus to identify genetic markers for meat quality. © 2014 Stichting International Foundation for Animal Genetics.

  3. Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects.

    NARCIS (Netherlands)

    Buelow, Elena; Bello González, Teresita D J; Fuentes, Susana; de Steenhuijsen Piters, Wouter A A; Lahti, Leo; Bayjanov, Jumamurat R; Majoor, Eline A M; Braat, Johanna C; van Mourik, Maaike S M; Oostdijk, Evelien A N; Willems, Rob J L; Bonten, Marc J M; van Passel, Mark W J; Smidt, Hauke; van Schaik, Willem

    2017-01-01

    The gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed "selective

  4. Identification of [4-[4-(methylsulfonyl)phenyl]-6-(trifluoromethyl)-2-pyrimidinyl] amines and ethers as potent and selective cyclooxygenase-2 inhibitors.

    Science.gov (United States)

    Swarbrick, Martin E; Beswick, Paul J; Gleave, Robert J; Green, Richard H; Bingham, Sharon; Bountra, Chas; Carter, Malcolm C; Chambers, Laura J; Chessell, Iain P; Clayton, Nick M; Collins, Sue D; Corfield, John A; Hartley, C David; Kleanthous, Savvas; Lambeth, Paul F; Lucas, Fiona S; Mathews, Neil; Naylor, Alan; Page, Lee W; Payne, Jeremy J; Pegg, Neil A; Price, Helen S; Skidmore, John; Stevens, Alexander J; Stocker, Richard; Stratton, Sharon C; Stuart, Alastair J; Wiseman, Joanne O

    2009-08-01

    A novel series of [4-[4-(methylsulfonyl)phenyl]-6-(trifluoromethyl)-2-pyrimidine-based cyclooxygenase-2 (COX-2) inhibitors, which have a different arrangement of substituents compared to the more common 1,2-diarylheterocycle based molecules, have been discovered. For example, 2-(butyloxy)-4-[4-(methylsulfonyl)phenyl]-6-(trifluoromethyl)pyrimidine (47), a member of the 2-pyrimidinyl ether series, has been shown to be a potent and selective inhibitor with a favourable pharmacokinetic profile, high brain penetration and good efficacy in rat models of hypersensitivity.

  5. Profiling the nucleobase and structure selectivity of anticancer drugs and other DNA alkylating agents by RNA sequencing.

    Science.gov (United States)

    Gillingham, Dennis; Sauter, Basilius

    2018-05-06

    Drugs that covalently modify DNA are components of most chemotherapy regimens, often serving as first-line treatments. Classically the chemical reactivity of DNA alkylators has been determined in vitro with short oligonucleotides. Here we use next generation RNA sequencing to report on the chemoselectivity of alkylating agents. We develop the method with the well-known clinically used DNA modifiying drugs streptozotocin and temozolomide, and then apply the technique to profile RNA modification with uncharacterized alkylation reactions such as with powerful electrophiles like trimethylsilyldiazomethane. The multiplexed and massively parallel format of NGS offers analyses of chemical reactivity in nucleic acids to be accomplished in less time with greater statistical power. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. The chemical profile of pyrrolizidine alkaloids from selected greek endemic boraginaceae plants determined by gas chromatography/mass spectrometry.

    Science.gov (United States)

    Damianakos, Harilaos; Jeziorek, Malgorzata; Pietrosiuk, Agnieszka; Chinou, Ioanna

    2014-01-01

    Four Greek endemic Boraginaceae plants, Onosma erecta Sibth. & Sm., Onosma kaheirei Teppner, Onosma leptantha Heldr., and Cynoglossum columnae L. (aerial parts), were screened for their content of pyrrolizidine alkaloids (PAs). TLC with the Mattocks-Molyneux visualization reagent was used as a preliminary qualitative test for PA or PA N-oxide detection. The extracts of the species found to contain PAs and their N-oxides were further analyzed by GC/MS, so as to identify their structures by means of the mass spectra and retention index values of known PAs already published in the literature. Twenty-three PAs were identified. For additional peaks, recognized as possible PAs by their MS pattern, no exact structures were tentatively suggested, as a result of lack of matching literature data. Furthermore, a quantitative PA profile of the species was obtained.

  7. Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes

    Directory of Open Access Journals (Sweden)

    Lotz Meredith J

    2008-01-01

    Full Text Available Abstract Background Gene expression data frequently contain missing values, however, most down-stream analyses for microarray experiments require complete data. In the literature many methods have been proposed to estimate missing values via information of the correlation patterns within the gene expression matrix. Each method has its own advantages, but the specific conditions for which each method is preferred remains largely unclear. In this report we describe an extensive evaluation of eight current imputation methods on multiple types of microarray experiments, including time series, multiple exposures, and multiple exposures × time series data. We then introduce two complementary selection schemes for determining the most appropriate imputation method for any given data set. Results We found that the optimal imputation algorithms (LSA, LLS, and BPCA are all highly competitive with each other, and that no method is uniformly superior in all the data sets we examined. The success of each method can also depend on the underlying "complexity" of the expression data, where we take complexity to indicate the difficulty in mapping the gene expression matrix to a lower-dimensional subspace. We developed an entropy measure to quantify the complexity of expression matrixes and found that, by incorporating this information, the entropy-based selection (EBS scheme is useful for selecting an appropriate imputation algorithm. We further propose a simulation-based self-training selection (STS scheme. This technique has been used previously for microarray data imputation, but for different purposes. The scheme selects the optimal or near-optimal method with high accuracy but at an increased computational cost. Conclusion Our findings provide insight into the problem of which imputation method is optimal for a given data set. Three top-performing methods (LSA, LLS and BPCA are competitive with each other. Global-based imputation methods (PLS, SVD, BPCA

  8. Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes.

    Science.gov (United States)

    Brock, Guy N; Shaffer, John R; Blakesley, Richard E; Lotz, Meredith J; Tseng, George C

    2008-01-10

    Gene expression data frequently contain missing values, however, most down-stream analyses for microarray experiments require complete data. In the literature many methods have been proposed to estimate missing values via information of the correlation patterns within the gene expression matrix. Each method has its own advantages, but the specific conditions for which each method is preferred remains largely unclear. In this report we describe an extensive evaluation of eight current imputation methods on multiple types of microarray experiments, including time series, multiple exposures, and multiple exposures x time series data. We then introduce two complementary selection schemes for determining the most appropriate imputation method for any given data set. We found that the optimal imputation algorithms (LSA, LLS, and BPCA) are all highly competitive with each other, and that no method is uniformly superior in all the data sets we examined. The success of each method can also depend on the underlying "complexity" of the expression data, where we take complexity to indicate the difficulty in mapping the gene expression matrix to a lower-dimensional subspace. We developed an entropy measure to quantify the complexity of expression matrixes and found that, by incorporating this information, the entropy-based selection (EBS) scheme is useful for selecting an appropriate imputation algorithm. We further propose a simulation-based self-training selection (STS) scheme. This technique has been used previously for microarray data imputation, but for different purposes. The scheme selects the optimal or near-optimal method with high accuracy but at an increased computational cost. Our findings provide insight into the problem of which imputation method is optimal for a given data set. Three top-performing methods (LSA, LLS and BPCA) are competitive with each other. Global-based imputation methods (PLS, SVD, BPCA) performed better on mcroarray data with lower complexity

  9. Variations in fatty acid composition, glucosinolate profile and some phyto chemical contents in selected oil seed rape (Brassica napus L.) cultivars

    Energy Technology Data Exchange (ETDEWEB)

    El-Din Saad El-Beltag, H.; Mohamed, A. A.

    2010-07-01

    Rapeseed (Brassica napus L.) is now the third most important source of edible oil in the world after soybean and palm oil. In this study seeds of five different rapeseed cultivars namely; pactol, silvo, topas, serw 4 and serw 6 were evaluated for their fatty acid composition, glucosinolate profile, amino acids, total tocopherols and phenolic content. Among all cultivars significant variability in fatty acids were observed. The oleic acid (C18:1) ranged from 56.31% to 58.67%, linoleic acid (C18:2) from 10.52% to 13.74%, {alpha}-linolenic acid (C18:3) from 8.83% to 10.32% and erucic acid (22:1) from 0.15% to 0.91%. The glucosinolate profile of rapeseed was also separated and identified using high-performance liquid chromatography. Small variations in the glucosinolate profile were observed among all tested cultivars; however, progoitrin and gluconapin were the major glucosinolate found. Additionally, silvo cultivar showed the highest total glucosinolate contents (5.97 {mu}mol/g dw). Generally, the contents of aspartic, glutamic, arginine and leucine were high, while the contents of tyrosine and isoleucine were low among all cultivars. For total tocopherols, the results indicated that both serw 6 and pactol cultivars had the highest total tocopherol contents (138.3 and 102.8 mg/100 g oil, respectively). Total phenolic contents varied from 28.0 to 35.4 mg/g dw. The highest total phenolic content was found in topas while the lowest value was detected in serw 6. These parameters; fatty acid contents, glucosinolate profile and amino acids together with total tocopherols and phenolic contents, could be taken into consideration by oilseed rape breeders as selection criteria for developing genotypes with modified seed quality traits in Brassica napus L. (Author)

  10. Temperature profile retrieval in axisymmetric combustion plumes using multilayer perceptron modeling and spectral feature selection in the infrared CO2 emission band.

    Science.gov (United States)

    García-Cuesta, Esteban; de Castro, Antonio J; Galván, Inés M; López, Fernando

    2014-01-01

    In this work, a methodology based on the combined use of a multilayer perceptron model fed using selected spectral information is presented to invert the radiative transfer equation (RTE) and to recover the spatial temperature profile inside an axisymmetric flame. The spectral information is provided by the measurement of the infrared CO2 emission band in the 3-5 μm spectral region. A guided spectral feature selection was carried out using a joint criterion of principal component analysis and a priori physical knowledge of the radiative problem. After applying this guided feature selection, a subset of 17 wavenumbers was selected. The proposed methodology was applied over synthetic scenarios. Also, an experimental validation was carried out by measuring the spectral emission of the exhaust hot gas plume in a microjet engine with a Fourier transform-based spectroradiometer. Temperatures retrieved using the proposed methodology were compared with classical thermocouple measurements, showing a good agreement between them. Results obtained using the proposed methodology are very promising and can encourage the use of sensor systems based on the spectral measurement of the CO2 emission band in the 3-5 μm spectral window to monitor combustion processes in a nonintrusive way.

  11. Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM analysis [v1; ref status: indexed, http://f1000r.es/2hj

    Directory of Open Access Journals (Sweden)

    Erin K. Hanson

    2013-12-01

    Full Text Available Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE or quantitative RT-PCR (qRT-PCR platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions, IL1F7 (skin, ALAS2 (blood, MMP10 (menstrual blood, HTN3 (saliva and TGM4 (semen.  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green. Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively

  12. Multiple flow profiles for two-phase flow in single microfluidic channels through site-selective channel coating.

    Science.gov (United States)

    Logtenberg, Hella; Lopez-Martinez, Maria J; Feringa, Ben L; Browne, Wesley R; Verpoorte, Elisabeth

    2011-06-21

    An approach to control two-phase flow systems in a poly(dimethylsiloxane) (PDMS) microfluidic device using spatially selective surface modification is demonstrated. Side-by-side flows of ethanol : water solutions containing different polymers are used to selectively modify both sides of a channel by laminar flow patterning. Introduction of air pockets during modification allows for control over the length of the channel section that is modified. This approach makes it possible to achieve slug flow and side-by-side flow of water : 1-octanol simultaneously within the same PDMS channel, without the need of additional structural elements. A key finding is that conditioning of the PDMS channels with 1-octanol before polymer deposition is crucial to achieving stable side-by-side flows.

  13. Quick survey for detection, identification and characterization of Acanthamoeba genotypes from some selected soil and water samples in Pakistan

    Directory of Open Access Journals (Sweden)

    Tania Tanveer

    2015-05-01

    Full Text Available Acanthamoeba is an opportunistic protozoan pathogen which is widely distributed in nature and plays a pivotal role in ecosystem. Acanthamoeba species may cause blinding keratitis and fatal granulomatous encephalitis involving central nervous system. In this study, we investigated the presence of Acanthamoeba in soil and water resources of Pakistan. Here, Acanthamoeba were recovered on non-nutrient agar plate lawn with E.coli and identified by morphological characteristics of the cyst. Furthermore PCR was performed with genus-specific primers followed by direct sequencing of the PCR product for molecular identification. Overall our PCR and sequencing results confirmed pathogenic genotypes including T4 and T15 from both soil and water samples. This is our first report of Acanthamoeba isolation from both soil and water resources of Pakistan which may serve as a potential treat to human health across the country.

  14. Chemical Profiling and Evaluation of Antioxidant and Anti-Microbial Properties of Selected Commercial Essential Oils: A Comparative Study

    OpenAIRE

    Lu?s, ?ngelo; Duarte, Ana Paula; Pereira, Lu?sa; Domingues, Fernanda

    2017-01-01

    Background: The last decades have seen an increased awareness by the scientific community of the extent of resistance to conventional antibiotics, particularly with respect to the emerging multidrug-resistant pathogenic microbes. Additionally, natural antioxidants have received significant attention among food professionals and consumers because of their assumed safety and potential therapeutic value. The aim of this work was to assess the antioxidant activities of eight selected commercial e...

  15. In vitro profiling of antimethicillin-resistant Staphylococcus aureus activity of thymoquinone against selected type and clinical strains.

    Science.gov (United States)

    Hariharan, P; Paul-Satyaseela, M; Gnanamani, A

    2016-03-01

    This study explores antimethicillin-resistant Staphylococcus aureus (MRSA) activity of a bioactive phytochemical constituent, thymoquinone obtained from the medicinal herb, Nigella sativa Linn. Based on initial assessment on crude extract of seeds of Nigella sativa Linn, the pure active constituent was employed in the study. A total of 99 MRSA strains which comprised of 40 types and 59 clinical strains were selected for the study. Minimum inhibitory concentration (MIC), bactericidal activity, postantibiotic effect (PAE) and propensity to select resistant mutants were determined using standard protocols. Results revealed that thymoquinone exhibited MIC in the range of 8-16 μg ml(-1) and MIC90 of 16 μg ml(-1) against MRSA strains. It was bactericidal to MRSA by demonstrating >3 log kill. It showed a longer PAE of 3·2 ± 0·2 h. Upon exposure to high-density inoculum of MRSA, it did not select resistant mutants. Transmission electron microscopy of thymoquinone-treated MRSA showed no lysis but damage to cell wall and cell membrane which corroborated well with the salt tolerance and bacteriolysis assays. In conclusion, MIC90 , bactericidal property, longer PAE, absence of resistant mutant selection and damages in cell membrane and cell wall imply a promising anti-MRSA activity of thymoquinone. This is the first detailed report on anti-MRSA activity of thymoquinone. The assessment was made with both type and clinical strains. Thymoquinone may be a potential lead compound which can be further optimized to discover novel anti-MRSA agents. © 2016 The Society for Applied Microbiology.

  16. Estimation of Leakage Potential of Selected Sites in Interstate and Tri-State Canals Using Geostatistical Analysis of Selected Capacitively Coupled Resistivity Profiles, Western Nebraska, 2004

    Science.gov (United States)

    Vrabel, Joseph; Teeple, Andrew; Kress, Wade H.

    2009-01-01

    With increasing demands for reliable water supplies and availability estimates, groundwater flow models often are developed to enhance understanding of surface-water and groundwater systems. Specific hydraulic variables must be known or calibrated for the groundwater-flow model to accurately simulate current or future conditions. Surface geophysical surveys, along with selected test-hole information, can provide an integrated framework for quantifying hydrogeologic conditions within a defined area. In 2004, the U.S. Geological Survey, in cooperation with the North Platte Natural Resources District, performed a surface geophysical survey using a capacitively coupled resistivity technique to map the lithology within the top 8 meters of the near-surface for 110 kilometers of the Interstate and Tri-State Canals in western Nebraska and eastern Wyoming. Assuming that leakage between the surface-water and groundwater systems is affected primarily by the sediment directly underlying the canal bed, leakage potential was estimated from the simple vertical mean of inverse-model resistivity values for depth levels with geometrically increasing layer thickness with depth which resulted in mean-resistivity values biased towards the surface. This method generally produced reliable results, but an improved analysis method was needed to account for situations where confining units, composed of less permeable material, underlie units with greater permeability. In this report, prepared by the U.S. Geological Survey in cooperation with the North Platte Natural Resources District, the authors use geostatistical analysis to develop the minimum-unadjusted method to compute a relative leakage potential based on the minimum resistivity value in a vertical column of the resistivity model. The minimum-unadjusted method considers the effects of homogeneous confining units. The minimum-adjusted method also is developed to incorporate the effect of local lithologic heterogeneity on water

  17. Identification of selected in vitro generated phase-I metabolites of the steroidal selective androgen receptor modulator MK-0773 for doping control purposes.

    Science.gov (United States)

    Lagojda, Andreas; Kuehne, Dirk; Krug, Oliver; Thomas, Andreas; Wigger, Tina; Karst, Uwe; Schänzer, Wilhelm; Thevis, Mario

    2016-01-01

    Research into developing anabolic agents for various therapeutic purposes has been pursued for decades. As the clinical utility of anabolic-androgenic steroids has been found to be limited because of their lack of tissue selectivity and associated off-target effects, alternative drug entities have been designed and are commonly referred to as selective androgen receptor modulators (SARMs). While most of these SARMs are of nonsteroidal structure, the drug candidate MK-0773 comprises a 4-aza-steroidal nucleus. Besides the intended therapeutic use, SARMs have been found to be illicitly distributed and misused as doping agents in sport, necessitating frequently updated doping control analytical assays. As steroidal compounds reportedly undergo considerable metabolic transformations, the phase-I metabolism of MK-0773 was simulated using human liver microsomal (HLM) preparations and electrochemical conversion. Subsequently, major metabolic products were identified and characterized employing liquid chromatography-high-resolution/high- accuracy tandem mass spectrometry with electrospray (ESI) and atmospheric pressure chemical ionization (APCI) as well as nuclear magnetic resonance (NMR) spectroscopy. MK-0773 produced numerous phase-I metabolites under the chosen in vitro incubation reactions, mostly resulting from mono- and bisoxygenation of the steroid. HLM yielded at least 10 monooxygenated species, while electrochemistry-based experiments resulted predominantly in three monohydroxylated metabolites. Elemental composition data and product ion mass spectra were generated for these analytes, ESI/APCI measurements corroborated the formation of at least two N-oxygenated metabolites, and NMR data obtained from electrochemistry-derived products supported structures suggested for three monohydroxylated compounds. Hereby, the hydroxylation of the A-ring located N- bound methyl group was found to be of particular intensity. In the absence of controlled elimination studies, the

  18. Coding-Sequence Identification and Transcriptional Profiling of Nine AMTs and Four NRTs From Tobacco Revealed Their Differential Regulation by Developmental Stages, Nitrogen Nutrition, and Photoperiod

    Directory of Open Access Journals (Sweden)

    Lai-Hua Liu

    2018-03-01

    Full Text Available Although many members encoding different ammonium- and nitrate-transporters (AMTs, NRTs were identified and functionally characterized from several plant species, little is known about molecular components for NH4+- and NO3- acquisition/transport in tobacco, which is often used as a plant model for biological studies besides its agricultural and industrial interest. We reported here the first molecular identification in tobacco (Nicotiana tabacum of nine AMTs and four NRTs, which are respectively divided into four (AMT1/2/3/4 and two (NRT1/2 clusters and whose functionalities were preliminarily evidenced by heterologous functional-complementation in yeast or Arabidopsis. Tissue-specific transcriptional profiling by qPCR revealed that NtAMT1.1/NRT1.1 mRNA occurred widely in leaves, flower organs and roots; only NtAMT1.1/1.3/2.1NRT1.2/2.2 were strongly transcribed in the aged leaves, implying their dominant roles in N-remobilization from source/senescent tissues. N-dependent expression analysis showed a marked upregulation of NtAMT1.1 in the roots by N-starvation and resupply with N including NH4+, suggesting a predominant action of NtAMT1.1 in NH4+ uptake/transport whenever required. The obvious leaf-expression of other NtAMTs e.g., AMT1.2 responsive to N indicates a major place, where they may play transport roles associated with plant N-status and (NH4+-N movement within aerial-parts. The preferentially root-specific transcription of NtNRT1.1/1.2/2.1 responsive to N argues their importance for root NO3- uptake and even sensing in root systems. Moreover, of all NtAMTs/NRTs, only NtAMT1.1/NRT1.1/1.2 showed their root-expression alteration in a typical diurnal-oscillation pattern, reflecting likely their significant roles in root N-acquisition regulated by internal N-demand influenced by diurnal-dependent assimilation and translocation of carbohydrates from shoots. This suggestion could be supported at least in part by sucrose- and MSX

  19. Coding-Sequence Identification and Transcriptional Profiling of Nine AMTs and Four NRTs From Tobacco Revealed Their Differential Regulation by Developmental Stages, Nitrogen Nutrition, and Photoperiod

    Science.gov (United States)

    Liu, Lai-Hua; Fan, Teng-Fei; Shi, Dong-Xue; Li, Chang-Jun; He, Ming-Jie; Chen, Yi-Yin; Zhang, Lei; Yang, Chao; Cheng, Xiao-Yuan; Chen, Xu; Li, Di-Qin; Sun, Yi-Chen

    2018-01-01

    Although many members encoding different ammonium- and nitrate-transporters (AMTs, NRTs) were identified and functionally characterized from several plant species, little is known about molecular components for NH4+- and NO3- acquisition/transport in tobacco, which is often used as a plant model for biological studies besides its agricultural and industrial interest. We reported here the first molecular identification in tobacco (Nicotiana tabacum) of nine AMTs and four NRTs, which are respectively divided into four (AMT1/2/3/4) and two (NRT1/2) clusters and whose functionalities were preliminarily evidenced by heterologous functional-complementation in yeast or Arabidopsis. Tissue-specific transcriptional profiling by qPCR revealed that NtAMT1.1/NRT1.1 mRNA occurred widely in leaves, flower organs and roots; only NtAMT1.1/1.3/2.1NRT1.2/2.2 were strongly transcribed in the aged leaves, implying their dominant roles in N-remobilization from source/senescent tissues. N-dependent expression analysis showed a marked upregulation of NtAMT1.1 in the roots by N-starvation and resupply with N including NH4+, suggesting a predominant action of NtAMT1.1 in NH4+ uptake/transport whenever required. The obvious leaf-expression of other NtAMTs e.g., AMT1.2 responsive to N indicates a major place, where they may play transport roles associated with plant N-status and (NH4+-)N movement within aerial-parts. The preferentially root-specific transcription of NtNRT1.1/1.2/2.1 responsive to N argues their importance for root NO3- uptake and even sensing in root systems. Moreover, of all NtAMTs/NRTs, only NtAMT1.1/NRT1.1/1.2 showed their root-expression alteration in a typical diurnal-oscillation pattern, reflecting likely their significant roles in root N-acquisition regulated by internal N-demand influenced by diurnal-dependent assimilation and translocation of carbohydrates from shoots. This suggestion could be supported at least in part by sucrose- and MSX-affected transcriptional

  20. [Mineral elements analysis of Momordica charantiap seeds by ICP-AES and fatty acid profile identification of seed oil by GC-MS].

    Science.gov (United States)

    Liu, Xiao-ru; Deng, Ze-yuan; Fan, Ya-wei; Li, Jing; Liu, Zhi-han

    2010-08-01

    In the present study, a special kind of Momordica charantia seeds produced in Hai Nan was selected and analyzed. Firstly, inductively coupled plasma-atomic emission spectrophotometry (ICP-AES) was used to determine the mineral elements. It was clear that the contents of K, Mg and P are the highest in the seeds; Cr and Zn takes up to 5.65% and 45.45% high, especially, which are rare in plant foods. These minerals, especially Cr and Zn might have a complex effect on those proteins or polysaccharides and form a stronger anticipation of hyperlipidemia, hyperglycemia and cholesterol. Secondly, seed oil was extracted by supercritical CO2 extraction with a yield ratio of 36.89, and the fatty acids were treated by methylation in alkaline process and purified by thin-layer chromatography, then analyzed by gas chromatography-mass spectrometer (GC-MS) identification. The saturated fatty acids (SFA) take up 36.712, and mainly are stearic acid; monounsaturated fatty acid (MUFA) is only 3.33% which is dominantly linoleic acid (LA); Polyunsaturated fatty acid (PUFA) accounted for 59.96%, and the alpha-eleostearic acid takes up 54.26% as the main fatty acids in all. The plentiful alpha-eleostearic acid leads to strong effects of inhibiting tumor cell proliferation, lowering blood fat, anti-cancer, anti-inflammatory and preventing cardiovascular diseases, and so on. Knowing clearly the mineral elements distribution and identifying the composition of fatty acid, especially the main fatty acids in the oil, are both of great guiding importance to further exploit the clinical and edible value in Momordica charantiap seeds.

  1. The [O III] Profiles of Infrared-selected Active Galactic Nuclei: More Powerful Outflows in the Obscured Population

    Science.gov (United States)

    DiPompeo, M. A.; Hickox, R. C.; Carroll, C. M.; Runnoe, J. C.; Mullaney, J. R.; Fischer, T. C.

    2018-03-01

    We explore the kinematics of ionized gas via the [O III] λ5007 emission lines in active galactic nuclei (AGNs) selected on the basis of their mid-infrared (IR) emission, and split into obscured and unobscured populations based on their optical‑IR colors. After correcting for differences in redshift distributions, we provide composite spectra of spectroscopically and photometrically defined obscured/Type 2 and unobscured/Type 1 AGNs from 3500 to 7000 Å. The IR-selected obscured sources contain a mixture of narrow-lined Type 2 AGNs and intermediate sources that have broad Hα emission and significantly narrower Hβ. Using both [O III] luminosities and AGN luminosities derived from optical‑IR spectral energy distribution fitting, we find evidence for enhanced large-scale obscuration in the obscured sources. In matched bins of luminosity we find that the obscured population typically has broader, more blueshifted [O III] emission than in the unobscured sample, suggestive of more powerful AGN-driven outflows. This trend is not seen in spectroscopically classified samples, and is unlikely to be entirely explained by orientation effects. In addition, outflow velocities increase from small to moderate AGN E(B ‑ V) values, before flattening out (as traced by FWHM) and even decreasing (as traced by blueshift). While difficult to fully interpret in a single physical model, due to both the averaging over populations and the spatially averaged spectra, these results agree with previous findings that simple geometric unification models are insufficient for the IR-selected AGN population, and may fit into an evolutionary model for obscured and unobscured AGNs.

  2. The profile of selected samples of Croatian athletes based on the items of sport jealousy scale (SJS

    Directory of Open Access Journals (Sweden)

    Sindik Joško

    2016-01-01

    Full Text Available The role of jealousy in sport, as a negative emotional reaction, accompanied by thoughts of inadequacy when compared to others, is the issue of this article. This study had a purpose to define the characteristic profiles of the Croatian athletes, based on single items of Sport Jealousy Scale (SJS II, labeled by several variables: gender, type of sport, age group. Purposive sample of 73 athletes competing at Croatian championships in different sports (football, bowling, volleyball and handball were examined with Croatian version of SJS-II. Three clusters obtained are similarly balanced, according to the number of cases in each cluster. The most simply explained, clusters clearly differentiate the most jealous, moderately jealous and slightly/low jealous athletes. Among the features of the athletes in each cluster, in the most jealous (first cluster are the athletes from team sports, women and older athletes. Females, bowling athletes, athletes from individual (coactive sports and the youngest athletes are the least jealous (grouped in third cluster.

  3. Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq.

    Science.gov (United States)

    Chang, Yiming K; Srivastava, Yogesh; Hu, Caizhen; Joyce, Adam; Yang, Xiaoxiao; Zuo, Zheng; Havranek, James J; Stormo, Gary D; Jauch, Ralf

    2017-01-25

    Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities. However, current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. We developed Coop-seq (cooperativity by sequencing) that is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment. We apply Coop-seq to 12 dimer pairs from the Sox and POU families of transcription factors using 324 unique sequences with changed half-site orientation, altered spacing and discrete randomization within the binding elements. The study reveals specific dimerization profiles of different Sox factors with Oct4. By contrast, Oct4 and the three neural class III POU factors Brn2, Brn4 and Oct6 assemble with Sox2 in a surprisingly indistinguishable manner. Two novel half-site configurations can support functional Sox/Oct dimerization in addition to known composite motifs. Moreover, Coop-seq uncovers a nucleotide switch within the POU half-site when spacing is altered, which is mirrored in genomic loci bound by Sox2/Oct4 complexes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. A novel strategy for global mapping of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry identification.

    Science.gov (United States)

    Shen, Bingquan; Zhang, Wanjun; Shi, Zhaomei; Tian, Fang; Deng, Yulin; Sun, Changqing; Wang, Guangshun; Qin, Weijie; Qian, Xiaohong

    2017-07-01

    O-GlcNAcylation is a kind of dynamic O-linked glycosylation of nucleocytoplasmic and mitochondrial proteins. It serves as a major nutrient sensor to regulate numerous biological processes including transcriptional regulation, cell metabolism, cellular signaling, and protein degradation. Dysregulation of cellular O-GlcNAcylated levels contributes to the etiologies of many diseases such as diabetes, neurodegenerative disease and cancer. However, deeper insight into the biological mechanism of O-GlcNAcylation is hampered by its extremely low stoichiometry and the lack of efficient enrichment approaches for large-scale identification by mass spectrometry. Herein, we developed a novel strategy for the global identification of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry analysis. Standard O-GlcNAc peptides can be efficiently enriched even in the presence of 500-fold more abundant non-O-GlcNAc peptides and identified by mass spectrometry with a low nanogram detection sensitivity. This strategy successfully achieved the first large-scale enrichment and characterization of O-GlcNAc proteins and peptides in human urine. A total of 474 O-GlcNAc peptides corresponding to 457 O-GlcNAc proteins were identified by mass spectrometry analysis, which is at least three times more than that obtained by commonly used enrichment methods. A large number of unreported O-GlcNAc proteins related to cell cycle, biological regulation, metabolic and developmental process were found in our data. The above results demonstrated that this novel strategy is highly efficient in the global enrichment and identification of O-GlcNAc peptides. These data provide new insights into the biological function of O-GlcNAcylation in human urine, which is correlated with the physiological states and pathological changes of human body and therefore indicate the potential of this strategy for biomarker discovery from human urine. Copyright

  5. A new laser vibrometry-based 2D selective intensity method for source identification in reverberant fields: part II. Application to an aircraft cabin

    International Nuclear Information System (INIS)

    Revel, G M; Martarelli, M; Chiariotti, P

    2010-01-01

    The selective intensity technique is a powerful tool for the localization of acoustic sources and for the identification of the structural contribution to the acoustic emission. In practice, the selective intensity method is based on simultaneous measurements of acoustic intensity, by means of a couple of matched microphones, and structural vibration of the emitting object. In this paper high spatial density multi-point vibration data, acquired by using a scanning laser Doppler vibrometer, have been used for the first time. Therefore, by applying the selective intensity algorithm, the contribution of a large number of structural sources to the acoustic field radiated by the vibrating object can be estimated. The selective intensity represents the distribution of the acoustic monopole sources on the emitting surface, as if each monopole acted separately from the others. This innovative selective intensity approach can be very helpful when the measurement is performed on large panels in highly reverberating environments, such as aircraft cabins. In this case the separation of the direct acoustic field (radiated by the vibrating panels of the fuselage) and the reverberant one is difficult by traditional techniques. The work shown in this paper is the application of part of the results of the European project CREDO (Cabin Noise Reduction by Experimental and Numerical Design Optimization) carried out within the framework of the EU. Therefore the aim of this paper is to illustrate a real application of the method to the interior acoustic characterization of an Alenia Aeronautica ATR42 ground test facility, Alenia Aeronautica being a partner of the CREDO project

  6. Identification of a domain within human TAF(I)48, a subunit of Selectivity Factor 1, that interacts with helix 2 of TBP.

    Science.gov (United States)

    Xu, Shuping; Hori, Roderick T

    2004-09-01

    RNA polymerase I transcription in human cells requires Selectivity Factor 1, a multisubunit complex composed of the TATA-box-binding protein (TBP) and three TBP-associated factors (TAFs) called TAF(I)48, TAF(I)63 and TAF(I)110. Each of the Selectivity Factor 1 subunits binds directly to the other three components, but these interactions have not been characterized. This study is the initial identification and analysis of a TBP-binding domain within a Selectivity Factor 1 TAF. The interaction between human TBP and human TAF(I)48 was initially examined using the yeast two-hybrid assay, and a TBP-binding domain was identified in the carboxyl-terminus of human (h)TAF(I)48. Consistent with this result, the hTAF(I)48 carboxyl-terminus was able to bind directly to TBP in protein-protein interaction assays. When mutations were introduced into the hTAF(I)48 carboxyl-terminus, we identified changes in uncharged and positive residues that affect its interaction with TBP. By examining TBP mutants, residues within and adjacent to helix 2 of TBP, previously demonstrated to interact with subunits of other TBP-containing complexes [Transcription Factor IID (TFIID) and TFIIIB] were also found to diminish its affinity for the carboxyl-terminus of hTAF(I)48. The regions of hTAF(I)48 and TBP that interact are compared to those identified within other complexes containing TBP.

  7. A Genetics Laboratory Module Involving Selection and Identification of Lysine Synthesis Mutants in the Yeast Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Jill B. Keeney

    2009-12-01

    Full Text Available We have developed a laboratory exercise, currently being used with college sophomores, which uses the yeast Saccharomyces cerevisiae to convey the concepts of amino acid biosynthesis, mutation, and gene complementation. In brief, selective medium is used to isolate yeast cells carrying a mutation in the lysine biosynthesis pathway. A spontaneous mutation in any one of three separate genetic loci will allow for growth on selective media; however, the frequency of mutations isolated from each locus differs. Following isolation of a mutated strain, students use complementation analysis to identify which gene contains the mutation. Since the yeast genome has been mapped and sequenced, students with access to the Internet can then research and develop hypotheses to explain the differences in frequencies of mutant genes obtained.

  8. Identification of potential nuclear reprogramming and differentiation factors by a novel selection method for cloning chromatin-binding proteins

    International Nuclear Information System (INIS)

    Wang Liu; Zheng Aihua; Yi Ling; Xu Chongren; Ding Mingxiao; Deng Hongkui

    2004-01-01

    Nuclear reprogramming is critical for animal cloning and stem cell creation through nuclear transfer, which requires extensive remodeling of chromosomal architecture involving dramatic changes in chromatin-binding proteins. To understand the mechanism of nuclear reprogramming, it is critical to identify chromatin-binding factors specify the reprogramming process. In this report, we have developed a high-throughput selection method, based on T7 phage display and chromatin immunoprecipitation, to isolate chromatin-binding factors expressed in mouse embryonic stem cells using primary mouse embryonic fibroblast chromatin. Seven chromatin-binding proteins have been isolated by this method. We have also isolated several chromatin-binding proteins involved in hepatocyte differentiation. Our method provides a powerful tool to rapidly and selectively identify chromatin-binding proteins. The method can be used to study epigenetic modification of chromatin during nuclear reprogramming, cell differentiation, and transdifferentiation

  9. Simultaneous Identification of Potential Pathogenicity Factors of Mycoplasma agalactiae in the Natural Ovine Host by Negative Selection

    OpenAIRE

    Hegde, Shivanand; Hegde, Shrilakshmi; Zimmermann, Martina; Flöck, Martina; Spergser, Joachim; Rosengarten, Renate; Chopra-Dewasthaly, Rohini

    2015-01-01

    Mycoplasmas possess complex pathogenicity determinants that are largely unknown at the molecular level. Mycoplasma agalactiae serves as a useful model to study the molecular basis of mycoplasma pathogenicity. The generation and in vivo screening of a transposon mutant library of M. agalactiae were employed to unravel its host colonization factors. Tn4001mod mutants were sequenced using a novel sequencing method, and functionally heterogeneous pools containing 15 to 19 selected mutants were sc...

  10. NESS038C6, a novel selective CB1 antagonist agent with anti-obesity activity and improved molecular profile.

    Science.gov (United States)

    Mastinu, Andrea; Pira, Marilena; Pani, Luca; Pinna, Gérard Aimè; Lazzari, Paolo

    2012-10-01

    The present work aims to study the effects induced by a chronic treatment with a novel CB1 antagonist (NESS038C6) in C57BL/6N diet-induced obesity (DIO) mice. Mice treated with NESS038C6 and fed with a fat diet (NESS038C6 FD) were compared with the following three reference experimental groups: DIO mice fed with the same fat diet used for NESS038C6 and treated with vehicle or the reference CB1 antagonist/inverse agonist rimonabant, "VH FD" and "SR141716 FD", respectively; DIO mice treated with vehicle and switched to a normal diet (VH ND). NESS038C6 chronic treatment (30 mg/kg/day for 31 days) determined a significant reduction in DIO mice weight relative to that of VH FD. The entity of the effect was comparable to that detected in both SR141716 FD and VH ND groups. Moreover, if compared to VH FD, NESS038C6 FD evidenced: (i) improvement of cardiovascular risk factors; (ii) significant decrease in adipose tissue leptin expression; (iii) increase in mRNA expression of hypothalamic orexigenic peptides and a decrease of anorexigenic peptides; (iv) expression increase of metabolic enzymes and peroxisome proliferator-activated receptor-α in the liver; (v) normalization of monoaminergic transporters and neurotrophic expression in mesolimbic area. However, in contrast to the case of rimonabant, the novel CB1 antagonist improved the disrupted expression profile of genes linked to the hunger-satiety circuit, without altering monoaminergic transmission. In conclusion, the novel CB1 antagonist compound NESS038C6 may represent a useful candidate agent for the treatment of obesity and its metabolic complications, without or with reduced side effects relative to those instead observed with rimonabant. Copyright © 2012 Elsevier B.V. All rights reserved.