WorldWideScience

Sample records for analysis involving tvs-m

  1. Development of multi-group spectral code TVS-M

    International Nuclear Information System (INIS)

    Lazarenko, A.P.; Pryanichnikov, A.V.; Kalugin, M.A.; Gurevich, M.I.

    2012-01-01

    This paper is dedicated to the latest version of TVS-M code - TVS-M 2007, which allows the neutron flux distribution inside fuel assemblies to be calculated without using the diffusion approximation. The new spatial calculation module PERST introduced in TVS-M code is based on the first collisions probability method and allows the scattering anisotropy to be accounted for. This paper presents some preliminary results calculated with the use of the new version of TVS-M code. (orig.)

  2. Development of multi-group spectral code TVS-M

    International Nuclear Information System (INIS)

    Lazarenko, A. P.; Pryanichnikov, A. V.; Kalugin, M. A.; Gurevich, M. I.

    2011-01-01

    This paper is dedicated to the latest version of TVS-M code - TVS-M 2007, which allows the neutron flux distribution inside fuel assemblies to be calculated without using the diffusion approximation. The new spatial calculation module PERST introduced in TBS-M code is based on the first collisions probability method and allows the scattering anisotropy to be accounted for. This paper presents some preliminary results calculated with the use of the new version of TVS-M code. (Authors)

  3. The Data Party: Involving Stakeholders in Meaningful Data Analysis

    Science.gov (United States)

    Franz, Nancy K.

    2013-01-01

    A hallmark of Extension includes the involvement of stakeholders in research and program needs assessment, design, implementation, evaluation, and reporting. A data party can be used to enhance this stakeholder involvement specifically in data analysis. This type of event can not only increase client participation in Extension programming and…

  4. Informational analysis involving application of complex information system

    Science.gov (United States)

    Ciupak, Clébia; Vanti, Adolfo Alberto; Balloni, Antonio José; Espin, Rafael

    The aim of the present research is performing an informal analysis for internal audit involving the application of complex information system based on fuzzy logic. The same has been applied in internal audit involving the integration of the accounting field into the information systems field. The technological advancements can provide improvements to the work performed by the internal audit. Thus we aim to find, in the complex information systems, priorities for the work of internal audit of a high importance Private Institution of Higher Education. The applied method is quali-quantitative, as from the definition of strategic linguistic variables it was possible to transform them into quantitative with the matrix intersection. By means of a case study, where data were collected via interview with the Administrative Pro-Rector, who takes part at the elaboration of the strategic planning of the institution, it was possible to infer analysis concerning points which must be prioritized at the internal audit work. We emphasize that the priorities were identified when processed in a system (of academic use). From the study we can conclude that, starting from these information systems, audit can identify priorities on its work program. Along with plans and strategic objectives of the enterprise, the internal auditor can define operational procedures to work in favor of the attainment of the objectives of the organization.

  5. Representation of analysis results involving aleatory and epistemic uncertainty.

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Jay Dean (ProStat, Mesa, AZ); Helton, Jon Craig (Arizona State University, Tempe, AZ); Oberkampf, William Louis; Sallaberry, Cedric J.

    2008-08-01

    Procedures are described for the representation of results in analyses that involve both aleatory uncertainty and epistemic uncertainty, with aleatory uncertainty deriving from an inherent randomness in the behavior of the system under study and epistemic uncertainty deriving from a lack of knowledge about the appropriate values to use for quantities that are assumed to have fixed but poorly known values in the context of a specific study. Aleatory uncertainty is usually represented with probability and leads to cumulative distribution functions (CDFs) or complementary cumulative distribution functions (CCDFs) for analysis results of interest. Several mathematical structures are available for the representation of epistemic uncertainty, including interval analysis, possibility theory, evidence theory and probability theory. In the presence of epistemic uncertainty, there is not a single CDF or CCDF for a given analysis result. Rather, there is a family of CDFs and a corresponding family of CCDFs that derive from epistemic uncertainty and have an uncertainty structure that derives from the particular uncertainty structure (i.e., interval analysis, possibility theory, evidence theory, probability theory) used to represent epistemic uncertainty. Graphical formats for the representation of epistemic uncertainty in families of CDFs and CCDFs are investigated and presented for the indicated characterizations of epistemic uncertainty.

  6. GANG INVOLVEMENT AMONG STREET-INVOLVED YOUTH IN A CANADIAN SETTING: A GENDER-BASED ANALYSIS

    Science.gov (United States)

    Marshall, Brandon DL; DeBeck, Kora; Simo, Annick; Kerr, Thomas; Wood, Evan

    2014-01-01

    Objectives Evidence suggests that gang involvement is associated with adverse health outcomes among high-risk youth. However, few studies have investigated the prevalence and correlates of gang affiliation among this population, particularly in Canada. We examined the relationship between self-reported gang involvement and early childhood traumatic experiences, social factors, and other behaviors in a study of drug-using, street-involved youth. Study Design Cross-Sectional Study Methods Data were derived from the At-Risk Youth Study (ARYS), a prospective study of street-involved youth in Vancouver, Canada. Between June 2009 and May 2011, participants were asked questions ascertaining lifetime gang involvement and gang affiliation in one’s social network. We examined the gender-specific correlates of gang involvement using stratified log-binomial regression analyses. Results Among 435 eligible participants, 94 (21.6%) reported gang involvement and 206 (47.4%) reported having friends in a gang. In gender-stratified models, males involved in gangs were more likely to be of Aboriginal ancestry (prevalence ratio [PR] = 1.63, 95% confidence interval [CI]: 1.09 – 2.44), have grown up in government care (PR = 2.03, 95%CI: 1.32 – 3.12), dealt drugs (PR = 2.52, 95%CI: 1.66 – 3.85), and been incarcerated (PR = 1.40, 95%CI: 1.29 – 2.80). Women involved in gangs were more likely to have reported a history of childhood sexual abuse (PR = 3.08, 95%CI: 1.15 – 8.27). Conclusions These results suggest that a variety of adverse experiences in early life are associated with an increased risk of gang affiliation among street-involved youth. Primary prevention strategies aiming to avert gang initiation among high-risk youth should seek to address childhood abuse and other traumatic experiences commonly experienced by this population. PMID:25542743

  7. Mutation analysis of the gene involved in adrenoleukodystrophy

    Energy Technology Data Exchange (ETDEWEB)

    Oost, B.A. van; Ligtenberg, M.J.L. [Univ. Hospital Nijmegen (Netherlands); Kemp, S.; Bolhuis, P.A. [Academic Medical Center, Amsterdam (Netherlands)

    1994-09-01

    A gene responsible for the X-linked genetic disorder adrenoleukodystrophy (ALD) that is characterized by demyelination of the nervous system and adrenocortical insufficiency has been identified by positional cloning. The gene encodes an ATP-binding transporter which is located in the peroxisomal membrane. Deficiency of the gene leads to accumulation of unsaturated very long chain fatty acids due to impaired peroxisomal {beta}-oxidation. A systematic analysis of the open reading frame of the ALD gene unraveled the mutations in 28 different families using reverse transcriptase-PCR followed by direct sequencing. No entire gene deletions or drastic promoter mutations have been detected. Only in one family did the mutation involved multiple exons. The remaining mutations were subtle alterations leading to missense (about 50%) or nonsense mutations, frameshifts or splice acceptor site defects. In one patient a single codon was missing. Mutations affecting a single amino acid were concentrated in the region between the third and fourth putative membrane spanning fragments and in the ATP-binding domain. This overview of mutations aids in the determination of structural and functional important regions and facilitates the screening for mutations in other ALD patients. The detection of mutations in virtually all ALD families tested indicates that the isolated gene is the only gene responsible for ALD located in Xq28.

  8. Coverage analysis of lists of genes involved in heterogeneous ...

    Indian Academy of Sciences (India)

    Genes involved in myopathies: 82 genes, based on the disease groups 'muscular dystrophies', 'congenital muscular dystrophies',. 'congenital ..... Spinal muscular atrophy, lower extremity-predominant, AD. 158600. EGR2 .... Mental retardation, stereotypic movements, epilepsy, and/or cerebral malformations. 613443.

  9. Cardiovascular involvement by osteosarcoma: an analysis of 20 patients

    Energy Technology Data Exchange (ETDEWEB)

    Yedururi, Sireesha; Morani, Ajaykumar C.; Gladish, Gregory W. [The University of Texas MD Anderson Cancer Center, Department of Diagnostic Radiology, Houston, TX (United States); Vallabhaneni, Srilakshmi [Medstar Harbor Hospital, Department of Internal Medicine, Baltimore, MD (United States); Anderson, Peter M. [Levine Children' s Hospital/Levine Cancer Institute, Department of Pediatrics Hematology/Oncology/BMT, Carolinas Healthcare System, Charlotte, NC (United States); Hughes, Dennis; Daw, Najat C. [The University of Texas MD Anderson Cancer Center, Division of Pediatrics, Houston, TX (United States); Wang, Wei-Lien [The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, TX (United States)

    2016-01-15

    Although hematogenous spread of osteosarcoma is well known, the imaging findings of cardiovascular involvement by osteosarcoma are seldom reported and can be difficult to recognize. The enhanced resolution of modern CT and MRI scanners may lead to better detection of cardiovascular involvement. To describe the key imaging findings and clinical behavior of cardiovascular involvement by osteosarcoma. We retrospectively reviewed the imaging findings and clinical characteristics of 20 patients with cardiovascular involvement by osteosarcoma identified by two pediatric radiologists from a review of imaging studies at our institution from 2007 to 2013. At initial diagnosis, the median age of the patients was 15.1 years (range 4.8-24.6 years), and 7 (35%) patients had detectable metastases. Median time to detection of cardiovascular metastases was 1.8 years (range 0-7.3 years). Sixteen patients died of disease; 4 have survived a median of 7.4 years since initial diagnosis. The sites of cardiovascular involvement were the systemic veins draining the primary and metastatic osteosarcoma, pulmonary arteries, pulmonary veins draining the pulmonary metastases, and heart. A dilated and mineralized terminal pulmonary arteriole is an early sign of metastatic osteosarcoma in the lung. Unfamiliarity with the imaging features resulted in under-recognition and misinterpretation of intravascular tumor thrombus as bland thrombus. Knowledge of imaging findings in the era of modern imaging modalities has enhanced our ability to detect cardiovascular involvement and lung metastases early and avoid misinterpreting tumor thrombus in draining systemic veins or pulmonary arteries as bland thrombus. (orig.)

  10. Cardiovascular involvement by osteosarcoma: an analysis of 20 patients

    International Nuclear Information System (INIS)

    Yedururi, Sireesha; Morani, Ajaykumar C.; Gladish, Gregory W.; Vallabhaneni, Srilakshmi; Anderson, Peter M.; Hughes, Dennis; Daw, Najat C.; Wang, Wei-Lien

    2016-01-01

    Although hematogenous spread of osteosarcoma is well known, the imaging findings of cardiovascular involvement by osteosarcoma are seldom reported and can be difficult to recognize. The enhanced resolution of modern CT and MRI scanners may lead to better detection of cardiovascular involvement. To describe the key imaging findings and clinical behavior of cardiovascular involvement by osteosarcoma. We retrospectively reviewed the imaging findings and clinical characteristics of 20 patients with cardiovascular involvement by osteosarcoma identified by two pediatric radiologists from a review of imaging studies at our institution from 2007 to 2013. At initial diagnosis, the median age of the patients was 15.1 years (range 4.8-24.6 years), and 7 (35%) patients had detectable metastases. Median time to detection of cardiovascular metastases was 1.8 years (range 0-7.3 years). Sixteen patients died of disease; 4 have survived a median of 7.4 years since initial diagnosis. The sites of cardiovascular involvement were the systemic veins draining the primary and metastatic osteosarcoma, pulmonary arteries, pulmonary veins draining the pulmonary metastases, and heart. A dilated and mineralized terminal pulmonary arteriole is an early sign of metastatic osteosarcoma in the lung. Unfamiliarity with the imaging features resulted in under-recognition and misinterpretation of intravascular tumor thrombus as bland thrombus. Knowledge of imaging findings in the era of modern imaging modalities has enhanced our ability to detect cardiovascular involvement and lung metastases early and avoid misinterpreting tumor thrombus in draining systemic veins or pulmonary arteries as bland thrombus. (orig.)

  11. Kinetics Parameters of VVER-1000 Core with 3 MOX Lead Test Assemblies To Be Used for Accident Analysis Codes

    International Nuclear Information System (INIS)

    Pavlovitchev, A.M.

    2000-01-01

    The present work is a part of Joint U.S./Russian Project with Weapons-Grade Plutonium Disposition in VVER Reactor and presents the neutronics calculations of kinetics parameters of VVER-1000 core with 3 introduced MOX LTAs. MOX LTA design has been studied in [1] for two options of MOX LTA: 100% plutonium and of ''island'' type. As a result, zoning i.e. fissile plutonium enrichments in different plutonium zones, has been defined. VVER-1000 core with 3 introduced MOX LTAs of chosen design has been calculated in [2]. In present work, the neutronics data for transient analysis codes (RELAP [3]) has been obtained using the codes chain of RRC ''Kurchatov Institute'' [5] that is to be used for exploitation neutronics calculations of VVER. Nowadays the 3D assembly-by-assembly code BIPR-7A and 2D pin-by-pin code PERMAK-A, both with the neutronics constants prepared by the cell code TVS-M, are the base elements of this chain. It should be reminded that in [6] TVS-M was used only for the constants calculations of MOX FAs. In current calculations the code TVS-M has been used both for UOX and MOX fuel constants. Besides, the volume of presented information has been increased and additional explications have been included. The results for the reference uranium core [4] are presented in Chapter 2. The results for the core with 3 MOX LTAs are presented in Chapter 3. The conservatism that is connected with neutronics parameters and that must be taken into account during transient analysis calculations, is discussed in Chapter 4. The conservative parameters values are considered to be used in 1-point core kinetics models of accident analysis codes

  12. Work zone fatal crashes involving large trucks, 2012 : [analysis brief].

    Science.gov (United States)

    2014-11-01

    In 2012, 30,800 fatal crashes took place on our Nations roadways, with 11.2 percent (3,464) involving at least 1 large truck. While the majority of all fatal crashes (98.2 percent) took place outside of a work zone in 2012, 547 fatal crashes (1.8 ...

  13. Analysis of Neural Systems Involved in Modulation of Memory Storage

    Science.gov (United States)

    1993-02-01

    blocked by concurrent infusion of low doses of the adrenergic agonist clenbuterol . Furthermore, low and otherwise ineffective doses of the adrenergic...we found that the retention-enhancing effects of clenbuterol were blocked by a low dose of the cholinergic antagonist atropine. In addition, a low dose...Involvement of the amygdala in the memory-enhancing effects of clenbuterol . Psychopharmacology, 1991, 104, 541-544. McGaugh, J.L. Neuromodulation and

  14. Rectal cancer: involved circumferential resection margin - a root cause analysis.

    Science.gov (United States)

    Youssef, H; Collantes, E C; Rashid, S H; Wong, L S; Baragwanath, P

    2009-06-01

    An involved circumferential resection margin (CRM) following surgery for rectal cancer is the strongest predictor of local recurrence and may represent a failure of the multidisciplinary team (MDT) process. The study analyses the causes of positive CRM in patients undergoing elective surgery for rectal cancer with respect to the decision-making process of the MDT, preoperative rectal cancer staging and surgical technique. From March 2002 to September 2005, data were collected prospectively on all patients undergoing elective rectal cancer surgery with curative intent. The data on all patients identified with positive CRM were analysed. Of 158 patients (male:female = 2.2:1) who underwent potentially curative surgery, 16 (10%) patients had a positive CRM on postoperative histology. Four were due to failure of the pelvic magnetic resonance imaging (MRI) staging scans to predict an involved margin, two with an equivocal CRM on MRI did not have preoperative radiotherapy, one had an inaccurate assessment of the site of primary tumour and in one intra-operative difficulty was encountered. No failure of staging or surgery was identified in the remaining eight of the 16 patients. Abdominoperineal resection (APR) was associated with a 26% positive CRM, compared with 5% for anterior resection. No single consistent cause was found for a positive CRM. The current MDT process and/or surgical technique may be inadequate for low rectal tumours requiring APR.

  15. Analysis of brand personality to involve event involvement and loyalty: A case study of Jakarta Fashion Week 2017

    Science.gov (United States)

    Nasution, A. H.; Rachmawan, Y. A.

    2018-04-01

    Fashion trend in the world changed extremely fast. Fashion has become the one of people’s lifestyle in the world. Fashion week events in several areas can be a measurement of fahion trend nowadays. There was a fashion week event in Indonesia called Jakarta Fashion Week (JFW) aims to show fashion trend to people who want to improve their fashion style. People will join some events if the event has involvement to them, hence they will come to that event again and again. Annually and continuously event is really important to create loyalty among people who are involved in it, in order to increase positive development towards the organizer in organizing the next event. Saving a huge amount from the marketing budget, and creating a higher quality event. This study aims to know the effect of 5 brand personality dimension to event involvement and loyalty in Jakarta Fashion Week (JFW). This study use quantitative confirmative method with Structural Equation Model (SEM) analysis technique. The sample of this study is 150 respondents who became a participant of Jakarta Fashion Week 2017. Result show that there was significant effect of 5 brand personality dimension to 3 dimension of event involvement and loyalty. Meanwhile, there was one dimension of event involvement called personal self-expression that has not effect to loyalty.

  16. Processing and analysis techniques involving in-vessel material generation

    Science.gov (United States)

    Schabron, John F [Laramie, WY; Rovani, Jr., Joseph F.

    2011-01-25

    In at least one embodiment, the inventive technology relates to in-vessel generation of a material from a solution of interest as part of a processing and/or analysis operation. Preferred embodiments of the in-vessel material generation (e.g., in-vessel solid material generation) include precipitation; in certain embodiments, analysis and/or processing of the solution of interest may include dissolution of the material, perhaps as part of a successive dissolution protocol using solvents of increasing ability to dissolve. Applications include, but are by no means limited to estimation of a coking onset and solution (e.g., oil) fractionating.

  17. VIDEO IMAGE CORRELATION METHOD INVOLVED IN DENTAL IMPLANTS’ ANALYSIS

    Directory of Open Access Journals (Sweden)

    SZÁVA Dániel-Tamás

    2014-09-01

    Full Text Available The authors offer useful details on a non-contact, experimental investigation tool, namely: the VIC-3D optical system, involved in the dental implants’ strain-state evaluation. The briefly-described facilities of this system seem to allow it’s deeply implementation in the dental practice, more exactly in the dental implants optimisation from stress-strain state point of view. The presented original testing bench, destined to evaluate the strain-field in the vicinity of the dental implants, mounted in some artificial mandibles, obtained by Rapid Prototyping, can be a first step in a modern and efficient approach of the dental implants. There are briefly presented some promising preliminary results.

  18. Immunohistochemical analysis of small plaque parapsoriasis: involvement of dendritic cells.

    Science.gov (United States)

    Zeybek, N Dilara; Asan, Esin; Erbil, A Hakan; Dagdeviren, Attila

    2008-01-01

    Small plaque parapsoriasis (SPP) is one of the cutaneous T-cell lymphoproliferative disorders. The aim of the present study was to show the antigenic profile of a subset of dendritic cells and lymphocytes in SPP in comparison with normal cells to provide data on the role of these two cell types in the pathogenesis of SPP. Skin biopsy specimens of lesions were obtained from 8 patients with SPP. Biopsies of the healthy skin from 9 control individuals were also analyzed. Immunohistochemistry was performed on the frozen tissue sections to reveal binding of anti-HLA Class II, anti-CD1a, anti-CD4, anti-CD8, anti-CD44, anti-CD45, and anti-CD68 monoclonal antibodies. There was a statistically significant increase in the number of CD1a(+), Langerhans cells (LCs), HLA-DR-immunoreactive and, CD1a-positive dermal dendritic cells and CD68(+) macrophages in the SPP group (p=0.008, 0.008, 0.002 and <0.0009, respectively). The number of lymphocytes positive for CD4, CD8 and CD45 was significantly higher than normal in the SPP group (p=0.015, <0.0009 and <0.0009, respectively). Our study demonstrates that both peptide- and lipid-based antigens are involved in the persistent antigenic exposure in SPP. Dendritic cells play a pivotal role in SPP by presenting antigens by both LC and dermal dendritic cells via MHC Class II and CD1a molecules. The CD68(+) macrophages are thought to be involved in the immune response in this pathology as an antigen-presenting cell.

  19. Coverage analysis of lists of genes involved in heterogeneous ...

    Indian Academy of Sciences (India)

    be targeted with second-tier Sanger sequencing can be iden- tified precisely for any sample of interest using the same cov- erage analysis workflow as used in our study for the deter- mination of mean sequence coverage values. Importantly, to avoid biases relating to variability among exome sequenc- ing runs, this should ...

  20. Analysis of genes involved in glycogen degradation in Escherichia coli.

    Science.gov (United States)

    Strydom, Lindi; Jewell, Jonathan; Meier, Michael A; George, Gavin M; Pfister, Barbara; Zeeman, Samuel; Kossmann, Jens; Lloyd, James R

    2017-02-01

    Escherichia coli accumulate or degrade glycogen depending on environmental carbon supply. Glycogen phosphorylase (GlgP) and glycogen debranching enzyme (GlgX) are known to act on the glycogen polymer, while maltodextrin phosphorylase (MalP) is thought to remove maltodextrins released by GlgX. To examine the roles of these enzymes in more detail, single, double and triple mutants lacking all their activities were produced. GlgX and GlgP were shown to act directly on the glycogen polymer, while MalP most likely catabolised soluble malto-oligosaccharides. Interestingly, analysis of a triple mutant lacking all three enzymes indicates the presence of another enzyme that can release maltodextrins from glycogen. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. An Analysis of the Traits and Motivations of College Students Involved in Service Organizations.

    Science.gov (United States)

    Winniford, Janet C.; And Others

    1995-01-01

    Analysis of students' volunteer efforts exhibited altruism's importance both in students' initial and continued involvement as volunteers; egoistic motivations also seemed important to students. Students more heavily involved in volunteer efforts cited altruistic motivations as more important in their continued involvement than in their initial…

  2. A Meta-Analysis: The Relationship between Father Involvement and Student Academic Achievement

    Science.gov (United States)

    Jeynes, William H.

    2015-01-01

    A meta-analysis was undertaken, including 66 studies, to determine the relationship between father involvement and the educational outcomes of urban school children. Statistical analyses were done to determine the overall impact and specific components of father involvement. The possible differing effects of paternal involvement by race were also…

  3. User involvement in health and social care education: a concept analysis.

    Science.gov (United States)

    Rhodes, Christine A

    2012-02-01

    This paper presents an evaluative discussion of the literature, and findings from a concept analysis which explores user involvement in the context of health and social care higher education in the United Kingdom. User involvement is increasingly a requirement in higher education and the purpose of the concept analysis was to clarify and elucidate the meaning and nature of the concept. Walker and Avant's (2005) eight step framework for concept analysis was used to provide understanding of the underlying attributes and a model for critique and meaningful evaluation and research. A structured search and discussion of contemporary literature was undertaken. A model case is identified along with antecedents, critical attributes and consequences. The complexities of involvement are delineated with a recommendation for robust research that explores the benefits of involvement. Copyright © 2011 Elsevier Ltd. All rights reserved.

  4. Molecular genetic analysis of activation-tagged transcription factors thought to be involved in photomorphogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Neff, Michael M.

    2011-06-23

    This is a final report for Department of Energy Grant No. DE-FG02-08ER15927 entitled “Molecular Genetic Analysis of Activation-Tagged Transcription Factors Thought to be Involved in Photomorphogenesis”. Based on our preliminary photobiological and genetic analysis of the sob1-D mutant, we hypothesized that OBP3 is a transcription factor involved in both phytochrome and cryptochrome-mediated signal transduction. In addition, we hypothesized that OBP3 is involved in auxin signaling and root development. Based on our preliminary photobiological and genetic analysis of the sob2-D mutant, we also hypothesized that a related gene, LEP, is involved in hormone signaling and seedling development.

  5. Types of parental involvement in CBT with anxious youth: a preliminary meta-analysis.

    Science.gov (United States)

    Manassis, Katharina; Lee, Trevor Changgun; Bennett, Kathryn; Zhao, Xiu Yan; Mendlowitz, Sandra; Duda, Stephanie; Saini, Michael; Wilansky, Pamela; Baer, Susan; Barrett, Paula; Bodden, Denise; Cobham, Vanessa E; Dadds, Mark R; Flannery-Schroeder, Ellen; Ginsburg, Golda; Heyne, David; Hudson, Jennifer L; Kendall, Philip C; Liber, Juliette; Masia-Warner, Carrie; Nauta, Maaike H; Rapee, Ronald M; Silverman, Wendy; Siqueland, Lynne; Spence, Susan H; Utens, Elisabeth; Wood, Jeffrey J

    2014-12-01

    Meta-analytic studies have not confirmed that involving parents in cognitive behavior therapy (CBT) for anxious children is therapeutically beneficial. There is also great heterogeneity in the type of parental involvement included. We investigated parental involvement focused on contingency management (CM) and transfer of control (TC) as a potential outcome moderator using a meta-analysis with individual patient data. Investigators of randomized controlled trials (RCTs) of CBT for anxious children, identified systematically, were invited to submit their data. Conditions in each RCT were coded based on type of parental involvement in CBT (i.e., low involvement, active involvement without emphasis on CM or TC, active involvement with emphasis on CM or TC). Treatment outcomes were compared using a 1-stage meta-analysis. All cases involved in active treatment (894 of 1,618) were included for subgroup analyses. Across all CBT groups, means of clinical severity, anxiety, and internalizing symptoms significantly decreased posttreatment and were comparable across groups. The group without emphasis on CM or TC showed a higher proportion with posttreatment anxiety diagnoses than the low-involvement group. Between posttreatment and 1-year follow-up, the proportion with anxiety diagnoses significantly decreased in CBT with active parental involvement with emphasis on CM or TC, whereas treatment gains were merely maintained in the other 2 groups. CBT for anxious children is an effective treatment with or without active parental involvement. However, CBT with active parental involvement emphasizing CM or TC may support long-term maintenance of treatment gains. RESULTS should be replicated as additional RCTs are published.

  6. Alcohol Involvement and the Five-Factor Model of Personality: A Meta-Analysis

    Science.gov (United States)

    Malouff, John M.; Thorsteinsson, Einar B.; Rooke, Sally E.; Schutte, Nicola S.

    2007-01-01

    The purpose of this meta-analysis was to quantify the relationship between the Five-Factor Model of personality and alcohol involvement and to identify moderators of the relationship. The meta-analysis included 20 studies, 119 effect sizes, and 7,886 participants. Possible moderators examined included: five-factor rating type (self vs. other);…

  7. Technique Feature Analysis or Involvement Load Hypothesis: Estimating Their Predictive Power in Vocabulary Learning.

    Science.gov (United States)

    Gohar, Manoochehr Jafari; Rahmanian, Mahboubeh; Soleimani, Hassan

    2018-02-05

    Vocabulary learning has always been a great concern and has attracted the attention of many researchers. Among the vocabulary learning hypotheses, involvement load hypothesis and technique feature analysis have been proposed which attempt to bring some concepts like noticing, motivation, and generation into focus. In the current study, 90 high proficiency EFL students were assigned into three vocabulary tasks of sentence making, composition, and reading comprehension in order to examine the power of involvement load hypothesis and technique feature analysis frameworks in predicting vocabulary learning. It was unraveled that involvement load hypothesis cannot be a good predictor, and technique feature analysis was a good predictor in pretest to posttest score change and not in during-task activity. The implications of the results will be discussed in the light of preparing vocabulary tasks.

  8. Analysis of factors associated with injury severity in crashes involving young New Zealand drivers

    DEFF Research Database (Denmark)

    Weiss, Harold B.; Kaplan, Sigal; Prato, Carlo Giacomo

    2014-01-01

    measures within youth-oriented road safety programs. The current study estimates discrete choice models of injury severity of crashes involving young drivers conditional on these crashes having occurred. The analysis examined a comprehensive set of single-vehicle and two-vehicle crashes involving at least......Young people are a risk to themselves and other road users, as motor vehicle crashes are the leading cause of their death. A thorough understanding of the most important factors associated with injury severity in crashes involving young drivers is important for designing well-targeted restrictive...... fit than a binary and a generalized ordered logit. Results show that the young drivers’ behavior, the presence of passengers and the involvement of vulnerable road users were the most relevant factors associated with higher injury severity in both single-vehicle and two-vehicle crashes. Seatbelt non...

  9. Service user involvement in mental health care: an evolutionary concept analysis.

    Science.gov (United States)

    Millar, Samantha L; Chambers, Mary; Giles, Melanie

    2016-04-01

    The concept of service user involvement is an evolving concept in the mental health-care literature. This study sought to explore and analyse the concept of service user involvement as used in within the field of mental health care. An evolutionary concept analysis was conducted using a literature-based sample extracted from an electronic database search. One hundred and thirty-four papers met the inclusion criteria and were analysed to discover key attributes, antecedents and consequences of service user involvement and to produce a definition of the concept. Five key attributes of service user involvement within the context of mental health care were identified: a person-centred approach, informed decision making, advocacy, obtaining service user views and feedback and working in partnership. Clarity of the attributes and definition of the concept of service user involvement aims to promote understanding of the concept among key stakeholders including mental health professionals, service users and community and voluntary organizations. The findings of the research have utility in the areas of theory and policy development, research on service user involvement in mental health care and service user involvement in mental health practice. Directions for further research regarding the concept are identified. © 2015 John Wiley & Sons Ltd.

  10. Impact of Incredible Years® on teacher perceptions of parental involvement: A latent transition analysis.

    Science.gov (United States)

    Thompson, Aaron M; Herman, Keith C; Stormont, Melissa A; Reinke, Wendy M; Webster-Stratton, Carolyn

    2017-06-01

    The purpose of the present study was to examine the impact of the Incredible Years® Teacher Classroom Management (IY TCM) training on teacher perceptions of parental involvement. A cluster randomized design was used to assign 42 classroom teachers to either an IY TCM training (n=19) or a control condition (n=23). Teachers rated parental involvement (i.e., bonding with teacher, parental involvement at school) for the families of 805 low income students (IY TCM=504, control=301). A latent profile transition analysis framework was used to model the effect of IY TCM on teacher perceptions of parental involvement from pre to posttest. Four profiles consisting of various patterns of high, medium, and low teacher perceptions of bonding with and involvement of parents emerged. Analyses of teacher profiles at baseline revealed teachers who felt parental involvement and bonding was low were also likely to rate students as having more externalizing behaviors, fewer social competencies, more attention deficit symptoms, and disruptive behaviors towards adults and peers compared to teachers with more adaptive profiles. Further analysis revealed that parents of teachers randomly assigned to IY TCM were more likely to transition to a more adaptive view of parental involvement at follow-up compared to teachers in the control condition. Because teacher perceptions of parental involvement may adversely impact teacher attitudes towards difficult students, findings from the present study support the promise of teacher training as an avenue for conferring protections for struggling students. Copyright © 2017 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

  11. Co-researching with people with learning disabilities: an experience of involvement in qualitative data analysis.

    Science.gov (United States)

    Tuffrey-Wijne, Irene; Butler, Gary

    2010-06-01

    People with learning disabilities have been included in research as co-researchers since the 1990s. However, there is limited literature about the processes of involving people with learning disabilities in the more intellectual and analytical stages of the research process. To examine the potential contribution of people with learning disabilities to data analysis in qualitative research. This article is a reflection on one research experience. The two authors include one researcher with and one without learning disabilities. They each describe their experience and understanding of user involvement in analysing the data of an ethnographic study of people with learning disabilities who had cancer. The researcher with learning disabilities was given extensive vignettes and extracts from the research field notes, and was supported to extract themes, which were cross-compared with the analysis of other members of the research team. The researcher with learning disabilities coped well with the emotive content of the data and with the additional support provided, he was able to extract themes that added validity to the overall analysis. His contribution complemented those of the other members of the research team. There were unexpected benefits, in particular, in terms of a more reciprocal and supportive relationship between the two researchers. It is possible and valuable to extend involvement to data analysis, but to avoid tokenism and maintain academic rigour, there must be a clear rationale for such involvement. Extra support, time and costs must be planned for.

  12. Hybrid transfinite element modeling/analysis of nonlinear heat conduction problems involving phase change

    Science.gov (United States)

    Tamma, Kumar K.; Railkar, Sudhir B.

    1988-01-01

    The present paper describes the applicability of hybrid transfinite element modeling/analysis formulations for nonlinear heat conduction problems involving phase change. The methodology is based on application of transform approaches and classical Galerkin schemes with finite element formulations to maintain the modeling versatility and numerical features for computational analysis. In addition, in conjunction with the above, the effects due to latent heat are modeled using enthalpy formulations to enable a physically realistic approximation to be dealt computationally for materials exhibiting phase change within a narrow band of temperatures. Pertinent details of the approach and computational scheme adapted are described in technical detail. Numerical test cases of comparative nature are presented to demonstrate the applicability of the proposed formulations for numerical modeling/analysis of nonlinear heat conduction problems involving phase change.

  13. Qualitative analysis of factors that increase and reduce involvement in gambling

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    Egidijus

    2015-12-01

    Full Text Available During the rapid development of gambling business, the number of pathological gamblers is increasing as well. The problem of pathological gambling is just as important as alcoholism or drug addiction. However, there is a lack of information and research of this topicin Lithuania. The aim of work: to investigate and analyse the factors that increase or reduce involvement in gambling. Research questions: 1 What factors increase involvement in gambling? 2 What factors reduce involvement in gambling? Critical case sampling was used for selection of the participants. Subjects were required to a have experience of involvement in gambling for at least one year; b have experience of negative impact of gambling on quality of life; c have at least 6 months of gambling abstinence. Five individuals participated in the research; all of them were males who live in Vilnius. Age of the participants varied from 19 to 45. Semi-structured interviews were used to collect data. Interviews were recorded and transcribed verbatim. The matic analysis of the data led to the identification of four major the matic categories: psychological factors; social relations; material well being; quality of life. There search results show that negatyve childhood experience, gambling friends, escaping from various troubles, disputes in family and high financial needs can increase involvement in gambling. Factors that reduce involvement in gambling are: feeling support of social environment, proper evaluation of financial position, awareness of one‘s own addiction to gambling and desire to change life.

  14. Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

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    Yonglong Yu

    2016-04-01

    Full Text Available Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20 during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

  15. A Multimodal Data Analysis Approach for Targeted Drug Discovery Involving Topological Data Analysis (TDA).

    Science.gov (United States)

    Alagappan, Muthuraman; Jiang, Dadi; Denko, Nicholas; Koong, Albert C

    In silico drug discovery refers to a combination of computational techniques that augment our ability to discover drug compounds from compound libraries. Many such techniques exist, including virtual high-throughput screening (vHTS), high-throughput screening (HTS), and mechanisms for data storage and querying. However, presently these tools are often used independent of one another. In this chapter, we describe a new multimodal in silico technique for the hit identification and lead generation phases of traditional drug discovery. Our technique leverages the benefits of three independent methods-virtual high-throughput screening, high-throughput screening, and structural fingerprint analysis-by using a fourth technique called topological data analysis (TDA). We describe how a compound library can be independently tested with vHTS, HTS, and fingerprint analysis, and how the results can be transformed into a topological data analysis network to identify compounds from a diverse group of structural families. This process of using TDA or similar clustering methods to identify drug leads is advantageous because it provides a mechanism for choosing structurally diverse compounds while maintaining the unique advantages of already established techniques such as vHTS and HTS.

  16. Genes involved in immunity and apoptosis are associated with human presbycusis based on microarray analysis.

    Science.gov (United States)

    Dong, Yang; Li, Ming; Liu, Puzhao; Song, Haiyan; Zhao, Yuping; Shi, Jianrong

    2014-06-01

    Genes involved in immunity and apoptosis were associated with human presbycusis. CCR3 and GILZ played an important role in the pathogenesis of presbycusis, probably through regulating chemokine receptor, T-cell apoptosis, or T-cell activation pathways. To identify genes associated with human presbycusis and explore the molecular mechanism of presbycusis. Hearing function was tested by pure-tone audiometry. Microarray analysis was performed to identify presbycusis-correlated genes by Illumina Human-6 BeadChip using the peripheral blood samples of subjects. To identify biological process categories and pathways associated with presbycusis-correlated genes, bioinformatics analysis was carried out by Gene Ontology Tree Machine (GOTM) and database for annotation, visualization, and integrated discovery (DAVID). Quantitative RT-PCR (qRT-PCR) was used to validate the microarray data. Microarray analysis identified 469 up-regulated genes and 323 down-regulated genes. Both the dominant biological processes by Gene Ontology (GO) analysis and the enriched pathways by Kyoto encyclopedia of genes and genomes (KEGG) and BIOCARTA showed that genes involved in immunity and apoptosis were associated with presbycusis. In addition, CCR3, GILZ, CXCL10, and CX3CR1 genes showed consistent difference between groups for both the gene chip and qRT-PCR data. The differences of CCR3 and GILZ between presbycusis patients and controls were statistically significant (p < 0.05).

  17. Analysis of Jmjd6 cellular localization and testing for its involvement in histone demethylation.

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    Phillip Hahn

    2010-10-01

    Full Text Available Methylation of residues in histone tails is part of a network that regulates gene expression. JmjC domain containing proteins catalyze the oxidative removal of methyl groups on histone lysine residues. Here, we report studies to test the involvement of Jumonji domain-containing protein 6 (Jmjd6 in histone lysine demethylation. Jmjd6 has recently been shown to hydroxylate RNA splicing factors and is known to be essential for the differentiation of multiple tissues and cells during embryogenesis. However, there have been conflicting reports as to whether Jmjd6 is a histone-modifying enzyme.Immunolocalization studies reveal that Jmjd6 is distributed throughout the nucleoplasm outside of regions containing heterochromatic DNA, with occasional localization in nucleoli. During mitosis, Jmjd6 is excluded from the nucleus and reappears in the telophase of the cell cycle. Western blot analyses confirmed that Jmjd6 forms homo-multimers of different molecular weights in the nucleus and cytoplasm. A comparison of mono-, di-, and tri-methylation states of H3K4, H3K9, H3K27, H3K36, and H4K20 histone residues in wildtype and Jmjd6-knockout cells indicate that Jmjd6 is not involved in the demethylation of these histone lysine residues. This is further supported by overexpression of enzymatically active and inactive forms of Jmjd6 and subsequent analysis of histone methylation patterns by immunocytochemistry and western blot analysis. Finally, treatment of cells with RNase A and DNase I indicate that Jmjd6 may preferentially associate with RNA/RNA complexes and less likely with chromatin.Taken together, our results provide further evidence that Jmjd6 is unlikely to be involved in histone lysine demethylation. We confirmed that Jmjd6 forms multimers and showed that nuclear localization of the protein involves association with a nucleic acid matrix.

  18. Analysis of Jmjd6 cellular localization and testing for its involvement in histone demethylation.

    Science.gov (United States)

    Hahn, Phillip; Wegener, Ivonne; Burrells, Alison; Böse, Jens; Wolf, Alexander; Erck, Christian; Butler, Danica; Schofield, Christopher J; Böttger, Angelika; Lengeling, Andreas

    2010-10-29

    Methylation of residues in histone tails is part of a network that regulates gene expression. JmjC domain containing proteins catalyze the oxidative removal of methyl groups on histone lysine residues. Here, we report studies to test the involvement of Jumonji domain-containing protein 6 (Jmjd6) in histone lysine demethylation. Jmjd6 has recently been shown to hydroxylate RNA splicing factors and is known to be essential for the differentiation of multiple tissues and cells during embryogenesis. However, there have been conflicting reports as to whether Jmjd6 is a histone-modifying enzyme. Immunolocalization studies reveal that Jmjd6 is distributed throughout the nucleoplasm outside of regions containing heterochromatic DNA, with occasional localization in nucleoli. During mitosis, Jmjd6 is excluded from the nucleus and reappears in the telophase of the cell cycle. Western blot analyses confirmed that Jmjd6 forms homo-multimers of different molecular weights in the nucleus and cytoplasm. A comparison of mono-, di-, and tri-methylation states of H3K4, H3K9, H3K27, H3K36, and H4K20 histone residues in wildtype and Jmjd6-knockout cells indicate that Jmjd6 is not involved in the demethylation of these histone lysine residues. This is further supported by overexpression of enzymatically active and inactive forms of Jmjd6 and subsequent analysis of histone methylation patterns by immunocytochemistry and western blot analysis. Finally, treatment of cells with RNase A and DNase I indicate that Jmjd6 may preferentially associate with RNA/RNA complexes and less likely with chromatin. Taken together, our results provide further evidence that Jmjd6 is unlikely to be involved in histone lysine demethylation. We confirmed that Jmjd6 forms multimers and showed that nuclear localization of the protein involves association with a nucleic acid matrix.

  19. Economics of alcohol-involved traffic crashes in the USA: an input-output analysis.

    Science.gov (United States)

    Zaloshnja, Eduard; Miller, Ted R; Lawrence, Bruce A

    2016-02-01

    Preventing traffic crashes reduces crash costs paid by employers and employees. The related savings filter through the economy, impacting its performance. This study is the first to measure the impact of traffic crash reduction on a national economy. It focuses on impaired driving crashes. We analysed the impact of the almost 50% alcohol-involved driving crash rate reduction from 1984-1986 to 2010 and the impact if such crashes in 2010 had not occurred. The analysis entered published estimates of costs that employers, consumers and governments paid because of US impaired-driving crashes as production costs and demand changes in Rutgers University's input-output model of the US economy. For example, reducing medical costs paid by employers lowers the cost of labour inputs to production while reducing vehicle repairs raises demand for other goods. Running the model at current and alternative crash rates revealed the impacts of crash reductions on economic output, gross domestic product (GDP), national income and employment. Alcohol-involved crash reductions since 1984-1986 increased economic output in 2010 by an estimated $20 billion, raised GDP by $10 billion, increased US income by $6.5 billion, and created 215 000 jobs. GDP gains from alcohol-involved crash reduction contributed 5% of the $200 million compounded average annual growth in US GDP from 1985 to 2013. Eliminating remaining alcohol-involved crashes would result in similar economic gains. Alcohol-involved crashes drag down the US economy. On average, each of the 25.5 billion miles Americans drove impaired in 2010 reduced economic output by $0.80. Those losses are preventable. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  20. [A spatially explicit analysis of traffic accidents involving pedestrians and cyclists in Berlin].

    Science.gov (United States)

    Lakes, Tobia

    2017-12-01

    In many German cities and counties, sustainable mobility concepts that strengthen pedestrian and cyclist traffic are promoted. From the perspectives of urban development, traffic planning and public healthcare, a spatially differentiated analysis of traffic accident data is decisive. 1) The identification of spatial and temporal patterns of the distribution of accidents involving cyclists and pedestrians, 2) the identification of hotspots and exploration of possible underlying causes and 3) the critical discussion of benefits and challenges of the results and the derivation of conclusions. Spatio-temporal distributions of data from accident statistics in Berlin involving pedestrians and cyclists from 2011 to 2015 were analysed with geographic information systems (GIS). While the total number of accidents remains relatively stable for pedestrian and cyclist accidents, the spatial distribution analysis shows, however, that there are significant spatial clusters (hotspots) of traffic accidents with a strong concentration in the inner city area. In a critical discussion, the benefits of geographic concepts are identified, such as spatially explicit health data (in this case traffic accident data), the importance of the integration of other data sources for the evaluation of the health impact of areas (traffic accident statistics of the police), and the possibilities and limitations of spatial-temporal data analysis (spatial point-density analyses) for the derivation of decision-supported recommendations and for the evaluation of policy measures of health prevention and of health-relevant urban development.

  1. Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

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    Vicente Martí-Centelles

    2012-01-01

    competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.

  2. A quantitative analysis of the reactions involved in stratospheric ozone depletion in the polar vortex core

    Science.gov (United States)

    Wohltmann, Ingo; Lehmann, Ralph; Rex, Markus

    2017-09-01

    We present a quantitative analysis of the chemical reactions involved in polar ozone depletion in the stratosphere and of the relevant reaction pathways and cycles. While the reactions involved in polar ozone depletion are well known, quantitative estimates of the importance of individual reactions or reaction cycles are rare. In particular, there is no comprehensive and quantitative study of the reaction rates and cycles averaged over the polar vortex under conditions of heterogeneous chemistry so far. We show time series of reaction rates averaged over the core of the polar vortex in winter and spring for all relevant reactions and indicate which reaction pathways and cycles are responsible for the vortex-averaged net change of the key species involved in ozone depletion, i.e., ozone, chlorine species (ClOx, HCl, ClONO2), bromine species, nitrogen species (HNO3, NOx) and hydrogen species (HOx). For clarity, we focus on one Arctic winter (2004-2005) and one Antarctic winter (2006) in a layer in the lower stratosphere around 54 hPa and show results for additional pressure levels and winters in the Supplement. Mixing ratios and reaction rates are obtained from runs of the ATLAS Lagrangian chemistry and transport model (CTM) driven by the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA-Interim reanalysis data. An emphasis is put on the partitioning of the relevant chemical families (nitrogen, hydrogen, chlorine, bromine and odd oxygen) and activation and deactivation of chlorine.

  3. Malonylome Analysis Reveals the Involvement of Lysine Malonylation in Metabolism and Photosynthesis in Cyanobacteria.

    Science.gov (United States)

    Ma, Yanyan; Yang, Mingkun; Lin, Xiaohuang; Liu, Xin; Huang, Hui; Ge, Feng

    2017-05-05

    As a recently validated reversible post translational modification, lysine malonylation regulates diverse cellular processes from bacteria to mammals, but its existence and function in photosynthetic organisms remain unknown. Cyanobacteria are the most ancient group of photosynthetic prokaryotes and contribute about 50% of the total primary production on Earth. Previously, we reported the lysine acetylome in the model cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis). Here we performed the first proteomic survey of lysine malonylation in Synechocystis using highly accurate tandem mass spectrometry in combination with affinity purification. We identified 598 lysine malonylation sites on 339 proteins with high confidence in total. A bioinformatic analysis suggested that these malonylated proteins may play various functions and were distributed in diverse subcellular compartments. Among them, many malonylated proteins were involved in cellular metabolism. The functional significance of lysine malonylation in the metabolic enzyme activity of phosphoglycerate kinase (PGK) was determined by site-specific mutagenesis and biochemical studies. Interestingly, 27 proteins involved in photosynthesis were found to be malonylated for the first time, suggesting that lysine malonylation may be involved in photosynthesis. Thus our results provide the first lysine malonylome in a photosynthetic organism and suggest a previously unexplored role of lysine malonylation in the regulation of metabolic processes and photosynthesis in Synechocystis as well as in other photosynthetic organisms.

  4. A quantitative analysis of the reactions involved in stratospheric ozone depletion in the polar vortex core

    Directory of Open Access Journals (Sweden)

    I. Wohltmann

    2017-09-01

    Full Text Available We present a quantitative analysis of the chemical reactions involved in polar ozone depletion in the stratosphere and of the relevant reaction pathways and cycles. While the reactions involved in polar ozone depletion are well known, quantitative estimates of the importance of individual reactions or reaction cycles are rare. In particular, there is no comprehensive and quantitative study of the reaction rates and cycles averaged over the polar vortex under conditions of heterogeneous chemistry so far. We show time series of reaction rates averaged over the core of the polar vortex in winter and spring for all relevant reactions and indicate which reaction pathways and cycles are responsible for the vortex-averaged net change of the key species involved in ozone depletion, i.e., ozone, chlorine species (ClOx, HCl, ClONO2, bromine species, nitrogen species (HNO3, NOx and hydrogen species (HOx. For clarity, we focus on one Arctic winter (2004–2005 and one Antarctic winter (2006 in a layer in the lower stratosphere around 54 hPa and show results for additional pressure levels and winters in the Supplement. Mixing ratios and reaction rates are obtained from runs of the ATLAS Lagrangian chemistry and transport model (CTM driven by the European Centre for Medium-Range Weather Forecasts (ECMWF ERA-Interim reanalysis data. An emphasis is put on the partitioning of the relevant chemical families (nitrogen, hydrogen, chlorine, bromine and odd oxygen and activation and deactivation of chlorine.

  5. Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes

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    Pablo Moscato

    2013-05-01

    Full Text Available While Illumina microarrays can be used successfully for detecting small gene expression changes due to their high degree of technical replicability, there is little information on how different normalization and differential expression analysis strategies affect outcomes. To evaluate this, we assessed concordance across gene lists generated by applying different combinations of normalization strategy and analytical approach to two Illumina datasets with modest expression changes. In addition to using traditional statistical approaches, we also tested an approach based on combinatorial optimization. We found that the choice of both normalization strategy and analytical approach considerably affected outcomes, in some cases leading to substantial differences in gene lists and subsequent pathway analysis results. Our findings suggest that important biological phenomena may be overlooked when there is a routine practice of using only one approach to investigate all microarray datasets. Analytical artefacts of this kind are likely to be especially relevant for datasets involving small fold changes, where inherent technical variation—if not adequately minimized by effective normalization—may overshadow true biological variation. This report provides some basic guidelines for optimizing outcomes when working with Illumina datasets involving small expression changes.

  6. Proteomic analysis of Daphnia magna hints at molecular pathways involved in defensive plastic responses

    Science.gov (United States)

    2014-01-01

    Background Phenotypic plasticity in defensive traits occurs in many species when facing heterogeneous predator regimes. The waterflea Daphnia is well-known for showing a variety of these so called inducible defences. However, molecular mechanisms underlying this plasticity are poorly understood so far. We performed proteomic analysis on Daphnia magna exposed to chemical cues of the predator Triops cancriformis. D. magna develops an array of morphological changes in the presence of Triops including changes of carapace morphology and cuticle hardening. Results Using the 2D-DIGE technique, 1500 protein spots could be matched and quantified. We discovered 179 protein spots with altered intensity when comparing Triops exposed animals to a control group, and 69 spots were identified using nano-LC MS/MS. Kairomone exposure increased the intensity of spots containing muscle proteins, cuticle proteins and chitin-modifying enzymes as well as enzymes of carbohydrate and energy metabolism. The yolk precursor protein vitellogenin decreased in abundance in 41 of 43 spots. Conclusion Identified proteins may be either directly involved in carapace stability or reflect changes in energy demand and allocation costs in animals exposed to predator kairomones. Our results present promising candidate proteins involved in the expression of inducible defences in Daphnia and enable further in depth analysis of this phenomenon. PMID:24762235

  7. The multiple imputation method: a case study involving secondary data analysis.

    Science.gov (United States)

    Walani, Salimah R; Cleland, Charles M

    2015-05-01

    To illustrate with the example of a secondary data analysis study the use of the multiple imputation method to replace missing data. Most large public datasets have missing data, which need to be handled by researchers conducting secondary data analysis studies. Multiple imputation is a technique widely used to replace missing values while preserving the sample size and sampling variability of the data. The 2004 National Sample Survey of Registered Nurses. The authors created a model to impute missing values using the chained equation method. They used imputation diagnostics procedures and conducted regression analysis of imputed data to determine the differences between the log hourly wages of internationally educated and US-educated registered nurses. The authors used multiple imputation procedures to replace missing values in a large dataset with 29,059 observations. Five multiple imputed datasets were created. Imputation diagnostics using time series and density plots showed that imputation was successful. The authors also present an example of the use of multiple imputed datasets to conduct regression analysis to answer a substantive research question. Multiple imputation is a powerful technique for imputing missing values in large datasets while preserving the sample size and variance of the data. Even though the chained equation method involves complex statistical computations, recent innovations in software and computation have made it possible for researchers to conduct this technique on large datasets. The authors recommend nurse researchers use multiple imputation methods for handling missing data to improve the statistical power and external validity of their studies.

  8. Phenotype Analysis Method for Identification of Gene Functions Involved in Asymmetric Division of Caenorhabditis elegans.

    Science.gov (United States)

    Yang, Sihai; Han, Xianhua; Tohsato, Yukako; Kyoda, Koji; Onami, Shuichi; Nishikawa, Ikuko; Chen, Yenwei

    2017-05-01

    In gene function analysis, it is arduous to identify gene function individually, and the way to screen out all involved genes according to a particular phenotype or disease usually shows us little information for a specific problem. We present a data-driven analysis system based on wild type (WT) embryos to study the concrete function of each gene associated with certain category of abnormal phenotypes. It can be applied to genes with very few RNAi embryos. Instead of presupposing the particular function of a gene, its function is confirmed by the statistical testing of built models. The scheme includes the following five: first, verify the to be detected genes and determine related recognized features according to the given category; second, compute the value of each feature based on WT embryos and merge them by principal component analysis (PCA); third, for each of the selected components of PCA, build a normal distribution and verify its normality; fourth, project the RNAi embryos to each component and probe them; and finally, analyze the more detailed functions of each gene based on the physical or biological meaning of each component. Choosing the first-round asymmetric division process of Caenorhabditis elegans as the phenotype, experimental results show that on the different aspects of the asymmetric division process, par-2, par-3, and let-754 are related to scalar differences; dcn-1 and mcm-5 are associated with the divergences of scalar variation, which may reflect the disaccord in development; and dcn-1, par-2, and par-3 are involved with morphological discrepancies.

  9. Identification and expression analysis of MATE genes involved in flavonoid transport in blueberry plants.

    Science.gov (United States)

    Chen, Li; Liu, Yushan; Liu, Hongdi; Kang, Limin; Geng, Jinman; Gai, Yuzhuo; Ding, Yunlong; Sun, Haiyue; Li, Yadong

    2015-01-01

    Multidrug and toxic compound extrusion (MATE) proteins are the most recently identified family of multidrug transporters. In plants, this family is remarkably large compared to the human and bacteria counterpart, highlighting the importance of MATE proteins in this kingdom. Here 33 Unigenes annotated as MATE transporters were found in the blueberry fruit transcriptome, of which eight full-length cDNA sequences were identified and cloned. These proteins are composed of 477-517 residues, with molecular masses ~54 kDa, and theoretical isoelectric points from 5.35 to 8.41. Bioinformatics analysis predicted 10-12 putative transmembrane segments for VcMATEs, and localization to the plasma membrane without an N-terminal signal peptide. All blueberry MATE proteins shared 32.1-84.4% identity, among which VcMATE2, VcMATE3, VcMATE5, VcMATE7, VcMATE8, and VcMATE9 were more similar to the MATE-type flavonoid transporters. Phylogenetic analysis showed VcMATE2, VcMATE3, VcMATE5, VcMATE7, VcMATE8 and VcMATE9 clustered with MATE-type flavonoid transporters, indicating that they might be involved in flavonoid transport. VcMATE1 and VcMATE4 may be involved in the transport of secondary metabolites, the detoxification of xenobiotics, or the export of toxic cations. Real-time quantitative PCR demonstrated that the expression profile of the eight VcMATE genes varied spatially and temporally. Analysis of expression and anthocyanin accumulation indicated that there were some correlation between the expression profile and the accumulation of anthocyanins. These results showed VcMATEs might be involved in diverse physiological functions, and anthocyanins across the membranes might be mutually maintained by MATE-type flavonoid transporters and other mechanisms. This study will enrich the MATE-based transport mechanisms of secondary metabolite, and provide a new biotechonology strategy to develop better nutritional blueberry cultivars.

  10. 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.

  11. Analysis of crucial molecules involved in herniated discs and degenerative disc disease

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    Zhigang Qu

    2013-01-01

    Full Text Available OBJECTIVES: Herniated discs and degenerative disc disease are major health problems worldwide. However, their pathogenesis remains obscure. This study aimed to explore the molecular mechanisms of these ailments and to identify underlying therapeutic targets. MATERIAL AND METHODS: Using the GSE23130 microarray datasets downloaded from the Gene Expression Omnibus database, differentially co-expressed genes and links were identified using the differentially co-expressed gene and link method with a false discovery rate ,0.25 as a significant threshold. Subsequently, the underlying molecular mechanisms of the differential co-expression of these genes were investigated using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. In addition, the transcriptional regulatory relationship was also investigated. RESULTS: Through the analysis of the gene expression profiles of different specimens from patients with these diseases, 539 differentially co-expressed genes were identified for these ailments. The ten most significant signaling pathways involving the differentially co-expressed genes were identified by enrichment analysis. Among these pathways, apoptosis and extracellular matrix-receptor interaction pathways have been reported to be related to these diseases. A total of 62 pairs of regulatory relationships between transcription factors and their target genes were identified as critical for the pathogenesis of these diseases. CONCLUSION: The results of our study will help to identify the mechanisms responsible for herniated discs and degenerative disc disease and provides a theoretical basis for further therapeutic study.

  12. Analysis of crucial molecules involved in herniated discs and degenerative disc disease.

    Science.gov (United States)

    Qu, Zhigang; Miao, Weiwei; Zhang, Qi; Wang, Zhenyu; Fu, Changfeng; Han, Jinhua; Liu, Yi

    2013-01-01

    Herniated discs and degenerative disc disease are major health problems worldwide. However, their pathogenesis remains obscure. This study aimed to explore the molecular mechanisms of these ailments and to identify underlying therapeutic targets. Using the GSE23130 microarray datasets downloaded from the Gene Expression Omnibus database, differentially co-expressed genes and links were identified using the differentially co-expressed gene and link method with a false discovery rate ,0.25 as a significant threshold. Subsequently, the underlying molecular mechanisms of the differential co-expression of these genes were investigated using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. In addition, the transcriptional regulatory relationship was also investigated. Through the analysis of the gene expression profiles of different specimens from patients with these diseases, 539 differentially co-expressed genes were identified for these ailments. The ten most significant signaling pathways involving the differentially co-expressed genes were identified by enrichment analysis. Among these pathways, apoptosis and extracellular matrix-receptor interaction pathways have been reported to be related to these diseases. A total of 62 pairs of regulatory relationships between transcription factors and their target genes were identified as critical for the pathogenesis of these diseases. The results of our study will help to identify the mechanisms responsible for herniated discs and degenerative disc disease and provides a theoretical basis for further therapeutic study.

  13. Transcriptome analysis of genes involved in defence response in Polyporus umbellatus with Armillaria mellea infection.

    Science.gov (United States)

    Liu, Meng-Meng; Xing, Yong-Mei; Zhang, Da-Wei; Guo, Shun-Xing

    2015-11-03

    Polyporus umbellatus, a species symbiotic with Armillaria mellea and it also exhibits substantial defence response to Armillaria mellea infection. There are no genomics resources databases for understanding the molecular mechanism underlying the infection stress of P. umbellatus. Therefore, we performed a large-scale transcriptome sequencing of this fungus with A. mellea infection using Illumina sequencing technology. The assembly of the clean reads resulted in 120,576 transcripts, including 38,444 unigenes. Additionally, we performed a gene expression profiling analysis upon infection treatment. The results indicated significant differences in the gene expression profiles between the control and the infection group. In total, 10933 genes were identified between the two groups. Based on the differentially expressed genes, a Gene Ontology annotation analysis showed many defence-relevant categories. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways. Furthermore, the expression patterns of 13 putative genes that are involved in defence response resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The sequenced genes covered a considerable proportion of the P. umbellatus transcriptome, and the expression results may be useful to strengthen the knowledge on the defence response of this fungus defend against Armillaria mellea invasion.

  14. Identification and expression analysis of candidate genes involved in carotenoid biosynthesis in chickpea seeds

    Directory of Open Access Journals (Sweden)

    Mohammad Kazem Rezaei

    2016-12-01

    Full Text Available Plant carotenoids have a key role in preventing various diseases in human because of their antioxidant and provitamin A properties. Chickpea is a good source of carotenoid among legumes and its diverse germplasm and genome accessibility makes it a good model for carotenogenesis studies. The structure, location and copy numbers of genes involved in carotenoid biosynthesis were retrieved from the chickpea genome. The majority of the single nucleotide polymorphism (SNPs within these genes across five diverse chickpea cultivars was synonymous mutation. We examined the expression of the carotenogenesis genes and their association with carotenoid concentration at different seed development stages of five chickpea cultivars. Total carotenoid concentration ranged from 22 μg g-1 in yellow cotyledon kabuli to 44 μg g-1 in green cotyledon desi at 32 days post anthesis (DPA. The majority of carotenoids in chickpea seeds consists of lutein and zeaxanthin. The expression of the selected 19 genes involved in carotenoid biosynthesis pathway showed common pattern across five cultivars with higher expression at 8 and/or 16 DPA then dropped considerably at 24 and 32 DPA. Almost all genes were up-regulated in CDC Jade cultivar. Correlation analysis between gene expression and carotenoid concentration showed that the genes involved in the primary step of carotenoid biosynthesis pathway including carotenoid desaturase and isomerase positively correlated with various carotenoid components in chickpea seeds. A negative correlation was found between hydroxylation activity and provitamin A concentration in the seeds. The highest provitamin A concentration including β-carotene and β-cryptoxanthin were found in green cotyledon chickpea cultivars.

  15. Anti-neutrophil cytoplasmic antibody-associated vasculitis with renal involvement: Analysis of 89 cases.

    Science.gov (United States)

    Caravaca-Fontán, Fernando; Yerovi, Estefanía; Delgado-Yagu E, María; Galeano, Cristina; Pampa-Saico, Saúl; Tenorio, Maria Teresa; Liaño, Fernando

    2017-01-06

    The anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis with renal involvement are associated with high morbi-mortality. In this study we analyse if the prognosis of these diseases have improved in recent years, and which factors influence the outcomes. Retrospective single-centre observational study, which included all patients diagnosed with microscopic polyangiitis and granulomatosis with polyangiitis with renal involvement in the last 25 years. Demographic, clinical and biochemical parameters of prognostic interest were recorded. The differences between four chronological periods were analysed, along with the determinants of a poor outcome (death or end-stage renal disease). Eighty-nine patients were included (mean age 64±15 years). Sixty-four patients (72%) had microscopic polyangiitis and 25 (28%) granulomatosis with polyangiitis. During the study period, 37 (42%) patients died. Through Cox regression analysis, the best determinants of mortality were the initial glomerular filtration rate (HR 0.911; P=.003), Charlson comorbidity index (HR 1.513; P<.0001) and tobacco smoking (HR 1.816; P=.003). 35% developed end-stage renal disease, and the best determinants (by competing-risk regression) were: initial glomerular filtration rate (sub-hazard ratio [SHR]: 0.791; P<.0001), proteinuria (SHR: 1.313; P<.0001), and smoking status (SHR: 1.848; P=.023). No differences were found in patients' mortality or renal survival between the different study periods. Prognosis of anti-neutrophil cytoplasm antibodies vasculitis with renal involvement treated with conventional immunosuppressive therapy remains unsatisfactory, and continues to have increased long-term complications and mortality. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

  16. The Involvement of Girls and Boys with Bullying: An Analysis of Gender Differences

    Directory of Open Access Journals (Sweden)

    Marta Angélica Iossi Silva

    2013-12-01

    Full Text Available This exploratory and cross-sectional study aimed to identify the prevalence of bullying in a group of students and analyze the data regarding the gender of those involved in the violence. A questionnaire adapted from Olweus was applied in seven elementary education schools in Portugal. The sample consisted of 387 students between 7 and 14 years old. Data are presented in terms of descriptive statistics and differences between proportions were analyzed using chi-square tests. The gender analysis of victimization and aggression shows that boys and girls are both victims and aggressors, and there are significant differences in involvement in bullying between genders and the roles played. Boys are victims more often when considering different types of bullying, although significant differences were only found for physical aggression. Strategies that include gender roles are a priority for prevention and careful attention to this phenomenon in the school context. The questions addressed contribute to a broader understanding of the phenomenon, emphasizing the differential participation of boys and girls in bullying.

  17. Comparative Transcriptome Analysis Identifies Putative Genes Involved in the Biosynthesis of Xanthanolides in Xanthium strumarium L.

    Directory of Open Access Journals (Sweden)

    Yuanjun Li

    2016-08-01

    Full Text Available Xanthium strumarium L. is a traditional Chinese herb belonging to the Asteraceae family. The major bioactive components of this plant are sesquiterpene lactones, which include the xanthanolides. To date, the biogenesis of xanthanolides, especiallytheir downstream pathway, remains largely unknown. In X. strumarium, xanthanolides primarily accumulate in its glandular trichomes. To identify putative gene candidates involved in the biosynthesis of xanthanolides, three X. strumarium transcriptomes, which were derived from the young leaves of two different cultivars and the purified glandular trichomes from one of the cultivars, were constructed in this study. In total, 157 million clean reads were generated and assembled into 91,861 unigenes, of which 59,858 unigenes were successfully annotated. All the genes coding for known enzymes in the upstream pathway to the biosynthesis of xanthanolides were present in the X. strumarium transcriptomes. From a comparative analysis of the X. strumarium transcriptomes, this study identified a number of gene candidates that are putatively involved in the downstream pathway to the synthesis of xanthanolides, such as four unigenes encoding CYP71 P450s, 50 unigenes for dehydrogenases, and 27 genes for acetyltransferases. The possible functions of these four CYP71 candidates are extensively discussed. In addition, 116 transcription factors that were highly expressed in X. strumarium glandular trichomes were also identified. Their possible regulatory roles in the biosynthesis of sesquiterpene lactones are discussed. The global transcriptomic data for X. strumarium should provide a valuable resource for further research into the biosynthesis of xanthanolides.

  18. Quantitative LC-MS/MS Analysis of Proteins Involved in Metastasis of Breast Cancer

    Science.gov (United States)

    Goto, Rieko; Nakamura, Yasushi; Takami, Tomonori; Sanke, Tokio; Tozuka, Zenzaburo

    2015-01-01

    The purpose of this study was to develop quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods for the analysis of proteins involved in metastasis of breast cancer for diagnosis and determining disease prognosis, as well as to further our understand of metastatic mechanisms. We have previously demonstrated that the protein type XIV collagen may be specifically expressed in metastatic tissues by two dimensional LC-MS/MS. In this study, we developed quantitative LC-MS/MS methods for type XIV collagen. Type XIV collagen was quantified by analyzing 2 peptides generated by digesting type XIV collagen using stable isotope-labeled peptides. The individual concentrations were equivalent between 2 different peptides of type XIV collagen by evaluation of imprecise transitions and using the best transition for the peptide concentration. The results indicated that type XIV collagen is highly expressed in metastatic tissues of patients with massive lymph node involvement compared to non-metastatic tissues. These findings were validated by quantitative real-time RT-PCR. Further studies on type XIV collagen are desired to verify its role as a prognostic factor and diagnosis marker for metastasis. PMID:26176947

  19. Analysis of miRNAs Involved in Mouse Brain Damage upon Enterovirus 71 Infection.

    Science.gov (United States)

    Yang, Xiaoxia; Xie, Jing; Jia, Leili; Liu, Nan; Liang, Yuan; Wu, Fuli; Liang, Beibei; Li, Yongrui; Wang, Jinyan; Sheng, Chunyu; Li, Hao; Liu, Hongbo; Ma, Qiuxia; Yang, Chaojie; Du, Xinying; Qiu, Shaofu; Song, Hongbin

    2017-01-01

    Enterovirus 71 (EV71) infects the central nervous system (CNS) and causes brainstem encephalitis in children. MiRNAs have been found to play various functions in EV71 infection in human cell lines. To identify potential miRNAs involved in the inflammatory injury in CNS, our study, for the first time, performed a miRNA microarray assay in vivo using EV71 infected mice brains. Twenty differentially expressed miRNAs were identified (four up- and 16 down-regulated) and confirmed by qRT-PCR. The target genes of these miRNAs were analyzed using KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, revealing that the miRNAs were mainly involved in the regulation of inflammation and neural system function. MiR-150-5p, -3082-5p, -3473a, -468-3p, -669n, -721, -709, and -5107-5p that regulate MAPK and chemokine signaling were all down-regulated, which might result in increased cytokine production. In addition, miR-3473a could also regulate focal adhesion and leukocyte trans-endothelial migration, suggesting a role in virus-induced blood-brain barrier disruption. The miRNAs and pathways identified in this study could help to understand the intricate interactions between EV71 and the brain injury, offering new insight for the future research of the molecular mechanism of EV71 induced brainstem encephalitis.

  20. Methodology for Design and Analysis of Reactive Distillation Involving Multielement Systems

    DEFF Research Database (Denmark)

    Jantharasuk, Amnart; Gani, Rafiqul; Górak, Andrzej

    2011-01-01

    A new methodology for design and analysis of reactive distillation has been developed. In this work, the elementbased approach, coupled with a driving force diagram, has been extended and applied to the design of a reactive distillation column involving multielement (multicomponent) systems....... The transformation of ordinary systems to element-based ones and the aggregation of non-key elements allow the important design parameters, such as the number of stages, feed stage and minimum reflux ratio, to be determined by using simple diagrams similar to those regularly employed for non-reactive systems...... consisting of two components. Based on this methodology, an optimal design configuration is identified using the equivalent binary-element-driving force diagram. Two case studies of methyl acetate (MeOAc) synthesis and methyl-tert-butyl ether (MTBE) synthesis have been considered to demonstrate...

  1. Nurses Writing about Psychiatric Nurses' Involvement in Killings during the Nazi Era: A Preliminary Discourse Analysis.

    Science.gov (United States)

    Holmes, Colin A; McAllister, Margaret; Crowther, Andrew

    2016-01-01

    Nurses actively killed people in Nazi Europe between 1939 and 1945. The so-called ‘science of eugenics’ underpinned Nazi ideology, used to further the Nazi racist agenda. Edicts sanctioned selection and medically supervised killing of people, and nurses, principally in mental hospitals, participated in the killing of between 100–300 thousand patients. Erroneously termed ‘euthanasia', there were three phases: the initial programme involving children, the T4 adult programme, and ‘wild euthanasia'. Unofficial killings also took place before 1939. This paper uses discourse analysis to map and analyse published texts which explore the role of nurses in Nazi Germany. The aim is to identify its characteristics as a body of literature, to note strengths and weaknesses, emphases and silences, and to note aspects that need further exploration. It acknowledges that how these events are to be understood and represented in contemporary discourse constitutes a significant problem for historians of nursing.

  2. Egalitarianism and Achievement in the Involvement of Others in Consumer Decisions: A Functional Analysis.

    Science.gov (United States)

    Miller, Duane I.

    1980-01-01

    Studied how egalitaranism and success through individual achievement, were expressed in the involvement of others in consumer decisions. Results found egalitarians involved others in seeking more information. Individual achievement subjects delegated more decision responsibility for non-ego involving decisions. Suggests involvement of others could…

  3. Identification and analysis of novel genes involved in gravitropism of Arabidopsis thaliana.

    Science.gov (United States)

    Morita, Miyo T.; Tasaka, Masao; Masatoshi Taniguchi, .

    2012-07-01

    Gravitropism is a continuous control with regard to the orientation and juxtaposition of the various parts of the plant body in response to gravity. In higher plants, the relative directional change of gravity is mainly suscepted in specialized cells called statocytes, followed by signal conversion from physical information into physiological information within the statocytes. We have studied the early process of shoot gravitropism, gravity sensing and signaling process, mainly by molecular genetic approach. In Arabidopsis shoot, statocytes are the endodermal cells. sgr1/scarcrow (scr) and sgr7/short-root (shr) mutants fail to form the endodermis and to respond to gravity in their inflorescence stems. Since both SGR1/SCR and SGR7/SHR are transcriptional factors, at least a subset of their downstream genes can be expected to be involved in gravitropism. In addition, eal1 (endodermal-amyloplast less 1), which exhibits no gravitropism in inflorescence stem but retains ability to form endodermis, is a hypomorphic allele of sgr7/shr. Take advantage of these mutants, we performed DNA microarray analysis and compared gene expression profiles between wild type and the mutants. We found that approx. 40 genes were commonly down-regulated in these mutants and termed them DGE (DOWN-REGULATED GENE IN EAL1) genes. DGE1 has sequence similarity to Oryza sativa LAZY1 that is involved in shoot gravitropism of rice. DGE2 has a short region homologous to DGE1. DTL (DGE TWO-LIKE}) that has 54% identity to DGE2 is found in Arabidopsis genome. All three genes are conserved in angiosperm but have no known functional domains or motifs. We analyzed T-DNA insertion for these genes in single or multiple combinations. In dge1 dge2 dtl triple mutant, gravitropic response of shoot, hypocotyl and root dramatically reduced. Now we are carrying out further physiological and molecular genetic analysis of the triple mutant.

  4. Phylogenetic analysis of proteins involved in the stringent response in plant cells.

    Science.gov (United States)

    Ito, Doshun; Ihara, Yuta; Nishihara, Hidenori; Masuda, Shinji

    2017-07-01

    The nucleotide (p)ppGpp is a second messenger that controls the stringent response in bacteria. The stringent response modifies expression of a large number of genes and metabolic processes and allows bacteria to survive under fluctuating environmental conditions. Recent genome sequencing analyses have revealed that genes responsible for the stringent response are also found in plants. These include (p)ppGpp synthases and hydrolases, RelA/SpoT homologs (RSHs), and the pppGpp-specific phosphatase GppA/Ppx. However, phylogenetic relationship between enzymes involved in bacterial and plant stringent responses is as yet generally unclear. Here, we investigated the origin and evolution of genes involved in the stringent response in plants. Phylogenetic analysis and primary structures of RSH homologs from different plant phyla (including Embryophyta, Charophyta, Chlorophyta, Rhodophyta and Glaucophyta) indicate that RSH gene families were introduced into plant cells by at least two independent lateral gene transfers from the bacterial Deinococcus-Thermus phylum and an unidentified bacterial phylum; alternatively, they were introduced into a proto-plant cell by a lateral gene transfer from the endosymbiotic cyanobacterium followed by gene loss of an ancestral RSH gene in the cyanobacterial linage. Phylogenetic analysis of gppA/ppx families indicated that plant gppA/ppx homologs form an individual cluster in the phylogenetic tree, and show a sister relationship with some bacterial gppA/ppx homologs. Although RSHs contain a plastidial transit peptide at the N terminus, GppA/Ppx homologs do not, suggesting that plant GppA/Ppx homologs function in the cytosol. These results reveal that a proto-plant cell obtained genes for the stringent response by lateral gene transfer events from different bacterial phyla and have utilized them to control metabolism in plastids and the cytosol.

  5. Study of covariances involved in the k0 method of neutron activation analysis

    International Nuclear Information System (INIS)

    Cardoso, Vanderlei

    2011-01-01

    This work aimed the development of a methodology for the treatment of uncertainty in the k 0 Method for Neutron Activation Analysis (NAA), comprehensively and accurately, by applying the covariance analysis methodology. All parameters involved in determining the concentration of a given element were analyzed with criteria in order to establish the correlations among them. Also established were the possible correlations between the concentrations of different elements for the same sample and for different samples. This procedure generated a large number of correlations that have been rigorously addressed. Data for analysis were obtained experimentally by means of irradiations performed at 24A irradiation position, near the core of the IEA-R1 research reactor, located at IPEN-CNEN/SP. The parameters α and f, characterizing the neutron field were determined by applying several methods from the literature. A detailed statistical treatment was applied to each measurement, verifying the various uncertainties and partial correlations. In order to deepen the study, targets of 64 Zn and 68 Zn were chosen, for which the nuclear parameters k 0 and Q 0 showed discrepancies in the literature in order to determine them experimentally. For 64 Zn, the values for these parameters resulted 5.63(8) x 10 -3 and 1.69(6), respectively. For 68 Zn they resulted 4.00(6) x 10 -4 and 2.34(4), respectively. These values were compared with data from the literature. The Monte Carlo method was applied at various stages of study, to allow accurate determination of some parameters needed for the complete data analysis. (author)

  6. Parallel analysis of tagged deletion mutants efficiently identifies genes involved in endoplasmic reticulum biogenesis.

    Science.gov (United States)

    Wright, Robin; Parrish, Mark L; Cadera, Emily; Larson, Lynnelle; Matson, Clinton K; Garrett-Engele, Philip; Armour, Chris; Lum, Pek Yee; Shoemaker, Daniel D

    2003-07-30

    Increased levels of HMG-CoA reductase induce cell type- and isozyme-specific proliferation of the endoplasmic reticulum. In yeast, the ER proliferations induced by Hmg1p consist of nuclear-associated stacks of smooth ER membranes known as karmellae. To identify genes required for karmellae assembly, we compared the composition of populations of homozygous diploid S. cerevisiae deletion mutants following 20 generations of growth with and without karmellae. Using an initial population of 1,557 deletion mutants, 120 potential mutants were identified as a result of three independent experiments. Each experiment produced a largely non-overlapping set of potential mutants, suggesting that differences in specific growth conditions could be used to maximize the comprehensiveness of similar parallel analysis screens. Only two genes, UBC7 and YAL011W, were identified in all three experiments. Subsequent analysis of individual mutant strains confirmed that each experiment was identifying valid mutations, based on the mutant's sensitivity to elevated HMG-CoA reductase and inability to assemble normal karmellae. The largest class of HMG-CoA reductase-sensitive mutations was a subset of genes that are involved in chromatin structure and transcriptional regulation, suggesting that karmellae assembly requires changes in transcription or that the presence of karmellae may interfere with normal transcriptional regulation. Copyright 2003 John Wiley & Sons, Ltd.

  7. The Relationship among Egyptian Adolescents' Perception of Parental Involvement, Academic Achievement, and Achievement Goals: A Mediational Analysis

    Science.gov (United States)

    Abd-El-Fattah, Sabry M.

    2006-01-01

    A structural equation modelling analysis was used to test the mediating effect of achievement goal factors on the relationship between Egyptian adolescents' perception of parental involvement and academic achievement. The perception of Parental Involvement Scale and Achievement Goal Questionnaire was administered to a sample of 255 first-year…

  8. Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis.

    Science.gov (United States)

    Xie, Jianbo; Tian, Jiaxing; Du, Qingzhang; Chen, Jinhui; Li, Ying; Yang, Xiaohui; Li, Bailian; Zhang, Deqiang

    2016-05-01

    Gibberellins (GAs) regulate a wide range of important processes in plant growth and development, including photosynthesis. However, the mechanism by which GAs regulate photosynthesis remains to be understood. Here, we used multi-gene association to investigate the effect of genes in the GA-responsive pathway, as constructed by RNA sequencing, on photosynthesis, growth, and wood property traits, in a population of 435 Populus tomentosa By analyzing changes in the transcriptome following GA treatment, we identified many key photosynthetic genes, in agreement with the observed increase in measurements of photosynthesis. Regulatory motif enrichment analysis revealed that 37 differentially expressed genes related to photosynthesis shared two essential GA-related cis-regulatory elements, the GA response element and the pyrimidine box. Thus, we constructed a GA-responsive pathway consisting of 47 genes involved in regulating photosynthesis, including GID1, RGA, GID2, MYBGa, and 37 photosynthetic differentially expressed genes. Single nucleotide polymorphism (SNP)-based association analysis showed that 142 SNPs, representing 40 candidate genes in this pathway, were significantly associated with photosynthesis, growth, and wood property traits. Epistasis analysis uncovered interactions between 310 SNP-SNP pairs from 37 genes in this pathway, revealing possible genetic interactions. Moreover, a structural gene-gene matrix based on a time-course of transcript abundances provided a better understanding of the multi-gene pathway affecting photosynthesis. The results imply a functional role for these genes in mediating photosynthesis, growth, and wood properties, demonstrating the potential of combining transcriptome-based regulatory pathway construction and genetic association approaches to detect the complex genetic networks underlying quantitative traits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights

  9. Climateprediction.com: Public Involvement, Multi-Million Member Ensembles and Systematic Uncertainty Analysis

    Science.gov (United States)

    Stainforth, D. A.; Allen, M.; Kettleborough, J.; Collins, M.; Heaps, A.; Stott, P.; Wehner, M.

    2001-12-01

    The climateprediction.com project is preparing to carry out the first systematic uncertainty analysis of climate forecasts using large ensembles of GCM climate simulations. This will be done by involving schools, businesses and members of the public, and utilizing the novel technology of distributed computing. Each participant will be asked to run one member of the ensemble on their PC. The model used will initially be the UK Met Office's Unified Model (UM). It will be run under Windows and software will be provided to enable those involved to view their model output as it develops. The project will use this method to carry out large perturbed physics GCM ensembles and thereby analyse the uncertainty in the forecasts from such models. Each participant/ensemble member will therefore have a version of the UM in which certain aspects of the model physics have been perturbed from their default values. Of course the non-linear nature of the system means that it will be necessary to look not just at perturbations to individual parameters in specific schemes, such as the cloud parameterization, but also to the many combinations of perturbations. This rapidly leads to the need for very large, perhaps multi-million member ensembles, which could only be undertaken using the distributed computing methodology. The status of the project will be presented and the Windows client will be demonstrated. In addition, initial results will be presented from beta test runs using a demo release for Linux PCs and Alpha workstations. Although small by comparison to the whole project, these pilot results constitute a 20-50 member perturbed physics climate ensemble with results indicating how climate sensitivity can be substantially affected by individual parameter values in the cloud scheme.

  10. A Qualitative Analysis of Loneliness Dynamics Involved with College Long-Distance Relationships

    Science.gov (United States)

    Firmin, Michael W.; Firmin, Ruth L.; Lorenzen, Kailee

    2014-01-01

    The present phenomenological, qualitative research study involved in-depth interviews of all 16 female, sophomore students involved in respective distance relationships at a private, selective, comprehensive, Midwest university. Among other results found in the study, the present article specifically addressed the loneliness dynamics involved with…

  11. Including Fathers in the Picture: A Meta-Analysis of Parental Involvement and Students' Academic Achievement

    Science.gov (United States)

    Kim, Sung won; Hill, Nancy E.

    2015-01-01

    Extant research on parental involvement in education has been conducted largely without respect to which parent is involved. The implicit assumption is that family-school relationship frameworks function similarly for fathers and mothers. Although there is a growing body of research examining fathers' involvement in education, this assumption has…

  12. Resident Black Fathers' Involvement: A Comparative Analysis of Married and Unwed, Cohabitating Fathers

    Science.gov (United States)

    Perry, Armon R.; Harmon, Dana K.; Leeper, James

    2012-01-01

    Increasing fathers' involvement with their children has become a priority in recent years. Marriage promotion programs have been offered as the primary vehicles for increasing paternal involvement. Although marriage is likely to provide fathers with increased access and opportunity for paternal involvement, much less is known about the ways in…

  13. Systems analysis of gene ontology and biological pathways involved in post-myocardial infarction responses.

    Science.gov (United States)

    Nguyen, Nguyen T; Lindsey, Merry L; Jin, Yu-Fang

    2015-01-01

    Pathway analysis has been widely used to gain insight into essential mechanisms of the response to myocardial infarction (MI). Currently, there exist multiple pathway databases that organize molecular datasets and manually curate pathway maps for biological interpretation at varying forms of organization. However, inconsistencies among different databases in pathway descriptions, frequently due to conflicting results in the literature, can generate incorrect interpretations. Furthermore, although pathway analysis software provides detailed images of interactions among molecules, it does not exhibit how pathways interact with one another or with other biological processes under specific conditions. We propose a novel method to standardize descriptions of enriched pathways for a set of genes/proteins using Gene Ontology terms. We used this method to examine the relationships among pathways and biological processes for a set of condition-specific genes/proteins, represented as a functional biological pathway-process network. We applied this algorithm to a set of 613 MI-specific proteins we previously identified. A total of 96 pathways from Biocarta, KEGG, and Reactome, and 448 Gene Ontology Biological Processes were enriched with these 613 proteins. The pathways were represented as Boolean functions of biological processes, delivering an interactive scheme to organize enriched information with an emphasis on involvement of biological processes in pathways. We extracted a network focusing on MI to demonstrate that tyrosine phosphorylation of Signal Transducer and Activator of Transcription (STAT) protein, positive regulation of collagen metabolic process, coagulation, and positive/negative regulation of blood coagulation have immediate impacts on the MI response. Our method organized biological processes and pathways in an unbiased approach to provide an intuitive way to identify biological properties of pathways under specific conditions. Pathways from different

  14. System-Wide Analysis Reveals a Complex Network of Tumor-Fibroblast Interactions Involved in Tumorigenicity

    Science.gov (United States)

    Rajaram, Megha; Li, Jinyu; Egeblad, Mikala; Powers, R. Scott

    2013-01-01

    Many fibroblast-secreted proteins promote tumorigenicity, and several factors secreted by cancer cells have in turn been proposed to induce these proteins. It is not clear whether there are single dominant pathways underlying these interactions or whether they involve multiple pathways acting in parallel. Here, we identified 42 fibroblast-secreted factors induced by breast cancer cells using comparative genomic analysis. To determine what fraction was active in promoting tumorigenicity, we chose five representative fibroblast-secreted factors for in vivo analysis. We found that the majority (three out of five) played equally major roles in promoting tumorigenicity, and intriguingly, each one had distinct effects on the tumor microenvironment. Specifically, fibroblast-secreted amphiregulin promoted breast cancer cell survival, whereas the chemokine CCL7 stimulated tumor cell proliferation while CCL2 promoted innate immune cell infiltration and angiogenesis. The other two factors tested had minor (CCL8) or minimally (STC1) significant effects on the ability of fibroblasts to promote tumor growth. The importance of parallel interactions between fibroblasts and cancer cells was tested by simultaneously targeting fibroblast-secreted amphiregulin and the CCL7 receptor on cancer cells, and this was significantly more efficacious than blocking either pathway alone. We further explored the concept of parallel interactions by testing the extent to which induction of critical fibroblast-secreted proteins could be achieved by single, previously identified, factors produced by breast cancer cells. We found that although single factors could induce a subset of genes, even combinations of factors failed to induce the full repertoire of functionally important fibroblast-secreted proteins. Together, these results delineate a complex network of tumor-fibroblast interactions that act in parallel to promote tumorigenicity and suggest that effective anti-stromal therapeutic strategies

  15. Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis

    International Nuclear Information System (INIS)

    Gao, Wei-Min; Haab, Brian B; Hanash, Samir M; Kuick, Rork; Orchekowski, Randal P; Misek, David E; Qiu, Ji; Greenberg, Alissa K; Rom, William N; Brenner, Dean E; Omenn, Gilbert S

    2005-01-01

    Cancer serum protein profiling by mass spectrometry has uncovered mass profiles that are potentially diagnostic for several common types of cancer. However, direct mass spectrometric profiling has a limited dynamic range and difficulties in providing the identification of the distinctive proteins. We hypothesized that distinctive profiles may result from the differential expression of relatively abundant serum proteins associated with the host response. Eighty-four antibodies, targeting a wide range of serum proteins, were spotted onto nitrocellulose-coated microscope slides. The abundances of the corresponding proteins were measured in 80 serum samples, from 24 newly diagnosed subjects with lung cancer, 24 healthy controls, and 32 subjects with chronic obstructive pulmonary disease (COPD). Two-color rolling-circle amplification was used to measure protein abundance. Seven of the 84 antibodies gave a significant difference (p < 0.01) for the lung cancer patients as compared to healthy controls, as well as compared to COPD patients. Proteins that exhibited higher abundances in the lung cancer samples relative to the control samples included C-reactive protein (CRP; a 13.3 fold increase), serum amyloid A (SAA; a 2.0 fold increase), mucin 1 and α-1-antitrypsin (1.4 fold increases). The increased expression levels of CRP and SAA were validated by Western blot analysis. Leave-one-out cross-validation was used to construct Diagonal Linear Discriminant Analysis (DLDA) classifiers. At a cutoff where all 56 of the non-tumor samples were correctly classified, 15/24 lung tumor patient sera were correctly classified. Our results suggest that a distinctive serum protein profile involving abundant proteins may be observed in lung cancer patients relative to healthy subjects or patients with chronic disease and may have utility as part of strategies for detecting lung cancer

  16. A 10-Year Analysis of Head and Neck Injuries Involving Nonpowder Firearms.

    Science.gov (United States)

    Dandu, Kartik V; Carniol, Eric T; Sanghvi, Saurin; Baredes, Soly; Eloy, Jean Anderson

    2017-05-01

    Objectives Firearms have an enduring and visible presence within American culture. However, the public health impact of nonpowder firearms and other "toy" guns has not been fully studied. These guns-including BB guns (ie, ball bearing), paintball guns, and pellet guns-are typically marketed to a younger audience. The objective of this study is to analyze head and neck injuries related to nonpowder firearms. Study Design Cross-sectional analysis of a national database. Setting Academic medical center. Subjects and Methods The National Electronic Injury Surveillance System was queried for head and neck injuries involving nonpowder guns, including air, BB, and pellet guns, and associated ammunition. Analysis of age, sex, incidence, injury location, and diagnosis was performed. Results From 2005 to 2014, there were 1695 cases recorded, or 55,060 estimated emergency room visits, due to injuries related to nonpowder guns and fired ammunition. The majority of patients were male (80.9%). These injuries were most common in children 6 to 12 years of age (37.9%), followed by those 13 to 18 years old (27.1%) and adults (≥19 years old; 17.8%), while preschool children (0-5 years) represented 17.2%. The most common injury diagnosis was penetrating foreign body (34.9%), followed by lacerations (24.3%) and contusions/abrasions (13.7%). Conclusion Nonpowder and other nonlethal firearm-related injuries to the head and neck region are a frequent source of emergency room visits nationally. Safety measures and public education on a mainstream level are required.

  17. Analysis of the Proteolytic Processing of ABCA3: Identification of Cleavage Site and Involved Proteases.

    Directory of Open Access Journals (Sweden)

    Nicole Hofmann

    Full Text Available ABCA3 is a lipid transporter in the limiting membrane of lamellar bodies in alveolar type II cells. Mutations in the ABCA3 gene cause respiratory distress syndrome in new-borns and childhood interstitial lung disease. ABCA3 is N-terminally cleaved by an as yet unknown protease, a process believed to regulate ABCA3 activity.The exact site where ABCA3 is cleaved was localized using mass spectrometry (MS. Proteases involved in ABCA3 processing were identified using small molecule inhibitors and siRNA mediated gene knockdown. Results were verified by in vitro digestion of a synthetic peptide substrate mimicking ABCA3's cleavage region, followed by MS analysis.We found that cleavage of ABCA3 occurs after Lys174 which is located in the proteins' first luminal loop. Inhibition of cathepsin L and, to a lesser extent, cathepsin B resulted in attenuation of ABCA3 cleavage. Both enzymes showed activity against the ABCA3 peptide in vitro with cathepsin L being more active.We show here that, like some other proteins of the lysosomal membrane, ABCA3 is a substrate of cathepsin L. Therefore, cathepsin L may represent a potential target to therapeutically influence ABCA3 activity in ABCA3-associated lung disease.

  18. Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410.

    Science.gov (United States)

    Yoneda, Aki; Wittmann, Bruce J; King, Jeremy D; Blankenship, Robert E; Dantas, Gautam

    2016-08-01

    Acaryochloris species are a genus of cyanobacteria that utilize chlorophyll (chl) d as their primary chlorophyll molecule during oxygenic photosynthesis. Chl d allows Acaryochloris to harvest red-shifted light, which gives them the ability to live in filtered light environments that are depleted in visible light. Although genomes of multiple Acaryochloris species have been sequenced, their analysis has not revealed how chl d is synthesized. Here, we demonstrate that Acaryochloris sp. CCMEE 5410 cells undergo chlorosis by nitrogen depletion and exhibit robust regeneration of chl d by nitrogen repletion. We performed a time course RNA-Seq experiment to quantify global transcriptomic changes during chlorophyll recovery. We observed upregulation of numerous known chl biosynthesis genes and also identified an oxygenase gene with a similar transcriptional profile as these chl biosynthesis genes, suggesting its possible involvement in chl d biosynthesis. Moreover, our data suggest that multiple prochlorophyte chlorophyll-binding homologs are important during chlorophyll recovery, and light-independent chl synthesis genes are more dominant than the light-dependent gene at the transcription level. Transcriptomic characterization of this organism provides crucial clues toward mechanistic elucidation of chl d biosynthesis.

  19. Analysis of the enzyme network involved in cattle milk production using graph theory.

    Science.gov (United States)

    Ghorbani, Sholeh; Tahmoorespur, Mojtaba; Masoudi Nejad, Ali; Nasiri, Mohammad; Asgari, Yazdan

    2015-06-01

    Understanding cattle metabolism and its relationship with milk products is important in bovine breeding. A systemic view could lead to consequences that will result in a better understanding of existing concepts. Topological indices and quantitative characterizations mostly result from the application of graph theory on biological data. In the present work, the enzyme network involved in cattle milk production was reconstructed and analyzed based on available bovine genome information using several public datasets (NCBI, Uniprot, KEGG, and Brenda). The reconstructed network consisted of 3605 reactions named by KEGG compound numbers and 646 enzymes that catalyzed the corresponding reactions. The characteristics of the directed and undirected network were analyzed using Graph Theory. The mean path length was calculated to be4.39 and 5.41 for directed and undirected networks, respectively. The top 11 hub enzymes whose abnormality could harm bovine health and reduce milk production were determined. Therefore, the aim of constructing the enzyme centric network was twofold; first to find out whether such network followed the same properties of other biological networks, and second, to find the key enzymes. The results of the present study can improve our understanding of milk production in cattle. Also, analysis of the enzyme network can help improve the modeling and simulation of biological systems and help design desired phenotypes to increase milk production quality or quantity.

  20. Looking for prosocial genes: ITRAQ analysis of proteins involved in MDMA-induced sociability in mice.

    Science.gov (United States)

    Kuteykin-Teplyakov, Konstantin; Maldonado, Rafael

    2014-11-01

    Social behavior plays a fundamental role in life of many animal species, allowing the interaction between individuals and sharing of experiences, needs, and goals across them. In humans, some neuropsychiatric diseases, including anxiety, posttraumatic stress disorder and autism spectrum disorders, are often characterized by impaired sociability. Here we report that N-Methyl-3,4-methylenedioxyamphetamine (MDMA, "Ecstasy") at low dose (3mg/kg) has differential effects on mouse social behavior. In some animals, MDMA promotes sociability without hyperlocomotion, whereas in other mice it elevates locomotor activity without affecting sociability. Both WAY-100635, a selective antagonist of 5-HT1A receptor, and L-368899, a selective oxytocin receptor antagonist, abolish prosocial effects of MDMA. Differential quantitative analysis of brain proteome by isobaric tag for relative and absolute quantification technology (iTRAQ) revealed 21 specific proteins that were highly correlated with sociability, and allowed to distinguish between entactogenic prosocial and hyperlocomotor effects of MDMA on proteome level. Our data suggest particular relevance of neurotransmission mediated by GABA B receptor, as well as proteins involved in energy maintenance for MDMA-induced sociability. Functional association network for differentially expressed proteins in cerebral cortex, hippocampus and amygdala were identified. These results provide new information for understanding the neurobiological substrate of sociability and may help to discover new therapeutic approaches to modulate social behavior in patients suffering from social fear and low sociability. Copyright © 2014 Elsevier B.V. and ECNP. All rights reserved.

  1. On the stability analysis of a general discrete-time population model involving predation and Allee effects

    International Nuclear Information System (INIS)

    Merdan, H.; Duman, O.

    2009-01-01

    This paper presents the stability analysis of equilibrium points of a general discrete-time population dynamics involving predation with and without Allee effects which occur at low population density. The mathematical analysis and numerical simulations show that the Allee effect has a stabilizing role on the local stability of the positive equilibrium points of this model.

  2. Interdependence of Depressive Symptoms, School Involvement, and Academic Performance between Adolescent Friends: A Dyadic Analysis

    Science.gov (United States)

    Chow, Chong Man; Tan, Cin Cin; Buhrmester, Duane

    2015-01-01

    Background: Friendships play an important role in the development of school involvement and academic performance during adolescence. This study examined the interdependence of depressive symptoms, school involvement, and academic performance between adolescent same-sex friends. Aims: Using cross-sectional data, we examined whether the link between…

  3. African American Fathers' Involvement in Home and Schools: An Interpretive Analysis of Their Beliefs and Experiences

    Science.gov (United States)

    Jones, Tomashu

    2012-01-01

    The lack of research about Black fathers and their involvement with schools was the primary motivation for this mixed method dissertation study. This discourse provides a much-needed account of what the nature is of Black father's involvement with schools, why and how they do it, and how student performance is influenced by Black fathers'…

  4. Proteomic analysis reveals metabolic and regulatory systems involved the syntrophic and axenic lifestyle of Syntrophomonas wolfei.

    Directory of Open Access Journals (Sweden)

    Jessica Rhea Sieber

    2015-02-01

    Full Text Available Microbial syntrophy is a vital metabolic interaction necessary for the complete oxidation of organic biomass to methane in all-anaerobic ecosystems. However, this process is thermodynamically constrained and represents an ecosystem-level metabolic bottleneck. To gain insight into the physiology of this process, a shotgun proteomic approach was used to quantify the protein landscape of the model syntrophic metabolizer, Syntrophomonas wolfei, grown axenically and syntrophically with Methanospirillum hungatei. Remarkably, the abundance of most proteins as represented by normalized spectral abundance factor (NSAF value changed very little between the pure and coculture growth conditions. Among the most abundant proteins detected were GroEL and GroES chaperonins, a small heat shock protein, and proteins involved in electron transfer, beta-oxidation, and ATP synthesis. Several putative energy conservation enzyme systems that utilize NADH and ferredoxin were present. The abundance of an EtfAB2 and the membrane-bound iron-sulfur oxidoreductase (Swol_0698 gene product delineated a potential conduit for electron transfer between acyl-CoA dehydrogenases and membrane redox carriers. Proteins detected only when S. wolfei was grown with M. hungatei included a zinc-dependent dehydrogenase with a GroES domain, whose gene is present in genomes in many organisms capable of syntrophy, and transcriptional regulators responsive to environmental stimuli or the physiological status of the cell. The proteomic analysis revealed an emphasis macromolecular stability and energy metabolism to S. wolfei and presence of regulatory mechanisms responsive to external stimuli and cellular physiological status.

  5. Parent-teen communication and pre-college alcohol involvement: a latent class analysis.

    Science.gov (United States)

    Abar, Caitlin C; Fernandez, Anne C; Wood, Mark D

    2011-12-01

    Although parent-adolescent communication has been identified as important in delaying the onset and escalation of alcohol use, both the strength and direction of observed associations have varied in prior research with adolescents and college students. The current study categorizes parents according to alcohol-related communication and relates these categories to other parenting factors and late adolescent alcohol involvement. As part of a larger study, 1007 college-bound teens and their parents were assessed. Teens were asked to report on their drinking behavior, and parents were asked about the occurrence of several specific alcohol-related communications with their teen, as well as additional parenting characteristics. Profiles of parent alcohol-related communication were derived using latent class analysis. Once the best fitting solution was determined, covariates were entered predicting class membership and investigating how classes were associated with additional parenting characteristics and teen alcohol use. A five-class solution provided the best fit to the data: Frequent, All Topics (28%); Moderate, All Topics (25%); Frequent, General Topics (25%); Frequent, Consequences and Limits (12%); and Infrequent, All Topics (10%). Covariate analyses demonstrated class differences with regard to parental modeling, monitoring, knowledge, and parent-teen relationship satisfaction, as well as for students' intentions to join fraternities/sororities and alcohol use. Findings from the current study add to a small but growing literature supporting the continuing influence of parents in late adolescence and suggest that the frequency and specificity of parent-teen communication are potentially informative for refined parent-based preventive interventions. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Transcriptomic analysis using olive varieties and breeding progenies identify candidate genes involved in plant architecture

    Directory of Open Access Journals (Sweden)

    Juan José eGonzález Plaza

    2016-03-01

    Full Text Available Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Little is known about how plant architecture is genetically determined in olive, were most of the existing varieties are traditional with an architecture poorly suited for modern growing and harvesting systems. In the present study, we have carried out microarray analysis of meristematic tissue to compare expression profiles of olive varieties displaying differences in architecture, as well as seedlings from their cross pooled on the basis of their sharing architecture-related phenotypes. The microarray used, previously developed by our group has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. Varieties with distinct architecture phenotypes and individuals from segregating progenies displaying opposite architecture features were used to link phenotype to expression. Here, we identify 2,252 differentially expressed genes associated to differences in plant architecture. Microarray results were validated by quantitative RT-PCR carried out on genes with functional annotation likely related to plant architecture. Twelve of these genes were further analyzed in individual seedlings of the corresponding pool. We also examined Arabidopsis mutants in putative orthologs of these targeted candidate genes, finding altered architecture for most of them. This supports a functional conservation between species and potential biological relevance of the candidate genes identified. This study is the first to identify genes associated to plant architecture in olive, and the results obtained could be of great help in future programs aimed at selecting phenotypes adapted to modern cultivation practices in this species.

  7. Transcriptomic Analysis Using Olive Varieties and Breeding Progenies Identifies Candidate Genes Involved in Plant Architecture.

    Science.gov (United States)

    González-Plaza, Juan J; Ortiz-Martín, Inmaculada; Muñoz-Mérida, Antonio; García-López, Carmen; Sánchez-Sevilla, José F; Luque, Francisco; Trelles, Oswaldo; Bejarano, Eduardo R; De La Rosa, Raúl; Valpuesta, Victoriano; Beuzón, Carmen R

    2016-01-01

    Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Little is known about how plant architecture is genetically determined in olive, were most of the existing varieties are traditional with an architecture poorly suited for modern growing and harvesting systems. In the present study, we have carried out microarray analysis of meristematic tissue to compare expression profiles of olive varieties displaying differences in architecture, as well as seedlings from their cross pooled on the basis of their sharing architecture-related phenotypes. The microarray used, previously developed by our group has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. Varieties with distinct architecture phenotypes and individuals from segregating progenies displaying opposite architecture features were used to link phenotype to expression. Here, we identify 2252 differentially expressed genes (DEGs) associated to differences in plant architecture. Microarray results were validated by quantitative RT-PCR carried out on genes with functional annotation likely related to plant architecture. Twelve of these genes were further analyzed in individual seedlings of the corresponding pool. We also examined Arabidopsis mutants in putative orthologs of these targeted candidate genes, finding altered architecture for most of them. This supports a functional conservation between species and potential biological relevance of the candidate genes identified. This study is the first to identify genes associated to plant architecture in olive, and the results obtained could be of great help in future programs aimed at selecting phenotypes adapted to modern cultivation practices in this species.

  8. Multilocus analysis of the Exophiala jeanselmei clade containing black yeasts involved in opportunistic disease in humans

    NARCIS (Netherlands)

    Zeng, J.; Feng, P.; Gerrits van den Ende, A.H.G.; Xi, L.; Harrak, M.J.; de Hoog, G.S.

    2014-01-01

    To confirm species delimitations in the ‘jeanselmei-clade’ in the Chaetothyriales, four independent markers were analysed, and phylogenetic trees were reconstructed using different algorithms. Reproductive isolation within the complex and reproductive modes in the species involved were determined,

  9. RNA Sequencing Analysis of Intracranial Aneurysm Walls Reveals Involvement of Lysosomes and Immunoglobulins in Rupture

    NARCIS (Netherlands)

    Kleinloog, Rachel; Verweij, Bon H.; van der Vlies, Pieter; Deelen, Patrick; Swertz, Morris A.; de Muynck, Louis; Van Damme, Philip; Giuliani, Fabrizio; Regli, Luca; van der Zwan, Albert; van der Sprenkel, Jan W. Berkelbach; Han, K. Sen; Gosselaar, Peter; van Rijen, Peter C.; Korkmaz, Emine; Post, Jan A.; Rinkel, Gabriel J. E.; Veldink, Jan H.; Ruigrok, Ynte M.

    Background and Purpose-Analyzing genes involved in development and rupture of intracranial aneurysms can enhance knowledge about the pathogenesis of aneurysms, and identify new treatment strategies. We compared gene expression between ruptured and unruptured aneurysms and control intracranial

  10. Practice nurse involvement in primary care depression management: an observational cost-effectiveness analysis

    OpenAIRE

    Gray, Jodi; Haji Ali Afzali, Hossein; Beilby, Justin; Holton, Christine; Banham, David; Karnon, Jonathan

    2014-01-01

    Background Most evidence on the effect of collaborative care for depression is derived in the selective environment of randomised controlled trials. In collaborative care, practice nurses may act as case managers. The Primary Care Services Improvement Project (PCSIP) aimed to assess the cost-effectiveness of alternative models of practice nurse involvement in a real world Australian setting. Previous analyses have demonstrated the value of high level practice nurse involvement in the manageme...

  11. Interdependence of depressive symptoms, school involvement, and academic performance between adolescent friends: A dyadic analysis.

    Science.gov (United States)

    Chow, Chong Man; Tan, Cin Cin; Buhrmester, Duane

    2015-09-01

    Friendships play an important role in the development of school involvement and academic performance during adolescence. This study examined the interdependence of depressive symptoms, school involvement, and academic performance between adolescent same-sex friends. Using cross-sectional data, we examined whether the link between depressive symptoms and academic performance would be mediated by school involvement at the intrapersonal (actor) and interpersonal (partner) levels. Data came from 155 pairs of same-sex adolescent friends (80 boys; M(age) = 16.17, SD = 0.44). The actor-partner interdependence model was used to examine the dyadic data and mediation hypotheses. Mediated actor effects showed that adolescents who had more depressive symptoms reported lower academic performance, and such an association was mediated by their own and their friend's lower school involvement. Mediated partner effects showed that adolescents who had more depressive symptoms also had a friend with lower academic performance, and such an association was mediated by both individuals' lower school involvement. This study provided evidence to support the broader interpersonal framework for understanding school involvement and academic performance. The current findings also have potential practical implications, especially for programmes targeted at addressing adolescents' school problems. © 2015 The British Psychological Society.

  12. A qualitative analysis of men's involvement in maternal and child health as a policy intervention in rural Central Malawi.

    Science.gov (United States)

    Mkandawire, Elizabeth; Hendriks, Sheryl L

    2018-01-19

    Men's involvement in maternal and child health presents an opportunity for the advancement of maternal and child nutrition as men often play a key role in decision-making particularly regarding women's reproductive health. While most research on men's involvement in maternal and child health has focused on men's participation in antenatal care, this study focuses specifically on men's involvement in maternal and child nutrition. The purpose of the study is to explore how men's involvement is conceptualised in rural Central Malawi, highlighting the key factors influencing men's involvement in maternal and child health. Focus group discussions and in-depth interviews were conducted with 26 informants and 44 community members. Critical policy was used as the theoretical framework to inform the analysis of research findings. In this study, we identified several factors that facilitate men's involvement in maternal and child health, but we also identified several barriers. Facilitators of men's involvement included: recognition by men of the impact of their involvement, pride, advocacy, incentives and disincentives and male champions. Barriers included socio-cultural beliefs, stigmatisation and opportunity costs. The study also found that there were several limitations that had unintended consequences on desired programme outcomes. These included: discriminating against women, marginalisation of married women and reinforcing men's decision-making roles. The study findings highlight the importance of involving men in maternal and child health for improved nutrition outcomes. We emphasise the need for nutrition policy-makers to be aware that gender dynamics are changing. It is no longer just women who are involved in nutrition activities, therefore policy-makers need to revise their approach to ensure that they consider men's role in nutrition.

  13. Moral transgression during the Vietnam War: a path analysis of the psychological impact of veterans' involvement in wartime atrocities.

    Science.gov (United States)

    Dennis, Paul A; Dennis, Nora M; Van Voorhees, Elizabeth E; Calhoun, Patrick S; Dennis, Michelle F; Beckham, Jean C

    2017-03-01

    Involvement in wartime combat often conveys a number of deleterious outcomes, including posttraumatic stress disorder (PTSD), depression, hostility, aggression, and suicidal ideation. Less studied is the effect of engagement in wartime atrocities, including witnessing and perpetrating abusive violence. This study employed path analysis to examine the direct effects of involvement in wartime atrocities on hostility, aggression, depression, and suicidal ideation independent of combat exposure, as well as the indirect effects via guilt and PTSD symptom severity among 603 help-seeking male Vietnam War veterans. Involvement in wartime atrocities was predictive of increased guilt, PTSD severity, hostility, aggression, depressive symptoms, and suicidal ideation after controlling for overall combat exposure. Combat-related guilt played a minor role in mediating the effect of atrocity involvement on depression and suicidal ideation. PTSD severity had a larger mediational effect. However, it still accounted for less than half of the total effect of involvement in wartime atrocities on hostility, aggression, and suicidal ideation. These findings highlight the heightened risk conveyed by involvement in wartime atrocities and suggest that the psychological sequelae experienced following atrocity involvement may extend well beyond guilt and PTSD.

  14. Fathers in Context: Comparative Analysis of Father Involvement in Bulgaria and the Netherlands

    NARCIS (Netherlands)

    N.A. Conkova (Nina); B.E. Ory (Brett)

    2016-01-01

    markdownabstractThis report compares father involvement with their children in Bulgaria and the Netherlands by examining country differences in family formation patterns, policy context, and cultural prescriptions regarding family life. In studying the time fathers spend with their children, it is

  15. Analysis of BRCA1 involvement in breast cancer in Indian women

    Indian Academy of Sciences (India)

    The involvement of the familial breast-ovarian cancer gene (BRCA1) in the molecular pathogenesis of breast cancer among Indian women is unknown. We have used a set of microsatellite polymorphisms to examine the frequency of allele loss at the BRCA1 region on chromosome 17q21, in a panel of 80 human breast ...

  16. Parent-Teen Communication and Pre-College Alcohol Involvement: A Latent Class Analysis

    OpenAIRE

    Abar, Caitlin C.; Fernandez, Anne C.; Wood, Mark D.

    2011-01-01

    Although parent-adolescent communication has been identified as important in delaying the onset and escalation of alcohol use, both the strength and direction of observed associations has varied in prior research with adolescents and college students. The current study categorizes parents according to alcohol-related communication and relates these categories to other parenting factors and late adolescent alcohol involvement.

  17. Community Involvement and Victimization at School: An Analysis through Family, Personal and Social Adjustment

    Science.gov (United States)

    Jimenez, Teresa Isabel; Musitu, Gonzalo; Ramos, Manuel Jesus; Murgui, Sergio

    2009-01-01

    The present study analyzes the impact of adolescents' community involvement on victimization by peers at school through various indicators of family, personal and social adjustment (openness of communication with mother and father, life satisfaction, social self-esteem, and loneliness). Participating in the project were 565 adolescents aged 11 to…

  18. Parent Involvement and Science Achievement: A Cross-Classified Multilevel Latent Growth Curve Analysis

    Science.gov (United States)

    Johnson, Ursula Y.; Hull, Darrell M.

    2014-01-01

    The authors examined science achievement growth at Grades 3, 5, and 8 and parent school involvement at the same time points using the Early Childhood Longitudinal Study-Kindergarten Class of 1998-1999. Data were analyzed using cross-classified multilevel latent growth curve modeling with time invariant and varying covariates. School-based…

  19. Clinical incidents involving students on placement: an analysis of incident reports to identify potential risk factors.

    Science.gov (United States)

    Gaida, J E; Maloney, S; Lo, K; Morgan, P

    2015-06-01

    Students are sometimes involved in incidents during clinical training. To the authors' knowledge, no quantitative studies of incidents specifically involving physiotherapy students on clinical placement are available in the literature. A retrospective audit (2008 to 2011) of incident reports involving physiotherapy students was conducted to identify the nature and features of incidents. The study aimed to determine if injuries to a student or patient were more or less likely when the supervisor was in close proximity, and whether students with lower academic performance in their preclinical semester were more likely to be involved in an incident. There were 19 care-delivery-related and three equipment-related incidents. There were no incidents of violent, aggressive or demeaning behaviour towards students. The incident rate was 9.0/100,000 student-hours for third-year students and 6.8/100,000 student-hours for fourth-year students. The majority of incidents (55%) occurred from 11 am to 12-noon and from 3 pm to 3.30 pm. Incidents more often resulted in patient or student injury when the supervisor was not in close proximity (approximately 50% vs approximately 20%), although the difference was not significant (P=0.336). The academic results of students involved in incidents were equivalent to the whole cohort in their preclinical semester {mean 75 [standard deviation (SD) 6] vs 76 (SD 7); P=0.488}. The unexpected temporal clustering of incidents warrants further investigation. Student fatigue may warrant attention as a potential contributor; however, contextual factors, such as staff workload, along with organisational systems, structures and procedures may be more relevant. The potential relationship between supervisor proximity and injury also warrants further exploration. The findings of the present study should be integrated into clinical education curricula and communicated to clinical educators. Copyright © 2014 Chartered Society of Physiotherapy. Published by

  20. Analysis of a postulated accident scenario involving loss of forced flow in a LMFBR

    International Nuclear Information System (INIS)

    Moreira, M.L.

    1985-01-01

    A model to analyse a postulated accident scenario involving loss of forced flow in the reactor vessel of a LMFBR is used. Five phases of the accident are analysed: Natural Circulation, Subcooled Boiling, Nucleate Boiling, Core Dryout and Cladding melt. The heat conduction in the fuel cladding, coolant and lower and upper plenum are calculated by a lump-parameter model. Physical data of a prototype LMFBR reactor were used for the calculation. (author)

  1. Bilateral involvement of a single cranial nerve: analysis of 578 cases.

    Science.gov (United States)

    Keane, James R

    2005-09-27

    The author reviewed 34 years of personal experience with inpatients in a large municipal hospital to analyze the seats and causes of involvement of single pairs of cranial nerves. Among 578 cases, the sixth (n = 234) and second (211) nerves predominated, followed by the fourth (48), seventh (30), third (27), and eighth (18) cranial nerves. Trauma (99), infection (94), tumor (92), increased intracranial pressure (85), vascular disease (74), and demyelination (66) were common causes.

  2. Learning from an analysis of closed malpractice litigation involving myocardial infarction.

    Science.gov (United States)

    Wu, Kuan-Han; Yen, Yung-Lin; Wu, Chien-Hung; Hwang, Chi-Yuan; Cheng, Shih-Yu

    2017-05-01

    To examine the epidemiologic data, identify the pattern of dispute, and determine clinical litigious errors by analyzing closed malpractice claims involving myocardial infarction (MI) in Taiwanese courts. A retrospective descriptive study was performed to analyze the verdicts pertaining to MI from the population-based database of the Taiwan judicial system between 2002 and 2013. The results of adjudication, involved specialists, primary dispute leading to lawsuits, and litigious errors were recorded. A total of 36 closed malpractice claims involving MI were included. The mean interval between the incident and litigation closure was 65.5 ± 28.3 months. Nearly 20% of the cases were judged against clinicians and the mean payment was $100639 ± 49617, while the mean imprisonment sentence was 4.3 ± 1.8 months. Cardiologists and emergency physicians were involved in 56.3% of cases, but won 92.6% of lawsuits, while other specialists lost nearly 25% of lawsuits. The most common dispute was misdiagnosis (38.9%), but this dispute had the lowest percentage of loss (7.1%). Disputes regarding delayed diagnosis were judged against the defendants in 50% of claims. Clinicians lost the lawsuit in the following conditions: 1) misdiagnosis of MI in patients with typical chest pain and known coronary artery risk factors; 2) failure to perform thoughtful evaluation and series investigations in patients suspicious of ischemic heart disease; 3) failure to perform indicated treatment to avoid disease progression. Medical practitioners should keep a high index of MI suspicion, especially if the diagnosis and treatment of MI are beyond their daily practice. Prudent patient reevaluation, serial ECG and cardiac enzyme testing, and early consultation are suggested to reduce malpractice liability. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  3. Truck-involved crashes injury severity analysis for different lighting conditions on rural and urban roadways.

    Science.gov (United States)

    Uddin, Majbah; Huynh, Nathan

    2017-11-01

    This paper investigates factors affecting injury severity of crashes involving trucks for different lighting conditions on rural and urban roadways. It uses 2009-2013 Ohio crash data from the Highway Safety Information System. The explanatory factors include the occupant, vehicle, collision, roadway, temporal and environmental characteristics. Six separate mixed logit models were developed considering three lighting conditions (daylight, dark, and dark-lighted) on two area types (rural and urban). A series of log-likelihood ratio tests were conducted to validate that these six separate models by lighting conditions and area types are warranted. The model results suggest major differences in both the combination and the magnitude of impact of variables included in each model. Some variables were significant only in one lighting condition but not in other conditions. Similarly, some variables were found to be significant in one area type but not in other area type. These differences show that the different lighting conditions and area types do in fact have different contributing effects on injury severity in truck-involved crashes, further highlighting the importance of examining crashes based on lighting conditions on rural and urban roadways. Age and gender of occupant (who is the most severely injured in a crash), truck types, AADT, speed, and weather condition were found to be factors that have significantly different levels of impact on injury severity in truck-involved crashes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. ANALYSIS OF THE TEACHERS’ INVOLVEMENT IN THE DISCUSSION OF THE APPLICATION OF THE FEDERAL STATE EDUCATIONAL STANDARDS VIA ONLINE RESOURCES

    Directory of Open Access Journals (Sweden)

    С Н Вачкова

    2017-12-01

    Full Text Available This article presents the research results of the teachers’ involvement extent in current problems emerging in educational activities. The paper discusses the concept of involvement, its functions and scientific approaches to its analysis; suggests the original definition and structure of this concept, describes the chosen methodology of its analysis, database research and the nature of the sample, analysis tools. The base of the present research was the Internet portal “Public expertise of normative documents in education”. There is a detailed description of quantitative results, the indicators of teachers’ participation in discussing problems of education in relation to normative educational documents of Federal state educational standards of primary, basic and secondary general education. The research results showed the indicators of teachers’ activity and the expressed problems in application the Federal state educational standards.

  5. Prospect Theory and the Risks Involved in Decision-Making: Content Analysis in ProQuest Articles

    Directory of Open Access Journals (Sweden)

    Sady Darcy da Silva-Junior

    2016-04-01

    Full Text Available In this study, the objective is to perform content analysis on articles of a reliable database, dealing with the prospect theory and the risks involved in the decision making process, evaluating some criteria for the theoretical and methodological approaches that allow a joint analysis and comparative. Therefore, a search in ProQuest database was performed which resulted in 15 articles that were submitted to content analysis process, based on the evaluation of nine factors identified by researchers. Among the results highlight the critical attitude to the prospect theory, in contrast to the assertion of his representative capacity of real situations and application in various situations.

  6. Analysis of risk factors of involvement of seminal vesicles in patients with prostate cancer undergoing radical prostatectomy

    Directory of Open Access Journals (Sweden)

    Marcos F. Dall'Oglio

    2004-12-01

    Full Text Available OBJECTIVE: To determine through preoperative serum PSA level, Gleason score on biopsy and percentage of fragments affected by tumor on biopsy, the probability of involvement of the seminal vesicles. MATERIALS AND METHODS: During the period between March 1991 to December 2002, we selected 899 patients undergoing radical prostatectomy for treatment of localized prostate adenocarcinoma. The analyzed preoperative variables were PSA, percentage of positive fragments and Gleason score on the biopsy. Pre-operative PSA was divided in scales from 0 to 4.0 ng/mL, 4.1 to 10 ng/mL, 10.1 to 20 ng/mL and > 20 ng/mL, Gleason score was categorized in scales from 2 to 6. 7 and 8 to 10, and the percentage of affected fragments was divided in 0 to 25%, 25.1% to 50%, 50.1% to 75%, and 75.1% to 100%. All these variables were correlated with the involvement of seminal vesicles in the surgical specimen. RESULTS: Of the 899 patients under study, approximately 11% (95% CI, [9% - 13%] had involvement of seminal vesicles. On the multivariate analysis, when PSA was < 4, the Gleason score was 2 to 6, and less than 25% of fragments were involved on the biopsy, only 3.6%, 7.6% and 6.2% of patients respectively, had involvement of seminal vesicles. On the multivariate analysis, we observed that PSA, Gleason score and the percentage of involved fragments were independent prognostic factors for invasion of seminal vesicles. CONCLUSION: The preoperative variables used in the present study allow the identification of men with minimal risk (lower than 5% if involvement of seminal vesicles.

  7. Assessing the economic impact of paternal involvement: a comparison of the generalized linear model versus decision analysis trees.

    Science.gov (United States)

    Salihu, Hamisu M; Salemi, Jason L; Nash, Michelle C; Chandler, Kristen; Mbah, Alfred K; Alio, Amina P

    2014-08-01

    Lack of paternal involvement has been shown to be associated with adverse pregnancy outcomes, including infant morbidity and mortality, but the impact on health care costs is unknown. Various methodological approaches have been used in cost minimization and cost effectiveness analyses and it remains unclear how cost estimates vary according to the analytic strategy adopted. We illustrate a methodological comparison of decision analysis modeling and generalized linear modeling (GLM) techniques using a case study that assesses the cost-effectiveness of potential father involvement interventions. We conducted a 12-year retrospective cohort study using a statewide enhanced maternal-infant database that contains both clinical and nonclinical information. A missing name for the father on the infant's birth certificate was used as a proxy for lack of paternal involvement, the main exposure of this study. Using decision analysis modeling and GLM, we compared all infant inpatient hospitalization costs over the first year of life. Costs were calculated from hospital charges using department-level cost-to-charge ratios and were adjusted for inflation. In our cohort of 2,243,891 infants, 9.2% had a father uninvolved during pregnancy. Lack of paternal involvement was associated with higher rates of preterm birth, small-for-gestational age, and infant morbidity and mortality. Both analytic approaches estimate significantly higher per-infant costs for father uninvolved pregnancies (decision analysis model: $1,827, GLM: $1,139). This paper provides sufficient evidence that healthcare costs could be significantly reduced through enhanced father involvement during pregnancy, and buttresses the call for a national program to involve fathers in antenatal care.

  8. Are the risk and protective factors similar for gang-involved, pressured-to-join, and non-gang-involved youth? A social-ecological analysis.

    Science.gov (United States)

    Merrin, Gabriel J; Hong, Jun Sung; Espelage, Dorothy L

    2015-11-01

    This study examines the risk and protective factors for gang involvement among subgroups of youth (i.e., current or former gang members, youth who resisted gang membership, and non-gang-involved youth) using the social-ecological framework. Middle and high school students (N = 17,366) from school districts in a large Midwestern county participated. Results indicated that males were more likely than females to be involved in gangs. For the individual context, our findings indicate that racial and ethnic minorities, females, and youth with depression/suicidal ideation are likely to be at risk for gang involvement. For the family context, we found that having gang-involved family members and family dysfunction are related to youth gang involvement. For the peer context, peers' alcohol and drug use and bullying were significantly associated with gang involvement. For the school context, as our results demonstrate, youth who perceived fair treatment from teachers and other adults in school and those with a sense of belonging in school are more likely to avoid gang membership. For the neighborhood context, we found that presence of adult support in the neighborhood and perceived neighborhood safety are negatively associated with gang membership. Findings suggest that gang prevention efforts need to target multiple ecologies that surround and influence youth. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

  9. ESTs analysis reveals putative genes involved in symbiotic seed germination in Dendrobium officinale.

    Directory of Open Access Journals (Sweden)

    Ming-Ming Zhao

    Full Text Available Dendrobiumofficinale (Orchidaceae is one of the world's most endangered plants with great medicinal value. In nature, D. officinale seeds must establish symbiotic relationships with fungi to germinate. However, the molecular events involved in the interaction between fungus and plant during this process are poorly understood. To isolate the genes involved in symbiotic germination, a suppression subtractive hybridization (SSH cDNA library of symbiotically germinated D. officinale seeds was constructed. From this library, 1437 expressed sequence tags (ESTs were clustered to 1074 Unigenes (including 902 singletons and 172 contigs, which were searched against the NCBI non-redundant (NR protein database (E-value cutoff, e(-5. Based on sequence similarity with known proteins, 579 differentially expressed genes in D. officinale were identified and classified into different functional categories by Gene Ontology (GO, Clusters of orthologous Groups of proteins (COGs and Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. The expression levels of 15 selected genes emblematic of symbiotic germination were confirmed via real-time quantitative PCR. These genes were classified into various categories, including defense and stress response, metabolism, transcriptional regulation, transport process and signal transduction pathways. All transcripts were upregulated in the symbiotically germinated seeds (SGS. The functions of these genes in symbiotic germination were predicted. Furthermore, two fungus-induced calcium-dependent protein kinases (CDPKs, which were upregulated 6.76- and 26.69-fold in SGS compared with un-germinated seeds (UGS, were cloned from D. officinale and characterized for the first time. This study provides the first global overview of genes putatively involved in D. officinale symbiotic seed germination and provides a foundation for further functional research regarding symbiotic relationships in orchids.

  10. Renal involvement in primary antiphospholipid syndrome: retrospective analysis of 160 patients.

    Science.gov (United States)

    Sinico, Renato Alberto; Cavazzana, Ilaria; Nuzzo, Monica; Vianelli, Monica; Napodano, Pietro; Scaini, Patrizia; Tincani, Angela

    2010-07-01

    The objective of this study was to evaluate the prevalence, clinicopathologic features, and outcome of renal involvement in a large cohort of patients with primary antiphospholipid syndrome (PAPS). We retrospectively examined medical records of 160 patients with a diagnosis of PAPS of two general hospitals of northern Italy between 1985 and 2008. There were 140 women and 20 men. Mean age was 35+/-12 yr. PAPS was characterized by thrombotic events in 41.2%, fetal loss in 39.4%, and both in 19.4%. Signs of renal abnormalities were present in 14 (8.7%) patients. All patients had proteinuria, in the nephrotic range in five; four patients had moderate chronic renal insufficiency, and one had end-stage kidney disease (ESKD). Two patients presented with acute renal failure and one with nephritic syndrome. Ten patients underwent a renal biopsy, which showed a membranous glomerulonephritis in four, proliferative glomerulonephritis in two, thrombotic microangiopathy in two, and vascular lesions consistent with chronic antiphospholipid antibodies nephropathy in two. Patients with renal involvement were older (41.8 versus 34.3 years; P=0.0269), more frequently lupus anticoagulant positive (92.3 versus 48.9%; P=0.0068), and had hypocomplementemia (P<0.05). Renal abnormalities are present in approximately 9% of patients with PAPS. In addition to APS nephropathy, the prevailing picture is membranous nephropathy. Outcome and long-term follow-up usually are good. Not all of the clinical manifestations of PAPS can be ascribed to thrombotic mechanisms. The heterogeneity of renal involvement confirms the presence of a continuum between systemic lupus erythematosus and PAPS.

  11. Practice nurse involvement in primary care depression management: an observational cost-effectiveness analysis.

    Science.gov (United States)

    Gray, Jodi; Haji Ali Afzali, Hossein; Beilby, Justin; Holton, Christine; Banham, David; Karnon, Jonathan

    2014-01-14

    Most evidence on the effect of collaborative care for depression is derived in the selective environment of randomised controlled trials. In collaborative care, practice nurses may act as case managers. The Primary Care Services Improvement Project (PCSIP) aimed to assess the cost-effectiveness of alternative models of practice nurse involvement in a real world Australian setting. Previous analyses have demonstrated the value of high level practice nurse involvement in the management of diabetes and obesity. This paper reports on their value in the management of depression. General practices were assigned to a low or high model of care based on observed levels of practice nurse involvement in clinical-based activities for the management of depression (i.e. percentage of depression patients seen, percentage of consultation time spent on clinical-based activities). Linked, routinely collected data was used to determine patient level depression outcomes (proportion of depression-free days) and health service usage costs. Standardised depression assessment tools were not routinely used, therefore a classification framework to determine the patient's depressive state was developed using proxy measures (e.g. symptoms, medications, referrals, hospitalisations and suicide attempts). Regression analyses of costs and depression outcomes were conducted, using propensity weighting to control for potential confounders. Capacity to determine depressive state using the classification framework was dependent upon the level of detail provided in medical records. While antidepressant medication prescriptions were a strong indicator of depressive state, they could not be relied upon as the sole measure. Propensity score weighted analyses of total depression-related costs and depression outcomes, found that the high level model of care cost more (95% CI: -$314.76 to $584) and resulted in 5% less depression-free days (95% CI: -0.15 to 0.05), compared to the low level model. However

  12. Placing the topical session on stakeholder involvement tools perspective: Rapporteur's analysis

    International Nuclear Information System (INIS)

    Vari, Anna

    2003-01-01

    The topical session discussed the following questions: - How to decide which of the various dialogue tools fits a waste management process, decision phase, and desired outcomes? - How to evaluate whether the dialogue process has been successful or not? - What can be expected, what should practitioners watch out for when applying some of the more commonly-used tools? This report summarises the responses given to the above questions by session contributors, and compares them with some general findings in public participation research. It was argued by most that although public participation will not guarantee an automatic success of the waste management programme, without it decision makers likely will be heading for tremendous difficulties. The public will not be contented by information only, but demands to be involved in the decision making process. Very strong motivation is needed to participate in a complex deliberation process that includes learning about or analysing a wide range of technical and non-technical issues, as well as gradually working out solutions or plans that are acceptable to all parties. Accomplishing such participation is an even more significant effort when it is a 'spare time', unpaid occupation. Under these conditions, the persons who attend all consultation meetings tend to be the ones who feel strongly against the project and who may not be open to the type of dialogue that decision makers would like to engage with them. As in other risk management and political situations, it is the very definition of 'what is at risk', and 'what should be done about it' that is brought to the fore. All these facts were recognised as significant challenges to the participation process. According to session participants, however, there are no alternatives or shortcuts to public involvement as a tool to make the decision making process in RWM transparent and acceptable. Most agreed that efforts should be allocated to using

  13. Peptidomic Analysis of Fetal Heart Tissue for Identification of Endogenous Peptides Involved in Tetralogy of Fallot.

    Science.gov (United States)

    Zhang, Jingjing; Liang, Dong; Cheng, Qing; Cao, Li; Wu, Yun; Wang, Yan; Han, Shuping; Yu, Zhangbin; Cui, Xianwei; Xu, Tianhui; Ma, Dingyuan; Hu, Ping; Xu, Zhengfeng

    2017-06-01

    Tetralogy of fallot (TOF) is one of the most prevalent types of congenital heart diseases. As a category of bioactive molecules, peptides have been proved to participate in various biological processes. However, the role of endogenous peptides in the pathogenesis of TOF has not been studied. In this study, we performed a comparative peptidomic profile in the fetal heart of TOF and the control group for the first time by liquid chromatography-tandem mass spectrometry. Our data demonstrated that a total of 201 peptides derived from 176 precursor proteins were differentially expressed in the heart tissues of TOF fetuses compared with normal controls, including 41 upregulated peptides and 160 downregulated peptides. After analyzing the characteristics of these differentially expressed peptides and their precursor proteins, we found that these peptides were potentially involved in different biological processes, especially cardiogenesis and congenital anomaly of the cardiovascular system. Interestingly, we detected several extracellular matrix-derived peptides involved in our differentially expressed peptidomic profile. In summary, our study constructed a comparative peptidomic profile from the heart tissues of TOF fetuses and normal controls, and it identified a series of peptides that could potentially participate in heart development and TOF formation. The emergence of our peptidomics study indicated a new perspective to explore the pathogenesis of abnormal heart morphology, especially TOF.

  14. Analysis of systemic lupus erythematosus (SLE) involving the central nervous system by magnetic resonance imaging (MRI)

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Kimihiro; Hara, Masako; Nakajima, Shinji and others

    1989-04-01

    Involvement of the central nervous system (CNS) commonly occurs in systemic lupus erythematosus (SLE). But definitive diagnosis remains difficult even with computed tomography (CT). In this study, we used the recently developed technique, magnetic resonance imaging (MRI) for CNS lupus and compared it with CT scans. CT was performed with a General Electric 8800 CT/T scanner. MRI was performed using a Mitsubishi Electric MMI-150 S. Ten patients with CNS lupus were divided into 3 groups. Group I included 4 cases with neurological manifestations alone. All lesions seen on CT were also detected by MRI, with greater clarity and extent. Furthermore, MRI depicted several microinfarcts in white matter without symptoms. Group II included 5 cases with psychiatric features alone. MRI detected a thalamic microinfarct in only one case while CT showed no abnormality in all cases. Group III included 1 case with both neurological and psychiatric symptoms. MRI demonstrated a small infarct of midbrain corresponding with neurological symptoms, more clearly than CT. Therefore MRI demonstrates the degree of brain involvement in SLE more accurately than CT. (author).

  15. Analysis of systemic lupus erythematosus (SLE) involving the central nervous system by magnetic resonance imaging (MRI)

    International Nuclear Information System (INIS)

    Suzuki, Kimihiro; Hara, Masako; Nakajima, Shinji

    1989-01-01

    Involvement of the central nervous system (CNS) commonly occurs in systemic lupus erythematosus (SLE). But definitive diagnosis remains difficult even with computed tomography (CT). In this study, we used the recently developed technique, magnetic resonance imaging (MRI) for CNS lupus and compared it with CT scans. CT was performed with a General Electric 8800 CT/T scanner. MRI was performed using a Mitsubishi Electric MMI-150 S. Ten patients with CNS lupus were divided into 3 groups. Group I included 4 cases with neurological manifestations alone. All lesions seen on CT were also detected by MRI, with greater clarity and extent. Furthermore, MRI depicted several microinfarcts in white matter without symptoms. Group II included 5 cases with psychiatric features alone. MRI detected a thalamic microinfarct in only one case while CT showed no abnormality in all cases. Group III included 1 case with both neurological and psychiatric symptoms. MRI demonstrated a small infarct of midbrain corresponding with neurological symptoms, more clearly than CT. Therefore MRI demonstrates the degree of brain involvement in SLE more accurately than CT. (author)

  16. Meta-analysis of SNPs involved in variance heterogeneity using Levene's test for equal variances

    Science.gov (United States)

    Deng, Wei Q; Asma, Senay; Paré, Guillaume

    2014-01-01

    Meta-analysis is a commonly used approach to increase the sample size for genome-wide association searches when individual studies are otherwise underpowered. Here, we present a meta-analysis procedure to estimate the heterogeneity of the quantitative trait variance attributable to genetic variants using Levene's test without needing to exchange individual-level data. The meta-analysis of Levene's test offers the opportunity to combine the considerable sample size of a genome-wide meta-analysis to identify the genetic basis of phenotypic variability and to prioritize single-nucleotide polymorphisms (SNPs) for gene–gene and gene–environment interactions. The use of Levene's test has several advantages, including robustness to departure from the normality assumption, freedom from the influence of the main effects of SNPs, and no assumption of an additive genetic model. We conducted a meta-analysis of the log-transformed body mass index of 5892 individuals and identified a variant with a highly suggestive Levene's test P-value of 4.28E-06 near the NEGR1 locus known to be associated with extreme obesity. PMID:23921533

  17. Analysis of proteins involved in the production of MAA׳s in two Cyanobacteria Synechocystis PCC 6803 and Anabaena cylindrica.

    Science.gov (United States)

    Rahman, Md Akhlaqur; Sinha, Sukrat; Sachan, Shephali; Kumar, Gaurav; Singh, Shailendra Kumar; Sundaram, Shanthy

    2014-01-01

    Mycosporine- like amino acids (MAAs) are small (MAAs is presumed to occur via the first part of shikimate pathway. In the present work two cyanobacteria Synechocystis PCC 6803 and Anabaena cylindrica were tested for their ability to synthesize MAAs and protein involved in the production of MAAs. It was found that protein sequence 3-phosphoshikimate 1-carboxyvinyltransferase is involved in producing mycosporine glycine in Synechocystis PCC 6803 and 3-dehydroquinate synthase is involved for producing shinorine in Anabaena cylindrica. Phylogenetic and bioinformatic analysis of Mycosporine like amino acid producing protein sequence of both cyanobacterial species Synechocystis PCC 6803 and Anabaena cylindrica provide a useful framework to understand the relationship of the different forms and how they have evolved from a common ancestor. These products seem to be conserved but the residues are prone to variation which might be due the fact that different cyanobacteria show different physiological process in response of Ultraviolet stress.

  18. Analysis of Hazards Associated with a Process Involving Uranium Metal and Uranium Hydride Powders

    Energy Technology Data Exchange (ETDEWEB)

    Bullock, J.S.

    2000-05-01

    An analysis of the reaction chemistry and operational factors associated with processing uranium and uranium hydride powders is presented, focusing on a specific operation in the Development Division which was subjected to the Job Hazard Analysis (JHA) process. Primary emphasis is on the thermodynamic factors leading to pyrophoricity in common atmospheres. The discussion covers feed powders, cold-pressed and hot-pressed materials, and stray material resulting from the operations. The sensitivity of the various forms of material to pyrophoricity in common atmospheres is discussed. Operational recommendations for performing the work described are given.

  19. Association analysis of schizophrenia on 18 genes involved in neuronal migration

    DEFF Research Database (Denmark)

    Kähler, Anna K; Djurovic, Srdjan; Kulle, Bettina

    2008-01-01

    Several lines of evidence support the theory of schizophrenia (SZ) being a neurodevelopmental disorder. The structural, cytoarchitectural and functional brain abnormalities reported in patients with SZ, might be due to aberrant neuronal migration, since the final position of neurons affects...... neuronal function, morphology, and formation of synaptic connections. We have investigated the putative association between SZ and gene variants engaged in the neuronal migration process, by performing an association study on 839 cases and 1,473 controls of Scandinavian origin. Using a gene-wide approach...... significant. Further studies in independent samples are needed, including upcoming genome wide association study results, but our data suggest that MDGA1 is a new SZ susceptibility gene, and that altered neuronal migration is involved in SZ pathology....

  20. Connectivity analysis of suggestive brain areas involved in middle ear pressure regulation in humans

    DEFF Research Database (Denmark)

    SA, Sami; Gaihede, Michael

    2010-01-01

    of these distinct mechanisms were found. CONCLUSION:: The human mastoid as well as the Eustachian tube was capable of active counter-regulation of the MEP in short-term experimental pressure changes in healthy ears. Thus, these 2 systems seemed to function in a complementary way, where the mastoid was related......HYPOTHESIS:: Middle ear pressure (MEP) is actively regulated by both the Eustachian tube and the mastoid air cell system. BACKGROUND:: MEP is a highly significant factor involved in many clinical conditions related to otitis media. Basic knowledge on its overall regulation remains insufficient......, but the Eustachian tube and mastoid gas exchange are important factors. The main focus has been aimed at the tube; however, evidence points to the mastoid as equally important. More detailed methods are demanded to study their complementary functions. METHODS:: A catheter was inserted into the mastoid of 12 human...

  1. Association analysis of schizophrenia on 18 genes involved in neuronal migration

    DEFF Research Database (Denmark)

    Kähler, Anna K; Djurovic, Srdjan; Kulle, Bettina

    2008-01-01

    , tagSNPs in 18 candidate genes have been genotyped, with gene products involved in the neuron-to-glial cell adhesion, interactions with the DISC1 protein and/or rearrangements of the cytoskeleton. Of the 289 markers tested, 19 markers located in genes MDGA1, RELN, ITGA3, DLX1, SPARCL1, and ASTN1......, attained nominal significant P-values (P glial cells. Eight markers obtained nominal significance in both tests, and were located......Several lines of evidence support the theory of schizophrenia (SZ) being a neurodevelopmental disorder. The structural, cytoarchitectural and functional brain abnormalities reported in patients with SZ, might be due to aberrant neuronal migration, since the final position of neurons affects...

  2. Network Analysis of MPO and Other Relevant Proteins Involved in Diabetic Foot Ulcer and Other Diabetic Complications.

    Science.gov (United States)

    Saumya, Mathew; Subin, E K; Suchithra, T V

    2017-09-13

    Network analysis and visualization of genes are very important to understand large complex biological data in a better manner. Large data on genes and proteins in the biological systems are analyzed on the occurrence, interactions, co-expression, and co-regulations of various genes. Here we have visualized the genes involved in type 1 diabetes (T1D), type 2 diabetes (T2D), and foot ulcer condition to put light on the corrective measures to the problem of impaired healing. The goal of this study was to identify the important genes involved in the pathogenesis of diabetes complications and foot ulcer and its association with the free radical-producing enzyme, the myeloperoxidase (MPO). In this study, we have used bioinformatics tools for the analysis of 24 genes that play a major role in diabetes mellitus and its complications, especially diabetic foot ulcer to reveal the relation between the genes and proteins involved in these disease conditions. We could conclude from the network model that MPO is related to foot ulcer and involved in pathogenesis of various co-associated diseases, such as oxidative stress, inflammation, peripheral vascular disease, and other related diabetes complications.

  3. Volunteering in adolescence and young adulthood crime involvement: a longitudinal analysis from the add health study.

    Science.gov (United States)

    Ranapurwala, Shabbar I; Casteel, Carri; Peek-Asa, Corinne

    2016-12-01

    Experiences in adolescence may have a lasting impact on adulthood. The objective of this study is to evaluate the association between adolescent (12-18 years of age) volunteerism with the incidence of illegal behaviors, arrests, and convictions in adulthood (>18 years of age). We conducted a retrospective cohort study using secondary data from the National Longitudinal Study of Adolescent to Adult Health. Students from grades 7-12 were recruited in 1994-1995 (n = 20,745), and then followed in 2001-2002 (n = 14,322) and in 2008-2009 (n = 12,288). In 2000-2001, participants were retrospectively asked about their volunteering experience from 12 to 18 years of age. Consequently, participants were divided into non-volunteers, self-volunteers, adult-required volunteers, and court-ordered volunteers. Groups were compared for rates of illegal behaviors, arrest, and convictions in adulthood (>18 years of age) using weighted generalized linear mixed negative binomial models while accounting for sampling design. Relative to non-volunteers, self-volunteers reported 11 % fewer illegal behaviors (RR: 0.89, 95 % CI: 0.80, 0.99), 31 % fewer arrests (RR: 0.69, 95 %: 0.57, 0.85), and 39 % fewer convictions (RR: 0.61, 95 % CI: 0.47, 0.79) by age 18-28 years, and 28 % fewer illegal behaviors, 53 % fewer arrests, and 36 % fewer convictions by age 24-34. In comparison the adult-required volunteers also reported fewer arrests and convictions; however, they reported more illegal behaviors than the non-volunteers. The court-ordered volunteers reported higher rates of criminal involvement than the non-volunteers, throughout. This study suggests that volunteering in adolescence may reduce crime involvement in adulthood.

  4. Lactose metabolism in Lactobacillus bulgaricus: analysis of the primary structure and expression of the genes involved.

    Science.gov (United States)

    Leong-Morgenthaler, P; Zwahlen, M C; Hottinger, H

    1991-01-01

    The genes coding for the lactose permease and beta-galactosidase, two proteins involved in the metabolism of lactose by Lactobacillus bulgaricus, have been cloned, expressed, and found functional in Escherichia coli. The nucleotide sequences of these genes and their flanking regions have been determined, showing the presence of two contiguous open reading frames (ORFs). One of these ORFs codes for the lactose permease gene, and the other codes for the beta-galactosidase gene. The lactose permease gene is located in front of the beta-galactosidase gene, with 3 bp in the intergenic region. The two genes are probably transcribed as one operon. Primer extension studies have mapped a promoter upstream from the lactose permease gene but not the beta-galactosidase gene. This promoter is similar to those found in E. coli with general characteristics of GC-rich organisms. In addition, the sequences around the promoter contain a significantly higher number of AT base pairs (80%) than does the overall L. bulgaricus genome, which is rich in GC (GC content of 54%). The amino acid sequences obtained from translation of the ORFs are found to be highly homologous (similarity of 75%) to those from Streptococcus thermophilus. The first 460 amino acids of the lactose permease shows homology to the melibiose transport protein of E. coli. Little homology was found between the lactose permease of L. bulgaricus and E. coli, but the residues which are involved in the binding and the transport of lactose are conserved. The carboxy terminus is similar to that of the enzyme III of several phosphoenolpyruvate-dependent phosphotransferase systems. Images PMID:1705929

  5. Understanding opioid overdose characteristics involving prescription and illicit opioids: A mixed methods analysis.

    Science.gov (United States)

    Yarborough, Bobbi Jo H; Stumbo, Scott P; Janoff, Shannon L; Yarborough, Micah T; McCarty, Dennis; Chilcoat, Howard D; Coplan, Paul M; Green, Carla A

    2016-10-01

    Opioid abuse and misuse are significant public health issues. The CDC estimated 72% of pharmaceutical-related overdose deaths in the US in 2012 involved opioids. While studies of opioid overdoses have identified sociodemographic characteristics, agents used, administration routes, and medication sources associated with overdoses, we know less about the context and life circumstances of the people who experience these events. We analyzed interviews (n=87) with survivors of opioid overdoses or family members of decedents. Individuals experiencing overdoses were members of a large integrated health system. Using ICD codes for opioid overdoses and poisonings, we identified participants from five purposefully derived pools of health-plan members who had: 1) prescriptions for OxyContin(®) or single-ingredient sustained-release oxycodone, 2) oxycodone single-ingredient immediate release, 3) other long-acting opioids, 4) other short-acting opioids, or 5) no active opioid prescriptions. Individuals who experienced opioid overdoses abused and misused multiple medications/drugs; experienced dose-related miscommunications or medication-taking errors; had mental health and/or substance use conditions; reported chronic pain; or had unstable resources or family/social support. Many had combinations of these risks. Most events involved polysubstance use, often including benzodiazepines. Accidental overdoses were commonly the result of abuse or misuse, some in response to inadequately treated chronic pain or, less commonly, medication-related mistakes. Suicide attempts were frequently triggered by consecutive negative life events. To identify people at greater risk of opioid overdose, efforts should focus on screening for prescribed and illicit polysubstance use, impaired cognition, and changes in life circumstances, psychosocial risks/supports, and pain control. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  6. Experience in the analysis of accidents and incidents involving the transport of radioactive materials

    International Nuclear Information System (INIS)

    Warner-Jones, S.M.; Hughes, J.S.; Shaw, K.B.

    2002-01-01

    Some half a million packages containing radioactive materials are transported to, from and within the UK annually. Accidents and incidents involving these shipments are rare. However, there is always the potential for such an event, which could lead to a release of the contents of a package or an increase in radiation level caused by damaged shielding. These events could result in radiological consequences for transport workers. As transport occurs in the public environment, such events could also lead to radiation exposures of members of the public. The UK Department for Transport (DfT), together with the Health and Safety Executive (HSE) have supported, for almost 20 years, work to compile, analyse and report on accidents and incidents that occur during the transport of radioactive materials. Annual reports on these events have been produced for twelve years. The details of these events are recorded in the Radioactive Materials Transport Event Database (RAMTED) maintained by the National Radiological Protection Board on behalf of the DfT and HSE. Information on accidents and incidents dates back to 1958. RAMTED currently includes information of 708 accidents and incidents, covering the period 1958 to 2000. This paper presents a summary of the data covering this period, identifying trends and lessons learned together with a discussion of some examples. It was found that, historically, the most significant exposures were received as a result of accidents involving the transport of industrial radiography sources. However, the frequency and severity of these events has decreased considerably in the later years of this study due to improvements in training, awareness and equipment. The International Atomic Energy Agency and the Nuclear Energy Agency, have established the international nuclear event scale (INES), which is described in detail in a users' guide. The INES has been revised to fully include transport events, and the information in RAMTED has been reviewed

  7. Magnetic resonance imaging for diagnosis of mandibular involvement from head and neck cancers: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Chunjie Li

    Full Text Available BACKGROUND: Diagnosis of mandibular involvement caused by head and neck cancers is critical for treatment. We performed a meta-analysis to determine the diagnostic efficacy of MR for distinguishing mandibular involvement caused by head and neck cancers. METHODS: Thirteen databases were searched electronically and hand-searching was also done. Two reviewers conducted study inclusion, data extractions, and quality assessment of the studies independently. Meta-disc 1.4 and STATA 11.0 were used to conduct the meta-analysis. RESULTS: 16 studies involving a total of 490 participants underwent MR examinations and were accounted for in this meta-analysis. Among the included studies, 2 had high risk of bias, while the rest had unclear risk of bias. Meta-regression showed that the slight clinical and methodological heterogeneities did not influence the outcome (P>0.05. Meta-analysis indicated that the MR for the diagnosis of mandibular involvement had a pooled sensitivity (SEN of 78%, specificity (SPE of 83%, positive likelihood ratio (+LR of 3.80, negative likelihood ratio (-LR of 0.28, diagnostic odds ratio (DOR of 28.94, area under curve (AUC of 0.9110, and Q* of 0.8432. Two studies detected the diagnostic efficacy of MR for the mandibular medullar invasion, and only one study reported the inferior alveolar canal invasion, which made it impossible to include it in our meta-analysis. In comparing to CT, MR had a higher SEN without statistical significance (P = 0.08, but a significantly lower SPE (P = 0.04. The synthesized diagnostic efficacy (AUC and Q* on mandibular involvement was similar between the two modalities (P>0.05. CONCLUSIONS: Present clinical evidence showed that MR had an acceptable diagnostic value in detecting mandibular involvement caused by head and neck cancers. MR exceeded CT in diagnosing patients with mandibular invasion (higher sensitivity than CT but was less efficacious to exclude patients without the mandibular invasion

  8. Integrative analysis for finding genes and networks involved in diabetes and other complex diseases

    DEFF Research Database (Denmark)

    Bergholdt, R.; Størling, Zenia, Marian; Hansen, Kasper Lage

    2007-01-01

    We have developed an integrative analysis method combining genetic interactions, identified using type 1 diabetes genome scan data, and a high-confidence human protein interaction network. Resulting networks were ranked by the significance of the enrichment of proteins from interacting regions. W...

  9. Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis

    Directory of Open Access Journals (Sweden)

    Dmitry A Ravcheev

    2016-02-01

    Full Text Available Ubiquinone and menaquinone are membrane lipid-soluble carriers of electrons that are essential for cellular respiration. Eukaryotic cells can synthesize ubiquinone but not menaquinone, whereas prokaryotes can synthesize both quinones. So far, most of the human gut microbiome (HGM studies have been based on metagenomic analysis. Here, we applied an analysis of individual HGM genomes to the identification of ubiquinone and menaquinone biosynthetic pathways. In our opinion, the shift from metagenomics to analysis of individual genomes is a pivotal milestone in investigation of bacterial communities, including the HGM. The key results of this study are as follows. (i The distribution of the canonical pathways in the HGM genomes was consistent with previous reports and with the distribution of the quinone-dependent reductases for electron acceptors. (ii The comparative genomics analysis identified four alternative forms of the previously known enzymes for quinone biosynthesis. (iii Genes for the previously unknown part of the futalosine pathway were identified, and the corresponding biochemical reactions were proposed. We discuss the remaining gaps in the menaquinone and ubiquinone pathways in some of the microbes, which indicate the existence of further alternate genes or routes. Together, these findings provide further insight into the biosynthesis of quinones in bacteria and the physiology of the HGM.

  10. Data, analysis and modeling of physical properties for process designof systems involving lipids

    DEFF Research Database (Denmark)

    Cunico, Larissa; Ceriani, Roberta; Sarup, Bent

    2013-01-01

    Pure component and mixture properties are necessary for synthesis, design, and analysis of processes forthe production of edible oils, fats, biodiesel, and other lipids. The lack of measured data for these systemsmakes it necessary to develop reliable predictive models based on limited data. We...

  11. Analysis of Waveguide Devices Involving Lateral and Transverse Perfect Magnetic Wall Boundary Conditions by the Mode-Matching Method

    Science.gov (United States)

    Polo-López, Lucas; Ruiz-Cruz, Jorge A.; Montejo-Garai, José R.; Rebollar, Jesús M.

    2017-09-01

    This contribution presents the analysis of waveguide problems involving general boundary conditions of perfect magnetic wall. This type of boundary condition is used in electromagnetic solvers very commonly when the device under analysis has physical symmetry, in order to speed up the computation time. This paper is focused on extending its use in problems having this type of boundary condition in the lateral and transverse walls of the waveguides involved in the problem. The presented formulation, based on the mode-matching method, will be applied to classical waveguide devices, but also to address radiating problems with a novel formulation. Different applications will be targeted, and the simulation results will be compared with those obtained by other numerical techniques (based on different solvers), validating the presented approach as another suitable tool for computer-aided design.

  12. Comparative Transcriptome Analysis to Reveal Genes Involved in Wheat Hybrid Necrosis

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    Yong Zhang

    2014-12-01

    Full Text Available Wheat hybrid necrosis is an interesting genetic phenomenon that is found frequently and results in gradual death or loss of productivity of wheat. However, the molecular basis and mechanisms of this genetic phenomenon are still not well understood. In this study, the transcriptomes of wheat hybrid necrosis F1 and its parents (Neimai 8 and II469 were investigated using digital gene expression (DGE. A total of 1300 differentially expressed genes were identified, indicating that the response to hybrid necrosis in wheat is complicated. The assignments of the annotated genes based on Gene Ontology (GO revealed that most of the up-regulated genes belong to “universal stress related”, “DNA/RNA binding”, “protein degradation” functional groups, while the down-regulated genes belong to “carbohydrate metabolism” and “translation regulation” functional groups. These findings suggest that these pathways were affected by hybrid necrosis. Our results provide preliminarily new insight into the underlying molecular mechanisms of hybrid necrosis and will help to identify important candidate genes involved in wheat hybrid necrosis.

  13. Comparative transcriptome analysis to reveal genes involved in wheat hybrid necrosis.

    Science.gov (United States)

    Zhang, Yong; Cheng, Yan; Guo, Jiahui; Yang, Ennian; Liu, Cheng; Zheng, Xuelian; Deng, Kejun; Zhou, Jianping

    2014-12-16

    Wheat hybrid necrosis is an interesting genetic phenomenon that is found frequently and results in gradual death or loss of productivity of wheat. However, the molecular basis and mechanisms of this genetic phenomenon are still not well understood. In this study, the transcriptomes of wheat hybrid necrosis F1 and its parents (Neimai 8 and II469) were investigated using digital gene expression (DGE). A total of 1300 differentially expressed genes were identified, indicating that the response to hybrid necrosis in wheat is complicated. The assignments of the annotated genes based on Gene Ontology (GO) revealed that most of the up-regulated genes belong to "universal stress related", "DNA/RNA binding", "protein degradation" functional groups, while the down-regulated genes belong to "carbohydrate metabolism" and "translation regulation" functional groups. These findings suggest that these pathways were affected by hybrid necrosis. Our results provide preliminarily new insight into the underlying molecular mechanisms of hybrid necrosis and will help to identify important candidate genes involved in wheat hybrid necrosis.

  14. Acetylome analysis reveals the involvement of lysine acetylation in biosynthesis of antibiotics in Bacillus amyloliquefaciens.

    Science.gov (United States)

    Liu, Lin; Wang, Guangyuan; Song, Limin; Lv, Binna; Liang, Wenxing

    2016-01-29

    Lysine acetylation is a major post-translational modification that plays an important regulatory role in almost every aspects in both eukaryotes and prokaryotes. Bacillus amyloliquefaciens, a Gram-positive bacterium, is very effective for the control of plant pathogens. However, very little is known about the function of lysine acetylation in this organism. Here, we conducted the first lysine acetylome in B. amyloliquefaciens through a combination of highly sensitive immune-affinity purification and high-resolution LC-MS/MS. Overall, we identified 3268 lysine acetylation sites in 1254 proteins, which account for 32.9% of the total proteins in this bacterium. Till date, this is the highest ratio of acetylated proteins that have been identified in bacteria. Acetylated proteins are associated with a variety of biological processes and a large fraction of these proteins are involved in metabolism. Interestingly, for the first time, we found that about 71.1% (27/38) and 78.6% (22/28) of all the proteins tightly related to the synthesis of three types of pepketides and five families of lipopeptides were acetylated, respectively. These findings suggest that lysine acetylation plays a critical role in the regulation of antibiotics biosynthesis. These data serves as an important resource for further elucidation of the physiological role of lysine acetylation in B. amyloliquefaciens.

  15. Analysis of the transcriptome of Isodon rubescens and key enzymes involved in terpenoid biosynthesis

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    Xiuhong Su

    2016-05-01

    Full Text Available Isodon rubescens is an important medicinal plant in China that has been shown to reduce tumour growth due to the presence of the compound oridonin. In an effort to facilitate molecular research on oridonin biosynthesis, we reported the use of next generation massively parallel sequencing technologies and de novo transcriptome assembly to gain a comprehensive overview of I. rubescens transcriptome. In our study, a total of 50,934,276 clean reads, 101,640 transcripts and 44,626 unigenes were generated through de novo transcriptome assembly. A number of unigenes – 23,987, 10,263, 7359, 18,245, 17,683, 19,485, 9361 – were annotated in the National Center for Biotechnology Information (NCBI non-redundant protein (Nr, NCBI nucleotide sequences (Nt, Kyoto Encyclopedia of Genes and Genomes (KEGG Orthology (KO, Swiss-Prot, protein family (Pfam, gene ontology (GO, eukaryotic ortholog groups (KOG databases, respectively. Furthermore, the annotated unigenes were functionally classified according to the GO, KOG and KEGG. Based on these results, candidate genes encoding enzymes involved in terpenoids backbone biosynthesis were detected. Our data provided the most comprehensive sequence resource available for the study on I. rubescens, as well as demonstrated the effective use of Illumina sequencing and de novo transcriptome assembly on a species lacking genomic information.

  16. Analysis of multiple components involved in the interaction between Cryptococcus neoformans and Acanthamoeba castellanii.

    Science.gov (United States)

    Rizzo, Juliana; Albuquerque, Priscila C; Wolf, Julie M; Nascimento, Renata; Pereira, Marcos D; Nosanchuk, Joshua D; Rodrigues, Marcio L

    Cryptococcus neoformans is an environmental fungus that can cause lethal meningoencephalitis in immunocompromised individuals. The mechanisms by which environmental microbes become pathogenic to mammals are still obscure, but different studies suggest that fungal virulence evolved from selection imposed by environmental predators. The soil-living Acanthamoeba castellanii is a well-known predator of C. neoformans. In this work, we evaluated the participation of C. neoformans virulence-associated structures in the interaction of fungal cells with A. castellanii. Fungal extracellular vesicles (EVs) and the polysaccharide glucuronoxylomannan (GXM) were internalized by A. castellanii with no impact on the viability of amoebal cells. EVs, but not free GXM, modulated antifungal properties of A. castellanii by inducing enhanced yeast survival. Phagocytosis of C. neoformans by amoebal cells and the pathogenic potential in a Galleria mellonella model were not affected by EVs, but previous interactions with A. castellanii rendered fungal cells more efficient in killing this invertebrate host. This observation was apparently associated with marked amoeba-induced changes in surface architecture and increased resistance to both oxygen- and nitrogen-derived molecular species. Our results indicate that multiple components with the potential to impact pathogenesis are involved in C. neoformans environmental interactions. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  17. A Meta-analysis of Central Lymph Node Metastasis for Predicting Lateral Involvement in Papillary Thyroid Carcinoma.

    Science.gov (United States)

    Lan, Xiabin; Sun, Wei; Zhang, Hao; Dong, Wenwu; Wang, Zhihong; Zhang, Ting

    2015-11-01

    Whether central lymph node metastasis is a reliable indicator of lateral lymph node metastasis in papillary thyroid carcinoma remains obscure. To investigate the value of central lymph node metastasis for predicting lateral compartment involvement, we performed a meta-analysis of published studies. A systematic literature search of PubMed, EMBASE, and Chinese National Knowledge Infrastructure databases was completed, and the reference lists of the identified articles and prior relevant reviews were examined. Two reviewers extracted data and assessed the quality of eligible studies independently. Odds ratios and 95% confidence intervals were pooled through a random effects meta-analysis model. Twenty-one studies were eligible and further analyzed in this meta-analysis. The risk of lateral lymph node metastasis was significantly higher in the central lymph node-positive group than in the negative group (odds ratio = 7.64, 95% confidence interval: 5.59-10.44), with moderate heterogeneity across studies (P = .007, I(2) = 48.6%). Subgroup analyses and sensitivity analysis suggested that the results were consistent and credible. However, Begg's funnel plot and Egger linear regression test revealed a likelihood of publication bias (P = .000). This meta-analysis suggests that central lymph node metastasis is valuable for predicting lateral compartment involvement in patients with papillary thyroid carcinoma. For those patients with central lymph node metastasis, additional attention should be paid to the lateral neck, as the risk of lateral lymph node metastasis was significantly higher in the central lymph node-positive group than in the negative group. Further studies regarding appropriate management for patients with high risk of lateral involvement are needed. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2015.

  18. And yet it moves! Involving transient flow conditions is the logical next step for WHPA analysis

    Science.gov (United States)

    Rodriguez-Pretelin, A.; Nowak, W.

    2017-12-01

    As the first line of defense among different safety measures, Wellhead Protection Areas (WHPAs) have been broadly used to protect drinking water wells against sources of pollution. In most cases, their implementation relies on simplifications, such as assuming homogeneous or zonated aquifer conditions or considering steady-state flow scenarios. Obviously, both assumptions inevitably invoke errors. However, while uncertainty due to aquifer heterogeneity has been extensively studied in the literature, the impact of transient flow conditions have received yet very little attention. For instance, WHPA maps in the offices of water supply companies are fixed maps derived from steady-state models although the actual catchment out there are transient. To mitigate high computational costs, we approximate transiency by means of a dynamic superposition of steady-state flow solutions. Then, we analyze four transient drivers that often appear on the seasonal scale: (I) regional groundwater flow direction, (II) strength of the regional hydraulic gradient, (III) natural recharge to the groundwater and (IV) pumping rate. The integration of transiency in WHPA analysis leads to time-frequency maps. They express for each location the temporal frequency of catchment membership. Furthermore, we account for the uncertainty due to incomplete knowledge on geological and transiency conditions, solved through Monte Carlo simulations. The main contribution of this study, is to show the need of enhancing groundwater well protection by considering transient flow considerations during WHPA analysis. To support and complement our statement, we demonstrate that 1) each transient driver imprints an individual spatial pattern in the required WHPA, ranking their influence through a global sensitivity analysis. 2) We compare the influence of transient conditions compared to geological uncertainty in terms of areal WHPA demand. 3) We show that considering geological uncertainty alone is insufficient

  19. Proteomic analysis of pathways involved in estrogen-induced growth and apoptosis of breast cancer cells.

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    Zhang-Zhi Hu

    Full Text Available Estrogen is a known growth promoter for estrogen receptor (ER-positive breast cancer cells. Paradoxically, in breast cancer cells that have been chronically deprived of estrogen stimulation, re-introduction of the hormone can induce apoptosis.Here, we sought to identify signaling networks that are triggered by estradiol (E2 in isogenic MCF-7 breast cancer cells that undergo apoptosis (MCF-7:5C versus cells that proliferate upon exposure to E2 (MCF-7. The nuclear receptor co-activator AIB1 (Amplified in Breast Cancer-1 is known to be rate-limiting for E2-induced cell survival responses in MCF-7 cells and was found here to also be required for the induction of apoptosis by E2 in the MCF-7:5C cells. Proteins that interact with AIB1 as well as complexes that contain tyrosine phosphorylated proteins were isolated by immunoprecipitation and identified by mass spectrometry (MS at baseline and after a brief exposure to E2 for two hours. Bioinformatic network analyses of the identified protein interactions were then used to analyze E2 signaling pathways that trigger apoptosis versus survival. Comparison of MS data with a computationally-predicted AIB1 interaction network showed that 26 proteins identified in this study are within this network, and are involved in signal transduction, transcription, cell cycle regulation and protein degradation.G-protein-coupled receptors, PI3 kinase, Wnt and Notch signaling pathways were most strongly associated with E2-induced proliferation or apoptosis and are integrated here into a global AIB1 signaling network that controls qualitatively distinct responses to estrogen.

  20. Microarray Analysis of the Molecular Mechanism Involved in Parkinson’s Disease

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    Cheng Tan

    2018-01-01

    Full Text Available Purpose. This study aimed to investigate the underlying molecular mechanisms of Parkinson’s disease (PD by bioinformatics. Methods. Using the microarray dataset GSE72267 from the Gene Expression Omnibus database, which included 40 blood samples from PD patients and 19 matched controls, differentially expressed genes (DEGs were identified after data preprocessing, followed by Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG pathway enrichment analyses. Protein-protein interaction (PPI network, microRNA- (miRNA- target regulatory network, and transcription factor- (TF- target regulatory networks were constructed. Results. Of 819 DEGs obtained, 359 were upregulated and 460 were downregulated. Two GO terms, “rRNA processing” and “cytoplasm,” and two KEGG pathways, “metabolic pathways” and “TNF signaling pathway,” played roles in PD development. Intercellular adhesion molecule 1 (ICAM1 was the hub node in the PPI network; hsa-miR-7-5p, hsa-miR-433-3p, and hsa-miR-133b participated in PD pathogenesis. Six TFs, including zinc finger and BTB domain-containing 7A, ovo-like transcriptional repressor 1, GATA-binding protein 3, transcription factor dp-1, SMAD family member 1, and quiescin sulfhydryl oxidase 1, were related to PD. Conclusions. “rRNA processing,” “cytoplasm,” “metabolic pathways,” and “TNF signaling pathway” were key pathways involved in PD. ICAM1, hsa-miR-7-5p, hsa-miR-433-3p, hsa-miR-133b, and the abovementioned six TFs might play important roles in PD development.

  1. In silico analysis of cacao (Theobroma cacao L.) genes that involved in pathogen and disease responses

    Science.gov (United States)

    Agung, Muhammad Budi; Budiarsa, I. Made; Suwastika, I. Nengah

    2017-02-01

    Cocoa bean is one of the main commodities from Indonesia for the world, which still have problem regarding yield degradation due to pathogens and disease attack. Developing robust cacao plant that genetically resistant to pathogen and disease attack is an ideal solution in over taking on this problem. The aim of this study was to identify Theobroma cacao genes on database of cacao genome that homolog to response genes of pathogen and disease attack in other plant, through in silico analysis. Basic information survey and gene identification were performed in GenBank and The Arabidopsis Information Resource database. The In silico analysis contains protein BLAST, homology test of each gene's protein candidates, and identification of homologue gene in Cacao Genome Database using data source "Theobroma cacao cv. Matina 1-6 v1.1" genome. Identification found that Thecc1EG011959t1 (EDS1), Thecc1EG006803t1 (EDS5), Thecc1EG013842t1 (ICS1), and Thecc1EG015614t1 (BG_PPAP) gene of Cacao Genome Database were Theobroma cacao genes that homolog to plant's resistance genes which highly possible to have similar functions of each gene's homologue gene.

  2. Flutter Analysis of RX-420 Balistic Rocket Fin Involving Rigid Body Modes of Rocket Structures

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    Novi Andria

    2013-03-01

    Full Text Available Flutter is a phenomenon that has brought a catastrophic failure to the flight vehicle structure. In this experiment, flutter was analyzed for its symmetric and antisymmetric configuration to understand the effect of rocket rigid modes to the fin flutter characteristic. This research was also expected to find out the safety level of RX-420 structure design. The analysis was performed using half rocket model. Fin structure used in this research was a fin which has semispan 600 mm, thickness 12 mm, chord root 700 mm, chord tip 400 mm, made by Al 6061-T651, double spar configuration with skin thickness of 2 mm. Structural dynamics and flutter stability were analyzed using finite element software implemented on MSC. Nastran. The analysis shows that the antisymmetric flutter mode is more critical than symmetric flutter mode. At sea level altitude, antisymmetric flutter occurs at 6.4 Mach, and symmetric flutter occurs at 10.15 Mach. Compared to maximum speed of RX-420 which is 4.5 Mach at altitude 11 km or equivalent to 2.1 Mach at sea level, it can be concluded that the RX-420 structure design is safe, and flutter will not occur during flight.

  3. Personal values Involved in choosing a College: Analysis Using the Means-End Chain Approach

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    Lílian Carolina Viana

    2014-04-01

    Full Text Available The investigation the reasons for choice of products and services by consumers stands out as relevant in the area of ​​market studies, as well as notes management for any organization. Through the Theory of Means-End Chain proposed by Gutman (1982, which relates the “means” (attributes and benefits linked to the consumption of products or services with the “ends” in terms of personal values achieved, it is possible understand of the meanings that consumers attribute the choice of products and services in a more abstract level. Thus, the objective of this study is to understand what aspects, considering attributes, consequences and personal values ​​guide the behavior of students in choosing the nursing course at a private institution of higher education. Based on the theory mentioned it was adopted the technique laddering, in-depth interview and analysis methodology and representation of the hierarchical value map, which was interpreted and analyzed in order to understand the cognitive structure of students’ choice.The analysis of the results indicate that students are guided primarily by hedonistic values of happiness itself the choice of nursing in college studied.

  4. Transcriptome Analysis of Red Swamp Crawfish Procambarus clarkii Reveals Genes Involved in Gonadal Development

    Science.gov (United States)

    Jiang, Hucheng; Xing, Zhijun; Lu, Wei; Qian, Zhaojun; Yu, Hongwei; Li, Jiale

    2014-01-01

    Background The red swamp crawfish, Procambarus clarkii, has become one of the most economically important cultured species in China. Currently, little is known about the gonadal development of this species. Isolation and characterization of genes are an initial step towards understanding gonadal development of P. clarkii. Results Using the 454 pyrosequencing technology, we obtained a total of 1,134,993 high quality sequence reads from the crawfish testis and ovary libraries. We aimed to identify different genes with a potential role in gonad development. The assembly formed into 22,652 isotigs, distributed by GO analysis across 55 categories in the three ontologies, ‘molecular function’, ‘cellular component’, and ‘biological processes’. Comparative transcript analysis showed that 1,720 isotigs in the ovary were up-regulated and 2138 isotigs were down-regulated. Several gonad development related genes, such as vitellogenin, cyclin B, cyclin-dependent kinases 2, Dmc1 and ubiquitin were identified. Quantitative real-time PCR verified the expression profiles of 14 differentially expressed genes, and confirmed the reliability of the 454 pyrosequencing. Conclusions Our findings provide an archive for future research on gonadal development at a molecular level in P. clarkii and other crustacean. This data will be helpful to develop new ideas for artificial regulation of the reproductive process in crawfish aquaculture. PMID:25118947

  5. Dynamic Game Analysis of Coal Electricity Market Involving Multi-Interests

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    Yu Xiaobao

    2016-01-01

    Full Text Available The coal consumption of China reached 2.75 billion tons of standard coal in 2013, which accounted for 67.5% of total energy consumption and more than 50% of global coal consumption. Therefore, the impact of coal price is huge on coal market and even energy market in China. As a large consumer of coal, thermal power enterprise has a strong sensitivity to coal price. In order to balance the rising cost of enterprises due to coal price, we need to analyze the interests of multiple stakeholders. Firstly, this paper combined the Nash equilibrium and cobweb model and proposed the characteristics in different cobweb model. Then, for coal, power, and energy companies, the dynamic game analysis model is constructed. This model gives a game analysis in four scenarios and quantifies the decision of each stakeholder in different coal prices. Finally, the impact figure of different coal prices on each stakeholder has been drawn. The impacts of different coal or thermal power prices on different markets have been put forward, so relevant policy recommendations have been proposed combined with the cobweb model.

  6. School-based extracurricular activity involvement and adolescent self-esteem: a growth-curve analysis.

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    Kort-Butler, Lisa A; Hagewen, Kellie J

    2011-05-01

    Research on adolescent self-esteem indicates that adolescence is a time in which individuals experience important changes in their physical, cognitive, and social identities. Prior research suggests that there is a positive relationship between an adolescent's participation in structured extracurricular activities and well-being in a variety of domains, and some research indicates that these relationships may be dependent on the type of activities in which adolescents participate. Building on previous research, a growth-curve analysis was utilized to examine self-esteem trajectories from adolescence (age 14) to young adulthood (age 26). Using 3 waves of data from National Longitudinal Study of Adolescent Health (n = 5,399; 47.8% male), the analysis estimated a hierarchical growth-curve model emphasizing the effects of age and type of school-based extracurricular activity portfolio, including sports and school clubs, on self-esteem. The results indicated that age had a linear relationship with self-esteem over time. Changes in both the initial level of self-esteem and the growth of self-esteem over time were significantly influenced by the type of extracurricular activity portfolio. The findings were consistent across race and sex. The results support the utility of examining the longitudinal impact of portfolio type on well-being outcomes.

  7. Learning to work together - lessons from a reflective analysis of a research project on public involvement.

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    Howe, A; Mathie, E; Munday, D; Cowe, M; Goodman, C; Keenan, J; Kendall, S; Poland, F; Staniszewska, S; Wilson, P

    2017-01-01

    Patient and public involvement (PPI) in research is very important, and funders and the NHS all expect this to happen. What this means in practice, and how to make it really successful, is therefore an important research question. This article analyses the experience of a research team using PPI, and makes recommendations on strengthening PPI in research. There were different PPI roles in our study - some people were part of the research team: some were on the advisory group; and there were patient groups who gave specific feedback on how to make research work better for their needs. We used minutes, other written documents, and structured individual and group reflections to learn from our own experiences over time. The main findings were:- for researchers and those in a PPI role to work in partnership, project structures must allow flexibility and responsiveness to different people's ideas and needs; a named link person can ensure support; PPI representatives need to feel fully included in the research; make clear what is expected for all roles; and ensure enough time and funding to allow meaningful involvement. Some roles brought more demands but also more rewards than others - highlighting that it is important that people giving up their time to help with research experience gains from doing so. Those contributing to PPI on a regular basis may want to learn new skills, rather than always doing the same things. Researchers and the public need to find ways to develop roles in PPI over time. We also found that, even for a team with expertise in PPI, there was a need both for understanding of different ways to contribute, and an evolving 'normalisation' of new ways of working together over time, which both enriched the process and the outputs. Background Patient and public involvement (PPI) is now an expectation of research funders, in the UK, but there is relatively little published literature on what this means in practice - nor is there much evaluative research

  8. Vertebral Augmentation Involving Vertebroplasty or Kyphoplasty for Cancer-Related Vertebral Compression Fractures: An Economic Analysis

    Science.gov (United States)

    2016-01-01

    Background Untreated vertebral compression fractures can have serious clinical consequences and impose a considerable impact on patients' quality of life and on caregivers. Since non-surgical management of these fractures has limited effectiveness, vertebral augmentation procedures are gaining acceptance in clinical practice for pain control and fracture stabilization. The objective of this analysis was to determine the cost-effectiveness and budgetary impact of kyphoplasty or vertebroplasty compared with non-surgical management for the treatment of vertebral compression fractures in patients with cancer. Methods We performed a systematic review of health economic studies to identify relevant studies that compare the cost-effectiveness of kyphoplasty or vertebroplasty with non-surgical management for the treatment of vertebral compression fractures in adults with cancer. We also performed a primary cost-effectiveness analysis to assess the clinical benefits and costs of kyphoplasty or vertebroplasty compared with non-surgical management in the same population. We developed a Markov model to forecast benefits and harms of treatments, and corresponding quality-adjusted life years and costs. Clinical data and utility data were derived from published sources, while costing data were derived using Ontario administrative sources. We performed sensitivity analyses to examine the robustness of the results. In addition, a 1-year budget impact analysis was performed using data from Ontario administrative sources. Two scenarios were explored: (a) an increase in the total number of vertebral augmentation procedures performed among patients with cancer in Ontario, maintaining the current proportion of kyphoplasty versus vertebroplasty; and (b) no increase in the total number of vertebral augmentation procedures performed among patients with cancer in Ontario but an increase in the proportion of kyphoplasties versus vertebroplasties. Results The base case considered each of

  9. Comparative Analysis of the Factors Necessitating Commercial Banks and Manufacturing Firms’ Involvement in Corporate Social Responsibility in Nigeria

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    Abiola Idowu

    2016-11-01

    Full Text Available This research investigates the factors necessitating commercial banks and manufacturing firms’ involvement in Corporate Social Responsibility (CSR in Nigeria comparatively. The research took place in Lagos State in South-west geo-political zone in Nigeria. The survey research design was used in this research. Moreover, the purposive sampling was used in selecting five commercial banks and five manufacturing firms. Primary data were gathered with the aid of questionnaire from 216 respondents out of 250 selected respondents from bank and 205 respondents out of 250 selected respondents from manufacturing firms. Fifty copies of the questionnaires were distributed to each company. All respondents selected were involved in CSR activities of their companies. Factors necessitating companies’ involvement in CSR were examined with Analysis of Variance. The research reveals that t-test value is -0.39 and p-value is 0.8, which shows that there is no significant difference between factors necessitating of the commercial banks and manufacturing firms’ involvement in CSR. The research recommends that corporate organizations should give attention to CSR initiatives as these lead to improvement of customers loyalty, improvement of the positive image of the organization, improved relationship with local communities,   and enhances shareholders values as well as improved relations with public authorities amongst others.

  10. A meta-analysis of perceptual and cognitive functions involved in useful-field-of-view test performance.

    Science.gov (United States)

    Woutersen, Karlijn; Guadron, Leslie; van den Berg, Albert V; Boonstra, F Nienke; Theelen, Thomas; Goossens, Jeroen

    2017-12-01

    The useful-field-of-view (UFOV) test measures the amount of information someone can extract from a visual scene in one glance. Its scores show relatively strong relationships with everyday activities. The UFOV test consists of three computer tests, suggested to measure processing speed and central vision, divided attention, and selective attention. However, other functions seem to be involved as well. In order to investigate the contribution of these suggested and other perceptual and cognitive functions, we performed a meta-analysis of 116 Pearson's correlation coefficients between UFOV scores and other test scores reported in 18 peer-reviewed articles. We divided these correlations into nine domains: attention, executive functioning, general cognition, memory, spatial ability, visual closure, contrast sensitivity, visual processing speed, and visual acuity. A multivariate mixed-effects model analysis revealed that each domain correlated significantly with each of the UFOV subtest scores. These correlations were stronger for Subtests 2 and 3 than for Subtest 1. Furthermore, some domains were more strongly correlated to the UFOV than others across subtests. We did not find interaction effects between subtest and domain, indicating that none of the UFOV subtests is more selectively sensitive to a particular domain than the others. Thus, none of the three UFOV subtests seem to measure one clear construct. Instead, a range of visual and cognitive functions is involved. Perhaps this is the reason for the UFOV's high ecological validity, as it involves many functions at once, making it harder to compensate if one of them fails.

  11. Identification and analysis of key residues involved in folding and binding of protein-carbohydrate complexes.

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    Gromiha, Michael; Shanmugam, N R Siva; Selvin, J Fermin Angelo; Veluraja, K

    2018-02-21

    Protein-carbohydrate interactions play vital roles in several biological processes in living organisms. The comparative analysis of binding site residues along with stabilizing residues in protein-carbohydrate complexes provides ample insights to understand the structure, function and recognition mechanism. In this work, we have identified 2.45% binding site residues in a non-redundant dataset of 1130 complexes using distance-based criteria and 7.07% stabilizing residues using the concepts of hydrophobicity, long-range interactions and conservation of residues. Further, 5.9% of binding and 2.04% of stabilizing residues are common to each other, which are termed as key residues. The key residues have been analyzed based on protein classes, carbohydrate types, gene ontology functional classifications, amino acid preference and structure-based parameters. We found that all-β, α+β and α/β have more key residues than other protein classes and most of the KRs are present in β-strands, which shows their importance in stability and binding of complexes. On the ligand side, L-saccharide has the highest number of key residues and it has a high percentage of KRs in SRs and BRs than other carbohydrate types. Further, polar and charged residues have a high tendency to serve as key residues. Classifications based on gene ontology terms revealed that Lys is preferred in all the three groups: molecular functions, biological processes and cellular components. Key residues have 6 to 9 contacts within the protein and make only one contact with the carbohydrate ligand. These contacts are dominant to form polar-nonpolar contacts followed by the contacts between charged atoms. Further, the influence of sequence and structural parameters such as surrounding hydrophobicity, solvent accessibility, secondary structure, long-range order and conservation score has been discussed. This analysis helps in understanding the interplay between stability and binding in protein

  12. Epidemiological analysis of bacterial strains involved in hospital infection in a University Hospital from Brazil

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    MORAES Bianca Aguiar de

    2000-01-01

    Full Text Available Hospital infections cause an increase in morbidity and mortality of hospitalized patients with significant rise in hospital costs. The aim of this work was an epidemiological analysis of hospital infection cases occurred in a public University Hospital in Rio de Janeiro. Hence, 238 strains were isolated from 14 different clinical materials of 166 patients hospitalized in the period between August 1995 and July 1997. The average age of the patients was 33.4 years, 72.9% used antimicrobials before having a positive culture. The most common risk conditions were surgery (19.3%, positive HIV or AIDS (18.1% and lung disease (16.9%. 24 different bacterial species were identified, S. aureus (21% and P. aeruginosa (18.5% were predominant. Among 50 S. aureus isolated strains 36% were classified as MRSA (Methicillin Resistant S. aureus. The Gram negative bacteria presented high resistance to aminoglycosides and cephalosporins. A diarrhea outbreak, detected in high-risk neonatology ward, was caused by Salmonella serovar Infantis strain, with high antimicrobial resistance and a plasmid of high molecular weight (98Mda containing virulence genes and positive for R factor.

  13. Quantitative Proteomic Analysis of Differentially Expressed Protein Profiles Involved in Pancreatic Ductal Adenocarcinoma

    Science.gov (United States)

    Kuo, Kung-Kai; Kuo, Chao-Jen; Chiu, Chiang-Yen; Liang, Shih-Shin; Huang, Chun-Hao; Chi, Shu-Wen; Tsai, Kun-Bow; Chen, Chiao-Yun; Hsi, Edward; Cheng, Kuang-Hung; Chiou, Shyh-Horng

    2016-01-01

    Objectives The aim of this study was to identify differentially expressed proteins among various stages of pancreatic ductal adenocarcinoma (PDAC) by shotgun proteomics using nano-liquid chromatography coupled tandem mass spectrometry and stable isotope dimethyl labeling. Methods Differentially expressed proteins were identified and compared based on the mass spectral differences of their isotope-labeled peptide fragments generated from protease digestion. Results Our quantitative proteomic analysis of the differentially expressed proteins with stable isotope (deuterium/hydrogen ratio, ≥2) identified a total of 353 proteins, with at least 5 protein biomarker proteins that were significantly differentially expressed between cancer and normal mice by at least a 2-fold alteration. These 5 protein biomarker candidates include α-enolase, α-catenin, 14-3-3 β, VDAC1, and calmodulin with high confidence levels. The expression levels were also found to be in agreement with those examined by Western blot and histochemical staining. Conclusions The systematic decrease or increase of these identified marker proteins may potentially reflect the morphological aberrations and diseased stages of pancreas carcinoma throughout progressive developments leading to PDAC. The results would form a firm foundation for future work concerning validation and clinical translation of some identified biomarkers into targeted diagnosis and therapy for various stages of PDAC. PMID:26262590

  14. Analysis of Pigeon (Columba Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation.

    Directory of Open Access Journals (Sweden)

    Ying Wang

    Full Text Available Monochromatic light is widely applied to promote poultry reproductive performance, yet little is currently known regarding the mechanism by which light wavelengths affect pigeon reproduction. Recently, high-throughput sequencing technologies have been used to provide genomic information for solving this problem. In this study, we employed Illumina Hiseq 2000 to identify differentially expressed genes in ovary tissue from pigeons under blue and white light conditions and de novo transcriptome assembly to construct a comprehensive sequence database containing information on the mechanisms of follicle development. A total of 157,774 unigenes (mean length: 790 bp were obtained by the Trinity program, and 35.83% of these unigenes were matched to genes in a non-redundant protein database. Gene description, gene ontology, and the clustering of orthologous group terms were performed to annotate the transcriptome assembly. Differentially expressed genes between blue and white light conditions included those related to oocyte maturation, hormone biosynthesis, and circadian rhythm. Furthermore, 17,574 SSRs and 533,887 potential SNPs were identified in this transcriptome assembly. This work is the first transcriptome analysis of the Columba ovary using Illumina technology, and the resulting transcriptome and differentially expressed gene data can facilitate further investigations into the molecular mechanism of the effect of blue light on follicle development and reproduction in pigeons and other bird species.

  15. Analysis of events resulting from an accident involving a transport aircraft carrying plutonium oxide

    International Nuclear Information System (INIS)

    Lombard, J.; Hubert, P.; Pages, P.

    1988-03-01

    This study assesses the impact on health of an aircraft accident resulting in the release into the atmosphere of the reprocessing product PuO 2 . The consequences associated with the inhalation of the initial cloud, the passage into suspension of the powder deposited on the ground and the contamination of the food chain were therefore evaluated as a function of the quantity released. It was deduced that the risk of inhalation is by far the greatest. The countermeasures likely to be implemented during emergency action were subjected to analysis. In particular, it appeared that the impact of the first cloud could not really be mitigated but that it was possible to take effective action against the other consequences. Research was undertaken to establish tolerable release quantities which could if necessary be used as acceptance criteria for packaging tests. This indicated that a release in the range 10-100 g would give rise to controllable consequences, at least in a rural environment. The calculations relating to the estimation of the acute toxicity associated with the inhalation of Plutonium and details of the emergency action plan are given in appendix

  16. Systematic Triple-Mutant Analysis Uncovers Functional Connectivity between Pathways Involved in Chromosome Regulation

    Directory of Open Access Journals (Sweden)

    James E. Haber

    2013-06-01

    Full Text Available Genetic interactions reveal the functional relationships between pairs of genes. In this study, we describe a method for the systematic generation and quantitation of triple mutants, termed triple-mutant analysis (TMA. We have used this approach to interrogate partially redundant pairs of genes in S. cerevisiae, including ASF1 and CAC1, two histone chaperones. After subjecting asf1Δ cac1Δ to TMA, we found that the Swi/Snf Rdh54 protein compensates for the absence of Asf1 and Cac1. Rdh54 more strongly associates with the chromatin apparatus and the pericentromeric region in the double mutant. Moreover, Asf1 is responsible for the synthetic lethality observed in cac1Δ strains lacking the HIRA-like proteins. A similar TMA was carried out after deleting both CLB5 and CLB6, cyclins that regulate DNA replication, revealing a strong functional connection to chromosome segregation. This approach can reveal functional redundancies that cannot be uncovered through traditional double-mutant analyses.

  17. Risk factor analysis for involvement of resection margins in gastric and esophagogastric junction cancer: an Italian multicenter study.

    Science.gov (United States)

    Bissolati, Massimiliano; Desio, Matteo; Rosa, Fausto; Rausei, Stefano; Marrelli, Daniele; Baiocchi, Gian Luca; De Manzoni, Giovanni; Chiari, Damiano; Guarneri, Giovanni; Pacelli, Fabio; De Franco, Lorenzo; Molfino, Sarah; Cipollari, Chiara; Orsenigo, Elena

    2017-01-01

    Resection margin (RM) involvement is associated with negative prognosis after gastrectomy. Intraoperative frozen section (IFS) analysis allows radical resection to be achieved in a single operation but is time-consuming and resource-consuming. The aim of this study was to assess risk factors associated with RM involvement to identify patients who would benefit from IFS analysis. We retrospectively analyzed patients who underwent gastrectomy with curative intent for gastric or esophagogastric junction (EGJ) cancer from 2000 to 2014 in six Italian hospitals. RM status was assessed by IFS analysis and/or definitive histopathology examination. A set of 21 potential risk factors were compared in a multivariate analysis between patients with positive RMs on IFS analysis or definitive histopathology examination and a control cohort of similar patients with negative RMs, with the samples stratified into three subgroups (T1, T2-T4 Lauren intestinal pattern, T2-T4 Lauren diffuse/mixed pattern). One hundred forty-five patients had positive RMs. Survival was significantly worse in positive RM patients than in negative RM patients (89.5 months vs 28.9 months). Multivariate analysis showed that in T1 cancers a margin distance of less than 2 cm is a risk factor for RM involvement (odds ratio 15.7), in T2-T4 intestinal pattern cancers, serosa invasion (odds ratio 6.0), EGJ location (odds ratio 4.1), and a margin distance of less than 3 cm (odds ratio 4.0) are independent risk factors, and in T2-T4 diffuse/mixed pattern cancers, lymphatic infiltration (odds ratio 4.2), tumor diameter greater than 4 cm (odds ratio 3.5), EGJ location (odds ratio 2.8), and serosa invasion (odds ratio 2.2) are independent risk factors. Survival after gastrectomy is negatively affected by positive RMs. IFS analysis should be routinely used in patients with a high risk of positive RMs, especially in diffuse pattern cancers.

  18. Comparative genomic analysis of duplicated homoeologous regions involved in the resistance of Brassica napus to stem canker

    Directory of Open Access Journals (Sweden)

    Berline eFopa Fomeju

    2015-09-01

    Full Text Available All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the

  19. Featured Article: Transcriptional landscape analysis identifies differently expressed genes involved in follicle-stimulating hormone induced postmenopausal osteoporosis.

    Science.gov (United States)

    Maasalu, Katre; Laius, Ott; Zhytnik, Lidiia; Kõks, Sulev; Prans, Ele; Reimann, Ene; Märtson, Aare

    2017-01-01

    Osteoporosis is a disorder associated with bone tissue reorganization, bone mass, and mineral density. Osteoporosis can severely affect postmenopausal women, causing bone fragility and osteoporotic fractures. The aim of the current study was to compare blood mRNA profiles of postmenopausal women with and without osteoporosis, with the aim of finding different gene expressions and thus targets for future osteoporosis biomarker studies. Our study consisted of transcriptome analysis of whole blood serum from 12 elderly female osteoporotic patients and 12 non-osteoporotic elderly female controls. The transcriptome analysis was performed with RNA sequencing technology. For data analysis, the edgeR package of R Bioconductor was used. Two hundred and fourteen genes were expressed differently in osteoporotic compared with non-osteoporotic patients. Statistical analysis revealed 20 differently expressed genes with a false discovery rate of less than 1.47 × 10 -4 among osteoporotic patients. The expression of 10 genes were up-regulated and 10 down-regulated. Further statistical analysis identified a potential osteoporosis mRNA biomarker pattern consisting of six genes: CACNA1G, ALG13, SBK1, GGT7, MBNL3, and RIOK3. Functional ingenuity pathway analysis identified the strongest candidate genes with regard to potential involvement in a follicle-stimulating hormone activated network of increased osteoclast activity and hypogonadal bone loss. The differentially expressed genes identified in this study may contribute to future research of postmenopausal osteoporosis blood biomarkers.

  20. A risk adjusted cost-effectiveness analysis of alternative models of nurse involvement in obesity management in primary care.

    Science.gov (United States)

    Karnon, J; Ali Afzali, H Haji; Gray, J; Holton, C; Banham, D; Beilby, J

    2013-03-01

    Controlled evaluations are subject to uncertainty regarding their replication in the real world, particularly around systems of service provision. Using routinely collected data, we undertook a risk adjusted cost-effectiveness (RAC-E) analysis of alternative applied models of primary health care for the management of obese adult patients. Models were based on the reported level of involvement of practice nurses (registered or enrolled nurses working in general practice) in the provision of clinical-based activities. Linked, routinely collected clinical data describing clinical outcomes (weight, BMI, and obesity-related complications) and resource use (primary care, pharmaceutical, and hospital resource use) were collected. Potential confounders were controlled for using propensity weighted regression analyses. Relative to low level involvement of practice nurses in the provision of clinical-based activities to obese patients, high level involvement was associated with lower costs and better outcomes (more patients losing weight, and larger mean reductions in BMI). Excluding hospital costs, high level practice nurse involvement was associated with slightly higher costs. Incrementally, the high level model gets one additional obese patient to lose weight at an additional cost of $6,741, and reduces mean BMI by an additional one point at an additional cost of $563 (upper 95% confidence interval $1,547). Converted to quality adjusted life year (QALY) gains, the results provide a strong indication that increased involvement of practice nurses in clinical activities is associated with additional health benefits that are achieved at reasonable additional cost. Dissemination activities and incentives are required to encourage general practices to better integrate practice nurses in the active provision of clinical services. Copyright © 2013 The Obesity Society.

  1. Unlawful occupation of Inner-City Buildings: A Constitutional Analysis of the Rights and Obligations involved

    Directory of Open Access Journals (Sweden)

    Janke Strydom

    2014-11-01

    Full Text Available The unlawful occupation of inner-city buildings in South Africa has led to a number of legal disputes between vulnerable occupiers and individual landowners that highlight the conflict between individuals' constitutional right not to be evicted in an arbitrary manner and property owners' constitutional right not to be deprived of property arbitrarily. The cause of this tension is a shortage of affordable housing options for low-income households in the inner cities, a fact which shows that the state is evidently struggling to give effect to its housing obligation embodied in section 26(1 and (2 of the Constitution. In the majority of cases the courts assume that any interference with private landowners' rights beyond a temporary nature would be unjustifiable, but they do this without undertaking a proper constitutional analysis to determine whether a further limitation of the individual landowner's property rights might be justifiable and non-arbitrary in the circumstances of each case. In general the courts can allow, suspend or refuse the eviction of unlawful occupiers, provided that the order does not amount to an arbitrary deprivation of property. Nevertheless, in some instances the arbitrary deprivation of property is unavoidable, despite the court's best efforts to protect property entitlements. These eviction cases show the limits of the courts' powers both to provide adequate solutions to protect owners' property rights and to give effect to the constitutional housing provision. In the light of three eviction cases, namely Blue Moonlight, Modderklip and Olivia Road, this article explains the role of the court and the local authority, together with the entitlements and social obligations of inner-city landowners within the framework of the property clause, in order to analyse the constitutionality of the courts' decisions and to suggest ways in which the inner-city housing shortage may be addressed more effectively. This article also

  2. The case for multimodal analysis of atypical interaction: questions, answers and gaze in play involving a child with autism.

    Science.gov (United States)

    Muskett, Tom; Body, Richard

    2013-01-01

    Conversation analysis (CA) continues to accrue interest within clinical linguistics as a methodology that can enable elucidation of structural and sequential orderliness in interactions involving participants who produce ostensibly disordered communication behaviours. However, it can be challenging to apply CA to re-examine clinical phenomena that have initially been defined in terms of linguistics, as a logical starting point for analysis may be to focus primarily on the organisation of language ("talk") in such interactions. In this article, we argue that CA's methodological power can only be fully exploited in this research context when a multimodal analytic orientation is adopted, where due consideration is given to participants' co-ordinated use of multiple semiotic resources including, but not limited to, talk (e.g., gaze, embodied action, object use and so forth). To evidence this argument, a two-layered analysis of unusual question-answer sequences in a play episode involving a child with autism is presented. It is thereby demonstrated that only when the scope of enquiry is broadened to include gaze and other embodied action can an account be generated of orderliness within these sequences. This finding has important implications for CA's application as a research methodology within clinical linguistics.

  3. RNA-Seq analysis of rice roots reveals the involvement of post-transcriptional regulation in response to cadmium stress

    Directory of Open Access Journals (Sweden)

    Luqing eZheng

    2015-12-01

    Full Text Available Widely-spread cadmium (Cd pollution in the soil threatens both crop production and human health. How plants deal with the excess Cd are largely unknown. To evaluate the molecular mechanism by which plants respond to Cd stress, rice seedlings were treated with two concentrations of Cd and subjected to deep RNA sequencing. Comprehensive RNA-Seq analysis of rice roots under two gradients of Cd treatment revealed 1,169 Cd toxicity-responsive genes. These genes were involved in the reactive oxygen species scavenging system, stress response, cell wall formation, ion transport, and signal transduction. Nine out of 93 predicted long non coding RNAs (lncRNAs were detected as Cd-responsive lncRNAs due to their high correlation with the Cd stress response. In addition, we analyzed alternative splicing (AS events under different Cd concentrations. 476 differential alternatively spliced genes with 542 aberrant splicing events were identified. GO analysis indicated that these genes were highly enriched in oxidation reduction and cellular response to chemical stimulus. Real-time qRT-PCR validation analysis strengthened the reliability of our RNA-Seq results. The results suggest that post-transcriptional AS regulation may also be involved in plant responses to high Cd stress.

  4. Label-free quantitative proteomic analysis reveals strong involvement of complement alternative and terminal pathways in human glomerular sclerotic lesions.

    Science.gov (United States)

    Zhang, Ying; Xu, Bo; Kinoshita, Naohiko; Yoshida, Yutaka; Tasaki, Masayuki; Fujinaka, Hidehiko; Magdeldin, Sameh; Yaoita, Eishin; Yamamoto, Tadashi

    2015-06-18

    Since glomerular sclerosis frequently accompanies various glomerular diseases at the end stages, it is challenging to differentiate ubiquitous biological processes underlying this pathology from those critically involved in specific diseases. Furthermore, in-depth proteomic profile of human glomerular sclerosis remains limited. In this study, human glomeruli with intermediate (i-GS) and advanced (GS) sclerotic lesions, which were excluded from specific renal diseases and assumed to be aging-related, were laser captured from macroscopically normal cortex distant from urological carcinoma, and subjected to label-free quantitative proteomic analysis. We explicate an evident increase of membrane attack complex in i-GS and GS with an up-going tendency, which is accompanied by increasing of inhibitory regulators of alternative and terminal pathways. GO annotation and IPA pathway analysis agree to these results. Proteomic findings are validated by immunohistochemical studies which indicate that alternative and terminal pathways are positively involved in the glomerular sclerosis seen in distinct renal diseases. Furthermore, proteomic analysis also demonstrates remarkable increases of complement factor B in GS and TGF-ß1 in both GS and i-GS. Identification of complement factor B implicates that on-site activation of alternative pathway may occur in injured glomeruli and stepwise increase of TGF-ß1 suggests its contribution to the progression of glomerulosclerosis. This study provides in-depth quantitative proteomic profiles of human glomeruli with intermediate and advanced sclerotic lesions. It reveals that the over-expression of alternative and terminal pathway components is significantly involved in human glomerulosclerosis seen in distinct renal diseases. Proteomic identification of the increased TGF-ß1 provides supporting evidence for the role of podocyte apoptosis leading to human glomerulosclerosis. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Quantitative Proteomic Analysis of Mosquito C6/36 Cells Reveals Host Proteins Involved in Zika Virus Infection.

    Science.gov (United States)

    Xin, Qi-Lin; Deng, Cheng-Lin; Chen, Xi; Wang, Jun; Wang, Shao-Bo; Wang, Wei; Deng, Fei; Zhang, Bo; Xiao, Gengfu; Zhang, Lei-Ke

    2017-06-15

    Zika virus (ZIKV) is an emerging arbovirus belonging to the genus Flavivirus of the family Flaviviridae During replication processes, flavivirus manipulates host cell systems to facilitate its replication, while the host cells activate antiviral responses. Identification of host proteins involved in the flavivirus replication process may lead to the discovery of antiviral targets. The mosquitoes Aedes aegypti and Aedes albopictus are epidemiologically important vectors for ZIKV, and effective restrictions of ZIKV replication in mosquitoes will be vital in controlling the spread of virus. In this study, an iTRAQ-based quantitative proteomic analysis of ZIKV-infected Aedes albopictus C6/36 cells was performed to investigate host proteins involved in the ZIKV infection process. A total of 3,544 host proteins were quantified, with 200 being differentially regulated, among which CHCHD2 can be upregulated by ZIKV infection in both mosquito C6/36 and human HeLa cells. Our further study indicated that CHCHD2 can promote ZIKV replication and inhibit beta interferon (IFN-β) production in HeLa cells, suggesting that ZIKV infection may upregulate CHCHD2 to inhibit IFN-I production and thus promote virus replication. Bioinformatics analysis of regulated host proteins highlighted several ZIKV infection-regulated biological processes. Further study indicated that the ubiquitin proteasome system (UPS) plays roles in the ZIKV entry process and that an FDA-approved inhibitor of the 20S proteasome, bortezomib, can inhibit ZIKV infection in vivo Our study illustrated how host cells respond to ZIKV infection and also provided a candidate drug for the control of ZIKV infection in mosquitoes and treatment of ZIKV infection in patients. IMPORTANCE ZIKV infection poses great threats to human health, and there is no FDA-approved drug available for the treatment of ZIKV infection. During replication, ZIKV manipulates host cell systems to facilitate its replication, while host cells activate

  6. Transcriptome analysis of skeletal muscle tissue to identify genes involved in pre-slaughter stress response in pigs

    Directory of Open Access Journals (Sweden)

    Vincenzo Russo

    2010-01-01

    Full Text Available The knowledge of genes and molecular processes controlling stress reactions and involved in the genetic system determining resistance to stress in pigs could be important for the improvement of meat quality. This research aimed to compare the expression profiles of skeletal muscle between physically stressed and not stressed pigs of different breeds immediately before slaughter. DNA microarray analysis showed that different functional categories of genes are up-regulated in stressed compared to not stressed pigs and relevant differences among breeds were found.

  7. Determination of trace amounts of uranium in silicate materials by means of neutron activation analysis involving rapid radiochemical separation

    International Nuclear Information System (INIS)

    Ebihara, M.; Tomura, Kenji; Masutani, M.

    1987-01-01

    Uranium is determined in silicate materials such as standard rocks and a meteorite by radiochemical neutron activation analysis. The gamma-ray intensity of 239 U was measured with a planar type pure germanium detector system. The obtained data are mostly consistent with the literature values. Compared with a non-destructive method, the present method was found to improve the sensitivity by at least a factor of ten. Several errors which might be involved in the authors' RNAA procedures were examined and their degrees were evaluated. (author)

  8. ANALYSIS OF STRATEGIC MANAGEMENT for ECOTOURISM DEVELOPMENT TOWARD COMMUNITY INVOLVEMENT AND NATURAL CONSERVATION at TM GUNUNG HALIMUN SALAK

    Directory of Open Access Journals (Sweden)

    Kurniawan Gilang Widagdyo

    2015-08-01

    Full Text Available This study was conducted in order to analyze ecotourism development within Taman Nasional Gunung Halimun Salak (TNGHS area and determine association among its elements which is ecotourism activities, community involvement, and natural conservation. To convey comprehensive and factual result, theoretical considerations appear as basis for this study as well as qualitative and quantitative analysis. Some theories tend to be guidance that will be confront with qualitative data that was obtain from interview with several expertise and community’s representative and compare with questionnaire distribution to determine how significant association occur between those three variables. The statistical analysis explains that ecotourism deliver positive impact toward local community and natural conservationDOI: 10.15408/etk.v11i1.1871

  9. Risk Factors Associated with Renal Involvement in Childhood Henoch-Schönlein Purpura: A Meta-Analysis

    Science.gov (United States)

    Chan, Han; Tang, Yan-Ling; Lv, Xiao-Hang; Zhang, Gao-Fu; Wang, Mo; Yang, Hai-Ping; Li, Qiu

    2016-01-01

    Background and objective Henoch-Schönlein purpura (HSP) is an important cause of chronic kidney disease in children. This meta-analysis identified risk factors associated with renal involvement in childhood HSP. Methods PubMed, Embase, and Web of Science were searched. The quality of all eligible studies was assessed using the Newcastle-Ottawa scale criteria. An analysis of possible risk factors was conducted to report the odds ratio (OR) and weighted mean difference (WMD). Results Thirteen studies (2398 children) revealed 20 possible and 13 significant risk factors associated with renal involvement in HSP, with the following meta-analysis estimates of OR and WMD, with 95% confidence intervals: older age (0.90, 0.61–1.19); age > 10 y (3.13, 1.39–7.07); male gender (1.36, 1.07–1.74); abdominal pain (1.94,1.24–3.04); gastrointestinal bleeding (1.86, 1.30–2.65); severe bowel angina (3.38, 1.17–9.80); persistent purpura (4.02, 1.22–13.25); relapse (4.70, 2.42–9.14); WBC > 15 × 109/L (2.42, 1.39–4.22); platelets > 500 × 109/L (2.98, 1.22–7.25); elevated antistreptolysin O (ASO) (2.17, 1.29–3.64); and decreased complement component 3 (C3) (3.13, 1.62–6.05). Factors not significantly associated with renal involvement were: blood pressure; orchitis; elevated C-reactive protein; elevated erythrocyte sedimentation rate (ESR); and elevated serum IgA/IgE or IgG. Arthritis/arthralgia may be a risk factor according to the criteria of the American College of Rheumatology (1.41, 1.01–1.96). Conclusion The following are associated with renal involvement in pediatric HSP: male gender; > 10 y old; severe gastrointestinal symptoms (abdominal pain, gastrointestinal bleeding, and severe bowel angina); arthritis/arthralgia; persistent purpura or relapse; WBC > 15 × 109/L; platelets > 500 × 109/L; elevated ASO; and low C3. Relevant clinical interventions for these risk factors may exert positive effects on the prevention of kidney disease during the early

  10. Transcriptional sequencing and analysis of major genes involved in the adventitious root formation of mango cotyledon segments.

    Science.gov (United States)

    Li, Yun-He; Zhang, Hong-Na; Wu, Qing-Song; Muday, Gloria K

    2017-06-01

    A total of 74,745 unigenes were generated and 1975 DEGs were identified. Candidate genes that may be involved in the adventitious root formation of mango cotyledon segment were revealed. Adventitious root formation is a crucial step in plant vegetative propagation, but the molecular mechanism of adventitious root formation remains unclear. Adventitious roots formed only at the proximal cut surface (PCS) of mango cotyledon segments, whereas no roots were formed on the opposite, distal cut surface (DCS). To identify the transcript abundance changes linked to adventitious root development, RNA was isolated from PCS and DCS at 0, 4 and 7 days after culture, respectively. Illumina sequencing of libraries generated from these samples yielded 62.36 Gb high-quality reads that were assembled into 74,745 unigenes with an average sequence length of 807 base pairs, and 33,252 of the assembled unigenes at least had homologs in one of the public databases. Comparative analysis of these transcriptome databases revealed that between the different time points at PCS there were 1966 differentially expressed genes (DEGs), while there were only 51 DEGs for the PCS vs. DCS when time-matched samples were compared. Of these DEGs, 1636 were assigned to gene ontology (GO) classes, the majority of that was involved in cellular processes, metabolic processes and single-organism processes. Candidate genes that may be involved in the adventitious root formation of mango cotyledon segment are predicted to encode polar auxin transport carriers, auxin-regulated proteins, cell wall remodeling enzymes and ethylene-related proteins. In order to validate RNA-sequencing results, we further analyzed the expression profiles of 20 genes by quantitative real-time PCR. This study expands the transcriptome information for Mangifera indica and identifies candidate genes involved in adventitious root formation in cotyledon segments of mango.

  11. Health Risk Behavior Among Justice Involved Male and Female Youth: Exploratory, Multi-Group Latent Class Analysis.

    Science.gov (United States)

    Dembo, Richard; Faber, Jessica; Cristiano, Jennifer; DiClemente, Ralph J; Krupa, Julie M; Terminello, Asha; Wareham, Jennifer

    2017-11-10

    Youth involved in the juvenile justice system experience a disproportionate prevalence of serious mental health issues, substance abuse, and are at an increased risk of engaging in risky sexual practices. Gender differences exist, with girls at a markedly greater risk of acquiring a sexually transmitted disease. The present study seeks to determine if there are subgroups of male and female youth who differ in their health risk behavior. If so, do any male or female subgroups at different levels of health risk differ in regard to their sociodemographic and psychological factors, and finally, what are intervention/service delivery implications of these differences. Youth were participants in an innovative health service at a centralized intake facility located in a large southeastern U.S. city. Latent class analysis and multinomial logistic regression is utilized to examine the heterogeneity of health risk behaviors across gender groups in a sample of 777 newly arrested youth. Results indicate a three class solution provided the optimal fit with the data for each gender group: a Lower Health Risk group, a Higher Health Risk group, and a Highest Health Risk group. Multinomial logistic regression analysis identified significant sociodemographic and depression effects among both male and female youth. Conclusions/Importance: Youth characterized by risky sexually behavior, elevated depression, and drug involvement should be the focus of integrated intervention services. This study documents the critical need for front end, juvenile justice intake facilities to provide behavioral and public health screening, with treatment follow-up, on newly arrested youth.

  12. Identification and expression analysis of BoMF25, a novel polygalacturonase gene involved in pollen development of Brassica oleracea.

    Science.gov (United States)

    Lyu, Meiling; Liang, Ying; Yu, Youjian; Ma, Zhiming; Song, Limin; Yue, Xiaoyan; Cao, Jiashu

    2015-06-01

    BoMF25 acts on pollen wall. Polygalacturonase (PG) is a pectin-digesting enzyme involved in numerous plant developmental processes and is described to be of critical importance for pollen wall development. In the present study, a PG gene, BoMF25, was isolated from Brassica oleracea. BoMF25 is the homologous gene of At4g35670, a PG gene in Arabidopsis thaliana with a high expression level at the tricellular pollen stage. Collinear analysis revealed that the orthologous gene of BoMF25 in Brassica campestris (syn. B. rapa) genome was probably lost because of genome deletion and reshuffling. Sequence analysis indicated that BoMF25 contained four classical conserved domains (I, II, III, and IV) of PG protein. Homology and phylogenetic analyses showed that BoMF25 was clustered in Clade F. The putative promoter sequence, containing classical cis-acting elements and pollen-specific motifs, could drive green fluorescence protein expression in onion epidermal cells. Quantitative RT-PCR analysis suggested that BoMF25 was mainly expressed in the anther at the late stage of pollen development. In situ hybridization analysis also indicated that the strong and specific expression signal of BoMF25 existed in pollen grains at the mature pollen stage. Subcellular localization showed that the fluorescence signal was observed in the cell wall of onion epidermal cells, which suggested that BoMF25 may be a secreted protein localized in the pollen wall.

  13. Considerations of health benefit-cost analysis for activities involving ionizing radiation exposure and alternatives. Technical report

    International Nuclear Information System (INIS)

    1977-01-01

    The report deals with development of methodology for the health benefit-cost analysis of activities that result in radiation exposure to humans. It attempts to frame the problems and to communicate the necessary elements of the complex technical process required for this method of analysis. The main thrust of the report is to develop a methodology for analyzing the benefits and costs of these activities. Application of the methodology is demonstrated for nuclear power production and medical uses of radiation, but no definitive analysis is attempted. The report concludes that benefit-cost analysis can be effectively applied to these applications and that it provides a basis for more informed governmental decision-making and for public participation in evaluating the issues of radiation exposure. It notes, however, that for cases where national policy is involved, decisions must inevitably be made on the basis of value judgements to which such analyses can make only limited contributions. An important conclusion is that a significant reduction in radiation exposure to the population is apparently achievable by development of methods for eliminating unproductive medical X-ray exposure

  14. The productivity and cost-efficiency of models for involving nurse practitioners in primary care: a perspective from queueing analysis.

    Science.gov (United States)

    Liu, Nan; D'Aunno, Thomas

    2012-04-01

    To develop simple stylized models for evaluating the productivity and cost-efficiencies of different practice models to involve nurse practitioners (NPs) in primary care, and in particular to generate insights on what affects the performance of these models and how. The productivity of a practice model is defined as the maximum number of patients that can be accounted for by the model under a given timeliness-to-care requirement; cost-efficiency is measured by the corresponding annual cost per patient in that model. Appropriate queueing analysis is conducted to generate formulas and values for these two performance measures. Model parameters for the analysis are extracted from the previous literature and survey reports. Sensitivity analysis is conducted to investigate the model performance under different scenarios and to verify the robustness of findings. Employing an NP, whose salary is usually lower than a primary care physician, may not be cost-efficient, in particular when the NP's capacity is underutilized. Besides provider service rates, workload allocation among providers is one of the most important determinants for the cost-efficiency of a practice model involving NPs. Capacity pooling among providers could be a helpful strategy to improve efficiency in care delivery. The productivity and cost-efficiency of a practice model depend heavily on how providers organize their work and a variety of other factors related to the practice environment. Queueing theory provides useful tools to take into account these factors in making strategic decisions on staffing and panel size selection for a practice model. © Health Research and Educational Trust.

  15. RNA Sequencing and Coexpression Analysis Reveal Key Genes Involved in α-Linolenic Acid Biosynthesis in Perilla frutescens Seed

    Directory of Open Access Journals (Sweden)

    Tianyuan Zhang

    2017-11-01

    Full Text Available Perilla frutescen is used as traditional food and medicine in East Asia. Its seeds contain high levels of α-linolenic acid (ALA, which is important for health, but is scarce in our daily meals. Previous reports on RNA-seq of perilla seed had identified fatty acid (FA and triacylglycerol (TAG synthesis genes, but the underlying mechanism of ALA biosynthesis and its regulation still need to be further explored. So we conducted Illumina RNA-sequencing in seven temporal developmental stages of perilla seeds. Sequencing generated a total of 127 million clean reads, containing 15.88 Gb of valid data. The de novo assembly of sequence reads yielded 64,156 unigenes with an average length of 777 bp. A total of 39,760 unigenes were annotated and 11,693 unigenes were found to be differentially expressed in all samples. According to Kyoto Encyclopedia of Genes and Genomes (KEGG pathway analysis, 486 unigenes were annotated in the “lipid metabolism” pathway. Of these, 150 unigenes were found to be involved in fatty acid (FA biosynthesis and triacylglycerol (TAG assembly in perilla seeds. A coexpression analysis showed that a total of 104 genes were highly coexpressed (r > 0.95. The coexpression network could be divided into two main subnetworks showing over expression in the medium or earlier and late phases, respectively. In order to identify the putative regulatory genes, a transcription factor (TF analysis was performed. This led to the identification of 45 gene families, mainly including the AP2-EREBP, bHLH, MYB, and NAC families, etc. After coexpression analysis of TFs with highly expression of FAD2 and FAD3 genes, 162 TFs were found to be significantly associated with two FAD genes (r > 0.95. Those TFs were predicted to be the key regulatory factors in ALA biosynthesis in perilla seed. The qRT-PCR analysis also verified the relevance of expression pattern between two FAD genes and partial candidate TFs. Although it has been reported that some TFs

  16. Identification and functional analysis of gene cluster involvement in biosynthesis of the cyclic lipopeptide antibiotic pelgipeptin produced by Paenibacillus elgii

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    Qian Chao-Dong

    2012-09-01

    Full Text Available Abstract Background Pelgipeptin, a potent antibacterial and antifungal agent, is a non-ribosomally synthesised lipopeptide antibiotic. This compound consists of a β-hydroxy fatty acid and nine amino acids. To date, there is no information about its biosynthetic pathway. Results A potential pelgipeptin synthetase gene cluster (plp was identified from Paenibacillus elgii B69 through genome analysis. The gene cluster spans 40.8 kb with eight open reading frames. Among the genes in this cluster, three large genes, plpD, plpE, and plpF, were shown to encode non-ribosomal peptide synthetases (NRPSs, with one, seven, and one module(s, respectively. Bioinformatic analysis of the substrate specificity of all nine adenylation domains indicated that the sequence of the NRPS modules is well collinear with the order of amino acids in pelgipeptin. Additional biochemical analysis of four recombinant adenylation domains (PlpD A1, PlpE A1, PlpE A3, and PlpF A1 provided further evidence that the plp gene cluster involved in pelgipeptin biosynthesis. Conclusions In this study, a gene cluster (plp responsible for the biosynthesis of pelgipeptin was identified from the genome sequence of Paenibacillus elgii B69. The identification of the plp gene cluster provides an opportunity to develop novel lipopeptide antibiotics by genetic engineering.

  17. SYSTEMIC CRISIS MANAGEMENT AND THE IMPACT ON MONETARY POLICY. THE INVOLVEMENT OF CENTRAL BANKS. AN EMPIRICAL ANALYSIS

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    Adriana GIBA

    2011-09-01

    Full Text Available In a systemic crisis, many institutions in the financial system may face a lack of liquidity and central banks, as lenders of last resort, have to support them in order to ensure their financial stability. The question is: To what extent the involvement of central banks in systemic crises management, by providing liquidity to credit institutions, affects their ability to accomplish the central goal of monetary policy - price stability?To answer this question, through this study, we conducted an empiricalanalysis on the effect which central banks’ involvement in systemic crises management, through liquidity support, has on monetary policy objectives, mainly on price stability. Using a principal components analysis, we built a Monetary policy index and we developed a regression model between this index and the liquidity support provided by central banks in systemic crises.The conclusion we reached is that the provision of liquidity by the central bank to banking institutions in the system affects its monetary policy objectives only on the short -term. Specifically, providing liquidity support leads to an increase in both monetary aggregates and consumer price index in the first two years of the crisis, after which there is a significant dilution of this impact.

  18. The Discourse of Parent Involvement in Special Education: A Critical Analysis Linking Policy Documents to the Experiences of Mothers

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    Lai, Yuan; Vadeboncoeur, Jennifer A.

    2013-01-01

    Parent involvement is acknowledged as a crucial aspect of the education of students with special needs. However, the discourse of parent involvement represents parent involvement in limited ways, thereby controlling how and the extent to which parents can be involved in the education of their children. In this article, critical discourse analysis…

  19. High throughput analysis reveals dissociable gene expression profiles in two independent neural systems involved in the regulation of social behavior

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    Stevenson Tyler J

    2012-10-01

    Full Text Available Abstract Background Production of contextually appropriate social behaviors involves integrated activity across many brain regions. Many songbird species produce complex vocalizations called ‘songs’ that serve to attract potential mates, defend territories, and/or maintain flock cohesion. There are a series of discrete interconnect brain regions that are essential for the successful production of song. The probability and intensity of singing behavior is influenced by the reproductive state. The objectives of this study were to examine the broad changes in gene expression in brain regions that control song production with a brain region that governs the reproductive state. Results We show using microarray cDNA analysis that two discrete brain systems that are both involved in governing singing behavior show markedly different gene expression profiles. We found that cortical and basal ganglia-like brain regions that control the socio-motor production of song in birds exhibit a categorical switch in gene expression that was dependent on their reproductive state. This pattern is in stark contrast to the pattern of expression observed in a hypothalamic brain region that governs the neuroendocrine control of reproduction. Subsequent gene ontology analysis revealed marked variation in the functional categories of active genes dependent on reproductive state and anatomical localization. HVC, one cortical-like structure, displayed significant gene expression changes associated with microtubule and neurofilament cytoskeleton organization, MAP kinase activity, and steroid hormone receptor complex activity. The transitions observed in the preoptic area, a nucleus that governs the motivation to engage in singing, exhibited variation in functional categories that included thyroid hormone receptor activity, epigenetic and angiogenetic processes. Conclusions These findings highlight the importance of considering the temporal patterns of gene expression

  20. Evaluating public involvement in research design and grant development: Using a qualitative document analysis method to analyse an award scheme for researchers.

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    Baxter, Susan; Muir, Delia; Brereton, Louise; Allmark, Christine; Barber, Rosemary; Harris, Lydia; Hodges, Brian; Khan, Samaira; Baird, Wendy

    2016-01-01

    The National Institute for Health Research (NIHR) Research Design Service (RDS) for Yorkshire and Humber has been running a public involvement funding scheme since 2008. This scheme awards researchers a small amount of money to help them get involvement from patients and/or the public. Involvement activities take place at the time when researchers are planning studies, and when they are completing application forms to request funding for a proposed research project. After the public involvement activities researchers are asked to write a report for the RDS describing what they did with the public involvement funding. This study analysed those reports using an approach which included members of a public involvement panel in the data analysis process. The aim of the work was to see what the views and experiences of researchers who received funding were, and what might be learned for the future of the scheme. Twenty five reports were analysed. Four main themes were identified, these described: the added value of public involvement; aspects to consider when planning and designing public involvement; different roles of public contributors; and aspects of valuing public member contributions. The group approach to analysis was successful in enabling involvement of a variety of individuals in the process. The findings of the study provide evidence of the value of public involvement during the development of applications for research funding. The results also indicate that researchers recognise the variety in potential roles for the public in research, and acknowledge how involvement adds value to studies. Background A regional Research Design Service, funded by the National Institute for Health Research, introduced a small grant in 2008, to support public involvement (often known as patient and public involvement [PPI]) activities during the development of applications for research funding. Successful applicants are requested to submit a report detailing how the grant

  1. Cloning and Expression Analysis of Vvlcc3, a Novel and Functional Laccase Gene Possibly Involved in Stipe Elongation

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    Yuanping Lu

    2015-12-01

    Full Text Available Volvariella volvacea, usually harvested in its egg stage, is one of the most popular mushrooms in Asia. The rapid transition from the egg stage to elongation stage, during which the stipe stretches to almost full length leads to the opening of the cap and rupture of the universal veil, and is considered to be one of the main factors that negatively impacts the yield and value of V. volvacea. Stipe elongation is a common phenomenon in mushrooms; however, the mechanisms, genes and regulation involved in stipe elongation are still poorly understood. In order to study the genes related to the stipe elongation, we analyzed the transcription of laccase genes in stipe tissue of V. volvacea, as some laccases have been suggested to be involved in stipe elongation in Flammulina velutipes. Based on transcription patterns, the expression of Vvlcc3 was found to be the highest among the 11 laccase genes. Moreover, phylogenetic analysis showed that VvLCC3 has a high degree of identity with other basidiomycete laccases. Therefore, we selected and cloned a laccase gene, named Vvlcc3, a cDNA from V. volvacea, and expressed the cDNA in Pichia pastoris. The presence of the laccase signature L1-L4 on the deduced protein sequence indicates that the gene encodes a laccase. Phylogenetic analysis showed that VvLCC3 clusters with Coprinopsis cinerea laccases. The ability to catalyze ABTS (2,2’-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid oxidation proved that the product of the Vvlcc3 gene was a functional laccase. We also found that the expression of the Vvlcc3 gene in V. volvacea increased during button stage to the elongation stage; it reached its peak in the elongation stage, and then decreased in the maturation stage, which was similar to the trend in the expression of Fv-lac3 and Fv-lac5 in F. velutipes stipe tissue. The similar trend in expression level of these laccase genes of F. velutipes suggested that this gene could be involved in stipe elongation in V

  2. Multiple and substitute addictions involving prescription drugs misuse among 12th graders: gateway theory revisited with Market Basket Analysis.

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    Jayawardene, Wasantha Parakrama; YoussefAgha, Ahmed Hassan

    2014-01-01

    This study aimed to identify the sequential patterns of drug use initiation, which included prescription drugs misuse (PDM), among 12th-grade students in Indiana. The study also tested the suitability of the data mining method Market Basket Analysis (MBA) to detect common drug use initiation sequences in large-scale surveys. Data from 2007 to 2009 Annual Surveys of Alcohol, Tobacco, and Other Drug Use by Indiana Children and Adolescents were used for this study. A close-ended, self-administered questionnaire was used to ask adolescents about the use of 21 substance categories and the age of first use. "Support%" and "confidence%" statistics of Market Basket Analysis detected multiple and substitute addictions, respectively. The lifetime prevalence of using any addictive substance was 73.3%, and it has been decreasing during past few years. Although the lifetime prevalence of PDM was 19.2%, it has been increasing. Males and whites were more likely to use drugs and engage in multiple addictions. Market Basket Analysis identified common drug use initiation sequences that involved 11 drugs. High levels of support existed for associations among alcohol, cigarettes, and marijuana, whereas associations that included prescription drugs had medium levels of support. Market Basket Analysis is useful for the detection of common substance use initiation sequences in large-scale surveys. Before initiation of prescription drugs, physicians should consider the adolescents' risk of addiction. Prevention programs should address multiple addictions, substitute addictions, common sequences in drug use initiation, sex and racial differences in PDM, and normative beliefs of parents and adolescents in relation to PDM.

  3. Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signalling

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    Mehanathan eMuthamilarasan

    2015-10-01

    Full Text Available Transcription factors (TFs are major players in stress signalling and constitute an integral part of signalling networks. Among the major TFs, WRKY proteins play pivotal roles in regulation of transcriptional reprogramming associated with stress responses. In view of this, genome- and transcriptome-wide identification of WRKY TF family was performed in the C4 model plants, Setaria italica (SiWRKY and S. viridis (SvWRKY, respectively. The study identified 105 SiWRKY and 44 SvWRKY proteins that were computationally analysed for their physicochemical properties. Sequence alignment and phylogenetic analysis classified these proteins into three major groups, namely I, II and III with majority of WRKY proteins belonging to group II (53 SiWRKY and 23 SvWRKY, followed by group III (39 SiWRKY and 11 SvWRKY and group I (10 SiWRKY and 6 SvWRKY. Group II proteins were further classified into 5 subgroups (IIa to IIe based on their phylogeny. Domain analysis showed the presence of WRKY motif and zinc finger-like structures in these proteins along with additional domains in a few proteins. All SiWRKY genes were physically mapped on the S. italica genome and their duplication analysis revealed that 10 and 8 gene pairs underwent tandem and segmental duplications, respectively. Comparative mapping of SiWRKY and SvWRKY genes in related C4 panicoid genomes demonstrated the orthologous relationships between these genomes. In silico expression analysis of SiWRKY and SvWRKY genes showed their differential expression patterns in different tissues and stress conditions. Expression profiling of candidate SiWRKY genes in response to stress (dehydration and salinity and hormone treatments (abscisic acid, salicylic acid and methyl jasmonate suggested the putative involvement of SiWRKY066 and SiWRKY082 in stress and hormone signalling. These genes could be potential candidates for further characterization to delineate their functional roles in abiotic stress signalling.

  4. Transcriptome analysis of wheat seedling and spike tissues in the hybrid Jingmai 8 uncovered genes involved in heterosis.

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    Liu, Yong-Jie; Gao, Shi-Qing; Tang, Yi-Miao; Gong, Jie; Zhang, Xiao; Wang, Yong-Bo; Zhang, Li-Ping; Sun, Ren-Wei; Zhang, Quan; Chen, Zhao-Bo; Wang, Xiang; Guo, Cai-Juan; Zhang, Sheng-Quan; Zhang, Feng-Ting; Gao, Jian-Gang; Sun, Hui; Yang, Wei-Bing; Wang, Wei-Wei; Zhao, Chang-Ping

    2018-03-05

    Transcriptome analysis was carried out for wheat seedlings and spikes from hybrid Jingmai 8 and both inbred lines to unravel mechanisms underlying heterosis. Heterosis, known as one of the most successful strategies for increasing crop yield, has been widely exploited in plant breeding systems. Despite its great importance, the molecular mechanism underlying heterosis remains elusive. In the present study, RNA sequencing (RNA-seq) was performed on the seedling and spike tissues of the wheat (Triticum aestivum) hybrid Jingmai 8 (JM8) and its homozygous parents to unravel the underlying mechanisms of wheat heterosis. In total, 1686 and 2334 genes were identified as differentially expressed genes (DEGs) between the hybrid and the two inbred lines in seedling and spike tissues, respectively. Gene Ontology analysis revealed that DEGs from seedling tissues were significantly enriched in processes involved in photosynthesis and carbon fixation, and the majority of these DEGs expressed at a higher level in JM8 compared to both inbred lines. In addition, cell wall biogenesis and protein biosynthesis-related pathways were also significantly represented. These results confirmed that a combination of different pathways could contribute to heterosis. The DEGs between the hybrid and the two inbred progenitors from the spike tissues were significantly enriched in biological processes related to transcription, RNA biosynthesis and molecular function categories related to transcription factor activities. Furthermore, transcription factors such as NAC, ERF, and TIF-IIA were highly expressed in the hybrid JM8. These results may provide valuable insights into the molecular mechanisms underlying wheat heterosis.

  5. Complications of Oncoplastic Breast Surgery Involving Soft Tissue Transfer Versus Breast-Conserving Surgery: An Analysis of the NSQIP Database.

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    Cil, Tulin D; Cordeiro, Erin

    2016-10-01

    Oncoplastic breast surgery (OBS) aims to provide breast cancer patients with optimum oncologic outcomes and excellent cosmesis. We sought to determine if there is a difference in complications associated with OBS involving soft tissue transfer compared with the traditional breast-conserving surgical (BCS) approach. Analysis of the American College of Surgeons National Surgical Quality Improvement Program database was performed. Patients with breast cancer who underwent BCS from 2005 to 2014 were included in the study cohort, while patients undergoing concurrent high-risk non-breast surgery, male patients, and those with metastatic disease were excluded. Patients with concomitant current procedural terminology codes identifying soft tissue transfer were categorized as having OBS. Multivariable analysis was performed to determine the independent effect of OBS on postoperative morbidity. We identified 75,972 patients who underwent BCS for breast cancer between 2005 and 2014, of whom 1363 (1.8 %) underwent OBS with soft tissue transfer. Compared with the standard lumpectomy group, patients undergoing OBS were more likely to be younger, had a lower body mass index, were less likely to be smokers, and more often received neoadjuvant chemotherapy. OBS with soft tissue transfer also had a significantly longer operative time (83 vs. 59 min; p breast cancer treatment does not confer an increased risk of surgical complications, despite the longer operative time. This is important given the increasing use of oncoplastic surgery techniques within North America.

  6. Novel MLPA procedure using self-designed probes allows comprehensive analysis for CNVs of the genes involved in Hirschsprung disease

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    Antiñolo Guillermo

    2010-05-01

    Full Text Available Abstract Background Hirschsprung disease is characterized by the absence of intramural ganglion cells in the enteric plexuses, due to a fail during enteric nervous system formation. Hirschsprung has a complex genetic aetiology and mutations in several genes have been related to the disease. There is a clear predominance of missense/nonsense mutations in these genes whereas copy number variations (CNVs have been seldom described, probably due to the limitations of conventional techniques usually employed for mutational analysis. In this study, we have looked for CNVs in some of the genes related to Hirschsprung (EDNRB, GFRA1, NRTN and PHOX2B using the Multiple Ligation-dependent Probe Amplification (MLPA approach. Methods CNVs screening was performed in 208 HSCR patients using a self-designed set of MLPA probes, covering the coding region of those genes. Results A deletion comprising the first 4 exons in GFRA1 gene was detected in 2 sporadic HSCR patients and in silico approaches have shown that the critical translation initiation signal in the mutant gene was abolished. In this study, we have been able to validate the reliability of this technique for CNVs screening in HSCR. Conclusions The implemented MLPA based technique presented here allows CNV analysis of genes involved in HSCR that have not been not previously evaluated. Our results indicate that CNVs could be implicated in the pathogenesis of HSCR, although they seem to be an uncommon molecular cause of HSCR.

  7. Pathway analysis of bladder cancer genome-wide association study identifies novel pathways involved in bladder cancer development.

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    Chen, Meng; Rothman, Nathaniel; Ye, Yuanqing; Gu, Jian; Scheet, Paul A; Huang, Maosheng; Chang, David W; Dinney, Colin P; Silverman, Debra T; Figueroa, Jonine D; Chanock, Stephen J; Wu, Xifeng

    2016-07-01

    Genome-wide association studies (GWAS) are designed to identify individual regions associated with cancer risk, but only explain a small fraction of the inherited variability. Alternative approach analyzing genetic variants within biological pathways has been proposed to discover networks of susceptibility genes with additional effects. The gene set enrichment analysis (GSEA) may complement and expand traditional GWAS analysis to identify novel genes and pathways associated with bladder cancer risk. We selected three GSEA methods: Gen-Gen, Aligator, and the SNP Ratio Test to evaluate cellular signaling pathways involved in bladder cancer susceptibility in a Texas GWAS population. The candidate genetic polymorphisms from the significant pathway selected by GSEA were validated in an independent NCI GWAS. We identified 18 novel pathways ( P CACNA1S, COL4A2, SRC , and CACNA1C were associated with bladder cancer risk. Two CCNE1 variants, rs8102137 and rs997669, from cell cycle pathways showed the strongest associations; the CCNE1 signal at 19q12 has already been reported in previous GWAS. These findings offer additional etiologic insights highlighting the specific genes and pathways associated with bladder cancer development. GSEA may be a complementary tool to GWAS to identify additional loci of cancer susceptibility.

  8. Proteomic analysis of germinal vesicles in the domestic cat model reveals candidate nuclear proteins involved in oocyte competence acquisition.

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    Lee, P-C; Wildt, D E; Comizzoli, P

    2018-01-01

    Do nuclear proteins in the germinal vesicle (GV) contribute to oocyte competence acquisition during folliculogenesis? Proteomic analysis of GVs identified candidate proteins for oocyte competence acquisition, including a key RNA processing protein-heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2B1). The domestic cat GV, which is physiologically similar to the human GV, gains the intrinsic ability to resume meiosis and support early embryo development during the pre-antral-to-antral follicle transition. However, little is known about nuclear proteins that contribute to this developmental process. GVs were enriched from pre-antral (incompetent) and antral (competent) follicles from 802 cat ovaries. Protein lysates were subjected to quantitative proteomic analysis to identify differentially expressed proteins in GVs from the two follicular categories. Two biological replicates (from independent pools of ovaries) of pre-antral versus antral samples were labeled by tandem mass tags and then assessed by liquid chromatography-tandem mass spectrometry. Proteomic data were analyzed according to gene ontology and a protein-protein interaction network. Immunofluorescent staining and protein inhibition assays were used for validation. A total of 174 nuclear proteins was identified, with 54 being up-regulated and 22 down-regulated (≥1.5-fold) after antrum formation. Functional protein analysis through gene ontology over-representation tests revealed that changes in molecular network within the GVs during this transitional phase were related to chromatin reorganization, gene transcription, and maternal RNA processing and storage. Protein inhibition assays verified that hnRNPA2B1, a key nuclear protein identified, was required for oocyte meiotic maturation and subsequent blastocyst formation. Data are available via ProteomeXchange with identifier PXD007211. Proteins identified by proteomic comparison may (i) be involved in processes other than competence acquisition

  9. Whole-genome resequencing and transcriptomic analysis to identify genes involved in leaf-color diversity in ornamental rice plants.

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    Chang-Kug Kim

    Full Text Available Rice field art is a large-scale art form in which people design rice fields using various kinds of ornamental rice plants with different leaf colors. Leaf color-related genes play an important role in the study of chlorophyll biosynthesis, chloroplast structure and function, and anthocyanin biosynthesis. Despite the role of different metabolites in the traditional relationship between leaf and color, comprehensive color-specific metabolite studies of ornamental rice have been limited. We performed whole-genome resequencing and transcriptomic analysis of regulatory patterns and genetic diversity among different rice cultivars to discover new genetic mechanisms that promote enhanced levels of various leaf colors. We resequenced the genomes of 10 rice leaf-color accessions to an average of 40× reads depth and >95% coverage and performed 30 RNA-seq experiments using the 10 rice accessions sampled at three developmental stages. The sequencing results yielded a total of 1,814 × 106 reads and identified an average of 713,114 SNPs per rice accession. Based on our analysis of the DNA variation and gene expression, we selected 47 candidate genes. We used an integrated analysis of the whole-genome resequencing data and the RNA-seq data to divide the candidate genes into two groups: genes related to macronutrient (i.e., magnesium and sulfur transport and genes related to flavonoid pathways, including anthocyanidin biosynthesis. We verified the candidate genes with quantitative real-time PCR using transgenic T-DNA insertion mutants. Our study demonstrates the potential of integrated screening methods combined with genetic-variation and transcriptomic data to isolate genes involved in complex biosynthetic networks and pathways.

  10. Analysis of Cathepsin and Furin Proteolytic Enzymes Involved in Viral Fusion Protein Activation in Cells of the Bat Reservoir Host

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    El Najjar, Farah; Lampe, Levi; Baker, Michelle L.; Wang, Lin-Fa; Dutch, Rebecca Ellis

    2015-01-01

    Bats of different species play a major role in the emergence and transmission of highly pathogenic viruses including Ebola virus, SARS-like coronavirus and the henipaviruses. These viruses require proteolytic activation of surface envelope glycoproteins needed for entry, and cellular cathepsins have been shown to be involved in proteolysis of glycoproteins from these distinct virus families. Very little is currently known about the available proteases in bats. To determine whether the utilization of cathepsins by bat-borne viruses is related to the nature of proteases in their natural hosts, we examined proteolytic processing of several viral fusion proteins in cells derived from two fruit bat species, Pteropus alecto and Rousettus aegyptiacus. Our work shows that fruit bat cells have homologs of cathepsin and furin proteases capable of cleaving and activating both the cathepsin-dependent Hendra virus F and the furin-dependent parainfluenza virus 5 F proteins. Sequence analysis comparing Pteropus alecto furin and cathepsin L to proteases from other mammalian species showed a high degree of conservation; however significant amino acid variation occurs at the C-terminus of Pteropus alecto furin. Further analysis of furin-like proteases from fruit bats revealed that these proteases are catalytically active and resemble other mammalian furins in their response to a potent furin inhibitor. However, kinetic analysis suggests that differences may exist in the cellular localization of furin between different species. Collectively, these results indicate that the unusual role of cathepsin proteases in the life cycle of bat-borne viruses is not due to the lack of active furin-like proteases in these natural reservoir species; however, differences may exist between furin proteases present in fruit bats compared to furins in other mammalian species, and these differences may impact protease usage for viral glycoprotein processing. PMID:25706132

  11. Analysis of cathepsin and furin proteolytic enzymes involved in viral fusion protein activation in cells of the bat reservoir host.

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    Farah El Najjar

    Full Text Available Bats of different species play a major role in the emergence and transmission of highly pathogenic viruses including Ebola virus, SARS-like coronavirus and the henipaviruses. These viruses require proteolytic activation of surface envelope glycoproteins needed for entry, and cellular cathepsins have been shown to be involved in proteolysis of glycoproteins from these distinct virus families. Very little is currently known about the available proteases in bats. To determine whether the utilization of cathepsins by bat-borne viruses is related to the nature of proteases in their natural hosts, we examined proteolytic processing of several viral fusion proteins in cells derived from two fruit bat species, Pteropus alecto and Rousettus aegyptiacus. Our work shows that fruit bat cells have homologs of cathepsin and furin proteases capable of cleaving and activating both the cathepsin-dependent Hendra virus F and the furin-dependent parainfluenza virus 5 F proteins. Sequence analysis comparing Pteropus alecto furin and cathepsin L to proteases from other mammalian species showed a high degree of conservation; however significant amino acid variation occurs at the C-terminus of Pteropus alecto furin. Further analysis of furin-like proteases from fruit bats revealed that these proteases are catalytically active and resemble other mammalian furins in their response to a potent furin inhibitor. However, kinetic analysis suggests that differences may exist in the cellular localization of furin between different species. Collectively, these results indicate that the unusual role of cathepsin proteases in the life cycle of bat-borne viruses is not due to the lack of active furin-like proteases in these natural reservoir species; however, differences may exist between furin proteases present in fruit bats compared to furins in other mammalian species, and these differences may impact protease usage for viral glycoprotein processing.

  12. Identification and Expression Analysis of Medicago truncatula Isopentenyl Transferase Genes (IPTs Involved in Local and Systemic Control of Nodulation

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    Mahboobeh Azarakhsh

    2018-03-01

    Full Text Available Cytokinins are essential for legume plants to establish a nitrogen-fixing symbiosis with rhizobia. Recently, the expression level of cytokinin biosynthesis IPTs (ISOPENTENYLTRANSFERASES genes was shown to be increased in response to rhizobial inoculation in Lotus japonicus, Medicago truncatula and Pisum sativum. In addition to its well-established positive role in nodule primordium initiation in root cortex, cytokinin negatively regulates infection processes in the epidermis. Moreover, it was reported that shoot-derived cytokinin inhibits the subsequent nodule formation through AON (autoregulation of nodulation pathway. In L. japonicus, LjIPT3 gene was shown to be activated in the shoot phloem via the components of AON system, negatively affecting nodulation. However, in M. truncatula, the detailed analysis of MtIPTs expression, both in roots and shoots, in response to nodulation has not been performed yet, and the link between IPTs and AON has not been studied so far. In this study, we performed an extensive analysis of MtIPTs expression levels in different organs, focusing on the possible role of MtIPTs in nodule development. MtIPTs expression dynamics in inoculated roots suggest that besides its early established role in the nodule primordia development, cytokinin may be also important for later stages of nodulation. According to expression analysis, MtIPT3, MtIPT4, and MtIPT5 are activated in the shoots in response to inoculation. Among these genes, MtIPT3 is the only one the induction of which was not observed in leaves of the sunn-3 mutant defective in CLV1-like kinase, the key component of AON, suggesting that MtIPT3 is activated in the shoots in an AON-dependent manner. Taken together, our findings suggest that MtIPTs are involved in the nodule development at different stages, both locally in inoculated roots and systemically in shoots, where their expression can be activated in an AON-dependent manner.

  13. Comparative Transcriptome Analysis Reveal Candidate Genes Potentially Involved in Regulation of Primocane Apex Rooting in Raspberry (Rubus spp.).

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    Liu, Jianfeng; Ming, Yuetong; Cheng, Yunqing; Zhang, Yuchu; Xing, Jiyang; Sun, Yuqi

    2017-01-01

    Raspberries ( Rubus spp.) exhibit a unique rooting process that is initiated from the stem apex of primocane, conferring an unusual asexual mode of reproduction to this plant. However, the full complement of genes involved in this process has not been identified. To this end, the present study analyzed the transcriptomes of the Rubus primocane and floricane stem apex at three developmental stages by Digital Gene Expression profiling to identify genes that regulate rooting. Sequencing and de novo assembly yielded 26.82 Gb of nucleotides and 59,173 unigenes; 498, 7,346, 4,110, 7,900, 9,397, and 4,776 differently expressed genes were identified in paired comparisons of SAF1 (floricane at developmental stage 1) vs. SAP1 (primocane at developmental stage 1), SAF2 vs. SAP2, SAF3 vs. SAP3, SAP1 vs. SAP2, SAP1 vs. SAP3, and SAP2 vs. SAP3, respectively. SAP1 maintains an extension growth pattern; SAP2 then exhibits growth arrest and vertical (downward) gravitropic deflection; and finally, short roots begin to form on the apex of SAP3. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis of SAP1 vs. SAP2 revealed 12 pathways that were activated in response to shoot growth arrest and root differentiation, including circadian rhythm-plant (ko04712) and plant hormone signal transduction (ko04075). Our results indicate that genes related to circadian rhythm, ethylene and auxin signaling, shoot growth, and root development are potentially involved in the regulation of primocane apex rooting in Rubus . These findings provide a basis for elucidating the molecular mechanisms of primocane apex rooting in this economically valuable crop.

  14. Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma.

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    Li, Chaoxing; Liu, Li; Dinu, Valentin

    2018-01-01

    Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway's topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs. In addition, it is reported that the loss of connectivity is a common topological trait of cancer networks, which is an assumption of our method. Hence, from normal to cancer, the process of the network losing connectivity might be the process of disrupting the structure of the network, namely, the number of hub genes might be altered in cancer compared to that in normal or the distribution of topological ranks of genes might be altered. Based on this, we propose a new PageRank-based method called Pathways of Topological Rank Analysis (PoTRA) to detect pathways involved in cancer. We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fisher's exact test to test if the number of hub genes in each pathway is altered from normal to cancer. Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer. Hence, we use the Kolmogorov-Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes. We apply PoTRA to study hepatocellular carcinoma (HCC) and several subtypes of HCC. Very interestingly, we discover that all significant pathways in HCC are cancer-associated generally, while several significant pathways in subtypes

  15. Comparative proteome analysis of embryo and endosperm reveals central differential expression proteins involved in wheat seed germination.

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    He, Miao; Zhu, Chong; Dong, Kun; Zhang, Ting; Cheng, Zhiwei; Li, Jiarui; Yan, Yueming

    2015-04-08

    Wheat seeds provide a staple food and an important protein source for the world's population. Seed germination is vital to wheat growth and development and directly affects grain yield and quality. In this study, we performed the first comparative proteomic analysis of wheat embryo and endosperm during seed germination. The proteomic changes in embryo and endosperm during the four different seed germination stages of elite Chinese bread wheat cultivar Zhengmai 9023 were first investigated. In total, 74 and 34 differentially expressed protein (DEP) spots representing 63 and 26 unique proteins were identified in embryo and endosperm, respectively. Eight common DEP were present in both tissues, and 55 and 18 DEP were specific to embryo and endosperm, respectively. These identified DEP spots could be sorted into 13 functional groups, in which the main group was involved in different metabolism pathways, particularly in the reserves necessary for mobilization in preparation for seed germination. The DEPs from the embryo were mainly related to carbohydrate metabolism, proteometabolism, amino acid metabolism, nucleic acid metabolism, and stress-related proteins, whereas those from the endosperm were mainly involved in protein storage, carbohydrate metabolism, inhibitors, stress response, and protein synthesis. During seed germination, both embryo and endosperm had a basic pattern of oxygen consumption, so the proteins related to respiration and energy metabolism were up-regulated or down-regulated along with respiration of wheat seeds. When germination was complete, most storage proteins from the endosperm began to be mobilized, but only a small amount was degraded during germination. Transcription expression of six representative DEP genes at the mRNA level was consistent with their protein expression changes. Wheat seed germination is a complex process with imbibition, stirring, and germination stages, which involve a series of physiological, morphological, and

  16. Pathways of topological rank analysis (PoTRA: a novel method to detect pathways involved in hepatocellular carcinoma

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    Chaoxing Li

    2018-04-01

    Full Text Available Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway’s topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs. In addition, it is reported that the loss of connectivity is a common topological trait of cancer networks, which is an assumption of our method. Hence, from normal to cancer, the process of the network losing connectivity might be the process of disrupting the structure of the network, namely, the number of hub genes might be altered in cancer compared to that in normal or the distribution of topological ranks of genes might be altered. Based on this, we propose a new PageRank-based method called Pathways of Topological Rank Analysis (PoTRA to detect pathways involved in cancer. We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fisher’s exact test to test if the number of hub genes in each pathway is altered from normal to cancer. Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer. Hence, we use the Kolmogorov–Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes. We apply PoTRA to study hepatocellular carcinoma (HCC and several subtypes of HCC. Very interestingly, we discover that all significant pathways in HCC are cancer-associated generally, while several

  17. Comparative genomic analysis reveals a diverse repertoire of genes involved in prokaryote-eukaryote interactions within the Pseudovibrio genus.

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    Stefano eRomano

    2016-03-01

    Full Text Available Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage.Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus.Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche

  18. Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus.

    Science.gov (United States)

    Romano, Stefano; Fernàndez-Guerra, Antonio; Reen, F Jerry; Glöckner, Frank O; Crowley, Susan P; O'Sullivan, Orla; Cotter, Paul D; Adams, Claire; Dobson, Alan D W; O'Gara, Fergal

    2016-01-01

    Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage. Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus. Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche within its

  19. Transcriptome analysis and discovery of genes involved in immune pathways from hepatopancreas of microbial challenged mitten crab Eriocheir sinensis.

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    Xihong Li

    Full Text Available BACKGROUND: The Chinese mitten crab Eriocheir sinensis is an important economic crustacean and has been seriously attacked by various diseases, which requires more and more information for immune relevant genes on genome background. Recently, high-throughput RNA sequencing (RNA-seq technology provides a powerful and efficient method for transcript analysis and immune gene discovery. METHODS/PRINCIPAL FINDINGS: A cDNA library from hepatopancreas of E. sinensis challenged by a mixture of three pathogen strains (Gram-positive bacteria Micrococcus luteus, Gram-negative bacteria Vibrio alginolyticus and fungi Pichia pastoris; 10(8 cfu·mL(-1 was constructed and randomly sequenced using Illumina technique. Totally 39.76 million clean reads were assembled to 70,300 unigenes. After ruling out short-length and low-quality sequences, 52,074 non-redundant unigenes were compared to public databases for homology searching and 17,617 of them showed high similarity to sequences in NCBI non-redundant protein (Nr database. For function classification and pathway assignment, 18,734 (36.00% unigenes were categorized to three Gene Ontology (GO categories, 12,243 (23.51% were classified to 25 Clusters of Orthologous Groups (COG, and 8,983 (17.25% were assigned to six Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. Potentially, 24, 14, 47 and 132 unigenes were characterized to be involved in Toll, IMD, JAK-STAT and MAPK pathways, respectively. CONCLUSIONS/SIGNIFICANCE: This is the first systematical transcriptome analysis of components relating to innate immune pathways in E. sinensis. Functional genes and putative pathways identified here will contribute to better understand immune system and prevent various diseases in crab.

  20. Computational Analysis of Missense Variants of G Protein-Coupled Receptors Involved in the Neuroendocrine Regulation of Reproduction.

    Science.gov (United States)

    Min, Le; Nie, Min; Zhang, Anna; Wen, Junping; Noel, Sekoni D; Lee, Vivian; Carroll, Rona S; Kaiser, Ursula B

    2016-01-01

    Many missense variants in G protein-coupled receptors (GPCRs) involved in the neuroendocrine regulation of reproduction have been identified by phenotype-driven or large-scale exome sequencing. Computational functional prediction analysis is commonly performed to evaluate their impact on receptor function. To assess the performance and outcome of functional prediction analyses for these GPCRs, we performed a statistical analysis of the prediction performance of SIFT and PolyPhen-2 for variants with documented biological function as well as variants retrieved from Ensembl. We obtained missense variants with documented biological function testing from patients with reproductive disorders from a comprehensive literature search. Missense variants from individuals with known reproductive disorders were retrieved from the Human Gene Mutation Database. Missense variants from the general population were retrieved from the Ensembl genome database. The accuracies of SIFT and PolyPhen-2 were 83 and 85%, respectively. The performance of both prediction tools was greater in predicting loss-of-function variants (SIFT: 92%; PolyPhen-2: 95%) than in predicting variants that did not affect function (SIFT: 54%; PolyPhen-2: 57%). Concordance between SIFT and PolyPhen-2 did not improve accuracy. Surprisingly, approximately half of the variants retrieved from Ensembl were predicted as loss-of-function variants by SIFT (47%) and PolyPhen-2 (54%). Our findings provide new guidance for interpreting the results and limitations of computational functional prediction analyses for GPCRs and will help to determine which variants require biological function testing. In addition, our findings raise important questions regarding the link between genotype and phenotype in the general population. © 2015 S. Karger AG, Basel.

  1. Gonadal Transcriptome Analysis of Pacific Abalone Haliotis discus discus: Identification of Genes Involved in Germ Cell Development.

    Science.gov (United States)

    Yu, Lingyun; Xu, Dongdong; Ye, Huan; Yue, Huamei; Ooka, Shioh; Kondo, Hidehiro; Yazawa, Ryosuke; Takeuchi, Yutaka

    2018-04-03

    Little is known about the molecular mechanisms governing gonadal developmental processes in abalones. Here, we conducted transcriptome analysis of Pacific abalone Haliotis discus discus for gene discovery in the brain, ovary, testis, and unfertilized eggs. Among the annotated unigenes, 48.6% of unigenes were identified by Venn diagram analysis as having universal or tissue-specific expression. Twenty-three genes with gonad-biased gene ontology (GO) terms were first obtained. Secondly, 36 genes were found by screening known gene names related to germ cell development. Finally, 17 genes were obtained by querying the annotated unigene database for zygotically expressed gonadal genes (ovary and testis) and maternally expressed gonadal genes (ovary, testis, and unfertilized eggs) using keywords related to reproduction. To further verify tissue distribution pattern and subcellular localization of these genes, RT-PCR and in situ hybridization were performed using a unigene encoding a germ cell marker, vasa, as control. The results showed that vasa was expressed mainly in the early developmental stages of germ cells in both sexes. One of the candidate genes, vitelline envelope zona pellucida domain protein 12 (ZP12), was expressed in the primordial germ cells of immature gonad and early developmental stages of germ cells of the adult female. The results obtained from the present study suggest that vasa and ZP12 are involved in germ cell development of Pacific abalone and that ZP12 is an especially useful germ cell-specific marker in immature adults. The current gonadal transcriptome profile is an extensive resource for future reproductive molecular biology studies of this species.

  2. De novo transcriptome sequencing and comparative analysis to discover genes involved in ovarian maturity in Strongylocentrotus nudus.

    Science.gov (United States)

    Jia, Zhiying; Wang, Qiai; Wu, Kaikai; Wei, Zhenlin; Zhou, Zunchun; Liu, Xiaolin

    2017-09-01

    Strongylocentrotus nudus is an edible sea urchin, mainly harvested in China. Correlation studies indicated that S. nudus with larger diameter have a prolonged marketing time and better palatability owing to their precocious gonads and extended maturation process. However, the molecular mechanism underlying this phenomenon is still unknown. Here, transcriptome sequencing was applied to study the ovaries of adult S. nudus with different shell diameters to explore the possible mechanism. In this study, four independent cDNA libraries were constructed, including two from the big size urchins and two from the small ones using a HiSeq™2500 platform. A total of 88,581 unigenes were acquired with a mean length of 1354bp, of which 66,331 (74.88%) unigenes could be annotated using six major publicly available databases. Comparative analysis revealed that 353 unigenes were differentially expressed (with log2(ratio)≥1, FDR≤0.001) between the two groups. Of these, 20 differentially expressed genes (DEGs) were selected to confirm the accuracy of RNA-seq data by quantitative real-time RT-PCR. Furthermore, gene ontology and KEGG pathway enrichment analyses were performed to find the putative genes and pathways related to ovarian maturity. Eight unigenes were identified as significant DEGs involved in reproduction related pathways; these included Mos, Cdc20, Rec8, YP30, cytochrome P450 2U1, ovoperoxidase, proteoliaisin, and rendezvin. Our research fills the gap in the studies on the S. nudus ovaries using transcriptome analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Comparative Transcriptomic Analysis Reveals Candidate Genes and Pathways Involved in Larval Settlement of the Barnacle Megabalanus volcano.

    Science.gov (United States)

    Yan, Guoyong; Zhang, Gen; Huang, Jiaomei; Lan, Yi; Sun, Jin; Zeng, Cong; Wang, Yong; Qian, Pei-Yuan; He, Lisheng

    2017-10-27

    Megabalanus barnacle is one of the model organisms for marine biofouling research. However, further elucidation of molecular mechanisms underlying larval settlement has been hindered due to the lack of genomic information thus far. In the present study, cDNA libraries were constructed for cyprids, the key stage for larval settlement, and adults of Megabalanus volcano . After high-throughput sequencing and de novo assembly, 42,620 unigenes were obtained with a N50 value of 1532 bp. These unigenes were annotated by blasting against the NCBI non-redundant (nr), Swiss-Prot, Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Finally, 19,522, 15,691, 14,459, and 10,914 unigenes were identified correspondingly. There were 22,158 differentially expressed genes (DEGs) identified between two stages. Compared with the cyprid stage, 8241 unigenes were down-regulated and 13,917 unigenes were up-regulated at the adult stage. The neuroactive ligand-receptor interaction pathway (ko04080) was significantly enriched by KEGG enrichment analysis of the DEGs, suggesting that it possibly involved in larval settlement. Potential functions of three conserved allatostatin neuropeptide-receptor pairs and two light-sensitive opsin proteins were further characterized, indicating that they might regulate attachment and metamorphosis at cyprid stage. These results provided a deeper insight into the molecular mechanisms underlying larval settlement of barnacles.

  4. Identification and expression analysis of the genes involved in serotonin biosynthesis and transduction in the field cricket Gryllus bimaculatus.

    Science.gov (United States)

    Watanabe, T; Sadamoto, Hitoshi; Aonuma, H

    2011-10-01

    Serotonin (5-HT) modulates various aspects of behaviours such as aggressive behaviour and circadian behaviour in the cricket. To elucidate the molecular basis of the cricket 5-HT system, we identified 5-HT-related genes in the field cricket Gryllus bimaculatus DeGeer. Complementary DNA of tryptophan hydroxylase and phenylalanine-tryptophan hydroxylase, which convert tryptophan into 5-hydroxy-L-tryptophan (5-HTP), and that of aromatic L-amino acid decarboxylase, which converts 5-HTP into 5-HT, were isolated from a cricket brain cDNA library. In addition, four 5-HT receptor genes (5-HT(1A) , 5-HT(1B) , 5-HT(2α) , and 5-HT(7) ) were identified. Expression analysis of the tryptophan hydroxylase gene TRH and phenylalanine-tryptophan hydroxylase gene TPH, which are selectively involved in neuronal and peripheral 5-HT synthesis in Drosophila, suggested that two 5-HT synthesis pathways co-exist in the cricket neuronal tissues. The four 5-HT receptor genes were expressed in various tissues at differential expression levels, suggesting that the 5-HT system is widely distributed in the cricket. © 2011 The Authors. Insect Molecular Biology © 2011 The Royal Entomological Society.

  5. RNA-Seq mediated root transcriptome analysis of Chlorophytum borivilianum for identification of genes involved in saponin biosynthesis.

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    Kumar, Sunil; Kalra, Shikha; Singh, Baljinder; Kumar, Avneesh; Kaur, Jagdeep; Singh, Kashmir

    2016-01-01

    Chlorophytum borivilianum is an important species of liliaceae family, owing to its vital medicinal properties. Plant roots are used for aphrodisiac, adaptogen, anti-aging, health-restorative and health-promoting purposes. Saponins, are considered to be the principal bioactive components responsible for the wide variety of pharmacological properties of this plant. In the present study, we have performed de novo root transcriptome sequencing of C. borivilianum using Illumina Hiseq 2000 platform, to gain molecular insight into saponins biosynthesis. A total of 33,963,356 high-quality reads were obtained after quality filtration. Sequences were assembled using various programs which generated 97,344 transcripts with a size range of 100-5,216 bp and N50 value of 342. Data was analyzed against non-redundant proteins, gene ontology (GO), and enzyme commission (EC) databases. All the genes involved in saponins biosynthesis along with five full-length genes namely farnesyl pyrophosphate synthase, cycloartenol synthase, β-amyrin synthase, cytochrome p450, and sterol-3-glucosyltransferase were identified. Read per exon kilobase per million (RPKM)-based comparative expression profiling was done to study the differential regulation of the genes. In silico expression analysis of seven selected genes of saponin biosynthetic pathway was validated by qRT-PCR.

  6. Transcriptome analysis of grain-filling caryopses reveals involvement of multiple regulatory pathways in chalky grain formation in rice

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    Mao Bigang

    2010-12-01

    Full Text Available Abstract Background Grain endosperm chalkiness of rice is a varietal characteristic that negatively affects not only the appearance and milling properties but also the cooking texture and palatability of cooked rice. However, grain chalkiness is a complex quantitative genetic trait and the molecular mechanisms underlying its formation are poorly understood. Results A near-isogenic line CSSL50-1 with high chalkiness was compared with its normal parental line Asominori for grain endosperm chalkiness. Physico-biochemical analyses of ripened grains showed that, compared with Asominori, CSSL50-1 contains higher levels of amylose and 8 DP (degree of polymerization short-chain amylopectin, but lower medium length 12 DP amylopectin. Transcriptome analysis of 15 DAF (day after flowering caryopses of the isogenic lines identified 623 differential expressed genes (P Conclusion Extensive gene expression changes were detected during rice grain chalkiness formation. Over half of these differentially expressed genes are implicated in several important categories of genes, including signal transduction, transcription, carbohydrate metabolism and redox homeostasis, suggesting that chalkiness formation involves multiple metabolic and regulatory pathways.

  7. Methamphetamine use and rates of incarceration among street-involved youth in a Canadian setting: a cross-sectional analysis

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    Buxton Jane

    2009-08-01

    Full Text Available Abstract Background Given concerns over rising use of methamphetamine, especially among street-involved youth, and the links between exposure to the correctional system and the production of drug-related harm, we sought to assess the relationship between ever using methamphetamine and reporting ever being incarcerated in the At-Risk Youth Survey (ARYS in Vancouver, Canada. Methods The relationship between ever being imprisoned and ever using methamphetamine was estimated using a multivariate logistic regression analysis while also considering potentially confounding secondary demographic, social and behavioural variables. Results Of the 478 youth recruited into ARYS between September 2005 and October 2006, 385 (80.5% reported ever being incarcerated overnight or longer. In the multivariate model, methamphetamine use was independently associated with ever being incarcerated (Adjusted Odds Ratio: 1.79, 95% Confidence Interval [CI]: 1.03 – 3.13. Conclusion Incarceration was very common in this cohort and strongly linked with ever using methamphetamine. This finding is of concern and, along with the previously identified risks of drug-related harm associated with incarceration, supports the development of novel public policy, such as community-based drug treatment, to address the use of methamphetamine among street youth.

  8. Genome-Wide Identification and Analysis of TCP Transcription Factors Involved in the Formation of Leafy Head in Chinese Cabbage

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    Yan Liu

    2018-03-01

    Full Text Available Chinese cabbage (Brassica rapa L. ssp. pekinensis is a widely cultivated and economically important vegetable crop with typical leaf curvature. The TCP (Teosinte branched1, Cycloidea, Proliferating cell factor family proteins are plant-specific transcription factors (TFs and play important roles in many plant biological processes, especially in the regulation of leaf curvature. In this study, 39 genes encoding TCP TFs are detected on the whole genome of B. rapa. Based on the phylogenetic analysis of TCPs between Arabidopsis thaliana and Brassica rapa, TCP genes of Chinese cabbage are named from BrTCP1a to BrTCP24b. Moreover, the chromosomal location; phylogenetic relationships among B. rapa, A. thaliana, and rice; gene structures and protein conserved sequence alignment; and conserved domains are analyzed. The expression profiles of BrTCPs are analyzed in different tissues. To understand the role of Chinese cabbage TCP members in regulating the curvature of leaves, the expression patterns of all BrTCP genes are detected at three development stages essential for leafy head formation. Our results provide information on the classification and details of BrTCPs and allow us to better understand the function of TCPs involved in leaf curvature of Chinese cabbage.

  9. Correlation analysis of indicators of physical condition, health and physical fitness of soldiers involved in peacekeeping operations

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    S.S. Fedak

    2014-01-01

    Full Text Available Purpose: to identify the main physical qualities, which positively influence the physical state, health and military - professional career peacekeepers when performing tasks in different climatic conditions. Material : the study involved 98 military service under the contract the first age group (men. Analyzed contingent divided into groups according to climatic conditions of service: in the highlands - 37 person, in hot climates - 35 person, in towns and areas with limited space - 26 person. A correlation analysis between the results of running 100 meters, pulling, running 3 kilometre and indicators of the health and physical condition of the soldiers. Results : It was determined that the participation in peacekeeping missions in mountainous areas and in areas with a hot climate is the quality of the underlying physical endurance. With the participation in peacekeeping missions in populated areas and in areas with limited space - this is the strength and speed. Conclusions : on improving these physical qualities should focus during lessons in physical training of peacekeepers in the centers of immediate preparation for missions.

  10. Genetic Analysis of the Pathogenic Molecular Sub-phenotype Interferon Alpha Identifies Multiple Novel Loci Involved in Systemic Lupus Erythematosus

    Science.gov (United States)

    Kariuki, Silvia N.; Ghodke-Puranik, Yogita; Dorschner, Jessica M.; Chrabot, Beverly S.; Kelly, Jennifer A.; Tsao, Betty P.; Kimberly, Robert P.; Alarcón-Riquelme, Marta E.; Jacob, Chaim O.; Criswell, Lindsey A.; Sivils, Kathy L.; Langefeld, Carl D.; Harley, John B.; Skol, Andrew D.; Niewold, Timothy B.

    2014-01-01

    Systemic Lupus Erythematosus (SLE) is a chronic autoimmune disorder characterized by inflammation of multiple organ systems and dysregulated interferon responses. SLE is both genetically and phenotypically heterogeneous, greatly reducing the power of case-control studies in SLE. Elevated circulating interferon alpha (IFN-α) is a stable, heritable trait in SLE, which has been implicated in primary disease pathogenesis. 40–50% of patients have high IFN-α, and high levels correspond with clinical differences. To study genetic heterogeneity in SLE, we performed a case-case study comparing patients with high vs. low IFN-α in over 1550 SLE cases, including GWAS and replication cohorts. In meta-analysis, the top associations in European ancestry were PRKG1 rs7897633 (PMeta=2.75 × 10−8) and PNP rs1049564 (PMeta=1.24 × 10−7). We also found evidence for cross-ancestral background associations with the ANKRD44 and PLEKHF2 loci. These loci have not been previously identified in case-control SLE genetic studies. Bioinformatic analyses implicated these loci functionally in dendritic cells and natural killer cells, both of which are involved in IFN-α production in SLE. As case-control studies of heterogeneous diseases reach a limit of feasibility with respect to subject number and detectable effect size, the study of informative pathogenic subphenotypes becomes an attractive strategy for genetic discovery in complex disease. PMID:25338677

  11. Catalytic analysis of APOBEC3G involving real-time NMR spectroscopy reveals nucleic acid determinants for deamination.

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    Keisuke Kamba

    Full Text Available APOBEC3G (A3G is a single-stranded DNA-specific cytidine deaminase that preferentially converts cytidine to uridine at the third position of triplet cytosine (CCC hotspots. A3G restricts the infectivity of viruses, such as HIV-1, by targeting CCC hotspots scattered through minus DNA strands, reverse-transcribed from genomic RNA. Previously, we developed a real-time NMR method and elucidated the origin of the 3'→5' polarity of deamination of DNA by the C-terminal domain of A3G (CD2, which is a phenomenon by which a hotspot located closer to the 5'-end is deaminated more effectively than one less close to the 5'-end, through quantitative analysis involving nonspecific binding to and sliding along DNA. In the present study we applied the real-time NMR method to analyze the catalytic activity of CD2 toward DNA oligonucleotides containing a nucleotide analog at a single or multiple positions. Analyses revealed the importance of the sugar and base moieties throughout the consecutive 5 nucleotides, the CCC hotspot being positioned at the center. It was also shown that the sugar or base moieties of the nucleotides outside this 5 nucleotide recognition sequence are also relevant as to CD2's activity. Analyses involving DNA oligonucleotides having two CCC hotspots linked by a long sequence of either deoxyribonucleotides, ribonucleotides or abasic deoxyribonucleotides suggested that the phosphate backbone is required for CD2 to slide along the DNA strand and to exert the 3'→5' polarity. Examination of the effects of different salt concentrations on the 3'→5' polarity indicated that the higher the salt concentration, the less prominent the 3'→5' polarity. This is most likely the result of alleviation of sliding due to a decrease in the affinity of CD2 with the phosphate backbone at high salt concentrations. We also investigated the reactivity of substrates containing 5-methylcytidine (5mC or 5-hydroxymethylcytidine, and found that A3G exhibited low

  12. Patient Safety Incidents Involving Sick Children in Primary Care in England and Wales: A Mixed Methods Analysis.

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    Philippa Rees

    2017-01-01

    Full Text Available The UK performs poorly relative to other economically developed countries on numerous indicators of care quality for children. The contribution of iatrogenic harm to these outcomes is unclear. As primary care is the first point of healthcare contact for most children, we sought to investigate the safety of care provided to children in this setting.We undertook a mixed methods investigation of reports of primary care patient safety incidents involving sick children from England and Wales' National Reporting and Learning System between 1 January 2005 and 1 December 2013. Two reviewers independently selected relevant incident reports meeting prespecified criteria, and then descriptively analyzed these reports to identify the most frequent and harmful incident types. This was followed by an in-depth thematic analysis of a purposive sample of reports to understand the reasons underpinning incidents. Key candidate areas for strengthening primary care provision and reducing the risks of systems failures were then identified through multidisciplinary discussions. Of 2,191 safety incidents identified from 2,178 reports, 30% (n = 658 were harmful, including 12 deaths and 41 cases of severe harm. The children involved in these incidents had respiratory conditions (n = 387; 18%, injuries (n = 289; 13%, nonspecific signs and symptoms, e.g., fever (n = 281; 13%, and gastrointestinal or genitourinary conditions (n = 268; 12%, among others. Priority areas for improvement included safer systems for medication provision in community pharmacies; triage processes to enable effective and timely assessment, diagnosis, and referral of acutely sick children attending out-of-hours services; and enhanced communication for robust safety netting between professionals and parents. The main limitations of this study result from underreporting of safety incidents and variable data quality. Our findings therefore require further exploration in longitudinal studies utilizing

  13. Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity

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    Fuchs Thilo M

    2008-01-01

    Full Text Available Abstract Background Photorhabdus luminescens and Yersinia enterocolitica are both enteric bacteria which are associated with insects. P. luminescens lives in symbiosis with soil nematodes and is highly pathogenic towards insects but not to humans. In contrast, Y. enterocolitica is widely found in the environment and mainly known to cause gastroenteritis in men, but has only recently been shown to be also toxic for insects. It is expected that both pathogens share an overlap of genetic determinants that play a role within the insect host. Results A selective genome comparison was applied. Proteins belonging to the class of two-component regulatory systems, quorum sensing, universal stress proteins, and c-di-GMP signalling have been analysed. The interorganismic synopsis of selected regulatory systems uncovered common and distinct signalling mechanisms of both pathogens used for perception of signals within the insect host. Particularly, a new class of LuxR-like regulators was identified, which might be involved in detecting insect-specific molecules. In addition, the genetic overlap unravelled a two-component system that is unique for the genera Photorhabdus and Yersinia and is therefore suggested to play a major role in the pathogen-insect relationship. Our analysis also highlights factors of both pathogens that are expressed at low temperatures as encountered in insects in contrast to higher (body temperature, providing evidence that temperature is a yet under-investigated environmental signal for bacterial adaptation to various hosts. Common degradative metabolic pathways are described that might be used to explore nutrients within the insect gut or hemolymph, thus enabling the proliferation of P. luminescens and Y. enterocolitica in their invertebrate hosts. A strikingly higher number of genes encoding insecticidal toxins and other virulence factors in P. luminescens compared to Y. enterocolitica correlates with the higher virulence of P

  14. Patient Safety Incidents Involving Sick Children in Primary Care in England and Wales: A Mixed Methods Analysis.

    Science.gov (United States)

    Rees, Philippa; Edwards, Adrian; Powell, Colin; Hibbert, Peter; Williams, Huw; Makeham, Meredith; Carter, Ben; Luff, Donna; Parry, Gareth; Avery, Anthony; Sheikh, Aziz; Donaldson, Liam; Carson-Stevens, Andrew

    2017-01-01

    The UK performs poorly relative to other economically developed countries on numerous indicators of care quality for children. The contribution of iatrogenic harm to these outcomes is unclear. As primary care is the first point of healthcare contact for most children, we sought to investigate the safety of care provided to children in this setting. We undertook a mixed methods investigation of reports of primary care patient safety incidents involving sick children from England and Wales' National Reporting and Learning System between 1 January 2005 and 1 December 2013. Two reviewers independently selected relevant incident reports meeting prespecified criteria, and then descriptively analyzed these reports to identify the most frequent and harmful incident types. This was followed by an in-depth thematic analysis of a purposive sample of reports to understand the reasons underpinning incidents. Key candidate areas for strengthening primary care provision and reducing the risks of systems failures were then identified through multidisciplinary discussions. Of 2,191 safety incidents identified from 2,178 reports, 30% (n = 658) were harmful, including 12 deaths and 41 cases of severe harm. The children involved in these incidents had respiratory conditions (n = 387; 18%), injuries (n = 289; 13%), nonspecific signs and symptoms, e.g., fever (n = 281; 13%), and gastrointestinal or genitourinary conditions (n = 268; 12%), among others. Priority areas for improvement included safer systems for medication provision in community pharmacies; triage processes to enable effective and timely assessment, diagnosis, and referral of acutely sick children attending out-of-hours services; and enhanced communication for robust safety netting between professionals and parents. The main limitations of this study result from underreporting of safety incidents and variable data quality. Our findings therefore require further exploration in longitudinal studies utilizing case review

  15. Quantitative Analysis of Teachers' Perceptions of Parental Involvement and Communication in the Online School Environment

    Science.gov (United States)

    Brown, Amy K.

    2017-01-01

    Parent and family involvement is a familiar topic used by many researchers in the traditional education setting yet vastly under used as it applies to the online education setting. The purpose of this study was to explore and determine if there are any differences among online teachers' perceptions of parental involvement and communication in the…

  16. Transcriptomic Analysis Of Purified Embryonic Neural Stem Cells From Zebrafish Embryos Reveals Signalling Pathways Involved In Glycine-dependent Neurogenesis

    Directory of Open Access Journals (Sweden)

    Eric eSAMARUT

    2016-03-01

    Full Text Available How is the initial set of neurons correctly established during the development of the vertebrate central nervous system? In the embryo, glycine and GABA are depolarizing due the immature chloride gradient, which is only reversed to become hyperpolarizing later in post-natal development. We previously showed that glycine regulates neurogenesis via paracrine signalling that promotes calcium transients in neural stem cells (NSCs and their differentiation into interneurons within the spinal cord of the zebrafish embryo. However, the subjacent molecular mechanisms are not yet understood. Our previous work suggests that early neuronal progenitors were not differentiating correctly in the developing spinal cord. As a result, we aimed at identifying the downstream molecular mechanisms involved specifically in NSCs during glycine-dependent embryonic neurogenesis. Using a gfap:GFP transgenic line, we successfully purified NSCs by fluorescence-activated cell sorting (FACS from whole zebrafish embryos and in embryos in which the glycine receptor was knocked down. The strength of this approach is that it focused on the NSC population while tackling the biological issue in an in vivo context in whole zebrafish embryos. After sequencing the transcriptome by RNA-sequencing, we analyzed the genes whose expression was changed upon disruption of glycine signalling and we confirmed the differential expression by independent RTqPCR assay. While over a thousand genes showed altered expression levels, through pathway analysis we identified 14 top candidate genes belonging to five different canonical signalling pathways (signalling by calcium, TGF-beta, sonic hedgehog, Wnt and p53-related apoptosis that are likely to mediate the promotion of neurogenesis by glycine.

  17. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.

    Directory of Open Access Journals (Sweden)

    Sheri L Simmons

    2008-07-01

    Full Text Available Deeply sampled community genomic (metagenomic datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth approximately 20x. The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types ( approximately 94% sequence identity have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the

  18. Transcriptome analysis of Neisseria meningitidis in human whole blood and mutagenesis studies identify virulence factors involved in blood survival.

    Directory of Open Access Journals (Sweden)

    Hebert Echenique-Rivera

    2011-05-01

    Full Text Available During infection Neisseria meningitidis (Nm encounters multiple environments within the host, which makes rapid adaptation a crucial factor for meningococcal survival. Despite the importance of invasion into the bloodstream in the meningococcal disease process, little is known about how Nm adapts to permit survival and growth in blood. To address this, we performed a time-course transcriptome analysis using an ex vivo model of human whole blood infection. We observed that Nm alters the expression of ≈30% of ORFs of the genome and major dynamic changes were observed in the expression of transcriptional regulators, transport and binding proteins, energy metabolism, and surface-exposed virulence factors. In particular, we found that the gene encoding the regulator Fur, as well as all genes encoding iron uptake systems, were significantly up-regulated. Analysis of regulated genes encoding for surface-exposed proteins involved in Nm pathogenesis allowed us to better understand mechanisms used to circumvent host defenses. During blood infection, Nm activates genes encoding for the factor H binding proteins, fHbp and NspA, genes encoding for detoxifying enzymes such as SodC, Kat and AniA, as well as several less characterized surface-exposed proteins that might have a role in blood survival. Through mutagenesis studies of a subset of up-regulated genes we were able to identify new proteins important for survival in human blood and also to identify additional roles of previously known virulence factors in aiding survival in blood. Nm mutant strains lacking the genes encoding the hypothetical protein NMB1483 and the surface-exposed proteins NalP, Mip and NspA, the Fur regulator, the transferrin binding protein TbpB, and the L-lactate permease LctP were sensitive to killing by human blood. This increased knowledge of how Nm responds to adaptation in blood could also be helpful to develop diagnostic and therapeutic strategies to control the devastating

  19. Systematic review and meta-analysis of the influence of circumferential resection margin involvement on survival in patients with operable oesophageal cancer.

    Science.gov (United States)

    Chan, D S Y; Reid, T D; Howell, I; Lewis, W G

    2013-03-01

    The prognostic role and definition of circumferential resection margin (CRM) involvement in operable oesophageal cancer remain controversial. The College of American Pathologists (CAP) and Royal College of Pathologists (RCP) define CRM involvement as tumour found at the cut resection margin and within 1 mm of the cut margin respectively. This systematic review and meta-analysis was performed to determine the influence of CRM involvement on survival in operable oesophageal cancer. PubMed, MEDLINE and the Cochrane Library (January 1990 to June 2012) were searched for studies correlating CRM involvement with 5-year mortality. Statistical analysis of dichotomous variables was performed using the odds ratio (OR) as the summary statistic. Fourteen studies involving 2433 patients with oesophageal cancer who had undergone potentially curative oesophagectomy were analysed. Rates of CRM involvement were 15·3 per cent (173 of 1133) and 36·5 per cent (889 of 2433) according to the CAP and RCP criteria respectively. Overall 5-year mortality rates were significantly higher in patients with CRM involvement compared with CRM-negative patients according to both CAP (OR 4·02, 95 per cent confidence interval (c.i.) 2·25 to 7·20; P CRM involvement between 0·1 and 1 mm was associated with a significantly higher 5-year mortality rate than CRM-negative status (involvement more than 1 mm from CRM) (OR 2·05, 95 per cent c.i. 1·41 to 2·99; P CRM involvement is an important predictor of poor prognosis. CAP criteria differentiate a higher-risk group than RCP criteria, but overlook a patient group with similar poor outcomes. Copyright © 2013 British Journal of Surgery Society Ltd. Published by John Wiley & Sons, Ltd.

  20. Human cytosolic glutathione-S-transferases: quantitative analysis of expression, comparative analysis of structures and inhibition strategies of isozymes involved in drug resistance.

    Science.gov (United States)

    Mohana, Krishnamoorthy; Achary, Anant

    2017-08-01

    Glutathione-S-transferase (GST) inhibition is a strategy to overcome drug resistance. Several isoforms of human GSTs are present and they are expressed in almost all the organs. Specific expression levels of GSTs in various organs are collected from the human transcriptome data and analysis of the organ-specific expression of GST isoforms is carried out. The variations in the level of expressions of GST isoforms are statistically significant. The GST expression differs in diseased conditions as reported by many investigators and some of the isoforms of GSTs are disease markers or drug targets. Structure analysis of various isoforms is carried out and literature mining has been performed to identify the differences in the active sites of the GSTs. The xenobiotic binding H site is classified into H1, H2, and H3 and the differences in the amino acid composition, the hydrophobicity and other structural features of H site of GSTs are discussed. The existing inhibition strategies are compared. The advent of rational drug design, mechanism-based inhibition strategies, availability of high-throughput screening, target specific, and selective inhibition of GST isoforms involved in drug resistance could be achieved for the reversal of drug resistance and aid in the treatment of diseases.

  1. Comparative genomic analysis of a neurotoxigenic Clostridium species using partial genome sequence: Phylogenetic analysis of a few conserved proteins involved in cellular processes and metabolism.

    Science.gov (United States)

    Alam, Syed Imteyaz; Dixit, Aparna; Tomar, Arvind; Singh, Lokendra

    2010-04-01

    Clostridial organisms produce neurotoxins, which are generally regarded as the most potent toxic substances of biological origin and potential biological warfare agents. Clostridium tetani produces tetanus neurotoxin and is responsible for the fatal tetanus disease. In spite of the extensive immunization regimen, the disease is an important cause of death especially among neonates. Strains of C. tetani have not been genetically characterized except the complete genome sequencing of strain E88. The present study reports the genetic makeup and phylogenetic affiliations of an environmental strain of this bacterium with respect to C. tetani E88 and other clostridia. A shot gun library was constructed from the genomic DNA of C. tetani drde, isolated from decaying fish sample. Unique clones were sequenced and sequences compared with its closest relative C. tetani E88. A total of 275 clones were obtained and 32,457 bases of non-redundant sequence were generated. A total of 150 base changes were observed over the entire length of sequence obtained, including, additions, deletions and base substitutions. Of the total 120 ORFs detected, 48 exhibited closest similarity to E88 proteins of which three are hypothetical proteins. Eight of the ORFs exhibited similarity with hypothetical proteins from other organisms and 10 aligned with other proteins from unrelated organisms. There is an overall conservation of protein sequences among the two strains of C. tetani and. Selected ORFs involved in cellular processes and metabolism were subjected to phylogenetic analysis. Copyright 2009 Elsevier Ltd. All rights reserved.

  2. Managing stakeholder involvement in decision-making : A comparative analysis of six interactive processes in The Netherlands

    NARCIS (Netherlands)

    J. Edelenbos (Jurian); E-H. Klijn (Erik-Hans)

    2006-01-01

    textabstractInitiatives to encourage and stimulate the involvement of citizens but also various societal organisations in decision-making can be seen in a wide variety of European countries. Citizens panels, citizens charters, new forms of participation and other forms are being used to increase the

  3. High Stakes Testing Policy Issues in Education: An Analysis of Litigation Involving High Stakes Testing and the Denial of Diplomas

    Science.gov (United States)

    Winfield, Lisa M.

    2013-01-01

    This study analyzed the legal documents of cases involving the denial of a high school diploma as the result of not passing a high stakes exam in public education. The qualitative extrapolation of consistent themes in the court documents revealed information regarding the court's interpretation of the intersection of state authority to…

  4. Do Service Users with Intellectual Disabilities Want to Be Involved in the Risk Management Process? A Thematic Analysis

    Science.gov (United States)

    Kilcommons, Aoiffe M.; Withers, Paul; Moreno-Lopez, Agueda

    2012-01-01

    Background: Involving ID service users in risk decision making necessitates consideration of an individual's ability to assess the implications and associated risks and thus make an informed choice. This calls for research on service users' awareness and understanding of risk management (RM). Method: Thirteen people in a residential ID service who…

  5. Relationship of Power and Involvement to Working Alliance: A Multiple-Case Sequential Analysis of Brief Therapy.

    Science.gov (United States)

    Reandeau, Sharon Gardner; Wampold, Bruce E.

    1991-01-01

    Examined within-session interactional behavior in four brief-therapy cases, two characterized by high alliance and two by low alliance. Coded message units along dimensions of power and involvement. In all cases, there was general pattern of high power for therapists and low power for clients. High-alliance clients evidenced larger proportions of…

  6. CT-analysis of the course of gastrointestinal graft-versus-host disease-Patterns of involvement

    Energy Technology Data Exchange (ETDEWEB)

    Ketelsen, D., E-mail: dominik.ketelsen@med.uni-tuebingen.de [Department of Diagnostic and Interventional Radiology, Eberhard-Karls-University, Hoppe-Seyler-Str. 3, 72076 Tuebingen (Germany); Vogel, W.; Bethge, W.; Faul, C. [Department of Internal Medicine-Oncology, Eberhard-Karls-University, Ottfried-Mueller-Str. 5, 72070 Tuebingen (Germany); Claussen, C.D.; Horger, M. [Department of Diagnostic and Interventional Radiology, Eberhard-Karls-University, Hoppe-Seyler-Str. 3, 72076 Tuebingen (Germany)

    2011-07-15

    Objective: To describe the main patterns of distribution of gastrointestinal graft-versus-host disease (GVHD) and their chronological course. Methods: Twenty-five adult patients (17 men, 8 women, mean age 47 years) were enrolled from 11/2003 to 11/2007. All patients underwent abdominopelvic CT shortly after onset of GVHD-related symptoms and also at follow up. The mean number of CT examinations per patient was 3.2 {+-} 2.7 with a total of 81 in a median time period of 97 days after HCT. The gastrointestinal tract was divided into 7 segments. Gastrointestinal abnormalities were defined as follows: presence of wall thickening (>4 mm), increased mucosal enhancement, bowel dilatation (>3 cm for the small bowel, >8 cm for the colon), fluid-filled loops of the bowel, bowel loop separation and double-halo sign. Results: 40% (10/25) of the patients presented a classical pattern of evolution of involved segments by GI-GVHD. In these cases, especially the small bowel was initially involved showing a retreat with time towards the terminal ileum with longer length of stay in this location. 28% (7/25) of the patients presented with a nonclassical permanently migratory involvement of the GI jumping from one GI segment to another. Other 32% (8/25) of our patients revealed a nonclassical persistent, unchanged involvement pattern of GI involvement by GVHD at time. Conclusion: Contrary to existing reports, our data collected in 25 patients diagnosed with GI-GVHD after allogeneic hematopoietic stem cell transplantation suggest the presence of three different courses (classical, nonclassical migratory and nonclassical persistent) of this disorder. Awareness of this knowledge enables more accurate risk stratification.

  7. Analysis of the campground market in the Northeast, report III: a perspective on the camping-involvement cycle

    Science.gov (United States)

    Marvin W. Kottke; Malcolm I. Bevins; Gerald L. Cole; Kenneth J. Hock; Wilbur F. LaPage

    1975-01-01

    This is a report on a survey of 2,213 households and their potential for entering the camping market in 1973. One out of every two households was found to be in one of three stages of the camping-involvement cycle. Active campers included 21 percent of the sample, up by 2 percent since 1971; inactive campers, 20 percent, up by 6 percent; and potential campers, 9...

  8. Ambiguous involvement

    DEFF Research Database (Denmark)

    Dannesboe, Karen Ida

    2016-01-01

    This edited collection shows that good parenthood is neither fixed nor stable. The contributors show how parenthood is equally done by men, women and children, in and through practices involving different normative guidelines. The book explores how normative layers of parenthood are constituted...... by notions such as good childhood, family ideals, national public health and educational strategies. The authors illustrate how different versions of parenthood coexist and how complex sets of actions are demanded to fulfil today’s expectations of parenthood in Western societies. This interdisciplinary book...

  9. Adverse Events Involving Radiation Oncology Medical Devices: Comprehensive Analysis of US Food and Drug Administration Data, 1991 to 2015

    Energy Technology Data Exchange (ETDEWEB)

    Connor, Michael J. [Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California (United States); Department of Radiation Oncology, University of California Irvine School of Medicine, Irvine, California (United States); Marshall, Deborah C.; Moiseenko, Vitali; Moore, Kevin; Cervino, Laura; Atwood, Todd; Sanghvi, Parag; Mundt, Arno J.; Pawlicki, Todd [Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California (United States); Recht, Abram [Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts (United States); Hattangadi-Gluth, Jona A., E-mail: jhattangadi@ucsd.edu [Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California (United States)

    2017-01-01

    Purpose: Radiation oncology relies on rapidly evolving technology and highly complex processes. The US Food and Drug Administration collects reports of adverse events related to medical devices. We sought to characterize all events involving radiation oncology devices (RODs) from the US Food and Drug Administration's postmarket surveillance Manufacturer and User Facility Device Experience (MAUDE) database, comparing these with non–radiation oncology devices. Methods and Materials: MAUDE data on RODs from 1991 to 2015 were sorted into 4 product categories (external beam, brachytherapy, planning systems, and simulation systems) and 5 device problem categories (software, mechanical, electrical, user error, and dose delivery impact). Outcomes included whether the device was evaluated by the manufacturer, adverse event type, remedial action, problem code, device age, and time since 510(k) approval. Descriptive statistics were performed with linear regression of time-series data. Results for RODs were compared with those for other devices by the Pearson χ{sup 2} test for categorical data and 2-sample Kolmogorov-Smirnov test for distributions. Results: There were 4234 ROD and 4,985,698 other device adverse event reports. Adverse event reports increased over time, and events involving RODs peaked in 2011. Most ROD reports involved external beam therapy (50.8%), followed by brachytherapy (24.9%) and treatment planning systems (21.6%). The top problem types were software (30.4%), mechanical (20.9%), and user error (20.4%). RODs differed significantly from other devices in each outcome (P<.001). RODs were more likely to be evaluated by the manufacturer after an event (46.9% vs 33.0%) but less likely to be recalled (10.5% vs 37.9%) (P<.001). Device age and time since 510(k) approval were shorter among RODs (P<.001). Conclusions: Compared with other devices, RODs may experience adverse events sooner after manufacture and market approval. Close postmarket surveillance

  10. A Historical Analysis of the Quest for the Origins of Aging Macula Disorder, the Tissues Involved, and Its Terminology

    Science.gov (United States)

    de Jong, Paulus T.V.M.

    2016-01-01

    Although ocular tissues involved in aging macula disorder (AMD) were already known in 300 BC, the last type of photoreceptors was discovered only 10 years ago. The earliest descriptions of AMD appeared around 1850. It took over 150 years, till a clearer concept of AMD was formulated and even longer to grasp its pathophysiology. The uncertainty of researchers about the pathogenesis of AMD over the last century is reflected in its changing terminology. The evolution of this terminology is provided in a table to afford the reader a better insight into explanations proposed by researchers during this quest. PMID:27812291

  11. Comparative Transcriptome Analysis of Genes Involved in Anthocyanin Biosynthesis in Red and Green Walnut (Juglans regia L.

    Directory of Open Access Journals (Sweden)

    Yongzhou Li

    2017-12-01

    Full Text Available Fruit color is an important economic trait. The color of red walnut cultivars is mainly attributed to anthocyanins. The aim of this study was to explore the differences in the molecular mechanism of leaf and peel color change between red and green walnut. A reference transcriptome of walnut was sequenced and annotated to identify genes related to fruit color at the ripening stage. More than 290 million high-quality reads were assembled into 39,411 genes using a combined assembly strategy. Using Illumina digital gene expression profiling, we identified 4568 differentially expressed genes (DEGs between red and green walnut leaf and 3038 DEGs between red and green walnut peel at the ripening stage. We also identified some transcription factor families (MYB, bHLH, and WD40 involved in the control of anthocyanin biosynthesis. The trends in the expression levels of several genes encoding anthocyanin biosynthetic enzymes and transcription factors in the leaf and peel of red and green walnut were verified by quantitative real-time PCR. Together, our results identified the genes involved in anthocyanin accumulation in red walnut. These data provide a valuable resource for understanding the coloration of red walnut.

  12. Involvement of potential pathways in malignant transformation from Oral Leukoplakia to Oral Squamous Cell Carcinoma revealed by proteomic analysis

    Directory of Open Access Journals (Sweden)

    Li Jing

    2009-08-01

    Full Text Available Abstract Background Oral squamous cell carcinoma (OSCC is one of the most common forms of cancer associated with the presence of precancerous oral leukoplakia. Given the poor prognosis associated with oral leukoplakia, and the difficulties in distinguishing it from cancer lesions, there is an urgent need to elucidate the molecular determinants and critical signal pathways underlying the malignant transformation of precancerous to cancerous tissue, and thus to identify novel diagnostic and therapeutic target. Results We have utilized two dimensional electrophoresis (2-DE followed by ESI-Q-TOF-LC-MS/MS to identify proteins differentially expressed in six pairs of oral leukoplakia tissues with dysplasia and oral squamous cancer tissues, each pair was collected from a single patient. Approximately 85 differentially and constantly expressed proteins (> two-fold change, P Conclusion Varying levels of differentially expressed proteins were possibly involved in the malignant transformation of oral leukoplakia. Their expression levels, bioprocess, and interaction networks were analyzed using a bioinformatics approach. This study shows that the three homologs of PA28 may play an important role in malignant transformation and is an example of a systematic biology study, in which functional proteomics were constructed to help to elucidate mechanistic aspects and potential involvement of proteins. Our results provide new insights into the pathogenesis of oral cancer. These differentially expressed proteins may have utility as useful candidate markers of OSCC.

  13. Involvement of potential pathways in malignant transformation from Oral Leukoplakia to Oral Squamous Cell Carcinoma revealed by proteomic analysis

    Science.gov (United States)

    Wang, Zhi; Feng, Xiaodong; Liu, Xinyu; Jiang, Lu; Zeng, Xin; Ji, Ning; Li, Jing; Li, Longjiang; Chen, Qianming

    2009-01-01

    Background Oral squamous cell carcinoma (OSCC) is one of the most common forms of cancer associated with the presence of precancerous oral leukoplakia. Given the poor prognosis associated with oral leukoplakia, and the difficulties in distinguishing it from cancer lesions, there is an urgent need to elucidate the molecular determinants and critical signal pathways underlying the malignant transformation of precancerous to cancerous tissue, and thus to identify novel diagnostic and therapeutic target. Results We have utilized two dimensional electrophoresis (2-DE) followed by ESI-Q-TOF-LC-MS/MS to identify proteins differentially expressed in six pairs of oral leukoplakia tissues with dysplasia and oral squamous cancer tissues, each pair was collected from a single patient. Approximately 85 differentially and constantly expressed proteins (> two-fold change, P oral keratinocytes. Conclusion Varying levels of differentially expressed proteins were possibly involved in the malignant transformation of oral leukoplakia. Their expression levels, bioprocess, and interaction networks were analyzed using a bioinformatics approach. This study shows that the three homologs of PA28 may play an important role in malignant transformation and is an example of a systematic biology study, in which functional proteomics were constructed to help to elucidate mechanistic aspects and potential involvement of proteins. Our results provide new insights into the pathogenesis of oral cancer. These differentially expressed proteins may have utility as useful candidate markers of OSCC. PMID:19691830

  14. Proteomic analysis of ACTN4-interacting proteins reveals it's a putative involvement in mRNA metabolism

    International Nuclear Information System (INIS)

    Khotin, Mikhail; Turoverova, Lidia; Aksenova, Vasilisa; Barlev, Nikolai; Borutinskaite, Veronika Viktorija; Vener, Alexander; Bajenova, Olga; Magnusson, Karl-Eric; Pinaev, George P.; Tentler, Dmitri

    2010-01-01

    Alpha-actinin 4 (ACTN4) is an actin-binding protein. In the cytoplasm, ACTN4 participates in structural organisation of the cytoskeleton via cross-linking of actin filaments. Nuclear localisation of ACTN4 has also been reported, but no clear role in the nucleus has been established. In this report, we describe the identification of proteins associated with ACTN4 in the nucleus. A combination of two-dimensional gel electrophoresis (2D-GE) and MALDI-TOF mass-spectrometry revealed a large number of ACTN4-bound proteins that are involved in various aspects of mRNA processing and transport. The association of ACTN4 with different ribonucleoproteins suggests that a major function of nuclear ACTN4 may be regulation of mRNA metabolism and signaling.

  15. Replicating MISTERS: an epidemiological criminology framework analysis of a program for criminal justice-involved minority males in the community.

    Science.gov (United States)

    Potter, Roberto Hugh; Akers, Timothy A; Bowman, Daniel Richard

    2013-01-01

    The Men in STD Training and Empowerment Research Study (MISTERS) program and epidemiological criminology began their development in Atlanta at about the same time. MISTERS focuses on men recently released from jail to reduce both HIV/STD and crime-related risk factors through a brief educational intervention. This article examines ways in which MISTERS and epidemiological criminology have been used to inform one another in the replication of the MISTERS program in Orange County, Florida. Data from 110 MISTERS participants during the first 10 months of operation are analyzed to examine the overlapping occurrence of health and criminal risk behaviors in the men's lives. This provides a test of core hypotheses from the epidemiological criminology framework. This article also examines application of the epidemiological criminology framework to develop interventions to address health and crime risk factors simultaneously in Criminal Justice-Involved populations in the community.

  16. Involvement of multiple taste receptors in umami taste: analysis of gustatory nerve responses in metabotropic glutamate receptor 4 knockout mice.

    Science.gov (United States)

    Yasumatsu, Keiko; Manabe, Tomohiro; Yoshida, Ryusuke; Iwatsuki, Ken; Uneyama, Hisayuki; Takahashi, Ichiro; Ninomiya, Yuzo

    2015-02-15

    The taste receptor T1R1 + T1R3 heterodimer and metabotropic glutamate receptors (mGluR) may function as umami taste receptors. Here, we used mGluR4 knockout (mGluR4-KO) mice and examined the function of mGluR4 in peripheral taste responses of mice. The mGluR4-KO mice showed reduced responses to glutamate and L-AP4 (mGluR4 agonist) in the chorda tympani and glossopharyngeal nerves without affecting responses to other taste stimuli. Residual glutamate responses in mGluR4-KO mice were suppressed by gurmarin (T1R3 blocker) and AIDA (group I mGluR antagonist). The present study not only provided functional evidence for the involvement of mGluR4 in umami taste responses, but also suggested contributions of T1R1 + T1R3 and mGluR1 receptors in glutamate responses. Umami taste is elicited by L-glutamate and some other amino acids and is thought to be initiated by G-protein-coupled receptors. Proposed umami receptors include heterodimers of taste receptor type 1, members 1 and 3 (T1R1 + T1R3), and metabotropic glutamate receptors 1 and 4 (mGluR1 and mGluR4). Accumulated evidences support the involvement of T1R1 + T1R3 in umami responses in mice. However, little is known about the in vivo function of mGluR in umami taste. Here, we examined taste responses of the chorda tympani (CT) and the glossopharyngeal (GL) nerves in wild-type mice and mice genetically lacking mGluR4 (mGluR4-KO). Our results indicated that compared to wild-type mice, mGluR4-KO mice showed significantly smaller gustatory nerve responses to glutamate and L-(+)-2-amino-4-phosphonobutyrate (an agonist for group III mGluR) in both the CT and GL nerves without affecting responses to other taste stimuli. Residual glutamate responses in mGluR4-KO mice were not affected by (RS)-alpha-cyclopropyl-4-phosphonophenylglycine (an antagonist for group III mGluR), but were suppressed by gurmarin (a T1R3 blocker) in the CT and (RS)-1-aminoindan-1,5-dicarboxylic acid (an antagonist for group I mGluR) in the CT and GL nerve

  17. Identification of genes regulated by Wnt/β-catenin pathway and involved in apoptosis via microarray analysis

    Directory of Open Access Journals (Sweden)

    Chen Quan

    2006-09-01

    Full Text Available Abstract Background Wnt/β-catenin pathway has critical roles in development and oncogenesis. Although significant progress has been made in understanding the downstream signaling cascade of this pathway, little is known regarding Wnt/β-catenin pathway modification of the cellular apoptosis. Methods To identify potential genes regulated by Wnt/β-catenin pathway and involved in apoptosis, we used a stably integrated, inducible RNA interference (RNAi vector to specific inhibit the expression and the transcriptional activity of β-catenin in HeLa cells. Meanwhile, we designed an oligonucleotide microarray covering 1384 apoptosis-related genes. Using oligonucleotide microarrays, a series of differential expression of genes was identified and further confirmed by RT-PCR. Results Stably integrated inducible RNAi vector could effectively suppress β-catenin expression and the transcriptional activity of β-catenin/TCF. Meanwhile, depletion of β-catenin in this manner made the cells more sensitive to apoptosis. 130 genes involved in some important cell-apoptotic pathways, such as PTEN-PI3K-AKT pathway, NF-κB pathway and p53 pathway, showed significant alteration in their expression level after the knockdown of β-catenin. Conclusion Coupling RNAi knockdown with microarray and RT-PCR analyses proves to be a versatile strategy for identifying genes regulated by Wnt/β-catenin pathway and for a better understanding the role of this pathway in apoptosis. Some of the identified β-catenin/TCF directed or indirected target genes may represent excellent targets to limit tumor growth.

  18. Transcriptome analysis of the exocarp of apple fruit identifies light-induced genes involved in red color pigmentation.

    Science.gov (United States)

    Vimolmangkang, Sornkanok; Zheng, Danman; Han, Yuepeng; Khan, M Awais; Soria-Guerra, Ruth Elena; Korban, Schuyler S

    2014-01-15

    Although the mechanism of light regulation of color pigmentation of apple fruit is not fully understood, it has been shown that light can regulate expression of genes in the anthocyanin biosynthesis pathway by inducing transcription factors (TFs). Moreover, expression of genes encoding enzymes involved in this pathway may be coordinately regulated by multiple TFs. In this study, fruits on trees of apple cv. Red Delicious were covered with paper bags during early stages of fruit development and then removed prior to maturation to analyze the transcriptome in the exocarp of apple fruit. Comparisons of gene expression profiles of fruit covered with paper bags (dark-grown treatment) and those subjected to 14 h light treatment, following removal of paper bags, were investigated using an apple microarray of 40,000 sequences. Expression profiles were investigated over three time points, at one week intervals, during fruit development. Overall, 736 genes with expression values greater than two-fold were found to be modulated by light treatment. Light-induced products were classified into 19 categories with highest scores in primary metabolism (17%) and transcription (12%). Based on the Arabidopsis gene ontology annotation, 18 genes were identified as TFs. To further confirm expression patterns of flavonoid-related genes, these were subjected to quantitative RT-PCR (qRT-PCR) using fruit of red-skinned apple cv. Red Delicious and yellow-skinned apple cv. Golden Delicious. Of these, two genes showed higher levels of expression in 'Red Delicious' than in 'Golden Delicious', and were likely involved in the regulation of fruit red color pigmentation. © 2013 Elsevier B.V. All rights reserved.

  19. Anticipating forest and range land development in central Oregon (USA) for landscape analysis, with an example application involving mule deer

    Science.gov (United States)

    Jeffrey D. Kline; Alissa Moses; Theresa Burcsu

    2010-01-01

    Forest policymakers, public lands managers, and scientists in the Pacific Northwest (USA) seek ways to evaluate the landscape-level effects of policies and management through the multidisciplinary development and application of spatially explicit methods and models. The Interagency Mapping and Analysis Project (IMAP) is an ongoing effort to generate landscape-wide...

  20. An Age-Period-Cohort Analysis of Religious Involvement and Adult Self-Rated Health: Results from the USA, 1972-2008.

    Science.gov (United States)

    Zhang, Li

    2017-06-01

    This study conducts an age, period, cohort analysis of how religious involvement affects adult health across the life course and over time in the USA. Cross-classified random-effect models are used to examine data drawn from the General Social Survey, 1972-2008. The research shows clear life course patterns, time trends and birth cohort changes in the religious involvement and health relationship with period effects surpassing cohort effects. For the most part, the results show a loss of advantage in health with age for those who are more involved in religion. Period effects are mainly demonstrated by an overall downward trend of self-rated health (SRH) attributable to religious denominational differences and various levels of social integration. Unlike the period effects, the health disparities associated with religious denominational differences fluctuated when cohort progressed. These findings suggest that in general, the positive effect of religious involvement on SRH decreases with age and periods, but its influence on individual SRH fluctuates by cohort. It is expected that a downward trend in SRH attributable to religious involvement will carry on in future.

  1. Concepts involved in a proposed application of uncertainty analysis to the performance assessment of high-level nuclear waste isolation systems

    International Nuclear Information System (INIS)

    Maerker, R.E.

    1986-03-01

    This report introduces the concepts of a previously developed methodology which could readily be extended to the field of performance assessment for high-level nuclear waste isolation systems. The methodology incorporates sensitivities previously obtained with the GRESS code into an uncertainty analysis, from which propagated uncertainties in calculated responses may be derived from basic data uncertainties. Following a definition of terms, examples are provided illustrating commonly used conventions for describing the concepts of covariance and sensitivity. Examples of solutions to problems previously encountered in related fields involving uncertainty analysis and use of a generalized linear least-squares adjustment procedure are also presented. 5 refs., 14 tabs

  2. Meta-analysis identifies five novel loci associated with endometriosis highlighting key genes involved in hormone metabolism

    DEFF Research Database (Denmark)

    Sapkota, Yadav; Steinthorsdottir, Valgerdur; Morris, Andrew P

    2017-01-01

    Endometriosis is a heritable hormone-dependent gynecological disorder, associated with severe pelvic pain and reduced fertility; however, its molecular mechanisms remain largely unknown. Here we perform a meta-analysis of 11 genome-wide association case-control data sets, totalling 17,045 endomet......Endometriosis is a heritable hormone-dependent gynecological disorder, associated with severe pelvic pain and reduced fertility; however, its molecular mechanisms remain largely unknown. Here we perform a meta-analysis of 11 genome-wide association case-control data sets, totalling 17......,045 endometriosis cases and 191,596 controls. In addition to replicating previously reported loci, we identify five novel loci significantly associated with endometriosis risk (P... identified five secondary association signals, including two at the ESR1 locus, resulting in 19 independent single nucleotide polymorphisms (SNPs) robustly associated with endometriosis, which together explain up to 5.19% of variance in endometriosis. These results highlight novel variants in or near...

  3. Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses.

    Science.gov (United States)

    Luo, Jie; Xu, Pei; Cao, Peijian; Wan, Hongjian; Lv, Xiaonan; Xu, Shengchun; Wang, Gangjun; Cook, Melloni N; Jones, Byron C; Lu, Lu; Wang, Xusheng

    2018-01-01

    Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE) but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1), down-regulation in NOE but rescue in RSE (pattern 2), up-regulation in both restraint stress followed by a saline injection (RSS) and NOE, and further amplification in RSE (pattern 3), and up-regulation in RSS but reduction in both NOE and RSE (pattern 4). We further identified four functional subnetworks by superimposing protein-protein interactions (PPIs) to the 14 co-expression modules, including γ-aminobutyric acid receptor (GABA) signaling, glutamate signaling, neuropeptide signaling, cAMP-dependent signaling. We further performed module specificity analysis to identify modules that are specific to stress, alcohol, or stress-induced alcohol responses. Finally, we conducted causality analysis to link genetic variation to these identified modules, and anxiety behaviors after stress and alcohol treatments. This study underscores the importance of integrative analysis and offers new insights into the molecular networks underlying stress and alcohol responses.

  4. Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses

    Directory of Open Access Journals (Sweden)

    Jie Luo

    2018-04-01

    Full Text Available Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1, down-regulation in NOE but rescue in RSE (pattern 2, up-regulation in both restraint stress followed by a saline injection (RSS and NOE, and further amplification in RSE (pattern 3, and up-regulation in RSS but reduction in both NOE and RSE (pattern 4. We further identified four functional subnetworks by superimposing protein-protein interactions (PPIs to the 14 co-expression modules, including γ-aminobutyric acid receptor (GABA signaling, glutamate signaling, neuropeptide signaling, cAMP-dependent signaling. We further performed module specificity analysis to identify modules that are specific to stress, alcohol, or stress-induced alcohol responses. Finally, we conducted causality analysis to link genetic variation to these identified modules, and anxiety behaviors after stress and alcohol treatments. This study underscores the importance of integrative analysis and offers new insights into the molecular networks underlying stress and alcohol responses.

  5. Single cell analysis demonstrating somatic mosaicism involving 11p in a patient with paternal isodisomy and Beckwith-Wiedemann Syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Bischoff, F.Z.; McCaskill, C.; Subramanian, S. [Baylor College of Medicine, Houston, TX (United States)] [and others

    1994-09-01

    Beckwith-Wiedemann Syndrome (BWS) is characterized by numerous growth abnormalities including exomphalos, macroglossia, gigantism, and hemihypertrophy or hemihyperplasia. The {open_quotes}BWS gene{close_quotes} appears to be maternally repressed and is suspected to function as a growth factor or regulator of somatic growth, since activation of this gene through a variety of mechanisms appears to result in somatic overgrowth and tumor development. Mosaic paternal isodisomy of 11p has been observed previously by others in patients with BWS by Southern blot analysis of genomic DNA. The interpretation of these results was primarily based on the intensities of the hybridization signals for the different alleles. In our study, we demonstrate somatic mosaicism directly through PCR and single cell analysis. Peripheral blood was obtained from a patient with BWS and initial genomic DNA analysis by PCR was suggestive of somatic mosaicism for paternal isodisomy of 11p. Through micromanipulation, single cells were isolated and subjected to primer extention preamplification. Locus-specific microsatellite marker analyses by PCR were performed to determine the chromosome 11 origins in the preamplified individual cells. Two populations of cells were detected, a population of cells with normal biparental inheritance and a population of cells with paternal isodisomy of 11p and biparental disomy of 11q. Using the powerful approach of single cell analysis, the detected somatic mosaicism provides evidence for a mitotic recombinational event that has resulted in loss of the maternal 11p region and gain of a second copy of paternal 11p in some cells. The direct demonstration of mosaicism may explain the variable phenotypes and hemihypertrophy often observed in BWS.

  6. Amplitude histogram-based method of analysis of patch clamp recordings that involve extreme changes in channel activity levels.

    Science.gov (United States)

    Yakubovich, Daniel; Rishal, Ida; Dessauer, Carmen W; Dascal, Nathan

    2009-03-01

    Many ion channels show low basal activity, which is increased hundreds-fold by the relevant gating factor. A classical example is the activation G-protein-activated K(+) channels (GIRK) by Gbetagamma subunit dimer. The extent of activation (relative to basal current), R(a), is an important physiological parameter, usually readily estimated from whole cell recordings. However, calculation of R(a) often becomes non-trivial in multi-channel patches because of extreme changes in activity upon activation, from a seemingly single-channel pattern to a macroscopic one. In such cases, calculation of the net current flowing through the channels in the patch, I, before and after activation may require different methods of analysis. To address this problem, we utilized neuronal GIRK channels activated by purified Gbetagamma in excised patches of Xenopus oocytes. Channels were expressed at varying densities, from a few to several hundreds per patch. We present a simple and fast method of calculating I using amplitude histogram analysis and establish its accuracy by comparing with I calculated from event lists. This method allows the analysis of extreme changes in I in multichannel patches, which would be impossible using the standard methods of idealization and event list generation.

  7. Transcriptome analysis of ripe and unripe fruit tissue of banana identifies major metabolic networks involved in fruit ripening process.

    Science.gov (United States)

    Asif, Mehar Hasan; Lakhwani, Deepika; Pathak, Sumya; Gupta, Parul; Bag, Sumit K; Nath, Pravendra; Trivedi, Prabodh Kumar

    2014-12-02

    Banana is one of the most important crop plants grown in the tropics and sub-tropics. It is a climacteric fruit and undergoes ethylene dependent ripening. Once ripening is initiated, it proceeds at a fast rate making postharvest life short, which can result in heavy economic losses. During the fruit ripening process a number of physiological and biochemical changes take place and thousands of genes from various metabolic pathways are recruited to produce a ripe and edible fruit. To better understand the underlying mechanism of ripening, we undertook a study to evaluate global changes in the transcriptome of the fruit during the ripening process. We sequenced the transcriptomes of the unripe and ripe stages of banana (Musa accuminata; Dwarf Cavendish) fruit. The transcriptomes were sequenced using a 454 GSFLX-Titanium platform that resulted in more than 7,00,000 high quality (HQ) reads. The assembly of the reads resulted in 19,410 contigs and 92,823 singletons. A large number of the differentially expressed genes identified were linked to ripening dependent processes including ethylene biosynthesis, perception and signalling, cell wall degradation and production of aromatic volatiles. In the banana fruit transcriptomes, we found transcripts included in 120 pathways described in the KEGG database for rice. The members of the expansin and xyloglucan transglycosylase/hydrolase (XTH) gene families were highly up-regulated during ripening, which suggests that they might play important roles in the softening of the fruit. Several genes involved in the synthesis of aromatic volatiles and members of transcription factor families previously reported to be involved in ripening were also identified. A large number of differentially regulated genes were identified during banana fruit ripening. Many of these are associated with cell wall degradation and synthesis of aromatic volatiles. A large number of differentially expressed genes did not align with any of the databases and

  8. Program Director as Webmaster? Analysis of 131 Anesthesiology Department Web Sites and Program Director Web Site Involvement and Opinion Survey.

    Science.gov (United States)

    Daneshpayeh, Negin; Lee, Howard; Berger, Jeffrey

    2013-01-01

    The last formal review of academic anesthesiology department Web sites (ADWs) for content was conducted in 2009. ADWs have been rated as very important by medical students in researching residency training programs; however, the rapid evolution of sites require that descriptive statistics must be more current to be considered reliable. We set out to provide an updated overview of ADW content and to better understand residency program directors' (PD) role and comfort with ADWs. Two independent reviewers (ND and HL) analyzed all 131 Accreditation Council for Graduate Medical Education (ACGME) accredited ADWs. A binary system (Yes/No) was used to determine which features were present. Reviewer reliability was confirmed with inter-rater reliability and percentage agreement calculation. Additionally, a blinded electronic survey (Survey Monkey, Portland, OR) was sent to anesthesiology residency PDs via electronic mail investigating the audiences for ADWs, the frequency of updates and the degree of PD involvement. 13% of anesthesiology departments still lack a Web site with a homepage with links to the residency program and educational offerings (18% in 2009). Only half (55%) of Web sites contain information for medical students, including clerkship information. Furthermore, programs rarely contain up-to-date calendars (13%), accreditation cycle lengths (11%), accreditation dates (7%) or board pass rates (6%). The PD survey, completed by 42 of 131 PDs, noted a correlation (r = 0.36) between the number of years as PD and the frequency of Web site updates - less experienced PDs appear to update their sites more frequently (p = 0.03). Although 86% of PDs regarded a Web site as "very" important in recruitment, only 9% felt "very" comfortable with the skills required to advertise and market a Web site. Despite the overall increase in ADW content since 2009, privacy concerns, limited resources and time constraints may prevent PDs from providing the most up-to-date Web sites for

  9. Analysis of translocations that involve the NUP98 gene in patients with 11p15 chromosomal rearrangements.

    Science.gov (United States)

    Kobzev, Yuri N; Martinez-Climent, Jose; Lee, Sanggyu; Chen, Jianjun; Rowley, Janet D

    2004-12-01

    The NUP98 gene has been reported to be fused with at least 15 partner genes in leukemias with 11p15 translocations. We report the results of screening of cases with cytogenetically documented rearrangements of 11p15 and the subsequent identification of involvement of NUP98 and its partner genes. We identified 49 samples from 46 hematology patients with 11p15 (including a few with 11p14) abnormalities, and using fluorescence in situ hybridization (FISH), we found that NUP98 was disrupted in 7 cases. With the use of gene-specific FISH probes, in 6 cases, we identified the partner genes, which were PRRX1 (PMX1; in 2 cases), HOXD13, RAP1GDS1, HOXC13, and TOP1. In the 3 cases for which RNA was available, RT-PCR was performed, which confirmed the FISH results and identified the location of the breakpoints in patient cDNA. Our data confirm the previous findings that NUP98 is a recurrent target in various types of leukemia. Copyright 2004 Wiley-Liss, Inc.

  10. [Screening and analysis of coding SNPs of HLA-DQA1 gene involved in susceptibility for cervical cancer].

    Science.gov (United States)

    Li, Yan-Yun; Xing, Jun; Zhao, Lin-Sheng; Li, Yan-Ni; Wang, Yu-Chuan; Zhang, Wei-Ming

    2006-07-01

    Polymorphisms of human leukocyte antigen (HLA) gene play an important role in the development of cervical cancer. This study was to screen single nucleotide polymorphisms (SNPs) of HLA-DQA1 gene involved in susceptibility of cervical cancer by a bioinformatics approach, and analyze their correlations to abnormal gene functions. SNPs of HLA-DQA1 were screened from a public database dbSNP by SNPper software, and relevant FASTA subsequences were also obtained from dbSNP. PARSESNP software was used to analyze cSNPs. Two SNPs, rs9272693 and rs9272703, which may induce mis-sense mutation, were identified in codon region of HLA-DQA1 gene. A PSSM difference>10 was used to predict deleterious mutation. SNPper software in combination with PARSESNP software could be used to analyze SNPs of HLA-DQA1 gene and select the variants in a conserved region, and it provides an evaluation criterion. But the results need to be verified in cervical cancer patients and control populations.

  11. Troubled families and individualised solutions: an institutional discourse analysis of alcohol and drug treatment practices involving affected others.

    Science.gov (United States)

    Selbekk, Anne Schanche; Sagvaag, Hildegunn

    2016-09-01

    Research shows that members of the families with patients suffering from alcohol and other drug-related issues (AOD) experience stress and strain. An important question is, what options do AOD treatment have for them when it comes to support? To answer this, we interviewed directors and clinicians from three AOD treatment institutions in Norway. The study revealed that family-oriented practices are gaining ground as a 'going concern'. However, the relative position of family-orientation in the services, is constrained and shaped by three other going concerns related to: (i) discourse on health and illness, emphasising that addiction is an individual medical and psychological phenomenon, rather than a relational one; (ii) discourse on rights and involvement, emphasising the autonomy of the individual patient and their right to define the format of their own treatment; and (iii) discourse on management, emphasising the relationship between cost and benefit, where family-oriented practices are defined as not being cost-effective. All three discourses are connected to underpin the weight placed on individualised practices. Thus, the findings point to a paradox: there is a growing focus on the needs of children and affected family members, while the possibility of performing integrated work on families is limited. © 2016 Foundation for the Sociology of Health & Illness.

  12. Hallucinations in schizophrenia and Parkinson’s disease: an analysis of sensory modalities involved and the repercussion on patients

    Science.gov (United States)

    Llorca, P. M.; Pereira, B.; Jardri, R.; Chereau-Boudet, I.; Brousse, G.; Misdrahi, D.; Fénelon, G.; Tronche, A.-M.; Schwan, R.; Lançon, C.; Marques, A.; Ulla, M.; Derost, P.; Debilly, B.; Durif, F.; de Chazeron, I.

    2016-01-01

    Hallucinations have been described in various clinical populations, but they are neither disorder nor disease specific. In schizophrenia patients, hallucinations are hallmark symptoms and auditory ones are described as the more frequent. In Parkinson’s disease, the descriptions of hallucination modalities are sparse, but the hallucinations do tend to have less negative consequences. Our study aims to explore the phenomenology of hallucinations in both hallucinating schizophrenia patients and Parkinson’s disease patients using the Psycho-Sensory hAllucinations Scale (PSAS). The main objective is to describe the phenomena of these clinical symptoms in those two specific populations. Each hallucinatory sensory modality significantly differed between Parkinson’s disease and schizophrenia patients. Auditory, olfactory/gustatory and cœnesthetic hallucinations were more frequent in schizophrenia than visual hallucinations. The guardian angel item, usually not explored in schizophrenia, was described by 46% of these patients. The combination of auditory and visual hallucinations was the most frequent for both Parkinson’s disease and schizophrenia. The repercussion index summing characteristics of each hallucination (frequency, duration, negative aspects, conviction, impact, control and sound intensity) was always higher for schizophrenia. A broader view including widespread characteristics and interdisciplinary works must be encouraged to better understand the complexity of the process involved in hallucinations. PMID:27905557

  13. Time-course microarray analysis for identifying candidate genes involved in obesity-associated pathological changes in the mouse colon.

    Science.gov (United States)

    Bae, Yun Jung; Kim, Sung-Eun; Hong, Seong Yeon; Park, Taesun; Lee, Sang Gyu; Choi, Myung-Sook; Sung, Mi-Kyung

    2016-01-01

    Obesity is known to increase the risk of colorectal cancer. However, mechanisms underlying the pathogenesis of obesity-induced colorectal cancer are not completely understood. The purposes of this study were to identify differentially expressed genes in the colon of mice with diet-induced obesity and to select candidate genes as early markers of obesity-associated abnormal cell growth in the colon. C57BL/6N mice were fed normal diet (11% fat energy) or high-fat diet (40% fat energy) and were euthanized at different time points. Genome-wide expression profiles of the colon were determined at 2, 4, 8, and 12 weeks. Cluster analysis was performed using expression data of genes showing log 2 fold change of ≥1 or ≤-1 (twofold change), based on time-dependent expression patterns, followed by virtual network analysis. High-fat diet-fed mice showed significant increase in body weight and total visceral fat weight over 12 weeks. Time-course microarray analysis showed that 50, 47, 36, and 411 genes were differentially expressed at 2, 4, 8, and 12 weeks, respectively. Ten cluster profiles representing distinguishable patterns of genes differentially expressed over time were determined. Cluster 4, which consisted of genes showing the most significant alterations in expression in response to high-fat diet over 12 weeks, included Apoa4 (apolipoprotein A-IV), Ppap2b (phosphatidic acid phosphatase type 2B), Cel (carboxyl ester lipase), and Clps (colipase, pancreatic), which interacted strongly with surrounding genes associated with colorectal cancer or obesity. Our data indicate that Apoa4 , Ppap2b , Cel , and Clps are candidate early marker genes associated with obesity-related pathological changes in the colon. Genome-wide analyses performed in the present study provide new insights on selecting novel genes that may be associated with the development of diseases of the colon.

  14. Assisted reproduction involving gestational surrogacy: an analysis of the medical, psychosocial and legal issues: experience from a large surrogacy program.

    Science.gov (United States)

    Dar, Shir; Lazer, Tal; Swanson, Sonja; Silverman, Jan; Wasser, Cindy; Moskovtsev, Sergey I; Sojecki, Agata; Librach, Clifford L

    2015-02-01

    What are the medical, psychosocial and legal aspects of gestational surrogacy (GS), including pregnancy outcomes and complications, in a large series? Meticulous multidisciplinary teamwork, involving medical, legal and psychosocial input for both the intended parent(s) (IP) and the gestational carrier (GC), is critical to achieve a successful GS program. Small case series have described pregnancy rates of 17-50% for GS. There are no large case series and the medical, legal and psychological aspects of GS have not been addressed in most of these studies. To our knowledge, this is the largest reported GS case series. A retrospective cohort study was performed. Data were collected from 333 consecutive GC cycles between 1998 and 2012. There were 178 pregnancies achieved out of 333 stimulation cycles, including fresh and frozen transfers. The indications for a GC were divided into two groups. Those who have 'failed to carry', included women with recurrent implantation failure (RIF), recurrent pregnancy loss (RPL) and previous poor pregnancy outcome (n = 96; 132 cycles, pregnancy rate 50.0%). The second group consisted of those who 'cannot carry' including those with severe Asherman's syndrome, uterine malformations/uterine agenesis and maternal medical diseases (n = 108, 139 cycles, pregnancy rate 54.0%). A third group, of same-sex male couples and single men, were analyzed separately (n = 52, 62 cycles, pregnancy rate 59.7%). In 49.2% of cycles, autologous oocytes were used and 50.8% of cycles involved donor oocytes. The 'failed to carry' group consisted of 96 patients who underwent 132 cycles at a mean age of 40.3 years. There were 66 pregnancies (50.0%) with 17 miscarriages (25.8%) and 46 confirmed births (34.8%). The 'cannot carry pregnancy' group consisted of 108 patients who underwent 139 cycles at a mean age of 35.9 years. There were 75 pregnancies (54.0%) with 15 miscarriages (20.0%) and 56 confirmed births (40.3%). The pregnancy, miscarriage and live birth

  15. Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids

    Directory of Open Access Journals (Sweden)

    Kok-Keong Loke

    2017-02-01

    Full Text Available Background Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have been extensively studied due to its culinary and medicinal properties. There are only a few transcriptome sequences available for species from this important family of medicinal plants. The limited genetic information from the public expressed sequences tag (EST library hinders further study on molecular mechanisms underlying secondary metabolite production. Methods In this study, we performed a hybrid assembly of 454 and Illumina sequencing reads from Polygonum minus root and leaf tissues, respectively, to generate a combined transcriptome library as a reference. Results A total of 34.37 million filtered and normalized reads were assembled into 188,735 transcripts with a total length of 136.67 Mbp. We performed a similarity search against all the publicly available genome sequences and found similarity matches for 163,200 (86.5% of Polygonum minus transcripts, largely from Arabidopsis thaliana (58.9%. Transcript abundance in the leaf and root tissues were estimated and validated through RT-qPCR of seven selected transcripts involved in the biosynthesis of phenylpropanoids and flavonoids. All the transcripts were annotated against KEGG pathways to profile transcripts related to the biosynthesis of secondary metabolites. Discussion This comprehensive transcriptome profile will serve as a useful sequence resource for molecular genetics and evolutionary research on secondary metabolite biosynthesis in Polygonaceae family. Transcriptome assembly of Polygonum minus can be accessed at http://prims.researchfrontier.org/index.php/dataset/transcriptome.

  16. Comparative proteomic analysis of alfalfa revealed new salt and drought stress-related factors involved in seed germination.

    Science.gov (United States)

    Ma, Qiaoli; Kang, Junmei; Long, Ruicai; Zhang, Tiejun; Xiong, Junbo; Zhang, Kun; Wang, Tenghua; Yang, Qingchuan; Sun, Yan

    2017-07-01

    Salinity and drought are two major environmental factors that limit the growth and yield of many forage crops in semi-arid and arid regions. Alfalfa (Medicago sativa L.) is one of the most important forage crops in many countries. We aim to investigate the molecular mechanisms of alfalfa in response to salt and drought stresses in this study. Physiological and proteomic analyses were applied to examine the Zhongmu NO.3 alfalfa seed germination stage with 200 mM NaCl and 180 g·L -1 polyethylene glycol (PEG) treatments. The germination ability of the seed and the accumulation of osmotic solutes were quite different between the NaCl and PEG treatments. More than 800 protein spots were detected by proteomics technology on two-dimensional electrophoresis (2-DE) gels. The abundance of twenty-eight proteins were decreased or increased after salt and drought stress. Seventeen of these proteins were identified and classified into six functional categories through mass spectrometry (MS). The six groups involved in salt- and PEG-mediated stress included defense response, energy metabolism, protein synthesis and degradation, oxidative stress, carbohydrate metabolism-associated proteins, and unknown proteins. We discovered that some proteins related to carbohydrate metabolism and energy production increased in abundance under salt- and PEG-mediated drought stress. This demonstrates a common mechanism of energy consumption during abiotic stresses. Further study of these proteins with unknown function will provide insights into the molecular mechanisms of abiotic stress and the discovery of new candidate markers.

  17. Modeling economic costs of disasters and recovery involving positive effects of reconstruction: analysis using a dynamic CGE model

    Science.gov (United States)

    Xie, W.; Li, N.; Wu, J.-D.; Hao, X.-L.

    2013-11-01

    Disaster damages have negative effects on economy, whereas reconstruction investments have positive effects. The aim of this study is to model economic causes of disasters and recovery involving positive effects of reconstruction activities. Computable general equilibrium (CGE) model is a promising approach because it can incorporate these two kinds of shocks into a unified framework and further avoid double-counting problem. In order to factor both shocks in CGE model, direct loss is set as the amount of capital stock reduced on supply side of economy; A portion of investments restore the capital stock in existing period; An investment-driven dynamic model is formulated due to available reconstruction data, and the rest of a given country's saving is set as an endogenous variable. The 2008 Wenchuan Earthquake is selected as a case study to illustrate the model, and three scenarios are constructed: S0 (no disaster occurs), S1 (disaster occurs with reconstruction investment) and S2 (disaster occurs without reconstruction investment). S0 is taken as business as usual, and the differences between S1 and S0 and that between S2 and S0 can be interpreted as economic losses including reconstruction and excluding reconstruction respectively. The study showed that output from S1 is found to be closer to real data than that from S2. S2 overestimates economic loss by roughly two times that under S1. The gap in economic aggregate between S1 and S0 is reduced to 3% in 2011, a level that should take another four years to achieve under S2.

  18. Proteomic analysis reveals that proteasome subunit beta 6 is involved in hypoxia-induced pulmonary vascular remodeling in rats.

    Directory of Open Access Journals (Sweden)

    Jian Wang

    Full Text Available Chronic hypoxia (CH is known to be one of the major causes of pulmonary hypertension (PH, which is characterized by sustained elevation of pulmonary vascular resistance resulting from vascular remodeling. In this study, we investigated whether the ubiquitin proteasome system (UPS was involved in the mechanism of hypoxia-induced pulmonary vascular remodeling. We isolated the distal pulmonary artery (PA from a previously defined chronic hypoxic pulmonary hypertension (CHPH rat model, performed proteomic analyses in search of differentially expressed proteins belonging to the UPS, and subsequently identified their roles in arterial remodeling.Twenty-two proteins were differently expressed between the CH and normoxic group. Among them, the expression of proteasome subunit beta (PSMB 1 and PSMB6 increased after CH exposure. Given that PSMB1 is a well-known structural subunit and PSMB6 is a functional subunit, we sought to assess whether PSMB6 could be related to the multiple functional changes during the CHPH process. We confirmed the proteomic results by real-time PCR and Western blot. With the increase in quantity of the active subunit, proteasome activity in both cultured pulmonary artery smooth muscle cells (PASMCs and isolated PA from the hypoxic group increased. An MTT assay revealed that the proteasome inhibitor MG132 was able to attenuate the hypoxia-induced proliferation of PASMC in a dose-dependent manner. Knockdown of PSMB6 using siRNA also prevented hypoxia-induced proliferation.The present study revealed the association between increased PSMB6 and CHPH. CH up-regulated proteasome activity and the proliferation of PASMCs, which may have been related to increased PSMB6 expression and the subsequently enhanced functional catalytic sites of the proteasome. These results suggested an essential role of the proteasome during CHPH development, a novel finding requiring further study.

  19. Structural and functional analysis of validoxylamine A 7'-phosphate synthase ValL involved in validamycin A biosynthesis.

    Directory of Open Access Journals (Sweden)

    Lina Zheng

    Full Text Available Validamycin A (Val-A is an effective antifungal agent widely used in Asian countries as crop protectant. Validoxylamine A, the core structure and intermediate of Val-A, consists of two C(7-cyclitol units connected by a rare C-N bond. In the Val-A biosynthetic gene cluster in Streptomyces hygroscopicus 5008, the ORF valL was initially annotated as a validoxylamine A 7'-phosphate(V7P synthase, whose encoded 497-aa protein shows high similarity with trehalose 6-phosphate(T6P synthase. Gene inactivation of valL abolished both validoxylamine A and validamycin A productivity, and complementation with a cloned valL recovered 10% production of the wild-type in the mutant, indicating the involvement of ValL in validoxylamine A biosynthesis. Also we determined the structures of ValL and ValL/trehalose complex. The structural data indicates that ValL adopts the typical fold of GT-B protein family, featuring two Rossmann-fold domains and an active site at domain junction. The residues in the active site are arranged in a manner homologous to that of Escherichia coli (E.coli T6P synthase OtsA. However, a significant discrepancy is found in the active-site loop region. Also noticeable structural variance is found around the active site entrance in the apo ValL structure while the region takes an ordered configuration upon binding of product analog trehalose. Furthermore, the modeling of V7P in the active site of ValL suggests that ValL might have a similar SNi-like mechanism as OtsA.

  20. Structure-function analysis of STRUBBELIG, an Arabidopsis atypical receptor-like kinase involved in tissue morphogenesis.

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    Prasad Vaddepalli

    Full Text Available Tissue morphogenesis in plants requires the coordination of cellular behavior across clonally distinct histogenic layers. The underlying signaling mechanisms are presently being unraveled and are known to include the cell surface leucine-rich repeat receptor-like kinase STRUBBELIG in Arabidopsis. To understand better its mode of action an extensive structure-function analysis of STRUBBELIG was performed. The phenotypes of 20 EMS and T-DNA-induced strubbelig alleles were assessed and homology modeling was applied to rationalize their possible effects on STRUBBELIG protein structure. The analysis was complemented by phenotypic, cell biological, and pharmacological investigations of a strubbelig null allele carrying genomic rescue constructs encoding fusions between various mutated STRUBBELIG proteins and GFP. The results indicate that STRUBBELIG accepts quite some sequence variation, reveal the biological importance for the STRUBBELIG N-capping domain, and reinforce the notion that kinase activity is not essential for its function in vivo. Furthermore, individual protein domains of STRUBBELIG cannot be related to specific STRUBBELIG-dependent biological processes suggesting that process specificity is mediated by factors acting together with or downstream of STRUBBELIG. In addition, the evidence indicates that biogenesis of a functional STRUBBELIG receptor is subject to endoplasmic reticulum-mediated quality control, and that an MG132-sensitive process regulates its stability. Finally, STRUBBELIG and the receptor-like kinase gene ERECTA interact synergistically in the control of internode length. The data provide genetic and molecular insight into how STRUBBELIG regulates intercellular communication in tissue morphogenesis.

  1. Identification and function analysis of ras-related nuclear protein from Macrobrachium rosenbergii involved in Spiroplasma eriocheiris infection.

    Science.gov (United States)

    Ning, Mingxiao; Xiu, Yunji; Yuan, Meijun; Bi, Jingxiu; Liu, Min; Wei, Panpan; Yan, Yuye; Gu, Wei; Wang, Wen; Meng, Qingguo

    2017-11-01

    A ras-related nuclear protein (Ran) protein was obtained from Macrobrachium rosenbergii, named MrRan. Phylogenetic analysis results showed that MrRan was clustered in one group together with other crustaceans. Tissue distribution analysis revealed that MrRan was expressed mainly in gill, intestine and stomach, and expressed weakly in muscle. The MrRan expression levels in gill and hemocyte of prawns were significantly up-regulated after challenged by Spiroplasma eriocheiris. The copy number of S. eriocheiris in MrRan dsRNA injection group was significantly less than control groups during infection. Meanwhile, silencing MrRan obviously increased the survival rate of prawns. The subcellular localization experiment suggested that recombinant MrRan was mainly located in the nucleus, and relatively weak in the cytoplasm. Finally, over-expression in Drosophila S2 cell indicated that MrRan could increase copies of S. eriocheiris and decrease of cell viability. The present study suggested that MrRan participated in regulating the phagocytosis of S. eriocheiris in M. rosenbergii. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Comparative Genomic Analysis of Transgenic Poplar Dwarf Mutant Reveals Numerous Differentially Expressed Genes Involved in Energy Flow

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    Su Chen

    2014-09-01

    Full Text Available In our previous research, the Tamarix androssowii LEA gene (Tamarix androssowii late embryogenesis abundant protein Mrna, GenBank ID: DQ663481 was transferred into Populus simonii × Populus nigra. Among the eleven transgenic lines, one exhibited a dwarf phenotype compared to the wild type and other transgenic lines, named dwf1. To uncover the mechanisms underlying this phenotype, digital gene expression libraries were produced from dwf1, wild-type, and other normal transgenic lines, XL-5 and XL-6. Gene expression profile analysis indicated that dwf1 had a unique gene expression pattern in comparison to the other two transgenic lines. Finally, a total of 1246 dwf1-unique differentially expressed genes were identified. These genes were further subjected to gene ontology and pathway analysis. Results indicated that photosynthesis and carbohydrate metabolism related genes were significantly affected. In addition, many transcription factors genes were also differentially expressed in dwf1. These various differentially expressed genes may be critical for dwarf mutant formation; thus, the findings presented here might provide insight for our understanding of the mechanisms of tree growth and development.

  3. Gene-based meta-analysis of genome-wide association studies implicates new loci involved in obesity

    DEFF Research Database (Denmark)

    Hägg, Sara; Ganna, Andrea; Van Der Laan, Sander W

    2015-01-01

    To date, genome-wide association studies (GWASs) have identified >100 loci with single variants associated with body mass index (BMI). This approach may miss loci with high allelic heterogeneity; therefore, the aim of the present study was to use gene-based meta-analysis to identify regions...... of ANthropometric Traits (GIANT) consortium. Each cohort was tested for association between ∼2.4 million (Stage 1) or ∼200 000 (Stage 2) imputed or genotyped single variants and BMI, and summary statistics were subsequently meta-analyzed in 17 941 genes. We used the ‘VErsatile Gene-based Association Study’ (VEGAS......) approach to assign variants to genes and to calculate gene-based P-values based on simulations. The VEGAS method was applied to each cohort separately before a gene-based meta-analysis was performed. In Stage 1, two known (FTO and TMEM18) and six novel (PEX2, MTFR2, SSFA2, IARS2, CEP295 and TXNDC12) loci...

  4. Transcriptome analysis of genes involved in anthocyanins biosynthesis and transport in berries of black and white spine grapes (Vitis davidii).

    Science.gov (United States)

    Sun, Lei; Fan, Xiucai; Zhang, Ying; Jiang, Jianfu; Sun, Haisheng; Liu, Chonghuai

    2016-01-01

    The color of berry skin is an important economic trait for grape and is essentially determined by the components and content of anthocyanins. The fruit color of Chinese wild grapes is generally black, and the profile of anthocyanins in Chinese wild grapes is significantly different from that of Vitis vinifera . However, V. davidii is the only species that possesses white berry varieties among Chinese wild grape species. Thus, we performed a transcriptomic analysis to compare the difference of transcriptional level in black and white V. davidii , in order to find some key genes that are related to anthocyanins accumulation in V. davidii . The results of anthocyanins detection revealed that 3,5- O -diglucoside anthocyanins is the predominant anthocyanins in V. davidii . It showed obvious differences from V. vinifera in the profile of the composition of anthocyanins. The transcriptome sequencing by Illumina mRNA-Seq technology generated an average of 57 million 100-base pair clean reads from each sample. Differential gene expression analysis revealed thousands of differential expression genes (DEGs) in the pairwise comparison of different fruit developmental stages between and within black and white V. davidii . After the analysis of functional category enrichment and differential expression patterns of DEGs, 46 genes were selected as the candidate genes. Some genes have been reported as being related to anthocyanins accumulation, and some genes were newly found in our study as probably being related to anthocyanins accumulation. We inferred that 3AT (VIT_03s0017g00870) played an important role in anthocyanin acylation, GST4 (VIT_04s0079g00690) and AM2 (VIT_16s0050g00910) played important roles in anthocyanins transport in V. davidii . The expression of some selected DEGs was further confirmed by quantitative real-time PCR (qRT-PCR). The present study investigated the transcriptomic profiles of berry skin from black and white spine grapes at three fruit developmental

  5. Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cysIXHDNYZ gene cluster involved in assimilatory sulphate reduction

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    Albersmeier Andreas

    2005-09-01

    Full Text Available Abstract Background Corynebacterium glutamicum is a high-GC Gram-positive soil bacterium of great biotechnological importance for the production of amino acids. To facilitate the rational design of sulphur amino acid-producing strains, the pathway for assimilatory sulphate reduction providing the necessary reduced sulfur moieties has to be known. Although this pathway has been well studied in Gram-negative bacteria like Escherichia coli and low-GC Gram-positives like Bacillus subtilis, little is known for the Actinomycetales and other high-GC Gram-positive bacteria. Results The genome sequence of C. glutamicum was searched for genes involved in the assimilatory reduction of inorganic sulphur compounds. A cluster of eight candidate genes could be identified by combining sequence similarity searches with a subsequent synteny analysis between C. glutamicum and the closely related C. efficiens. Using mutational analysis, seven of the eight candidate genes, namely cysZ, cysY, cysN, cysD, cysH, cysX, and cysI, were demonstrated to be involved in the reduction of inorganic sulphur compounds. For three of the up to now unknown genes possible functions could be proposed: CysZ is likely to be the sulphate permease, while CysX and CysY are possibly involved in electron transfer and cofactor biosynthesis, respectively. Finally, the candidate gene designated fpr2 influences sulphur utilisation only weakly and might be involved in electron transport for the reduction of sulphite. Real-time RT-PCR experiments revealed that cysIXHDNYZ form an operon and that transcription of the extended cluster fpr2 cysIXHDNYZ is strongly influenced by the availability of inorganic sulphur, as well as L-cysteine. Mapping of the fpr2 and cysIXHDNYZ promoters using RACE-PCR indicated that both promoters overlap with binding-sites of the transcriptional repressor McbR, suggesting an involvement of McbR in the observed regulation. Comparative genomics revealed that large parts of

  6. A three-scale analysis of bacterial communities involved in rocks colonization and soil formation in high mountain environments.

    Science.gov (United States)

    Esposito, Alfonso; Ciccazzo, Sonia; Borruso, Luigimaria; Zerbe, Stefan; Daffonchio, Daniele; Brusetti, Lorenzo

    2013-10-01

    Alpha and beta diversities of the bacterial communities growing on rock surfaces, proto-soils, riparian sediments, lichen thalli, and water springs biofilms in a glacier foreland were studied. We used three molecular based techniques to allow a deeper investigation at different taxonomic resolutions: denaturing gradient gel electrophoresis, length heterogeneity-PCR, and automated ribosomal intergenic spacer analysis. Bacterial communities were mainly composed of Acidobacteria, Proteobacteria, and Cyanobacteria with distinct variations among sites. Proteobacteria were more represented in sediments, biofilms, and lichens; Acidobacteria were mostly found in proto-soils; and Cyanobacteria on rocks. Firmicutes and Bacteroidetes were mainly found in biofilms. UniFrac P values confirmed a significant difference among different matrices. Significant differences (P rocks which shared a more similar community structure, while at deep taxonomic resolution two distinct bacterial communities between lichens and rocks were found.

  7. Separation of Berberine Hydrochloride and Tetrahydropalmatine and Their Quantitative Analysis with Thin Layer Chromatography Involved with Ionic Liquids

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    Jing Lu

    2015-01-01

    Full Text Available [BMIM]OH was used in mobile and stationary phase of thin layer chromatography (TLC to analyze berberine hydrochloride and tetrahydropalmatine for the first time. Supported imidazole ionic liquid with hydroxide ion on silica gel (SiO2·Im+·OH− was synthesized through simple procedure and characterized by Fourier transform infrared spectroscopy (FT-IR, elemental analysis, and scanning electron microscope (SEM. Moreover, on the plates prepared by SiO2·Im+·OH−, the contents of the above alkaloids in the Chinese patent medicine (CPM of “Stomacheasy” capsule were successfully determined by TLC scanner. The key conditions and chromatographic behaviors were also investigated in detail. According to similar ways, ionic liquids (ILs also can be used in other planar chromatographies in two modes. This study is expected to be helpful in expanding the application of IL and its bonded silica gel in TLC separation field.

  8. Separation of Berberine Hydrochloride and Tetrahydropalmatine and Their Quantitative Analysis with Thin Layer Chromatography Involved with Ionic Liquids

    Science.gov (United States)

    Lu, Jing; Ma, Hong-yan; Zhang, Wei; Ma, Zhi-guo; Yao, Shun

    2015-01-01

    [BMIM]OH was used in mobile and stationary phase of thin layer chromatography (TLC) to analyze berberine hydrochloride and tetrahydropalmatine for the first time. Supported imidazole ionic liquid with hydroxide ion on silica gel (SiO2·Im+·OH−) was synthesized through simple procedure and characterized by Fourier transform infrared spectroscopy (FT-IR), elemental analysis, and scanning electron microscope (SEM). Moreover, on the plates prepared by SiO2·Im+·OH−, the contents of the above alkaloids in the Chinese patent medicine (CPM) of “Stomacheasy” capsule were successfully determined by TLC scanner. The key conditions and chromatographic behaviors were also investigated in detail. According to similar ways, ionic liquids (ILs) also can be used in other planar chromatographies in two modes. This study is expected to be helpful in expanding the application of IL and its bonded silica gel in TLC separation field. PMID:26609463

  9. Mutational analysis of amino acid residues involved in catalytic activity of a family 18 chitinase from tulip bulbs.

    Science.gov (United States)

    Suzukawa, Keisuke; Yamagami, Takeshi; Ohnuma, Takayuki; Hirakawa, Hideki; Kuhara, Satoru; Aso, Yoichi; Ishiguro, Masatsune

    2003-02-01

    We expressed chitinase-1 (TBC-1) from tulip bulbs (Tulipa bakeri) in E. coli cells and used site-directed mutagenesis to identify amino acid residues essential for catalytic activity. Mutations at Glu-125 and Trp-251 completely abolished enzyme activity, and activity decreased with mutations at Asp-123 and Trp-172 when glycolchitin was the substrate. Activity changed with the mutations of Trp-251 to one of several amino acids with side-chains of little hydrophobicity, suggesting that hydrophobic interaction of Trp-251 is important for the activity. Molecular dynamics (MD) simulation analysis with hevamine as the model compound showed that the distance between Asp-123 and Glu-125 was extended by mutation of Trp-251. Kinetic studies of Trp-251-mutated chitinases confirmed these various phenomena. The results suggested that Glu-125 and Trp-251 are essential for enzyme activity and that Trp-251 had a direct role in ligand binding.

  10. De Novo Transcriptome Analysis of Warburgia ugandensis to Identify Genes Involved in Terpenoids and Unsaturated Fatty Acids Biosynthesis.

    Science.gov (United States)

    Wang, Xin; Zhou, Chen; Yang, Xianpeng; Miao, Di; Zhang, Yansheng

    2015-01-01

    The bark of Warburgia ugandensis (Canellaceae family) has been used as a medicinal source for a long history in many African countries. The presence of diverse terpenoids and abundant polyunsaturated fatty acids (PUFAs) in this organ contributes to its broad range of pharmacological properties. Despite its medicinal and economic importance, the knowledge on the biosynthesis of terpenoid and unsaturated fatty acid in W. ugandensis bark remains largely unknown. Therefore, it is necessary to construct a genomic and/or transcriptomic database for the functional genomics study on W. ugandensis. The chemical profiles of terpenoids and fatty acids between the bark and leaves of W. ugandensis were compared by gas chromatography-mass spectrometry (GC-MS) analysis. Meanwhile, the transcriptome database derived from both tissues was created using Illumina sequencing technology. In total, about 17.1 G clean nucleotides were obtained, and de novo assembled into 72,591 unigenes, of which about 38.06% can be aligned to the NCBI non-redundant protein database. Many candidate genes in the biosynthetic pathways of terpenoids and unsaturated fatty acids were identified, including 14 unigenes for terpene synthases. Furthermore, 2,324 unigenes were discovered to be differentially expressed between both tissues; the functions of those differentially expressed genes (DEGs) were predicted by gene ontology enrichment and metabolic pathway enrichment analyses. In addition, the expression of 12 DEGs with putative roles in terpenoid and unsaturated fatty acid metabolic pathways was confirmed by qRT-PCRs, which was consistent with the data of the RNA-sequencing. In conclusion, we constructed a comprehensive transcriptome dataset derived from the bark and leaf of W. ugandensis, which forms the basis for functional genomics studies on this plant species. Particularly, the comparative analysis of the transcriptome data between the bark and leaf will provide critical clues to reveal the regulatory

  11. Conflict of interest reporting by authors involved in promotion of off-label drug use: an analysis of journal disclosures.

    Directory of Open Access Journals (Sweden)

    Aaron S Kesselheim

    Full Text Available Litigation documents reveal that pharmaceutical companies have paid physicians to promote off-label uses of their products through a number of different avenues. It is unknown whether physicians and scientists who have such conflicts of interest adequately disclose such relationships in the scientific publications they author.We collected whistleblower complaints alleging illegal off-label marketing from the US Department of Justice and other publicly available sources (date range: 1996-2010. We identified physicians and scientists described in the complaints as having financial relationships with defendant manufacturers, then searched Medline for articles they authored in the subsequent three years. We assessed disclosures made in articles related to the off-label use in question, determined the frequency of adequate disclosure statements, and analyzed characteristics of the authors (specialty, author position and articles (type, connection to off-label use, journal impact factor, citation count/year. We identified 39 conflicted individuals in whistleblower complaints. They published 404 articles related to the drugs at issue in the whistleblower complaints, only 62 (15% of which contained an adequate disclosure statement. Most articles had no disclosure (43% or did not mention the pharmaceutical company (40%. Adequate disclosure rates varied significantly by article type, with commentaries less likely to have adequate disclosure compared to articles reporting original studies or trials (adjusted odds ratio [OR] = 0.10, 95%CI = 0.02-0.67, p = 0.02. Over half of the authors (22/39, 56% made no adequate disclosures in their articles. However, four of six authors with ≥ 25 articles disclosed in about one-third of articles (range: 10/36-8/25 [28%-32%].One in seven authors identified in whistleblower complaints as involved in off-label marketing activities adequately disclosed their conflict of interest in subsequent journal publications. This is

  12. Conflict of interest reporting by authors involved in promotion of off-label drug use: an analysis of journal disclosures.

    Science.gov (United States)

    Kesselheim, Aaron S; Wang, Bo; Studdert, David M; Avorn, Jerry

    2012-01-01

    Litigation documents reveal that pharmaceutical companies have paid physicians to promote off-label uses of their products through a number of different avenues. It is unknown whether physicians and scientists who have such conflicts of interest adequately disclose such relationships in the scientific publications they author. We collected whistleblower complaints alleging illegal off-label marketing from the US Department of Justice and other publicly available sources (date range: 1996-2010). We identified physicians and scientists described in the complaints as having financial relationships with defendant manufacturers, then searched Medline for articles they authored in the subsequent three years. We assessed disclosures made in articles related to the off-label use in question, determined the frequency of adequate disclosure statements, and analyzed characteristics of the authors (specialty, author position) and articles (type, connection to off-label use, journal impact factor, citation count/year). We identified 39 conflicted individuals in whistleblower complaints. They published 404 articles related to the drugs at issue in the whistleblower complaints, only 62 (15%) of which contained an adequate disclosure statement. Most articles had no disclosure (43%) or did not mention the pharmaceutical company (40%). Adequate disclosure rates varied significantly by article type, with commentaries less likely to have adequate disclosure compared to articles reporting original studies or trials (adjusted odds ratio [OR] = 0.10, 95%CI = 0.02-0.67, p = 0.02). Over half of the authors (22/39, 56%) made no adequate disclosures in their articles. However, four of six authors with ≥ 25 articles disclosed in about one-third of articles (range: 10/36-8/25 [28%-32%]). One in seven authors identified in whistleblower complaints as involved in off-label marketing activities adequately disclosed their conflict of interest in subsequent journal publications. This is a much

  13. Conflict of Interest Reporting by Authors Involved in Promotion of Off-Label Drug Use: An Analysis of Journal Disclosures

    Science.gov (United States)

    Kesselheim, Aaron S.; Wang, Bo; Studdert, David M.; Avorn, Jerry

    2012-01-01

    Background Litigation documents reveal that pharmaceutical companies have paid physicians to promote off-label uses of their products through a number of different avenues. It is unknown whether physicians and scientists who have such conflicts of interest adequately disclose such relationships in the scientific publications they author. Methods and Findings We collected whistleblower complaints alleging illegal off-label marketing from the US Department of Justice and other publicly available sources (date range: 1996–2010). We identified physicians and scientists described in the complaints as having financial relationships with defendant manufacturers, then searched Medline for articles they authored in the subsequent three years. We assessed disclosures made in articles related to the off-label use in question, determined the frequency of adequate disclosure statements, and analyzed characteristics of the authors (specialty, author position) and articles (type, connection to off-label use, journal impact factor, citation count/year). We identified 39 conflicted individuals in whistleblower complaints. They published 404 articles related to the drugs at issue in the whistleblower complaints, only 62 (15%) of which contained an adequate disclosure statement. Most articles had no disclosure (43%) or did not mention the pharmaceutical company (40%). Adequate disclosure rates varied significantly by article type, with commentaries less likely to have adequate disclosure compared to articles reporting original studies or trials (adjusted odds ratio [OR] = 0.10, 95%CI = 0.02–0.67, p = 0.02). Over half of the authors (22/39, 56%) made no adequate disclosures in their articles. However, four of six authors with ≥25 articles disclosed in about one-third of articles (range: 10/36–8/25 [28%–32%]). Conclusions One in seven authors identified in whistleblower complaints as involved in off-label marketing activities adequately disclosed their conflict of

  14. Comparative Analysis of WRKY Genes Potentially Involved in Salt Stress Responses in Triticum turgidum L. ssp. durum

    Science.gov (United States)

    Yousfi, Fatma-Ezzahra; Makhloufi, Emna; Marande, William; Ghorbel, Abdel W.; Bouzayen, Mondher; Bergès, Hélène

    2017-01-01

    WRKY transcription factors are involved in multiple aspects of plant growth, development and responses to biotic stresses. Although they have been found to play roles in regulating plant responses to environmental stresses, these roles still need to be explored, especially those pertaining to crops. Durum wheat is the second most widely produced cereal in the world. Complex, large and unsequenced genomes, in addition to a lack of genomic resources, hinder the molecular characterization of tolerance mechanisms. This paper describes the isolation and characterization of five TdWRKY genes from durum wheat (Triticum turgidum L. ssp. durum). A PCR-based screening of a T. turgidum BAC genomic library using primers within the conserved region of WRKY genes resulted in the isolation of five BAC clones. Following sequencing fully the five BACs, fine annotation through Triannot pipeline revealed 74.6% of the entire sequences as transposable elements and a 3.2% gene content with genes organized as islands within oceans of TEs. Each BAC clone harbored a TdWRKY gene. The study showed a very extensive conservation of genomic structure between TdWRKYs and their orthologs from Brachypodium, barley, and T. aestivum. The structural features of TdWRKY proteins suggested that they are novel members of the WRKY family in durum wheat. TdWRKY1/2/4, TdWRKY3, and TdWRKY5 belong to the group Ia, IIa, and IIc, respectively. Enrichment of cis-regulatory elements related to stress responses in the promoters of some TdWRKY genes indicated their potential roles in mediating plant responses to a wide variety of environmental stresses. TdWRKY genes displayed different expression patterns in response to salt stress that distinguishes two durum wheat genotypes with contrasting salt stress tolerance phenotypes. TdWRKY genes tended to react earlier with a down-regulation in sensitive genotype leaves and with an up-regulation in tolerant genotype leaves. The TdWRKY transcripts levels in roots increased

  15. [Analysis on on-site rescue and traumatic features of victims involved in gas explosion accident in Hangzhou].

    Science.gov (United States)

    Wang, X G; Jin, R H; Liu, F P; Han, C M

    2017-10-20

    Objective: To investigate the situations of on-site rescue and traumatic features of victims involved in gas explosion accident in Hangzhou, so as to provide more data support for emergency medical rescues of the similar incidents of massive casualty. Methods: Two medical workers with a certain clinical experience were sent to Hangzhou 120 emergency medical centers to collect data of the on-site rescue on 21st July, 2017, including ambulance call-outs, on-site command and traffic conditions, and on-site triage and evacuation of the victims. They were then sent to the hospitals receiving the victims to investigate the situations of these victims including the general information (such as gender, age, admitted hospitals, and number of admission, discharge, and transferring in the first two weeks after the accident) and injury assessment [such as injury position and type, injury severity evaluation by New Injury Severity Scoring (NISS), and burn severity evaluation for victims with burns]. Results: (1) A total of 15 ambulances reached the accident site for rescue. The traffic and transportation were jammed and interrupted after this accident. On-site triage and distribution were disorderly conducted. (2) Clinical data of 53 victims were collected, including 24 males and 29 females, with the age of 8 to 70 (34±14) years old. They were sent into 6 hospitals in Hangzhou. Two victims died on the day of accident. Up to two weeks after this accident, 28 (52.8%) victims were discharged from the hospitals and received follow-up in outpatient department. Five victims with severe injuries were transferred to the other hospitals. (3) Based on the results of NISS, the injury severities were mild in 29 (54.7%) cases, moderate in 9 (17.0%) cases, serious in 3 (5.7%) cases, and severe in 12 (22.6%) cases. Those 2 dead victims were classified into the severe category due to the highest NISS score of 75. For all of the victims, skin and soft tissue defects were most common. Six (11

  16. Transcriptome analysis in prenatal IGF1-deficient mice identifies molecular pathways and target genes involved in distal lung differentiation.

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    Rosete Sofía Pais

    Full Text Available BACKGROUND: Insulin-like Growth Factor 1 (IGF1 is a multifunctional regulator of somatic growth and development throughout evolution. IGF1 signaling through IGF type 1 receptor (IGF1R controls cell proliferation, survival and differentiation in multiple cell types. IGF1 deficiency in mice disrupts lung morphogenesis, causing altered prenatal pulmonary alveologenesis. Nevertheless, little is known about the cellular and molecular basis of IGF1 activity during lung development. METHODS/PRINCIPAL FINDINGS: Prenatal Igf1(-/- mutant mice with a C57Bl/6J genetic background displayed severe disproportional lung hypoplasia, leading to lethal neonatal respiratory distress. Immuno-histological analysis of their lungs showed a thickened mesenchyme, alterations in extracellular matrix deposition, thinner smooth muscles and dilated blood vessels, which indicated immature and delayed distal pulmonary organogenesis. Transcriptomic analysis of Igf1(-/- E18.5 lungs using RNA microarrays identified deregulated genes related to vascularization, morphogenesis and cellular growth, and to MAP-kinase, Wnt and cell-adhesion pathways. Up-regulation of immunity-related genes was verified by an increase in inflammatory markers. Increased expression of Nfib and reduced expression of Klf2, Egr1 and Ctgf regulatory proteins as well as activation of ERK2 MAP-kinase were corroborated by Western blot. Among IGF-system genes only IGFBP2 revealed a reduction in mRNA expression in mutant lungs. Immuno-staining patterns for IGF1R and IGF2, similar in both genotypes, correlated to alterations found in specific cell compartments of Igf1(-/- lungs. IGF1 addition to Igf1(-/- embryonic lungs cultured ex vivo increased airway septa remodeling and distal epithelium maturation, processes accompanied by up-regulation of Nfib and Klf2 transcription factors and Cyr61 matricellular protein. CONCLUSIONS/SIGNIFICANCE: We demonstrated the functional tissue specific implication of IGF1 on fetal

  17. Genomic and proteomic analysis of Schizaphis graminum reveals cyclophilin proteins are involved in the transmission of cereal yellow dwarf virus.

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    Cecilia Tamborindeguy

    Full Text Available Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are transmitted by aphid vectors. The identification of aphid genes and proteins mediating virus transmission is critical to develop agriculturally sustainable virus management practices and to understand viral strategies for circulative movement in all insect vectors. Two cyclophilin B proteins, S28 and S29, were identified previously in populations of Schizaphisgraminum that differed in their ability to transmit the RPV strain of Cereal yellow dwarf virus (CYDV-RPV. The presence of S29 was correlated with F2 genotypes that were efficient virus transmitters. The present study revealed the two proteins were isoforms, and a single amino acid change distinguished S28 and S29. The distribution of the two alleles was determined in 12 F2 genotypes segregating for CYDV-RPV transmission capacity and in 11 genetically independent, field-collected S. graminum biotypes. Transmission efficiency for CYDV-RPV was determined in all genotypes and biotypes. The S29 isoform was present in all genotypes or biotypes that efficiently transmit CYDV-RPV and more specifically in genotypes that efficiently transport virus across the hindgut. We confirmed a direct interaction between CYDV-RPV and both S28 and S29 using purified virus and bacterially expressed, his-tagged S28 and S29 proteins. Importantly, S29 failed to interact with a closely related virus that is transported across the aphid midgut. We tested for in vivo interactions using an aphid-virus co-immunoprecipitation strategy coupled with a bottom-up LC-MS/MS analysis using a Q Exactive mass spectrometer. This analysis enabled us to identify a third cyclophilin protein, cyclophilin A, interacting directly or in complex with purified CYDV-RPV. Taken together, these data provide evidence that both cyclophilin A and B interact with CYDV-RPV, and these interactions may be important but not sufficient to mediate

  18. A Meta-Analysis of Retinoblastoma Copy Numbers Refines the List of Possible Driver Genes Involved in Tumor Progression

    Science.gov (United States)

    Kooi, Irsan E.; Mol, Berber M.; Massink, Maarten P. G.; de Jong, Marcus C.; de Graaf, Pim; van der Valk, Paul; Meijers-Heijboer, Hanne; Kaspers, Gertjan J. L.; Moll, Annette C.; te Riele, Hein; Cloos, Jacqueline; Dorsman, Josephine C.

    2016-01-01

    Background While RB1 loss initiates retinoblastoma development, additional somatic copy number alterations (SCNAs) can drive tumor progression. Although SCNAs have been identified with good concordance between studies at a cytoband resolution, accurate identification of single genes for all recurrent SCNAs is still challenging. This study presents a comprehensive meta-analysis of genome-wide SCNAs integrated with gene expression profiling data, narrowing down the list of plausible retinoblastoma driver genes. Methods We performed SCNA profiling of 45 primary retinoblastoma samples and eight retinoblastoma cell lines by high-resolution microarrays. We combined our data with genomic, clinical and histopathological data of ten published genome-wide SCNA studies, which strongly enhanced the power of our analyses (N = 310). Results Comprehensive recurrence analysis of SCNAs in all studies integrated with gene expression data allowed us to reduce candidate gene lists for 1q, 2p, 6p, 7q and 13q to a limited gene set. Besides the well-established driver genes RB1 (13q-loss) and MYCN (2p-gain) we identified CRB1 and NEK7 (1q-gain), SOX4 (6p-gain) and NUP205 (7q-gain) as novel retinoblastoma driver candidates. Depending on the sample subset and algorithms used, alternative candidates were identified including MIR181 (1q-gain) and DEK (6p gain). Remarkably, our study showed that copy number gains rarely exceeded change of one copy, even in pure tumor samples with 100% homozygosity at the RB1 locus (N = 34), which is indicative for intra-tumor heterogeneity. In addition, profound between-tumor variability was observed that was associated with age at diagnosis and differentiation grades. Interpretation Since focal alterations at commonly altered chromosome regions were rare except for 2p24.3 (MYCN), further functional validation of the oncogenic potential of the described candidate genes is now required. For further investigations, our study provides a refined and revised set

  19. Single-organ gallbladder vasculitis: characterization and distinction from systemic vasculitis involving the gallbladder. An analysis of 61 patients.

    Science.gov (United States)

    Hernández-Rodríguez, José; Tan, Carmela D; Rodríguez, E René; Hoffman, Gary S

    2014-11-01

    Systemic vasculitis (SV) involving abdominal structures usually has a poor prognosis. Gallbladder vasculitis (GV) has been reported as part of SV (GB-SV) and focal single-organ vasculitis (GB-SOV). We analyzed clinical and histologic characteristics of patients with GV to identify features that differentiate GB-SOV from the systemic forms of GV. To identify affected patients with GV we used pathology databases from our institution and an English-language PubMed search. Clinical manifestations, laboratory and histologic features, treatment administered, and outcomes were recorded. Patients were divided in 2 groups, GB-SOV and GB-SV. As in previous studies of single-organ vasculitis, GB-SOV was only considered to be a sustainable diagnosis if disease beyond the gallbladder was not apparent after a follow-up period of at least 6 months. Sixty-one well-characterized patients with GV were included (6 from our institution). There was no significant sex bias (32 female patients, 29 male). Median age was 52 years (range, 18-94 yr). GB-SOV was found in 20 (33%) and GB-SV in 41 (67%) patients. No differences were observed in age, sex frequency, or duration of gallbladder symptoms between groups. Past episodes of recurrent right-upper quadrant or abdominal pain and lithiasic cholecystitis were more frequent in GB-SOV patients, whereas acalculous cholecystitis occurred more often in GB-SV. In GB-SV, gallbladder-related symptoms occurred more often concomitantly with or after the systemic features, but they sometimes appeared before SV was fully developed (13.5%). Constitutional and musculoskeletal symptoms were reported only in GB-SV patients. Compared to GB-SOV, GB-SV patients presented more often with fever (62.5% vs 20%; p = 0.003) and exhibited higher erythrocyte sedimentation rate levels (80 ± 28 vs 37 ± 25 mm/h, respectively; p = 0.006). All GB-SV patients required glucocorticoids and 50% of them also received cytotoxic agents. Mortality in GB-SV was

  20. Detection of delta-ferrite to sigma transformation using metallographic techniques involving ferromagnetic colloid, color etching, and microprobe analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gray, R.J.; Sikka, V.K.; King, R.T.

    1976-01-01

    The mechanical properties of ferrite-containing austenitic stainless steel base metal and weldments are usually adversely affected by prolonged exposure to temperatures in the 482 to 900/sup 0/C (900 to 1652/sup 0/F) range. One cause of the property alteration is related to the transformation of relatively ductile delta-ferrite to less ductile sigma-phase. Attempts to identify sigma and delta-ferrite phases by color staining techniques alone are well documented; however, the results are often questionable due to the difficulty in maintaining consistent color identifications. This investigation is concerned with the microstructural responses of the ferromagnetic delta-ferrite phase and the paramagnetic sigma-phase to a ferromagnetic iron colloid in a magnetic field. Such positive or negative responses of the two phases to the colloid offer a more definitive identification. With this technique, the identification of small amounts of these phases in the microstructure is limited only by the highest magnification and resolution of the optical microscope. The procedure is substantiated in this metallographic study with microprobe analysis and color metallography. Several examples of the correlative use of these three techniques in identifying varying amounts of delta-ferrite ..-->.. sigma transformation are presented.

  1. Cognitive-behavioral high parental involvement treatments for pediatric obsessive-compulsive disorder: A meta-analysis.

    Science.gov (United States)

    Iniesta-Sepúlveda, Marina; Rosa-Alcázar, Ana I; Sánchez-Meca, Julio; Parada-Navas, José L; Rosa-Alcázar, Ángel

    2017-06-01

    A meta-analysis on the efficacy of cognitive-behavior-family treatment (CBFT) on children and adolescents with obsessive-compulsive disorder (OCD) was accomplished. The purposes of the study were: (a) to estimate the effect magnitude of CBFT in ameliorating obsessive-compulsive symptoms and reducing family accommodation on pediatric OCD and (b) to identify potential moderator variables of the effect sizes. A literature search enabled us to identify 27 studies that fulfilled our selection criteria. The effect size index was the standardized pretest-postest mean change index. For obsessive-compulsive symptoms, the adjusted mean effect size for CBFT was clinically relevant and statistically significant in the posttest (d adj =1.464). For family accommodation the adjusted mean effect size was also positive and statistically significant, but in a lesser extent than for obsessive-compulsive symptoms (d adj =0.511). Publication bias was discarded as a threat against the validity of the meta-analytic results. Large heterogeneity among effect sizes was found. Better results were found when CBFT was individually applied than in group (d + =2.429 and 1.409, respectively). CBFT is effective to reduce obsessive-compulsive symptoms, but offers a limited effect for family accommodation. Additional modules must be included in CBFT to improve its effectiveness on family accommodation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. The Source of Bacteria Involved in the Break-Down of Gammarus Pulex Faecal Pellets Using Image Analysis

    Science.gov (United States)

    Joyce, P.; Wotton, R.

    2005-05-01

    Bacteria survive passage through the gut of aquatic animals and are implicated in the break-down of POM (such as faecal pellets) in aquatic systems. There is evidence that bacteria that survive gut passage are the cause of the initial break-down of faecal pellets, rather than colonisation by bacteria from the environment. Gammarus is the dominant shredder in lowland permeable catchments ("chalk streams") in England and feeds on allochthonous detritus such as fallen leaves. Gammarus faecal pellets could form important pathways for transfer of organic matter in chalk streams. We incubated Gammarus faecal pellets for 80 days in stream water using combinations of treatments (autoclaving the stream water or pellets; fresh non-autoclaved stream water or pellets; reducing bacterial activity using Gentamicin; combinations of these treatments) to assess the role of surviving and colonising bacteria on the break-down process. Break-down was measured using image analysis. Results show that treatments with fresh pellets show much higher levels of break-down than fully autoclaved controls, treatments with fresh stream water but autoclaved pellets, or treatments with Gentamicin. Bacteria surviving gut passage therefore seem to play a greater role in faecal pellet break-down than those colonising from the environment.

  3. Solid Waste Management of Microcomputers in the City of Contagem/MG: An Analysis of Parties Involved

    Directory of Open Access Journals (Sweden)

    Claudio Jorge Cançado

    2012-06-01

    Full Text Available Among many issues related to solid waste, one stands out more and more, due to recent legislation linked to the area (National Policy on Solid Waste - Law 12.305/2010, which stresses the concept of reverse logistics, in which the producer is responsible for waste disposal related to the products manufactured by them. This study aims to perform an analysis of the disposal process of electronic waste from computers within the city limits of Contagem/ MG, in order to understand the reality of these wastes disposal, analyzing the population view, the management bodies and a recycling company, within the logic of reverse logistics. Data collection was the methodological procedure. The results showed that when it comes to recycling, there isn´t a chain that can incorporate these waste efficiently yet, showing the presence of only one company in the metropolitan region of Belo Horizonte, considering that the majority of screened waste is sent out of the State of Minas Gerais and abroad. In relation to the population, there is a repetition of the same mistakes from the past, with the overvaluation of economic growth at the expense of environmental issues. Finally, regarding the work, several limitations were found as lack of historical sales data, lack of data on the equipment life, the virtual absence of data from these items recycling.

  4. Transcriptome analysis revealed changes of multiple genes involved in immunity in Cynoglossus semilaevis during Vibrio anguillarum infection.

    Science.gov (United States)

    Zhang, Xiang; Wang, Shaolin; Chen, Songlin; Chen, Yadong; Liu, Yang; Shao, Changwei; Wang, Qilong; Lu, Yang; Gong, Guangye; Ding, Shaoxiong; Sha, Zhenxia

    2015-03-01

    Half-smooth tongue sole (Cynoglossus semilaevis) is one of the most valuable marine aquatic species in Northern China. Given to the rapid development of aquaculture industry, the C. semilaevis was subjected to disease-causing bacteria Vibrio anguillarum. It therefore is indispensable and urgent to understand the mechanism of C. semilaevis host defense against V. anguillarum infection. In the present study, the extensively analysis at the transcriptome level for V. Anguillarum disease in tongue sole was carried out. In total, 94,716 high quality contigs were generated from 75,884,572 clean reads in three libraries (HOSG, NOSG, and CG). 22,746 unigenes were identified when compared with SwissProt, an NR protein database and NT nucleotide database. 954 genes exhibiting the differentially expression at least one pair of comparison in all three libraries were identified. GO enrichment for these genes revealed gene response to biotic stimulus, immune system regulation, and immune response and cytokine production. Further, the pathways such as complement and coagulation cascades and Vibrio cholerae infection pathways were enriched in defensing of pathogen. Besides, 13,428 SSRs and 118,239 SNPs were detected in tongue sole, providing further support for genetic variation and marker-assisted selection in future. In summary, this study identifies several putative immune pathways and candidate genes deserving further investigation in the context of development of therapeutic regimens and lays the foundation for selecting resistant lines of C. semilaevis against V. anguillarum. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Proteomics analysis of global regulatory cascades involved in clavulanic acid production and morphological development in Streptomyces clavuligerus.

    Science.gov (United States)

    Ferguson, Nicole L; Peña-Castillo, Lourdes; Moore, Marcus A; Bignell, Dawn R D; Tahlan, Kapil

    2016-04-01

    The genus Streptomyces comprises bacteria that undergo a complex developmental life cycle and produce many metabolites of importance to industry and medicine. Streptomyces clavuligerus produces the β-lactamase inhibitor clavulanic acid, which is used in combination with β-lactam antibiotics to treat certain β-lactam resistant bacterial infections. Many aspects of how clavulanic acid production is globally regulated in S. clavuligerus still remains unknown. We conducted comparative proteomics analysis using the wild type strain of S. clavuligerus and two mutants (ΔbldA and ΔbldG), which are defective in global regulators and vary in their ability to produce clavulanic acid. Approximately 33.5 % of the predicted S. clavuligerus proteome was detected and 192 known or putative regulatory proteins showed statistically differential expression levels in pairwise comparisons. Interestingly, the expression of many proteins whose corresponding genes contain TTA codons (predicted to require the bldA tRNA for translation) was unaffected in the bldA mutant.

  6. Comparative microRNA-seq Analysis Depicts Candidate miRNAs Involved in Skin Color Differentiation in Red Tilapia

    Directory of Open Access Journals (Sweden)

    Lanmei Wang

    2018-04-01

    Full Text Available Differentiation and variation in body color has been a growing limitation to the commercial value of red tilapia. Limited microRNA (miRNA information is available on skin color differentiation and variation in fish so far. In this study, a high-throughput Illumina sequencing of sRNAs was conducted on three color varieties of red tilapia and 81,394,491 raw reads were generated. A total of 158 differentially expressed miRNAs (|log2(fold change| ≥ 1 and q-value ≤ 0.001 were identified. Target prediction and functional analysis of color-related miRNAs showed that a variety of putative target genes—including slc7a11, mc1r and asip—played potential roles in pigmentation. Moreover; the miRNA-mRNA regulatory network was illustrated to elucidate the pigmentation differentiation, in which miR-138-5p and miR-722 were predicted to play important roles in regulating the pigmentation process. These results advance our understanding of the molecular mechanisms of skin pigmentation differentiation in red tilapia.

  7. Comparative microRNA-seq Analysis Depicts Candidate miRNAs Involved in Skin Color Differentiation in Red Tilapia.

    Science.gov (United States)

    Wang, Lanmei; Zhu, Wenbin; Dong, Zaijie; Song, Feibiao; Dong, Juanjuan; Fu, Jianjun

    2018-04-16

    Differentiation and variation in body color has been a growing limitation to the commercial value of red tilapia. Limited microRNA (miRNA) information is available on skin color differentiation and variation in fish so far. In this study, a high-throughput Illumina sequencing of sRNAs was conducted on three color varieties of red tilapia and 81,394,491 raw reads were generated. A total of 158 differentially expressed miRNAs (|log₂(fold change)| ≥ 1 and q -value ≤ 0.001) were identified. Target prediction and functional analysis of color-related miRNAs showed that a variety of putative target genes—including slc7a11 , mc1r and asip —played potential roles in pigmentation. Moreover; the miRNA-mRNA regulatory network was illustrated to elucidate the pigmentation differentiation, in which miR-138-5p and miR-722 were predicted to play important roles in regulating the pigmentation process. These results advance our understanding of the molecular mechanisms of skin pigmentation differentiation in red tilapia.

  8. Alveolar process fractures in the permanent dentition. Part 1. Etiology and clinical characteristics. A retrospective analysis of 299 cases involving 815 teeth

    DEFF Research Database (Denmark)

    Andreasen, Jens Ove; Lauridsen, Eva

    2015-01-01

    AIM: To describe the etiology and clinical characteristics of alveolar process fractures treated in a regional trauma clinic. MATERIAL AND METHOD: The study is a retrospective descriptive analysis of 299 patients (180 males, 119 females; 815 permanent teeth) diagnosed with fractures of the alveolar...... process. RESULTS: Violence was the overall most frequent cause of injury in men (44%), whereas the three most common causes of this type of injury in women were violence (33%), falls (32%), or traffic injuries (26%). Fracture of the alveolar process occurred most frequently in the maxilla (74%) and less...... frequently in the mandible (26%). The majority of the fractures involved only two teeth (57%) but occasionally involved up to seven teeth. The age at fracture ranged from 5 to 90 years; alveolar process fractures occurred most frequently between 15 and 25 years of age (43%). Concomitant soft tissue injuries...

  9. Involving undergraduates in the annotation and analysis of global gene expression studies: creation of a maize shoot apical meristem expression database.

    Science.gov (United States)

    Buckner, Brent; Beck, Jon; Browning, Kate; Fritz, Ashleigh; Grantham, Lisa; Hoxha, Eneda; Kamvar, Zhian; Lough, Ashley; Nikolova, Olga; Schnable, Patrick S; Scanlon, Michael J; Janick-Buckner, Diane

    2007-06-01

    Through a multi-university and interdisciplinary project we have involved undergraduate biology and computer science research students in the functional annotation of maize genes and the analysis of their microarray expression patterns. We have created a database to house the results of our functional annotation of >4400 genes identified as being differentially regulated in the maize shoot apical meristem (SAM). This database is located at http://sam.truman.edu and is now available for public use. The undergraduate students involved in constructing this unique SAM database received hands-on training in an intellectually challenging environment, which has prepared them for graduate and professional careers in biological sciences. We describe our experiences with this project as a model for effective research-based teaching of undergraduate biology and computer science students, as well as for a rich professional development experience for faculty at predominantly undergraduate institutions.

  10. A Systematic Review and Meta-analysis of Interventions for Sexual Health Promotion Involving Serious Digital Games.

    Science.gov (United States)

    DeSmet, Ann; Shegog, Ross; Van Ryckeghem, Dimitri; Crombez, Geert; De Bourdeaudhuij, Ilse

    2015-04-01

    Serious games may be effective in promoting sexual health behavior. Their confidential nature may encourage users to discuss sensitive sexuality topics. Furthermore, they can tailor messages to the individual's needs and may be intrinsically motivating. This meta-analysis investigates the effectiveness of interventions for sexual health promotion that use serious games. A database search was conducted in PubMed, Web of Science, CINAHL, and PsycINFO for publications before the end of July 2013. Serious digital games studies measuring effects on behavior or its determinants, using a control condition, allowing the calculation of an effect size (Hedges' g, random-effects model) were included. Seven game studies for sexual health promotion were included. These showed positive effects on determinants (g=0.242; 95 percent confidence interval, 0.129, 0.356), albeit of small effect size. The effects on behavior, measured in only two studies, were not significant (g=0.456; 95 percent confidence interval, -0.649, 1.561). Most games did not use many game features that are considered to be immersive or enhancing flow. Instead, there was a strong reliance on pure gamification features, such as rewards and feedback. The effectiveness of the next generation of games may be enhanced by building on the behavioral change and educational gaming literatures (e.g., using role-play and simulation game formats, individual tailoring, offering adaptation in the difficulty of the challenge, and amount and timing of the feedback). There is a need for studies with rigorous evaluations of game effectiveness, longer-term follow-up, and using measures of behavior rather than merely their determinants.

  11. Analysis of gene expression of myo1c and inpp5k genes involved in endometrial adenocarcinoma

    International Nuclear Information System (INIS)

    Koul, A.M.; Nadeem, A.; Baryalai, P.

    2012-01-01

    Abstract: Inpp5k gene encodes a protein which plays a very vital role in a number of metabolic pathways. It is very significant in the glucose metabolism where it regulates the signalling of the insulin pathway. But the full molecular details of the pathways regulated by Inpp5k encoded protein are not known. It is speculated that Inpp5k gene expression is altered in case of endometrial adenocarcinoma. Myolc gene encodes for a protein called Myosin-lc which acts an actin-based molecular motor in the cells. II has been studied that this gene down-regulates during endometrial adenocarcinoma and colorectal cancers. In this study the expression analysis of these two was carried out using multiplex PCR. An endogenous control was used for this PCR. ACTS gene served as the endogenous control because of it being a house keeping gene. It thus shows a universal expression in all cells. Thus in this study the gene expression of Inpp5k and Myulc genes was comparatively analysed with ACTS gene. The results that came out of this study showed an over-expression of Inpp5k gene and down-regulation of myolc gene with respect to ACTS gene in cancer cell lines as was indicated by the previous studies with these genes. Expression of both genes i.e. Inpp5k and Myolc was statistically compared between normal and cancerous cell lines and was found statistically significant at a value of P< O.O I in most of the cases. (author)

  12. A Computational Approach From Gene to Structure Analysis of the Human ABCA4 Transporter Involved in Genetic Retinal Diseases.

    Science.gov (United States)

    Trezza, Alfonso; Bernini, Andrea; Langella, Andrea; Ascher, David B; Pires, Douglas E V; Sodi, Andrea; Passerini, Ilaria; Pelo, Elisabetta; Rizzo, Stanislao; Niccolai, Neri; Spiga, Ottavia

    2017-10-01

    The aim of this article is to report the investigation of the structural features of ABCA4, a protein associated with a genetic retinal disease. A new database collecting knowledge of ABCA4 structure may facilitate predictions about the possible functional consequences of gene mutations observed in clinical practice. In order to correlate structural and functional effects of the observed mutations, the structure of mouse P-glycoprotein was used as a template for homology modeling. The obtained structural information and genetic data are the basis of our relational database (ABCA4Database). Sequence variability among all ABCA4-deposited entries was calculated and reported as Shannon entropy score at the residue level. The three-dimensional model of ABCA4 structure was used to locate the spatial distribution of the observed variable regions. Our predictions from structural in silico tools were able to accurately link the functional effects of mutations to phenotype. The development of the ABCA4Database gathers all the available genetic and structural information, yielding a global view of the molecular basis of some retinal diseases. ABCA4 modeled structure provides a molecular basis on which to analyze protein sequence mutations related to genetic retinal disease in order to predict the risk of retinal disease across all possible ABCA4 mutations. Additionally, our ABCA4 predicted structure is a good starting point for the creation of a new data analysis model, appropriate for precision medicine, in order to develop a deeper knowledge network of the disease and to improve the management of patients.

  13. Graduated driver licensing and motor vehicle crashes involving teenage drivers: an exploratory age-stratified meta-analysis.

    Science.gov (United States)

    Zhu, Motao; Cummings, Peter; Chu, Haitao; Coben, Jeffrey H; Li, Guohua

    2013-02-01

    Graduated Driver Licensing (GDL) has been implemented in Australia, Canada, New Zealand, USA and Israel. We conducted an exploratory summary of available data to estimate whether GDL effects varied with age. We searched MEDLINE and other sources from 1991-2011. GDL evaluation studies with crashes resulting in injuries or deaths were eligible. They had to provide age-specific incidence rate ratios with CI or information for calculating these quantities. We included studies from individual states or provinces, but excluded national studies. We examined rates based on person-years, not license-years. Of 1397 papers, 144 were screened by abstract and 47 were reviewed. Twelve studies from 11 US states and one Canadian province were selected for meta-analysis for age 16, eight were selected for age 17, and four for age 18. Adjusted rate ratios were pooled using random effects models. The pooled adjusted rate ratios for the association of GDL presence with crash rates was 0.78 (95% CI 0.72 to 0.84) for age 16 years, 0.94 (95% CI 0.93 to 0.96) for 17 and 1.00 (95% CI 0.95 to 1.04) for 18. The difference between these three rate ratios was statistically significant: p<0.001. GDL policies were associated with a 22% reduction in crash rates among 16-year-old drivers, but only a 6% reduction for 17-year-old drivers. GDL showed no association with crashes among 18-year-old drivers. Because we had few studies to summarise, particularly for older adolescents, our findings should be considered exploratory.

  14. 454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides.

    Science.gov (United States)

    Zagrobelny, Mika; Scheibye-Alsing, Karsten; Jensen, Niels Bjerg; Møller, Birger Lindberg; Gorodkin, Jan; Bak, Søren

    2009-12-02

    . Pyrosequencing is an attractive approach to gain access to genes in the biosynthesis of bio-active natural products from insects and other organisms, for which the genome sequence is not known. Based on analysis of the Z. filipendulae transcriptome, promising gene candidates for biosynthesis of cyanogenic glucosides was identified, and the suitability of Z. filipendulae as a model system for cyanogenesis in insects is evident.

  15. 454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides

    Directory of Open Access Journals (Sweden)

    Jensen Niels

    2009-12-01

    convergent between plants and insects. Conclusion Pyrosequencing is an attractive approach to gain access to genes in the biosynthesis of bio-active natural products from insects and other organisms, for which the genome sequence is not known. Based on analysis of the Z. filipendulae transcriptome, promising gene candidates for biosynthesis of cyanogenic glucosides was identified, and the suitability of Z. filipendulae as a model system for cyanogenesis in insects is evident.

  16. Structural analysis of PseH, the Campylobacter jejuni N-acetyltransferase involved in bacterial O-linked glycosylation

    Energy Technology Data Exchange (ETDEWEB)

    Song, Wan Seok; Nam, Mi Sun; Namgung, Byeol [Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701 (Korea, Republic of); Yoon, Sung-il, E-mail: sungil@kangwon.ac.kr [Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701 (Korea, Republic of); Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 200-701 (Korea, Republic of)

    2015-03-20

    Campylobacter jejuni is a bacterium that uses flagella for motility and causes worldwide acute gastroenteritis in humans. The C. jejuni N-acetyltransferase PseH (cjPseH) is responsible for the third step in flagellin O-linked glycosylation and plays a key role in flagellar formation and motility. cjPseH transfers an acetyl group from an acetyl donor, acetyl coenzyme A (AcCoA), to the amino group of UDP-4-amino-4,6-dideoxy-N-acetyl-β-L-altrosamine to produce UDP-2,4-diacetamido-2,4,6-trideoxy-β-L-altropyranose. To elucidate the catalytic mechanism of cjPseH, crystal structures of cjPseH alone and in complex with AcCoA were determined at 1.95 Å resolution. cjPseH folds into a single-domain structure of a central β-sheet decorated by four α-helices with two continuously connected grooves. A deep groove (groove-A) accommodates the AcCoA molecule. Interestingly, the acetyl end of AcCoA points toward an open space in a neighboring shallow groove (groove-S), which is occupied by extra electron density that potentially serves as a pseudosubstrate, suggesting that the groove-S may provide a substrate-binding site. Structure-based comparative analysis suggests that cjPseH utilizes a unique catalytic mechanism of acetylation that has not been observed in other glycosylation-associated acetyltransferases. Thus, our studies on cjPseH will provide valuable information for the design of new antibiotics to treat C. jejuni-induced gastroenteritis. - Highlights: • cjPseH adopts a single-domain structure of a central β-sheet decorated by α-helices. • cjPseH features two continuously connected grooves on the protein surface. • Acetyl coenzyme A (AcCoA) binds into a deep groove of cjPseH in an ‘L’ shape. • The acetyl end of AcCoA points to a wide groove, a potential substrate-binding site.

  17. Acetylome analysis reveals the involvement of lysine acetylation in photosynthesis and carbon metabolism in the model cyanobacterium Synechocystis sp. PCC 6803.

    Science.gov (United States)

    Mo, Ran; Yang, Mingkun; Chen, Zhuo; Cheng, Zhongyi; Yi, Xingling; Li, Chongyang; He, Chenliu; Xiong, Qian; Chen, Hui; Wang, Qiang; Ge, Feng

    2015-02-06

    Cyanobacteria are the oldest known life form inhabiting Earth and the only prokaryotes capable of performing oxygenic photosynthesis. Synechocystis sp. PCC 6803 (Synechocystis) is a model cyanobacterium used extensively in research on photosynthesis and environmental adaptation. Posttranslational protein modification by lysine acetylation plays a critical regulatory role in both eukaryotes and prokaryotes; however, its extent and function in cyanobacteria remain unexplored. Herein, we performed a global acetylome analysis on Synechocystis through peptide prefractionation, antibody enrichment, and high accuracy LC-MS/MS analysis; identified 776 acetylation sites on 513 acetylated proteins; and functionally categorized them into an interaction map showing their involvement in various biological processes. Consistent with previous reports, a large fraction of the acetylation sites are present on proteins involved in cellular metabolism. Interestingly, for the first time, many proteins involved in photosynthesis, including the subunits of phycocyanin (CpcA, CpcB, CpcC, and CpcG) and allophycocyanin (ApcA, ApcB, ApcD, ApcE, and ApcF), were found to be lysine acetylated, suggesting that lysine acetylation may play regulatory roles in the photosynthesis process. Six identified acetylated proteins associated with photosynthesis and carbon metabolism were further validated by immunoprecipitation and Western blotting. Our data provide the first global survey of lysine acetylation in cyanobacteria and reveal previously unappreciated roles of lysine acetylation in the regulation of photosynthesis. The provided data set may serve as an important resource for the functional analysis of lysine acetylation in cyanobacteria and facilitate the elucidation of the entire metabolic networks and photosynthesis process in this model cyanobacterium.

  18. Malonylome analysis of rhizobacterium Bacillus amyloliquefaciens FZB42 reveals involvement of lysine malonylation in polyketide synthesis and plant-bacteria interactions.

    Science.gov (United States)

    Fan, Ben; Li, Yu-Long; Li, Lei; Peng, Xiao-Jun; Bu, Chen; Wu, Xiao-Qin; Borriss, Rainer

    2017-02-10

    Using the combination of affinity enrichment and high-resolution LC-MS/MS analysis, we performed a large-scale lysine malonylation analysis in the model representative of Gram-positive plant growth-promoting rhizobacteria (PGPR), Bacillus amyloliquefaciens FZB42. Altogether, 809 malonyllysine sites in 382 proteins were identified. The bioinformatic analysis revealed that lysine malonylation occurs on the proteins involved in a variety of biological functions including central carbon metabolism, fatty acid biosynthesis and metabolism, NAD(P) binding and translation machinery. A group of proteins known to be implicated in rhizobacterium-plant interaction were also malonylated; especially, the enzymes responsible for antibiotic production including polyketide synthases (PKSs) and nonribosomal peptide synthases (NRPSs) were highly malonylated. Furthermore, our analysis showed malonylation occurred on proteins structure with higher surface accessibility and appeared to be conserved in many bacteria but not in archaea. The results provide us valuable insights into the potential roles of lysine malonylation in governing bacterial metabolism and cellular processes. Although in mammalian cells some important findings have been discovered that protein malonylation is related to basic metabolism and chronic disease, few studies have been performed on prokaryotic malonylome. In this study, we determined the malonylation profiles of Bacillus amyloliquefaciens FZB42, a model organism of Gram-positive plant growth-promoting rhizobacteria. FZB42 is known for the extensive investigations on its strong ability of producing antimicrobial polyketides and its potent activities of stimulating plant growth. Our analysis shows that malonylation is highly related to the polyketide synthases and the proteins involved bacterial interactions with plants. The results not only provide one of the first malonylomes for exploring the biochemical nature of bacterial proteins, but also shed light on

  19. [Analysis on funds application of community based organizations involved in HIV/AIDS response and government financial investment in China, 2014].

    Science.gov (United States)

    Zhang, G; Zhu, Y X; Wang, P; Liu, P; Li, J F; Sha, S; Yang, W Z; Li, H

    2017-03-06

    Objective: To understand the government financial investments to community based organizations (CBO) involved in HIV/AIDS Control and Prevention of China and its influencing factors. Methods: Questionnaire of the situation of CBO involved in HIV/AIDS control and prevention were designed, and filled by the staff of Provincial Health Administrative Departments of 31 provinces (autonomous regions and municipalities). The research focused on the fields of CBO involved in HIV/AIDS response in 31 provinces (autonomous regions and municipalities), including intervention on HIV/AIDS high risk population (female sex worker (FSW), man who sex with man (MSM), drug user (DU) and case management and care for people living with HIV/AIDS (PLWH)). 29 valid questionnaires were collecting, with Shanxi Province and Inner Mongolia Autonomous Regions not filled. Questionnaire included financial supports from local governments, transfer payment from central government for CBO involved in HIV/AIDS response in 2014, and unit cost for CBO involved in HIV/AIDS control and prevention. Multivariate analysis was conducted on the project application and financial investment of community based organizations involved in HIV/AIDS control and prevention in 2014. Results: The total amount of CBO to apply for participation in AIDS prevention and control was 64 482 828 Yuan in 2014. The actual total amount of investment was 50 616 367 Yuan, The investment came from the central government funding, the provincial level government funding, the prefecture and county level government funding investment and other sources of funding. 22 of 28 provinces (autonomous regions and municipalities) received the funds from the central government finance, and median of investment funds 500 000 Yuan. 15 provinces (autonomous regions and municipalities) gained the funds from the provincial government finance, and median of investment funds 350 000 Yuan. 12 provinces (autonomous regions and municipalities) got the funds

  20. 18F-FDG PET for detecting recurrent head and neck cancer, local lymph node involvement and distant metastases. Comparison of qualitative visual and semiquantitative analysis

    International Nuclear Information System (INIS)

    Schmidt, M.; Schmalenbach, M.; Theissen, P.; Dietlein, M.; Eschner, W.; Schicha, H.; Jungehuelsing, M.; Schroeder, U.; Stennert, E.

    2004-01-01

    Aim: Assessment of the clinical value of 18 F-FDG-PET for detection of recurrent head and neck cancer, local lymph node involvement and distant metastases comparing a qualitative visual with a semiquantitative analysis (SUV values). Patients, methods: Retrospective evaluation of 73 18 F-FDG PET studies in 55 patients by use of a four-step qualitative visual grading system and calculation of standard uptake values in pathological lesions. Calculation of SUV values in normal regions for generating a map of physiological 18 F-FDG distribution. Correlation to histopathological findings and clinical follow-up. Results: 1. Qualitative visual analysis of 18 F-FDG PET studies: a) local recurrence sensitivity 79%, specificity 97%, positive predictive value 95%, negative predictive value 85%, and diagnostic accuracy 89%; b) local metastatic lymph nodes 100%, 95%, 85%, 100%, 96%; c) distant metastases 100%, 98%, 86%, 100%, 98%, respectively. 2. Semiquantitative analysis had only little incremental, non-significant value in comparison to qualitative visual analysis for the detection of a local recurrence in two patients: a) local recurrence: sensitivity 83%, specificity 100%, positive predictive value 100%, negative predictive value 88%, and diagnostic accuracy 93%; b) local metastatic lymph nodes or c) distant metastases did not change in comparison to qualitative visual analysis. Conclusion: 18 F-FDG PET is an effective tool for re-staging of patients with suspected recurrence after therapy for head and neck cancer. (orig.)

  1. Discovery of proteins involved in the interaction between prebiotics carbohydrates and probiotics & whole proteome analysis of the probiotic strain Bifidobacterium animalis susp. lactis BB-12

    DEFF Research Database (Denmark)

    Gilad, Ofir

    in the human gastrointestinal tract. Despite an increased scientific focus within this field, the mechanisms behind the beneficial effects exerted by pre- and probiotics are still far from fully understood. The purpose of the present industrial-PhD project was to identify proteins involved in interactions......Probiotic bacteria, which primarily belong to the genera Lactobascillus and Bifidobacterium, are live microorganisms that have been related to a variety of health-promoting effects. Prebiotics are indigestible food components that specifically stimulate the growth of probiotic organisms...... on these results and on chromatographic analysis of XOS consumption in BB-12 cultures, a model for XOS utilisation in BB-12 was established. The subsequent phase of the PhD project included extracellular proteome analysis, giving rise to the identification of 86 unique proteins. Of these proteins, 33...

  2. De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids

    Directory of Open Access Journals (Sweden)

    Megha Rai

    2017-12-01

    Full Text Available Aconitum carmichaelii is an important medicinal herb used widely in China, Japan, India, Korea, and other Asian countries. While extensive research on the characterization of metabolic extracts of A. carmichaelii has shown accumulation of numerous bioactive metabolites including aconitine and aconitine-type diterpene alkaloids, its biosynthetic pathway remains largely unknown. Biosynthesis of these secondary metabolites is tightly controlled and mostly occurs in a tissue-specific manner; therefore, transcriptome analysis across multiple tissues is an attractive method to identify the molecular components involved for further functional characterization. In order to understand the biosynthesis of secondary metabolites, Illumina-based deep transcriptome profiling and analysis was performed for four tissues (flower, bud, leaf, and root of A. carmichaelii, resulting in 5.5 Gbps clean RNA-seq reads assembled into 128,183 unigenes. Unigenes annotated as possible rate-determining steps of an aconitine-type biosynthetic pathway were highly expressed in the root, in accordance with previous reports describing the root as the accumulation site for these metabolites. We also identified 21 unigenes annotated as cytochrome P450s and highly expressed in roots, which represent candidate unigenes involved in the diversification of secondary metabolites. Comparative transcriptome analysis of A. carmichaelii with A. heterophyllum identified 20,232 orthogroups, representing 30,633 unigenes of A. carmichaelii, gene ontology enrichment analysis of which revealed essential biological process together with a secondary metabolic process to be highly enriched. Unigenes identified in this study are strong candidates for aconitine-type diterpene alkaloid biosynthesis, and will serve as useful resources for further validation studies.

  3. GC-MS Metabolomic Analysis to Reveal the Metabolites and Biological Pathways Involved in the Developmental Stages and Tissue Response of Panax ginseng

    Directory of Open Access Journals (Sweden)

    Jia Liu

    2017-03-01

    Full Text Available Ginsenosides, the major compounds present in ginseng, are known to have numerous physiological and pharmacological effects. The physiological processes, enzymes and genes involved in ginsenoside synthesis in P. ginseng have been well characterized. However, relatively little information is known about the dynamic metabolic changes that occur during ginsenoside accumulation in ginseng. To explore this topic, we isolated metabolites from different tissues at different growth stages, and identified and characterized them by using gas chromatography coupled with mass spectrometry (GC-MS. The results showed that a total of 30, 16, 20, 36 and 31 metabolites were identified and involved in different developmental stages in leaf, stem, petiole, lateral root and main root, respectively. To investigate the contribution of tissue to the biosynthesis of ginsenosides, we examined the metabolic changes of leaf, stem, petiole, lateral root and main root during five development stages: 1-, 2-, 3-, 4- and 5-years. The score plots of partial least squares-discriminate analysis (PLS-DA showed clear discrimination between growth stages and tissue samples. Kyoto Encyclopedia of Genes and Genomes (KEGG pathway analysis in the same tissue at different growth stages indicated profound biochemical changes in several pathways, including carbohydrate metabolism and pentose phosphate metabolism, in addition, the tissues displayed significant variations in amino acid metabolism, sugar metabolism and energy metabolism. These results should facilitate further dissection of the metabolic flux regulation of ginsenoside accumulation in different developmental stages or different tissues of ginseng.

  4. Transcriptome Analysis and Discovery of Genes Involved in Immune Pathways from Coelomocytes of Sea Cucumber (Apostichopus japonicus after Vibrio splendidus Challenge

    Directory of Open Access Journals (Sweden)

    Qiong Gao

    2015-07-01

    Full Text Available Vibrio splendidus is identified as one of the major pathogenic factors for the skin ulceration syndrome in sea cucumber (Apostichopus japonicus, which has vastly limited the development of the sea cucumber culture industry. In order to screen the immune genes involving Vibrio splendidus challenge in sea cucumber and explore the molecular mechanism of this process, the related transcriptome and gene expression profiling of resistant and susceptible biotypes of sea cucumber with Vibrio splendidus challenge were collected for analysis. A total of 319,455,942 trimmed reads were obtained, which were assembled into 186,658 contigs. After that, 89,891 representative contigs (without isoform were clustered. The analysis of the gene expression profiling identified 358 differentially expression genes (DEGs in the bacterial-resistant group, and 102 DEGs in the bacterial-susceptible group, compared with that in control group. According to the reported references and annotation information from BLAST, GO and KEGG, 30 putative bacterial-resistant genes and 19 putative bacterial-susceptible genes were identified from DEGs. The qRT-PCR results were consistent with the RNA-Seq results. Furthermore, many DGEs were involved in immune signaling related pathways, such as Endocytosis, Lysosome, MAPK, Chemokine and the ERBB signaling pathway.

  5. Transcriptome Profiling of Petal Abscission Zone and Functional Analysis of an Aux/IAA Family GeneRhIAA16Involved in Petal Shedding in Rose.

    Science.gov (United States)

    Gao, Yuerong; Liu, Chun; Li, Xiaodong; Xu, Haiqian; Liang, Yue; Ma, Nan; Fei, Zhangjun; Gao, Junping; Jiang, Cai-Zhong; Ma, Chao

    2016-01-01

    Roses are one of the most important cut flowers among ornamental plants. Rose flower longevity is largely dependent on the timing of petal shedding occurrence. To understand the molecular mechanism underlying petal abscission in rose, we performed transcriptome profiling of the petal abscission zone during petal shedding using Illumina technology. We identified a total of 2592 differentially transcribed genes (DTGs) during rose petal shedding. Gene ontology term enrichment and pathway analysis revealed that major biochemical pathways the DTGs were involved in included ethylene biosynthesis, starch degradation, superpathway of cytosolic glycolysis, pyruvate dehydrogenase and TCA cycle, photorespiration and the lactose degradation III pathway. This suggests that alterations in carbon metabolism are an important part of rose petal abscission. Among these DTGs, approximately 150 genes putatively encoding transcription factors were identified in rose abscission zone. These included zinc finger, WRKY, ERF, and Aux/IAA gene families, suggesting that petal abscission involves complex transcriptional reprogramming. Approximately 108 DTGs were related to hormone pathways, of which auxin and ethylene related DTGs were the largest groups including 52 and 41 genes, respectively. These also included 12 DTGs related to gibberellin and 6 DTGs in jasmonic acid pathway. Surprisingly, no DTGs involved in the biosynthesis/signaling of abscisic acid, cytokinin, brassinosteroid, and salicylic acid pathways were detected. Moreover, among DTGs related to auxin, we identified an Aux/IAA gene RhIAA16 that was up-regulated in response to petal shedding. Down-regulation of RhIAA16 by virus-induced gene silencing in rose promoted petal abscission, suggesting that RhIAA16 plays an important role in rose petal abscission.

  6. Transcriptome profiling of petal abscission zone and functional analysis of an Aux/IAA family gene RhIAA16 involved in petal shedding in rose

    Directory of Open Access Journals (Sweden)

    Yuerong Gao

    2016-09-01

    Full Text Available Roses are one of the most important cut flowers among ornamental plants. Rose flower longevity is largely dependent on the timing of petal shedding occurrence. To understand the molecular mechanism underlying petal abscission in rose, we performed transcriptome profiling of the petal abscission zone during petal shedding using Illumina technology. We identified a total of 2592 differentially transcribed genes (DTGs during rose petal shedding. Gene ontology term enrichment and pathway analysis revealed that major biochemical pathways the DTGs were involved in included ethylene biosynthesis, starch degradation, superpathway of cytosolic glycolysis, pyruvate dehydrogenase and TCA cycle, photorespiration and the lactose degradation III pathway. This suggests that alterations in carbon metabolism are an important part of rose petal abscission. Among these DTGs, approximately 150 genes putatively encoding transcription factors were identified in rose abscission zone. These included zinc finger, WRKY, ERF, and Aux/IAA gene families, suggesting that petal abscission involves complex transcriptional reprogramming. Approximately 108 DTGs were related to hormone pathways, of which auxin and ethylene related DTGs were the largest groups including 52 and 41 genes, respectively. These also included 12 DTGs related to gibberellin and 6 DTGs in jasmonic acid pathway. Surprisingly, no DTGs involved in the biosynthesis/signaling of abscisic acid, cytokinin, brassinosteroid, and salicylic acid pathways were detected. Moreover, among DTGs related to auxin, we identified an Aux/IAA gene RhIAA16 that was up-regulated in response to petal shedding. Down-regulation of RhIAA16 by virus-induced gene silencing in rose promoted petal abscission, suggesting that RhIAA16 plays an important role in rose petal abscission.

  7. Analysis for the presence of determinants involved in the transport of mercury across bacterial membrane from polluted water bodies of India.

    Science.gov (United States)

    Jan, Arif Tasleem; Azam, Mudsser; Choi, Inho; Ali, Arif; Haq, Qazi Mohd Rizwanul

    2016-01-01

    Mercury, which is ubiquitous and recalcitrant to biodegradation processes, threatens human health by escaping to the environment via various natural and anthropogenic activities. Non-biodegradability of mercury pollutants has necessitated the development and implementation of economic alternatives with promising potential to remove metals from the environment. Enhancement of microbial based remediation strategies through genetic engineering approaches provides one such alternative with a promising future. In this study, bacterial isolates inhabiting polluted sites were screened for tolerance to varying concentrations of mercuric chloride. Following identification, several Pseudomonas and Klebsiella species were found to exhibit the highest tolerance to both organic and inorganic mercury. Screened bacterial isolates were examined for their genetic make-up in terms of the presence of genes (merP and merT) involved in the transport of mercury across the membrane either alone or in combination to deal with the toxic mercury. Gene sequence analysis revealed that the merP gene showed 86-99% homology, while the merT gene showed >98% homology with previously reported sequences. By exploring the genes involved in imparting metal resistance to bacteria, this study will serve to highlight the credentials that are particularly advantageous for their practical application to remediation of mercury from the environment. Copyright © 2015 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  8. Analysis of RNA-Seq data reveals involvement of JAK/STAT signalling during leg regeneration in the cricket Gryllus bimaculatus.

    Science.gov (United States)

    Bando, Tetsuya; Ishimaru, Yoshiyasu; Kida, Takuro; Hamada, Yoshimasa; Matsuoka, Yuji; Nakamura, Taro; Ohuchi, Hideyo; Noji, Sumihare; Mito, Taro

    2013-03-01

    In the cricket Gryllus bimaculatus, missing distal parts of the amputated leg are regenerated from the blastema, a population of dedifferentiated proliferating cells that forms at the distal tip of the leg stump. To identify molecules involved in blastema formation, comparative transcriptome analysis was performed between regenerating and normal unamputated legs. Components of JAK/STAT signalling were upregulated more than twofold in regenerating legs. To verify their involvement, Gryllus homologues of the interleukin receptor Domeless (Gb'dome), the Janus kinase Hopscotch (Gb'hop) and the transcription factor STAT (Gb'Stat) were cloned, and RNAi was performed against these genes. Gb'dome(RNAi), Gb'hop(RNAi) and Gb'Stat(RNAi) crickets showed defects in leg regeneration. Blastema expression of Gb'cyclinE was decreased in the Gb'Stat(RNAi) cricket compared with that in the control. Hyperproliferation of blastema cells caused by Gb'fat(RNAi) or Gb'warts(RNAi) was suppressed by RNAi against Gb'Stat. The results suggest that JAK/STAT signalling regulates blastema cell proliferation during leg regeneration.

  9. Osteoprotegerin concentration and risk of cardiovascular outcomes in nine general population studies: Literature-based meta-analysis involving 26,442 participants.

    Science.gov (United States)

    Tschiderer, Lena; Willeit, Johann; Schett, Georg; Kiechl, Stefan; Willeit, Peter

    2017-01-01

    Recent experimental and epidemiological studies have suggested that osteoprotegerin, a key regulator in bone metabolism, may be involved in vascular calcification and atherosclerosis. Our aim was to reliably quantify the associations of osteoprotegerin concentration and incidence of first-ever cardiovascular disease outcomes in the general population. Using the electronic databases MEDLINE, EMBASE and Web of Science (January 1975 and April 2017, no language restrictions), nine relevant studies were identified involving a total of 26,442 participants recruited from the general population. Over a mean follow-up of 8.5 years, 2,160 cardiovascular disease, 2,123 coronary heart disease, and 1,102 stroke outcomes were recorded. Study-specific risk ratios were combined with random-effects meta-analysis. When comparing individuals in the top with those in the bottom third of osteoprotegerin concentration, the combined risk ratio was 1.83 (95% confidence interval: 1.46, 2.30; Posteoprotegerin in plasma rather than in serum (P = 0.005 for cardiovascular disease and 0.018 for coronary heart disease). Magnitudes of associations did not differ according to the proportion of males, geographical region, or osteoprotegerin assay manufacturer. There was no evidence for publication bias for any of the outcomes assessed (all P>0.05). Elevated osteoprotegerin concentration is associated with an increased risk of incident cardiovascular disease in the general population. The mechanisms underlying this observation deserve further investigation.

  10. Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect L-Lysine Production in Corynebacterium glutamicum.

    Science.gov (United States)

    Kim, Hong-Il; Kim, Jong-Hyeon; Park, Young-Jin

    2016-03-09

    Corynebacterium glutamicum is widely used for amino acid production. In the present study, 543 genes showed a significant change in their mRNA expression levels in L-lysine-producing C. glutamicum ATCC21300 than that in the wild-type C. glutamicum ATCC13032. Among these 543 differentially expressed genes (DEGs), 28 genes were up- or downregulated. In addition, 454 DEGs were functionally enriched and categorized based on BLAST sequence homologies and gene ontology (GO) annotations using the Blast2GO software. Interestingly, NCgl0071 (bioB, encoding biotin synthase) was expressed at levels ~20-fold higher in the L-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain. Five other genes involved in biotin metabolism or transport--NCgl2515 (bioA, encoding adenosylmethionine-8-amino-7-oxononanoate aminotransferase), NCgl2516 (bioD, encoding dithiobiotin synthetase), NCgl1883, NCgl1884, and NCgl1885--were also expressed at significantly higher levels in the L-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain, which we determined using both next-generation RNA sequencing and quantitative real-time PCR analysis. When we disrupted the bioB gene in C. glutamicum ATCC21300, L-lysine production decreased by approximately 76%, and the three genes involved in biotin transport (NCgl1883, NCgl1884, and NCgl1885) were significantly downregulated. These results will be helpful to improve our understanding of C. glutamicum for industrial amino acid production.

  11. Interactome analysis of transcriptional coactivator multiprotein bridging factor 1 unveils a yeast AP-1-like transcription factor involved in oxidation tolerance of mycopathogen Beauveria bassiana.

    Science.gov (United States)

    Chu, Xin-Ling; Dong, Wei-Xia; Ding, Jin-Li; Feng, Ming-Guang; Ying, Sheng-Hua

    2018-02-01

    Oxidation tolerance is an important determinant to predict the virulence and biocontrol potential of Beauveria bassiana, a well-known entomopathogenic fungus. As a transcriptional coactivator, multiprotein bridging factor 1 mediates the activity of transcription factor in diverse physiological processes, and its homolog in B. bassiana (BbMBF1) contributes to fungal oxidation tolerance. In this study, the BbMBF1-interactomes under oxidative stress and normal growth condition were deciphered by mass spectrometry integrated with the immunoprecipitation. BbMBF1p factor has a broad interaction with proteins that are involved in various cellular processes, and this interaction is dynamically regulated by oxidative stress. Importantly, a B. bassiana homolog of yeast AP-1-like transcription factor (BbAP-1) was specifically associated with the BbMBF1-interactome under oxidation and significantly contributed to fungal oxidation tolerance. In addition, qPCR analysis revealed that several antioxidant genes are jointly controlled by BbAP-1 and BbMBF1. Conclusively, it is proposed that BbMBF1p protein mediates BbAP-1p factor to transcribe the downstream antioxidant genes in B. bassiana under oxidative stress. This study demonstrates for the first time a proteomic view of the MBF1-interactome in fungi, and presents an initial framework to probe the transcriptional mechanism involved in fungal response to oxidation, which will provide a new strategy to improve the biocontrol efficacy of B. bassiana.

  12. De Novo Assembly, Functional Annotation and Comparative Analysis of Withania somnifera Leaf and Root Transcriptomes to Identify Putative Genes Involved in the Withanolides Biosynthesis

    Science.gov (United States)

    Gupta, Parul; Goel, Ridhi; Pathak, Sumya; Srivastava, Apeksha; Singh, Surya Pratap; Sangwan, Rajender Singh; Asif, Mehar Hasan; Trivedi, Prabodh Kumar

    2013-01-01

    Withania somnifera is one of the most valuable medicinal plants used in Ayurvedic and other indigenous medicine systems due to bioactive molecules known as withanolides. As genomic information regarding this plant is very limited, little information is available about biosynthesis of withanolides. To facilitate the basic understanding about the withanolide biosynthesis pathways, we performed transcriptome sequencing for Withania leaf (101L) and root (101R) which specifically synthesize withaferin A and withanolide A, respectively. Pyrosequencing yielded 8,34,068 and 7,21,755 reads which got assembled into 89,548 and 1,14,814 unique sequences from 101L and 101R, respectively. A total of 47,885 (101L) and 54,123 (101R) could be annotated using TAIR10, NR, tomato and potato databases. Gene Ontology and KEGG analyses provided a detailed view of all the enzymes involved in withanolide backbone synthesis. Our analysis identified members of cytochrome P450, glycosyltransferase and methyltransferase gene families with unique presence or differential expression in leaf and root and might be involved in synthesis of tissue-specific withanolides. We also detected simple sequence repeats (SSRs) in transcriptome data for use in future genetic studies. Comprehensive sequence resource developed for Withania, in this study, will help to elucidate biosynthetic pathway for tissue-specific synthesis of secondary plant products in non-model plant organisms as well as will be helpful in developing strategies for enhanced biosynthesis of withanolides through biotechnological approaches. PMID:23667511

  13. De novo assembly, functional annotation and comparative analysis of Withania somnifera leaf and root transcriptomes to identify putative genes involved in the withanolides biosynthesis.

    Directory of Open Access Journals (Sweden)

    Parul Gupta

    Full Text Available Withania somnifera is one of the most valuable medicinal plants used in Ayurvedic and other indigenous medicine systems due to bioactive molecules known as withanolides. As genomic information regarding this plant is very limited, little information is available about biosynthesis of withanolides. To facilitate the basic understanding about the withanolide biosynthesis pathways, we performed transcriptome sequencing for Withania leaf (101L and root (101R which specifically synthesize withaferin A and withanolide A, respectively. Pyrosequencing yielded 8,34,068 and 7,21,755 reads which got assembled into 89,548 and 1,14,814 unique sequences from 101L and 101R, respectively. A total of 47,885 (101L and 54,123 (101R could be annotated using TAIR10, NR, tomato and potato databases. Gene Ontology and KEGG analyses provided a detailed view of all the enzymes involved in withanolide backbone synthesis. Our analysis identified members of cytochrome P450, glycosyltransferase and methyltransferase gene families with unique presence or differential expression in leaf and root and might be involved in synthesis of tissue-specific withanolides. We also detected simple sequence repeats (SSRs in transcriptome data for use in future genetic studies. Comprehensive sequence resource developed for Withania, in this study, will help to elucidate biosynthetic pathway for tissue-specific synthesis of secondary plant products in non-model plant organisms as well as will be helpful in developing strategies for enhanced biosynthesis of withanolides through biotechnological approaches.

  14. Integrated Proteome Analysis of the Wheat Embryo and Endosperm Reveals Central Metabolic Changes Involved in the Water Deficit Response during Grain Development.

    Science.gov (United States)

    Gu, Aiqin; Hao, Pengchao; Lv, Dongwen; Zhen, Shoumin; Bian, Yanwei; Ma, Chaoying; Xu, Yanhao; Zhang, Wenying; Yan, Yueming

    2015-09-30

    The embryo and endosperm of wheat have different physiological functions and large differences in protein level. In this study, we performed the first integrated proteome analysis of wheat embryo and endosperm in response to the water deficit during grain development. In total, 155 and 130 differentially expressed protein (DEP) spots in the embryo and endosperm, respectively, were identified by nonlinear two-dimensional electrophoresis and tandem mass spectrometry. These DEPs in the embryo were mainly involved in stress/defense responses such as heat shock-related proteins (HSP) and peroxidase, whereas those in endosperm were mainly related to starch and storage protein synthesis such as α-amylase inhibitor and the globulin-1 S allele. In particular, some storage proteins such as avenin-like proteins and high-molecular weight glutenin subunit Dy12 displayed higher expression levels in the mature endosperm under a water deficit, which might contribute to the improvement in the quality of breadmaking.

  15. Gene expression analysis of overwintering mountain pine beetle larvae suggests multiple systems involved in overwintering stress, cold hardiness, and preparation for spring development

    Directory of Open Access Journals (Sweden)

    Jeanne A. Robert

    2016-07-01

    Full Text Available Cold-induced mortality has historically been a key aspect of mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae, population control, but little is known about the molecular basis for cold tolerance in this insect. We used RNA-seq analysis to monitor gene expression patterns of mountain pine beetle larvae at four time points during their overwintering period—early-autumn, late-autumn, early-spring, and late-spring. Changing transcript profiles over the winter indicates a multipronged physiological response from larvae that is broadly characterized by gene transcripts involved in insect immune responses and detoxification during the autumn. In the spring, although transcripts associated with developmental process are present, there was no particular biological process dominating the transcriptome.

  16. Evidence of Multiple Treponema Phylotypes Involved in Bovine Digital Dermatitis as Shown by 16S rRNA Gene Analysis and Fluorescence In Situ Hybridization

    DEFF Research Database (Denmark)

    Klitgaard, Kirstine; Boye, Mette; Capion, Nynne

    2008-01-01

    of the bacteria involved in DD lesions of cattle by using culture-independent molecular methods. Ten different phylotypes of Treponema were identified either by 16S rRNA gene sequencing of bacteria from DD lesions or by fluorescence in situ hybridization (FISH) analysis using phylotype-specific 16S r......RNA-directed oligonucleotide probes. Two phylotypes, phylotype 1 (PT1) and PT2, were not closely related to any characterized treponemal species. PT7 was 99.3% identical to Treponema denticola, while PT9 resembled T. vincentii by 96%. The remaining phylotypes, PT3, PT4, PT5, PT6, and PT8, and Treponema brennaborense had...... previously been isolated from DD lesions. Forty DD biopsy specimens were examined for Treponema by FISH. With one exception, all of the biopsy specimens revealed epidermotropic, intermingled infection with three or more different phylotypes (mean, 4.7). The most prevalent species were PT1 (95%), PT6 (93...

  17. Comparative Transcriptome Analysis of Adipose Tissues Reveals that ECM-Receptor Interaction Is Involved in the Depot-Specific Adipogenesis in Cattle.

    Directory of Open Access Journals (Sweden)

    Hyun-Jeong Lee

    Full Text Available Adipocytes mainly function as energy storage and endocrine cells. Adipose tissues showed the biological and genetic difference based on their depots. The difference of adipocytes between depots might be influenced by the inherent genetic programing for adipogenesis. We used RNA-seq technique to investigate the transcriptomes in 3 adipose tissues of omental (O, subcutaneous (S and intramuscular (I fats in cattle. Sequence reads were obtained from Illumina HiSeq2000 and mapped to the bovine genome using Tophat2. Differentially expressed genes (DEG between adipose tissues were detected by EdgeR. We identified 5797, 2156, and 5455 DEGs in the comparison between OI, OS, and IS respectively and also found 5657 DEGs in the comparison between the intramuscular and the combined omental and subcutaneous fats (C (FDR<0.01. Depot specifically up- and down- regulated DEGs were 853 in S, 48 in I, and 979 in O. The numbers of DEGs and functional annotation studies suggested that I had the different genetic profile compared to other two adipose tissues. In I, DEGs involved in the developmental process (eg. EGR2, FAS, and KLF7 were up-regulated and those in the immune system process were down-regulated. Many DEGs from the adipose tissues were enriched in the various GO terms of developmental process and KEGG pathway analysis showed that the ECM-receptor interaction was one of commonly enriched pathways in all of the 3 adipose tissues and also functioned as a sub-pathway of other enriched pathways. However, genes involved in the ECM-receptor interaction were differentially regulated depending on the depots. Collagens, main ECM constituents, were significantly up-regulated in S and integrins, transmembrane receptors, were up-regulated in I. Different laminins were up-regulated in the different depots. This comparative transcriptome analysis of three adipose tissues suggested that the interactions between ECM components and transmembrane receptors of fat cells

  18. In vivo versus in vitro protein abundance analysis of Shigella dysenteriae type 1 reveals changes in the expression of proteins involved in virulence, stress and energy metabolism

    Directory of Open Access Journals (Sweden)

    Donohue-Rolfe Arthur

    2011-06-01

    Full Text Available Abstract Background Shigella dysenteriae serotype 1 (SD1 causes the most severe form of epidemic bacillary dysentery. Quantitative proteome profiling of Shigella dysenteriae serotype 1 (SD1 in vitro (derived from LB cell cultures and in vivo (derived from gnotobiotic piglets was performed by 2D-LC-MS/MS and APEX, a label-free computationally modified spectral counting methodology. Results Overall, 1761 proteins were quantitated at a 5% FDR (false discovery rate, including 1480 and 1505 from in vitro and in vivo samples, respectively. Identification of 350 cytoplasmic membrane and outer membrane (OM proteins (38% of in silico predicted SD1 membrane proteome contributed to the most extensive survey of the Shigella membrane proteome reported so far. Differential protein abundance analysis using statistical tests revealed that SD1 cells switched to an anaerobic energy metabolism under in vivo conditions, resulting in an increase in fermentative, propanoate, butanoate and nitrate metabolism. Abundance increases of transcription activators FNR and Nar supported the notion of a switch from aerobic to anaerobic respiration in the host gut environment. High in vivo abundances of proteins involved in acid resistance (GadB, AdiA and mixed acid fermentation (PflA/PflB indicated bacterial survival responses to acid stress, while increased abundance of oxidative stress proteins (YfiD/YfiF/SodB implied that defense mechanisms against oxygen radicals were mobilized. Proteins involved in peptidoglycan turnover (MurB were increased, while β-barrel OM proteins (OmpA, OM lipoproteins (NlpD, chaperones involved in OM protein folding pathways (YraP, NlpB and lipopolysaccharide biosynthesis (Imp were decreased, suggesting unexpected modulations of the outer membrane/peptidoglycan layers in vivo. Several virulence proteins of the Mxi-Spa type III secretion system and invasion plasmid antigens (Ipa proteins required for invasion of colonic epithelial cells, and release

  19. Descriptive analysis of the verbal behavior of a therapist: a known-group validity analysis of the putative behavioral functions involved in clinical interaction.

    Science.gov (United States)

    Virues-Ortega, Javier; Montaño-Fidalgo, Montserrat; Froján-Parga, María Xesús; Calero-Elvira, Ana

    2011-12-01

    This study analyzes the interobserver agreement and hypothesis-based known-group validity of the Therapist's Verbal Behavior Category System (SISC-INTER). The SISC-INTER is a behavioral observation protocol comprised of a set of verbal categories representing putative behavioral functions of the in-session verbal behavior of a therapist (e.g., discriminative, reinforcing, punishing, and motivational operations). The complete therapeutic process of a clinical case of an individual with marital problems was recorded (10 sessions, 8 hours), and data were arranged in a temporal sequence using 10-min periods. Hypotheses based on the expected performance of the putative behavioral functions portrayed by the SISC-INTER codes across prevalent clinical activities (i.e., assessing, explaining, Socratic method, providing clinical guidance) were tested using autoregressive integrated moving average (ARIMA) models. Known-group validity analyses provided support to all hypotheses. The SISC-INTER may be a useful tool to describe therapist-client interaction in operant terms. The utility of reliable and valid protocols for the descriptive analysis of clinical practice in terms of verbal behavior is discussed. Copyright © 2011. Published by Elsevier Ltd.

  20. QTL Analysis of High Thermotolerance with Superior and Downgraded Parental Yeast Strains Reveals New Minor QTLs and Converges on Novel Causative Alleles Involved in RNA Processing

    Science.gov (United States)

    Yang, Yudi; Foulquié-Moreno, Maria R.; Clement, Lieven; Erdei, Éva; Tanghe, An; Schaerlaekens, Kristien; Dumortier, Françoise; Thevelein, Johan M.

    2013-01-01

    Revealing QTLs with a minor effect in complex traits remains difficult. Initial strategies had limited success because of interference by major QTLs and epistasis. New strategies focused on eliminating major QTLs in subsequent mapping experiments. Since genetic analysis of superior segregants from natural diploid strains usually also reveals QTLs linked to the inferior parent, we have extended this strategy for minor QTL identification by eliminating QTLs in both parent strains and repeating the QTL mapping with pooled-segregant whole-genome sequence analysis. We first mapped multiple QTLs responsible for high thermotolerance in a natural yeast strain, MUCL28177, compared to the laboratory strain, BY4742. Using single and bulk reciprocal hemizygosity analysis we identified MKT1 and PRP42 as causative genes in QTLs linked to the superior and inferior parent, respectively. We subsequently downgraded both parents by replacing their superior allele with the inferior allele of the other parent. QTL mapping using pooled-segregant whole-genome sequence analysis with the segregants from the cross of the downgraded parents, revealed several new QTLs. We validated the two most-strongly linked new QTLs by identifying NCS2 and SMD2 as causative genes linked to the superior downgraded parent and we found an allele-specific epistatic interaction between PRP42 and SMD2. Interestingly, the related function of PRP42 and SMD2 suggests an important role for RNA processing in high thermotolerance and underscores the relevance of analyzing minor QTLs. Our results show that identification of minor QTLs involved in complex traits can be successfully accomplished by crossing parent strains that have both been downgraded for a single QTL. This novel approach has the advantage of maintaining all relevant genetic diversity as well as enough phenotypic difference between the parent strains for the trait-of-interest and thus maximizes the chances of successfully identifying additional minor

  1. QTL analysis of high thermotolerance with superior and downgraded parental yeast strains reveals new minor QTLs and converges on novel causative alleles involved in RNA processing.

    Directory of Open Access Journals (Sweden)

    Yudi Yang

    Full Text Available Revealing QTLs with a minor effect in complex traits remains difficult. Initial strategies had limited success because of interference by major QTLs and epistasis. New strategies focused on eliminating major QTLs in subsequent mapping experiments. Since genetic analysis of superior segregants from natural diploid strains usually also reveals QTLs linked to the inferior parent, we have extended this strategy for minor QTL identification by eliminating QTLs in both parent strains and repeating the QTL mapping with pooled-segregant whole-genome sequence analysis. We first mapped multiple QTLs responsible for high thermotolerance in a natural yeast strain, MUCL28177, compared to the laboratory strain, BY4742. Using single and bulk reciprocal hemizygosity analysis we identified MKT1 and PRP42 as causative genes in QTLs linked to the superior and inferior parent, respectively. We subsequently downgraded both parents by replacing their superior allele with the inferior allele of the other parent. QTL mapping using pooled-segregant whole-genome sequence analysis with the segregants from the cross of the downgraded parents, revealed several new QTLs. We validated the two most-strongly linked new QTLs by identifying NCS2 and SMD2 as causative genes linked to the superior downgraded parent and we found an allele-specific epistatic interaction between PRP42 and SMD2. Interestingly, the related function of PRP42 and SMD2 suggests an important role for RNA processing in high thermotolerance and underscores the relevance of analyzing minor QTLs. Our results show that identification of minor QTLs involved in complex traits can be successfully accomplished by crossing parent strains that have both been downgraded for a single QTL. This novel approach has the advantage of maintaining all relevant genetic diversity as well as enough phenotypic difference between the parent strains for the trait-of-interest and thus maximizes the chances of successfully identifying

  2. CNS involvement and treatment with interferon-α are independent prognostic factors in Erdheim-Chester disease: a multicenter survival analysis of 53 patients.

    Science.gov (United States)

    Arnaud, Laurent; Hervier, Baptiste; Néel, Antoine; Hamidou, Mohamed A; Kahn, Jean-Emmanuel; Wechsler, Bertrand; Pérez-Pastor, Gemma; Blomberg, Bjørn; Fuzibet, Jean-Gabriel; Dubourguet, François; Marinho, António; Magnette, Catherine; Noel, Violaine; Pavic, Michel; Casper, Jochen; Beucher, Anne-Bérangère; Costedoat-Chalumeau, Nathalie; Aaron, Laurent; Salvatierra, Juan; Graux, Carlos; Cacoub, Patrice; Delcey, Véronique; Dechant, Claudia; Bindi, Pascal; Herbaut, Christiane; Graziani, Giorgio; Amoura, Zahir; Haroche, Julien

    2011-03-10

    Erdheim-Chester disease (ECD) is a rare form of non-Langerhans histiocytosis, with noncodified therapeutic management and high mortality. No treatment has yet been shown to improve survival in these patients. We conducted a multicenter prospective observational cohort study to assess whether extraskeletal manifestations and interferon-α treatment would influence survival in a large cohort of ECD patients. To achieve this goal, we thoroughly analyzed the clinical presentation of 53 patients with biopsy-proven ECD, and we performed a survival analysis using Cox proportional hazard model. Fifty-three patients (39 men and 14 women) with biopsy-proven ECD were followed up between November 1981 and November 2010. Forty-six patients (87%) received interferon-α and/or PEGylated interferon-α. Multivariate survival analysis using Cox proportional hazard model revealed that central nervous system involvement was an independent predictor of death (hazard ratio = 2.51; 95% confidence interval, 1.28-5.52; P = .006) in our cohort. Conversely, treatment with interferon-α was identified as an independent predictor of survival (hazard ratio = 0.32; 95% confidence interval, 0.14-0.70; P = .006). Although definitive confirmation would require a randomized controlled trial, these results suggest that interferon-α improves survival in ECD patients. This may be seen as a significant advance, as it is the first time a treatment is shown to improve survival in this multisystemic disease with high mortality.

  3. ACE (I/D polymorphism and response to treatment in coronary artery disease: a comprehensive database and meta-analysis involving study quality evaluation

    Directory of Open Access Journals (Sweden)

    Kitsios Georgios

    2009-06-01

    Full Text Available Abstract Background The role of angiotensin-converting enzyme (ACE gene insertion/deletion (I/D polymorphism in modifying the response to treatment modalities in coronary artery disease is controversial. Methods PubMed was searched and a database of 58 studies with detailed information regarding ACE I/D polymorphism and response to treatment in coronary artery disease was created. Eligible studies were synthesized using meta-analysis methods, including cumulative meta-analysis. Heterogeneity and study quality issues were explored. Results Forty studies involved invasive treatments (coronary angioplasty or coronary artery by-pass grafting and 18 used conservative treatment options (including anti-hypertensive drugs, lipid lowering therapy and cardiac rehabilitation procedures. Clinical outcomes were investigated by 11 studies, while 47 studies focused on surrogate endpoints. The most studied outcome was the restenosis following coronary angioplasty (34 studies. Heterogeneity among studies (p ACE I/D polymorphism on the response to treatment for the rest outcomes (coronary events, endothelial dysfunction, left ventricular remodeling, progression/regression of atherosclerosis, individual studies showed significance; however, results were discrepant and inconsistent. Conclusion In view of available evidence, genetic testing of ACE I/D polymorphism prior to clinical decision making is not currently justified. The relation between ACE genetic variation and response to treatment in CAD remains an unresolved issue. The results of long-term and properly designed prospective studies hold the promise for pharmacogenetically tailored therapy in CAD.

  4. Identification and Functional Analysis of microRNAs Involved in the Anther Development in Cotton Genic Male Sterile Line Yu98-8A

    Directory of Open Access Journals (Sweden)

    Xiaojie Yang

    2016-10-01

    Full Text Available Hybrid vigor contributes in a large way to the yield and quality of cotton (Gossypium hirsutum fiber. Although microRNAs play essential regulatory roles in flower induction and development, it is still unclear if microRNAs are involved in male sterility, as the regulatory molecular mechanisms of male sterility in cotton need to be better defined. In this study, two independent small RNA libraries were constructed and sequenced from the young buds collected from the sporogenous cell formation to the meiosis stage of the male sterile line Yu98-8A and the near-isogenic line. Sequencing revealed 1588 and 1536 known microRNAs and 347 and 351 novel miRNAs from male sterile and male fertile libraries, respectively. MicroRNA expression profiles revealed that 49 conserved and 51 novel miRNAs were differentially expressed. Bioinformatic and degradome analysis indicated the regulatory complexity of microRNAs during flower induction and development. Further RT-qPCR and physiological analysis indicated that, among the different Kyoto Encyclopedia Gene and Genomes pathways, indole-3-acetic acid and gibberellic acid signaling transduction pathways may play pivotal regulatory functions in male sterility.

  5. Construction of an in vivo system for functional analysis of the genes involved in sex pheromone production in the silkmoth, Bombyx mori.

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    Ken-Ichi eMoto

    2012-02-01

    Full Text Available Moths produce species-specific sex pheromones to attract conspecific mates. The biochemical processes that comprise sex pheromone biosynthesis are precisely regulated and a number of gene products are involved in this biosynthesis and regulation. In recent years, at least 300 EST clones have been isolated from Bombyx mori pheromone gland (PG specific cDNA libraries with some of those clones (i.e., B. mori PG-specific desaturase1 (Bmpgdesat1, PG-specific fatty-acyl reductase (pgFAR, PG-specific acyl-CoA-binding protein (pgACBP, B. mori fatty acid transport protein (BmFATP, B. mori lipid storage droplet protein-1 (BmLsd1 characterized and demonstrated to play a role in sex pheromone production. However, most of the EST clones have yet to be fully characterized and identified. To develop an efficient system for analyzing sex pheromone production-related genes, we investigated the feasibility of a novel gene analysis system using the upstream region of Bmpgdesat1 that should contain a PG-specific gene promoter in conjunction with piggyBac vector-mediated germ-line transformation. As a result, we have been able to obtain expression of our reporter gene (enhanced green fluorescent protein in the PG but not in other tissues of transgenic B. mori. Current results indicate that we have successfully constructed a novel in vivo gene analysis system for sex pheromone production in B. mori.

  6. Muscle transcriptome analysis reveals molecular pathways and biomarkers involved in extreme ultimate pH and meat defect occurrence in chicken.

    Science.gov (United States)

    Beauclercq, Stéphane; Hennequet-Antier, Christelle; Praud, Christophe; Godet, Estelle; Collin, Anne; Tesseraud, Sophie; Métayer-Coustard, Sonia; Bourin, Marie; Moroldo, Marco; Martins, Frédéric; Lagarrigue, Sandrine; Bihan-Duval, Elisabeth Le; Berri, Cécile

    2017-07-25

    The processing ability and sensory quality of chicken breast meat are highly related to its ultimate pH (pHu), which is mainly determined by the amount of glycogen in the muscle at death. To unravel the molecular mechanisms underlying glycogen and meat pHu variations and to identify predictive biomarkers of these traits, a transcriptome profiling analysis was performed using an Agilent custom chicken 8 × 60 K microarray. The breast muscle gene expression patterns were studied in two chicken lines experimentally selected for high (pHu+) and low (pHu-) pHu values of the breast meat. Across the 1,436 differentially expressed (DE) genes found between the two lines, many were involved in biological processes related to muscle development and remodelling and carbohydrate and energy metabolism. The functional analysis showed an intensive use of carbohydrate metabolism to produce energy in the pHu- line, while alternative catabolic pathways were solicited in the muscle of the pHu+ broilers, compromising their muscle development and integrity. After a validation step on a population of 278 broilers using microfluidic RT-qPCR, 20 genes were identified by partial least squares regression as good predictors of the pHu, opening new perspectives of screening broilers likely to present meat quality defects.

  7. Association of rs2228570 polymorphism of vitamin D receptor gene with degenerative disc disease: a meta-analysis involving 2947 subjects.

    Science.gov (United States)

    Zong, Qiang; Ni, Dongkui; Li, Lijun; Shi, Yubo

    2015-01-01

    This study aimed to explore the association between the rs2228570 polymorphism in the vitamin D receptor gene and degenerative disc disease (IDD), especially in European. We perform a meta-analysis to analyze the association after searching the relevant studies through China National Knowledge Infrastructure (CNKI), PubMed, Medline and EMBASE databases. And odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to evaluate the strength of the association. A total of 10 studies involving 1,465 cases and 1,482 controls were included in the meta-analysis. Overall, there was not significant risk between rs2228570 polymorphism and degenerative disc disease in any genetic models. In addition, stratified analyses by ethnicity revealed similar results. However, stratified analyses by others indicates an association between IDD and the FF genotype (OR=0.62, 95% CI=0.43- 0.90, P=0.486) in age =40, and the F allele (OR=0.84, 95% CI=0.73-0.96, P=0.992), FF genotype (OR=0.78, 95% CI=0.65-0.93, P=0.853) in sample size > 300, and ff genotype (OR=0.91, 95% CI=1.11-3.29, P=0.783), FF genotype (OR=0.70, 95% CI=0.51-0.96, P=0.258) in Northern European. This meta-analysis suggested that the rs2228570 polymorphism may not be associated with degenerative disc disease. However, there existed some diversities, especially in age 300, countries in Northern Europe, suggesting that carrying the VDR FokI F allele may be a protective factor against IDD development. But a large number of well-designed studies are still required to assess this polymorphism and degenerative disc disease.

  8. Evidence of multiple Treponema phylotypes involved in bovine digital dermatitis as shown by 16S rRNA gene analysis and fluorescence in situ hybridization.

    Science.gov (United States)

    Klitgaard, Kirstine; Boye, Mette; Capion, Nynne; Jensen, Tim K

    2008-09-01

    The etiopathogenesis of the skin disease digital dermatitis (DD), an important cause of lameness in cattle, remains uncertain. Microscopically, the disease appears to be polymicrobial, with spirochetes as the predominant bacteria. The objective of this study was to identify the main part of the bacteria involved in DD lesions of cattle by using culture-independent molecular methods. Ten different phylotypes of Treponema were identified either by 16S rRNA gene sequencing of bacteria from DD lesions or by fluorescence in situ hybridization (FISH) analysis using phylotype-specific 16S rRNA-directed oligonucleotide probes. Two phylotypes, phylotype 1 (PT1) and PT2, were not closely related to any characterized treponemal species. PT7 was 99.3% identical to Treponema denticola, while PT9 resembled T. vincentii by 96%. The remaining phylotypes, PT3, PT4, PT5, PT6, and PT8, and Treponema brennaborense had previously been isolated from DD lesions. Forty DD biopsy specimens were examined for Treponema by FISH. With one exception, all of the biopsy specimens revealed epidermotropic, intermingled infection with three or more different phylotypes (mean, 4.7). The most prevalent species were PT1 (95%), PT6 (93%), and PT3 (85%). While colonization by PT3 was confined to the surface of the epidermis, both PT1 and PT6 invaded deep into the stratum spinosum and were seen in ulcerated dermal papillae. In two cases, all 10 phylotypes were demonstrated. Furthermore, FISH with a Treponema group-specific probe showed that Treponema accounted for more than 90% of the total bacterial population in the biopsy specimens. These data strongly suggest that a group of apparently symbiotic Treponema species are involved as primary bacterial pathogens in DD.

  9. The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism.

    Science.gov (United States)

    Wang, Na; Wang, Ruoqing; Wang, Renkai; Tian, Yongsheng; Shao, Changwei; Jia, Xiaodong; Chen, Songlin

    2017-01-01

    Albinism, a phenomenon characterized by pigmentation deficiency on the ocular side of Japanese flounder (Paralichthys olivaceus), has caused significant damage. Limited mRNA and microRNA (miRNA) information is available on fish pigmentation deficiency. In this study, a high-throughput sequencing strategy was employed to identify the mRNA and miRNAs involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05). The next target prediction discovered a variety of putative target genes, of which, 134 genes including Tyrosinase (TYR), Tyrosinase-related protein 1 (TYRP1), Microphthalmia-associated transcription factor (MITF) were overlapped with differentially expressed genes derived from RNA-seq. These target genes were significantly enriched to 254 GO terms and 103 KEGG pathways (p<0.001). Of those, tyrosine metabolism, lysosomes, phototransduction pathways, etc., attracted considerable attention due to their involvement in regulating skin pigmentation. Expression patterns of differentially expressed mRNA and miRNAs were validated in 10 mRNA and 10 miRNAs by qRT-PCR. With high-throughput mRNA and miRNA sequencing and analysis, a series of interested mRNA and miRNAs involved in fish

  10. Monoarticular Hip Involvement in Pseudogout

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    Figen Kocyigit

    2015-01-01

    Full Text Available Pseudogout is the acutest form of arthritis in the elderly. Although clinical manifestations vary widely, polyarticular involvement is typical mimicking osteoarthritis or rheumatoid arthritis. Monoarticular involvement is relatively rare and is generally provoked by another medical condition. There are reported cases of hip involvement by pseudogout in monoarticular form. However, all of the cases were presented as septic arthritis. In this report, we present a case of monoarticular hip involvement mimicking soft tissue abscess. We confirmed the pseudogout diagnosis after ultrasonographic evaluation of the involved hip joint and pathological and biochemical analysis of synovial fluid analysis. Diagnosis is important to avoid unnecessary medical and surgical treatment in cases of the bizarre involvement of hip in pseudogout.

  11. Patient involvement in Danish health care

    DEFF Research Database (Denmark)

    Vrangbaek, Karsten

    2015-01-01

    for analysis of patient involvement in health care. This framework is used to analyze key governance features of patient involvement in Denmark based on previous research papers and reports describing patient involvement in Danish health care. FINDINGS: Patient involvement is important in Denmark...... implications for the development of patient involvement in health care. ORIGINALITY/VALUE: This paper fulfills a need to study different types of patient involvement and to develop a theoretical framework for characterizing and analyzing such involvement strategies....

  12. Involved Node Radiation Therapy

    DEFF Research Database (Denmark)

    Maraldo, Maja V; Aznar, Marianne C; Vogelius, Ivan R

    2012-01-01

    PURPOSE: The involved node radiation therapy (INRT) strategy was introduced for patients with Hodgkin lymphoma (HL) to reduce the risk of late effects. With INRT, only the originally involved lymph nodes are irradiated. We present treatment outcome in a retrospective analysis using this strategy...... to 36 Gy). Patients attended regular follow-up visits until 5 years after therapy. RESULTS: The 4-year freedom from disease progression was 96.4% (95% confidence interval: 92.4%-100.4%), median follow-up of 50 months (range: 4-71 months). Three relapses occurred: 2 within the previous radiation field......, and 1 in a previously uninvolved region. The 4-year overall survival was 94% (95% confidence interval: 88.8%-99.1%), median follow-up of 58 months (range: 4-91 months). Early radiation therapy toxicity was limited to grade 1 (23.4%) and grade 2 (13.8%). During follow-up, 8 patients died, none from HL, 7...

  13. Who and What Does Involvement Involve?

    DEFF Research Database (Denmark)

    Hansen, Jeppe Oute; Petersen, A.; Huniche, L.

    2015-01-01

    , and on what grounds, involvement of relatives is perceived in Danish psychiatry. Paradoxically, the current understanding of involvement of relatives fails to take into consideration the perspectives of the relatives per se and families that were being studied. By analyzing involvement from a discourse...... the responsibility toward the mental health of the ill individual as well as toward the psychological milieu of the family....

  14. Association between EHBP1 rs721048(A>G polymorphism and prostate cancer susceptibility: a meta-analysis of 17 studies involving 150,678 subjects

    Directory of Open Access Journals (Sweden)

    Ao X

    2015-07-01

    Full Text Available Xiang Ao,1,* Ying Liu,1,* Xiao-Yan Bai,1 Xinjian Qu,2 Zhaowei Xu,1 Gaolei Hu,1 Min Chen,1 Huijian Wu1,21Laboratory of Molecular Medicine & Pharmacy, School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 2Laboratory of Molecular Medicine & Pharmacy, School of Life Science and Medicine, Dalian University of Technology, Panjin, Liaoning, People’s Republic of China*These authors have contributed equally to this workBackground: EHBP1 rs721048(A was first identified as a prostate cancer (PCa risk in Caucasians by genome-wide association study, but subsequent replication studies involving Caucasian and other ethnicities did not produce consistent results. The aim of this study was to obtain a more definite association between rs721048(A and PCa risk.Methods: We comprehensively searched several databases updated to September 2014, including PubMed, Web of Science, EBSCO, and Google Scholar. Two authors independently screened and reviewed the eligibility of each study. The quality of the included studies was assessed by the Newcastle–Ottawa scale. The association of rs721048(A and PCa risk was assessed by pooling odds ratios (ORs with 95% confidence intervals (CIs.Results: A total of 17 studies, including 48,135 cases and 102,543 controls, published between 2008 and 2014 were included in the meta-analysis. Overall, the pooled analysis demonstrated that rs721048(A was significantly associated with the risk of PCa under the allele model (OR=1.14, 95% CI=1.11–1.17, P=0.000. Subgroup analysis based on ethnicity revealed a ­significant association between rs721048(A and PCa in Caucasian (OR=1.14, 95% CI=1.11–1.16, P=0.000, African descent (OR=1.11, 95% CI=1.01–1.23, P=0.025, and Asian (OR=1.35, 95% CI=1.12–1.64, P=0.002.Conclusion: Our results provided strong evidence that rs721048(A could be a risk factor for PCa.Keywords: EHBP1, rs721048, meta-analysis, prostate cancer

  15. Molecular Cloning, Characterization, and Functional Analysis of Acetyl-CoA C-Acetyltransferase and Mevalonate Kinase Genes Involved in Terpene Trilactone Biosynthesis from Ginkgo biloba

    Directory of Open Access Journals (Sweden)

    Qiangwen Chen

    2017-01-01

    Full Text Available Ginkgolides and bilobalide, collectively termed terpene trilactones (TTLs, are terpenoids that form the main active substance of Ginkgo biloba. Terpenoids in the mevalonate (MVA biosynthetic pathway include acetyl-CoA C-acetyltransferase (AACT and mevalonate kinase (MVK as core enzymes. In this study, two full-length (cDNAs encoding AACT (GbAACT, GenBank Accession No. KX904942 and MVK (GbMVK, GenBank Accession No. KX904944 were cloned from G. biloba. The deduced GbAACT and GbMVK proteins contain 404 and 396 amino acids with the corresponding open-reading frame (ORF sizes of 1215 bp and 1194 bp, respectively. Tissue expression pattern analysis revealed that GbAACT was highly expressed in ginkgo fruits and leaves, and GbMVK was highly expressed in leaves and roots. The functional complementation of GbAACT in AACT-deficient Saccharomyces cerevisiae strain Δerg10 and GbMVK in MVK-deficient strain Δerg12 confirmed that GbAACT mediated the conversion of mevalonate acetyl-CoA to acetoacetyl-CoA and GbMVK mediated the conversion of mevalonate to mevalonate phosphate. This observation indicated that GbAACT and GbMVK are functional genes in the cytosolic mevalonate (MVA biosynthesis pathway. After G. biloba seedlings were treated with methyl jasmonate and salicylic acid, the expression levels of GbAACT and GbMVK increased, and TTL production was enhanced. The cloning, characterization, expression and functional analysis of GbAACT and GbMVK will be helpful to understand more about the role of these two genes involved in TTL biosynthesis.

  16. Molecular Cloning, Characterization, and Functional Analysis of Acetyl-CoA C-Acetyltransferase and Mevalonate Kinase Genes Involved in Terpene Trilactone Biosynthesis from Ginkgo biloba.

    Science.gov (United States)

    Chen, Qiangwen; Yan, Jiaping; Meng, Xiangxiang; Xu, Feng; Zhang, Weiwei; Liao, Yongling; Qu, Jinwang

    2017-01-02

    Ginkgolides and bilobalide, collectively termed terpene trilactones (TTLs), are terpenoids that form the main active substance of Ginkgo biloba . Terpenoids in the mevalonate (MVA) biosynthetic pathway include acetyl-CoA C -acetyltransferase (AACT) and mevalonate kinase (MVK) as core enzymes. In this study, two full-length (cDNAs) encoding AACT ( GbAACT , GenBank Accession No. KX904942) and MVK ( GbMVK , GenBank Accession No. KX904944) were cloned from G. biloba . The deduced GbAACT and GbMVK proteins contain 404 and 396 amino acids with the corresponding open-reading frame (ORF) sizes of 1215 bp and 1194 bp, respectively. Tissue expression pattern analysis revealed that GbAACT was highly expressed in ginkgo fruits and leaves, and GbMVK was highly expressed in leaves and roots. The functional complementation of GbAACT in AACT-deficient Saccharomyces cerevisiae strain Δerg10 and GbMVK in MVK-deficient strain Δerg12 confirmed that GbAACT mediated the conversion of mevalonate acetyl-CoA to acetoacetyl-CoA and GbMVK mediated the conversion of mevalonate to mevalonate phosphate. This observation indicated that GbAACT and GbMVK are functional genes in the cytosolic mevalonate (MVA) biosynthesis pathway. After G. biloba seedlings were treated with methyl jasmonate and salicylic acid, the expression levels of GbAACT and GbMVK increased, and TTL production was enhanced. The cloning, characterization, expression and functional analysis of GbAACT and GbMVK will be helpful to understand more about the role of these two genes involved in TTL biosynthesis.

  17. Comparative genome analysis of an avirulent and two virulent strains of avian Pasteurella multocida reveals candidate genes involved in fitness and pathogenicity

    Science.gov (United States)

    2013-01-01

    Background Pasteurella multocida is the etiologic agent of fowl cholera, a highly contagious and severe disease of poultry causing significant mortality and morbidity throughout the world. All types of poultry are susceptible to fowl cholera. Turkeys are most susceptible to the peracute/acute forms of the disease while chickens are most susceptible to the acute and chronic forms of the disease. The whole genome of the Pm70 strain of P. multocida was sequenced and annotated in 2001. The Pm70 strain is not virulent to chickens and turkeys. In contrast, strains X73 and P1059 are highly virulent to turkeys, chickens, and other poultry species. In this study, we sequenced the genomes of P. multocida strains X73 and P1059 and undertook a detailed comparative genome analysis with the avirulent Pm70 strain. The goal of this study was to identify candidate genes in the virulent strains that may be involved in pathogenicity of fowl cholera disease. Results Comparison of virulent versus avirulent avian P. multocida genomes revealed 336 unique genes among the P1059 and/or X73 genomes compared to strain Pm70. Genes of interest within this subset included those encoding an L-fucose transport and utilization system, several novel sugar transport systems, and several novel hemagglutinins including one designated PfhB4. Additionally, substantial amino acid variation was observed in many core outer membrane proteins and single nucleotide polymorphism analysis confirmed a higher dN/dS ratio within proteins localized to the outer membrane. Conclusions Comparative analyses of highly virulent versus avirulent avian P. multocida identified a number of genomic differences that may shed light on the ability of highly virulent strains to cause disease in the avian host, including those that could be associated with enhanced virulence or fitness. PMID:23672515

  18. Clinical Outcomes of Gap Balancing vs Measured Resection in Total Knee Arthroplasty: A Systematic Review and Meta-Analysis Involving 2259 Subjects.

    Science.gov (United States)

    Li, Shuxiang; Luo, Xiaomin; Wang, Peng; Sun, Han; Wang, Kun; Sun, Xiaoliang

    2018-03-17

    The argument on the clinical effects between gap balancing (GB) and measured resection (MR) in total knee arthroplasty remains to be resolved. A systematic review and meta-analysis was performed to investigate which technique in total knee arthroplasty has better clinical effect. A total of 20 studies involving 2259 cases were included in the meta-analysis. The primary outcome measure was Knee Society Score (KSS), whereas the secondary outcomes included other function assessment systems (eg, range of motion, Western Ontario and McMaster University Osteoarthritis Index), radiological outcomes (eg, femoral component rotation, total outliers), revision rate, complications (eg, infection, loosening, instability), and surgical time. The GB technique was associated with statistically significant increases in the primary outcomes of KSS-function in 1 year. However, a mean difference of 2.12 points was below the minimal clinically important difference of 6 points. No differences were found in the analyses of KSS-knee and KSS-function in any other follow-up periods. Secondary outcome assessments showed significant decreased surgical time (mean difference, 16.18; P < .00001) for MR. Although statistically significant difference in favor of GB was identified in total outliers (risk ratio, 1.72, P = .0004), the 2 techniques were comparable in range of motion, Western Ontario and McMaster University Osteoarthritis Index, femoral component rotation, complications, and revision rate. We conclude that both techniques can result in equivalent results when done properly, and each surgeon must understand the strengths and weaknesses of each technique. Copyright © 2018 Elsevier Inc. All rights reserved.

  19. Moving towards a more inclusive patient and public involvement in health research paradigm: the incorporation of a trauma-informed intersectional analysis.

    Science.gov (United States)

    Shimmin, Carolyn; Wittmeier, Kristy D M; Lavoie, Josée G; Wicklund, Evan D; Sibley, Kathryn M

    2017-08-07

    The concept of patient engagement in health research has received growing international recognition over recent years. Yet despite some critical advancements, we argue that the concept remains problematic as it negates the very real complexities and context of people's lives. Though patient engagement conceptually begins to disrupt the identity of "researcher," and complicate our assumptions and understandings around expertise and knowledge, it continues to essentialize the identity of "patient" as a homogenous group, denying the reality that individuals' economic, political, cultural, subjective and experiential lives intersect in intricate and multifarious ways. Patient engagement approaches that do not consider the simultaneous interactions between different social categories (e.g. race, ethnicity, Indigeneity, gender, class, sexuality, geography, age, ability, immigration status, religion) that make up social identity, as well as the impact of systems and processes of oppression and domination (e.g. racism, colonialism, classism, sexism, ableism, homophobia) exclude the involvement of individuals who often carry the greatest burden of illness - the very voices traditionally less heard in health research. We contend that in order to be a more inclusive and meaningful approach that does not simply reiterate existing health inequities, it is important to reconceptualize patient engagement through a health equity and social justice lens by incorporating a trauma-informed intersectional analysis. This article provides key concepts to the incorporation of a trauma-informed intersectional analysis and important questions to consider when developing a patient engagement strategy in health research training, practice and evaluation. In redefining the identity of both "patient" and "researcher," spaces and opportunities to resist and renegotiate power within the intersubjective relations can be recognized and addressed, in turn helping to build trust, transparency and

  20. De novo characterization of the spleen transcriptome of the large yellow croaker (Pseudosciaena crocea and analysis of the immune relevant genes and pathways involved in the antiviral response.

    Directory of Open Access Journals (Sweden)

    Yinnan Mu

    Full Text Available The large yellow croaker (Pseudosciaena crocea is an economically important marine fish in China. To understand the molecular basis for antiviral defense in this species, we used Illumia paired-end sequencing to characterize the spleen transcriptome of polyriboinosinic:polyribocytidylic acid [poly(I:C]-induced large yellow croakers. The library produced 56,355,728 reads and assembled into 108,237 contigs. As a result, 15,192 unigenes were found from this transcriptome. Gene ontology analysis showed that 4,759 genes were involved in three major functional categories: biological process, cellular component, and molecular function. We further ascertained that numerous consensus sequences were homologous to known immune-relevant genes. Kyoto Encyclopedia of Genes and Genomes orthology mapping annotated 5,389 unigenes and identified numerous immune-relevant pathways. These immune-relevant genes and pathways revealed major antiviral immunity effectors, including but not limited to: pattern recognition receptors, adaptors and signal transducers, the interferons and interferon-stimulated genes, inflammatory cytokines and receptors, complement components, and B-cell and T-cell antigen activation molecules. Moreover, the partial genes of Toll-like receptor signaling pathway, RIG-I-like receptors signaling pathway, Janus kinase-Signal Transducer and Activator of Transcription (JAK-STAT signaling pathway, and T-cell receptor (TCR signaling pathway were found to be changed after poly(I:C induction by real-time polymerase chain reaction (PCR analysis, suggesting that these signaling pathways may be regulated by poly(I:C, a viral mimic. Overall, the antivirus-related genes and signaling pathways that were identified in response to poly(I:C challenge provide valuable leads for further investigation of the antiviral defense mechanism in the large yellow croaker.

  1. Genome-Wide Analysis of the RAV Family in Soybean and Functional Identification of GmRAV-03 Involvement in Salt and Drought Stresses and Exogenous ABA Treatment

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    Shu-Ping Zhao

    2017-06-01

    Full Text Available Transcription factors play vital roles in plant growth and in plant responses to abiotic stresses. The RAV transcription factors contain a B3 DNA binding domain and/or an APETALA2 (AP2 DNA binding domain. Although genome-wide analyses of RAV family genes have been performed in several species, little is known about the family in soybean (Glycine max L.. In this study, a total of 13 RAV genes, named as GmRAVs, were identified in the soybean genome. We predicted and analyzed the amino acid compositions, phylogenetic relationships, and folding states of conserved domain sequences of soybean RAV transcription factors. These soybean RAV transcription factors were phylogenetically clustered into three classes based on their amino acid sequences. Subcellular localization analysis revealed that the soybean RAV proteins were located in the nucleus. The expression patterns of 13 RAV genes were analyzed by quantitative real-time PCR. Under drought stresses, the RAV genes expressed diversely, up- or down-regulated. Following NaCl treatments, all RAV genes were down-regulated excepting GmRAV-03 which was up-regulated. Under abscisic acid (ABA treatment, the expression of all of the soybean RAV genes increased dramatically. These results suggested that the soybean RAV genes may be involved in diverse signaling pathways and may be responsive to abiotic stresses and exogenous ABA. Further analysis indicated that GmRAV-03 could increase the transgenic lines resistance to high salt and drought and result in the transgenic plants insensitive to exogenous ABA. This present study provides valuable information for understanding the classification and putative functions of the RAV transcription factors in soybean.

  2. De novo characterization of the spleen transcriptome of the large yellow croaker (Pseudosciaena crocea) and analysis of the immune relevant genes and pathways involved in the antiviral response

    KAUST Repository

    Mu, Yinnan

    2014-05-12

    The large yellow croaker (Pseudosciaena crocea) is an economically important marine fish in China. To understand the molecular basis for antiviral defense in this species, we used Illumia paired-end sequencing to characterize the spleen transcriptome of polyriboinosinic:polyribocytidylic acid [poly(I:C)]-induced large yellow croakers. The library produced 56,355,728 reads and assembled into 108,237 contigs. As a result, 15,192 unigenes were found from this transcriptome. Gene ontology analysis showed that 4,759 genes were involved in three major functional categories: biological process, cellular component, and molecular function. We further ascertained that numerous consensus sequences were homologous to known immune-relevant genes. Kyoto Encyclopedia of Genes and Genomes orthology mapping annotated 5,389 unigenes and identified numerous immune-relevant pathways. These immune-relevant genes and pathways revealed major antiviral immunity effectors, including but not limited to: pattern recognition receptors, adaptors and signal transducers, the interferons and interferon-stimulated genes, inflammatory cytokines and receptors, complement components, and B-cell and T-cell antigen activation molecules. Moreover, the partial genes of Toll-like receptor signaling pathway, RIG-I-like receptors signaling pathway, Janus kinase-Signal Transducer and Activator of Transcription (JAK-STAT) signaling pathway, and T-cell receptor (TCR) signaling pathway were found to be changed after poly(I:C) induction by real-time polymerase chain reaction (PCR) analysis, suggesting that these signaling pathways may be regulated by poly(I:C), a viral mimic. Overall, the antivirus-related genes and signaling pathways that were identified in response to poly(I:C) challenge provide valuable leads for further investigation of the antiviral defense mechanism in the large yellow croaker. © 2014 Mu et al.

  3. Work Experience and Work Involvement.

    Science.gov (United States)

    Lorence, Jon; Mortimer, Jeylan T.

    1981-01-01

    Examines the interrelations of work experience and psychological involvement in work among male college graduates over a 10-year period. Both the occupational socialization and the occupational selection hypotheses are supported by the data analysis. (Author/JOW)

  4. Genome-wide analysis of the HD-ZIP IV transcription factor family in Gossypium arboreum and GaHDG11 involved in osmotic tolerance in transgenic Arabidopsis.

    Science.gov (United States)

    Chen, Eryong; Zhang, Xueyan; Yang, Zhaoen; Wang, Xiaoqian; Yang, Zuoren; Zhang, Chaojun; Wu, Zhixia; Kong, Depei; Liu, Zhao; Zhao, Ge; Butt, Hamama Islam; Zhang, Xianlong; Li, Fuguang

    2017-06-01

    HD-ZIP IV proteins belong to the homeodomain-leucine zipper (HD-ZIP) transcription factor family and are involved in trichome development and drought stress in plants. Although some functions of the HD-ZIP IV group are well understood in Arabidopsis, little is known about their function in cotton. In this study, HD-ZIP genes were identified from three Gossypium species (G. arboreum, G. raimondii and G. hirsutum) and clustered into four families (HD-ZIP I, II, III and IV) to separate HD-ZIP IV from the other three families. Systematic analyses of phylogeny, gene structure, conserved domains, and expression profiles in different plant tissues and the expression patterns under osmotic stress in leaves were further conducted in G. arboreum. More importantly, ectopic overexpression of GaHDG11, a representative of the HD-ZIP IV family, confers enhanced osmotic tolerance in transgenic Arabidopsis plants, possibly due to elongated primary root length, lower water loss rates, high osmoprotectant proline levels, significant levels of antioxidants CAT, and/or SOD enzyme activity with reduced levels of MDA. Taken together, these observations may lay the foundation for future functional analysis of cotton HD-ZIP IV genes to unravel their biological roles in cotton.

  5. Identification of Putative Genes Involved in Bisphenol A Degradation Using Differential Protein Abundance Analysis of Sphingobium sp. BiD32.

    Science.gov (United States)

    Zhou, Nicolette A; Kjeldal, Henrik; Gough, Heidi L; Nielsen, Jeppe L

    2015-10-20

    Discharge of the endocrine disrupting compound bisphenol A (BPA) with wastewater treatment plant (WWTP) effluents into surface waters results in deleterious effects on aquatic life. Sphingobium sp. BiD32 was previously isolated from activated sludge based on its ability to degrade BPA. This study investigated BPA metabolism by Sphingobium sp. BiD32 using label-free quantitative proteomics. The genome of Sphingobium sp. BiD32 was sequenced to provide a species-specific platform for optimal protein identification. The bacterial proteomes of Sphingobium sp. BiD32 in the presence and absence of BPA were identified and quantified. A total of 2155 proteins were identified; 1174 of these proteins were quantified, and 184 of these proteins had a statistically significant change in abundance in response to the presence/absence of BPA (p ≤ 0.05). Proteins encoded by genes previously identified to be responsible for protocatechuate degradation were upregulated in the presence of BPA. The analysis of the metabolites from BPA degradation by Sphingobium sp. BiD32 detected a hydroxylated metabolite. A novel p-hydroxybenzoate hydroxylase enzyme detected by proteomics was implicated in the metabolic pathway associated with the detected metabolite. This enzyme is hypothesized to be involved in BPA degradation by Sphingobium sp. BiD32, and may serve as a future genetic marker for BPA degradation.

  6. The use of global transcriptional analysis to reveal the biological and cellular events involved in distinct development phases of Trichophyton rubrum conidial germination

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    Ding Guohui

    2007-04-01

    Full Text Available Abstract Background Conidia are considered to be the primary cause of infections by Trichophyton rubrum. Results We have developed a cDNA microarray containing 10250 ESTs to monitor the transcriptional strategy of conidial germination. A total of 1561 genes that had their expression levels specially altered in the process were obtained and hierarchically clustered with respect to their expression profiles. By functional analysis, we provided a global view of an important biological system related to conidial germination, including characterization of the pattern of gene expression at sequential developmental phases, and changes of gene expression profiles corresponding to morphological transitions. We matched the EST sequences to GO terms in the Saccharomyces Genome Database (SGD. A number of homologues of Saccharomyces cerevisiae genes related to signalling pathways and some important cellular processes were found to be involved in T. rubrum germination. These genes and signalling pathways may play roles in distinct steps, such as activating conidial germination, maintenance of isotropic growth, establishment of cell polarity and morphological transitions. Conclusion Our results may provide insights into molecular mechanisms of conidial germination at the cell level, and may enhance our understanding of regulation of gene expression related to the morphological construction of T. rubrum.

  7. Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis.

    Science.gov (United States)

    Fernandez, Paula; Di Rienzo, Julio; Fernandez, Luis; Hopp, H Esteban; Paniego, Norma; Heinz, Ruth A

    2008-01-26

    Considering that sunflower production is expanding to arid regions, tolerance to abiotic stresses as drought, low temperatures and salinity arises as one of the main constrains nowadays. Differential organ-specific sunflower ESTs (expressed sequence tags) were previously generated by a subtractive hybridization method that included a considerable number of putative abiotic stress associated sequences. The objective of this work is to analyze concerted gene expression profiles of organ-specific ESTs by fluorescence microarray assay, in response to high sodium chloride concentration and chilling treatments with the aim to identify and follow up candidate genes for early responses to abiotic stress in sunflower. Abiotic-related expressed genes were the target of this characterization through a gene expression analysis using an organ-specific cDNA fluorescence microarray approach in response to high salinity and low temperatures. The experiment included three independent replicates from leaf samples. We analyzed 317 unigenes previously isolated from differential organ-specific cDNA libraries from leaf, stem and flower at R1 and R4 developmental stage. A statistical analysis based on mean comparison by ANOVA and ordination by Principal Component Analysis allowed the detection of 80 candidate genes for either salinity and/or chilling stresses. Out of them, 50 genes were up or down regulated under both stresses, supporting common regulatory mechanisms and general responses to chilling and salinity. Interestingly 15 and 12 sequences were up regulated or down regulated specifically in one stress but not in the other, respectively. These genes are potentially involved in different regulatory mechanisms including transcription/translation/protein degradation/protein folding/ROS production or ROS-scavenging. Differential gene expression patterns were confirmed by qRT-PCR for 12.5% of the microarray candidate sequences. Eighty genes isolated from organ-specific cDNA libraries

  8. Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis

    Directory of Open Access Journals (Sweden)

    Paniego Norma

    2008-01-01

    Full Text Available Abstract Background Considering that sunflower production is expanding to arid regions, tolerance to abiotic stresses as drought, low temperatures and salinity arises as one of the main constrains nowadays. Differential organ-specific sunflower ESTs (expressed sequence tags were previously generated by a subtractive hybridization method that included a considerable number of putative abiotic stress associated sequences. The objective of this work is to analyze concerted gene expression profiles of organ-specific ESTs by fluorescence microarray assay, in response to high sodium chloride concentration and chilling treatments with the aim to identify and follow up candidate genes for early responses to abiotic stress in sunflower. Results Abiotic-related expressed genes were the target of this characterization through a gene expression analysis using an organ-specific cDNA fluorescence microarray approach in response to high salinity and low temperatures. The experiment included three independent replicates from leaf samples. We analyzed 317 unigenes previously isolated from differential organ-specific cDNA libraries from leaf, stem and flower at R1 and R4 developmental stage. A statistical analysis based on mean comparison by ANOVA and ordination by Principal Component Analysis allowed the detection of 80 candidate genes for either salinity and/or chilling stresses. Out of them, 50 genes were up or down regulated under both stresses, supporting common regulatory mechanisms and general responses to chilling and salinity. Interestingly 15 and 12 sequences were up regulated or down regulated specifically in one stress but not in the other, respectively. These genes are potentially involved in different regulatory mechanisms including transcription/translation/protein degradation/protein folding/ROS production or ROS-scavenging. Differential gene expression patterns were confirmed by qRT-PCR for 12.5% of the microarray candidate sequences. Conclusion

  9. Supplementary Material for: Identification of the genes involved in odorant reception and detection in the palm weevil Rhynchophorus ferrugineus, an important quarantine pest, by antennal transcriptome analysis

    KAUST Repository

    Antony, Binu

    2016-01-01

    Abstract Background The Red Palm Weevil (RPW) Rhynchophorus ferrugineus (Oliver) is one of the most damaging invasive insect species in the world. This weevil is highly specialized to thrive in adverse desert climates, and it causes major economic losses due to its effects on palm trees around the world. RPWs locate palm trees by means of plant volatile cues and use an aggregation pheromone to coordinate a mass-attack. Here we report on the high throughput sequencing of the RPW antennal transcriptome and present a description of the highly expressed chemosensory gene families. Results Deep sequencing and assembly of the RPW antennal transcriptome yielded 35,667 transcripts with an average length of 857 bp and identified a large number of highly expressed transcripts of odorant binding proteins (OBPs), chemosensory proteins (CSPs), odorant receptors/co-receptors (ORs/Orcos), sensory neuron membrane proteins (SNMPs), gustatory receptors (GRs) and ionotropic receptors (IRs). In total, 38 OBPs, 12 CSPs, 76 ORs, 1 Orco, 6 SNMPs, 15 GRs and 10 IRs were annotated in the R. ferrugineus antennal transcriptome. A comparative transcriptome analysis with the bark beetle showed that 25 % of the blast hits were unique to R. ferrugineus, indicating a higher, more complete transcript coverage for R. ferrugineus. We categorized the RPW ORs into seven subfamilies of coleopteran ORs and predicted two new subfamilies of ORs. The OR protein sequences were compared with those of the flour beetle, the cerambycid beetle and the bark beetle, and we identified coleopteran-specific, highly conserved ORs as well as unique ORs that are putatively involved in RPW aggregation pheromone detection. We identified 26 Minus-C OBPs and 8 Plus-C OBPs and grouped R. ferrugineus OBPs into different OBP-subfamilies according to phylogeny, which indicated significant species-specific expansion and divergence in R. ferrugineus. We also identified a diverse family of CSP proteins, as well as a coleopteran

  10. Identification of the genes involved in odorant reception and detection in the palm weevil Rhynchophorus ferrugineus, an important quarantine pest, by antennal transcriptome analysis.

    Science.gov (United States)

    Antony, Binu; Soffan, Alan; Jakše, Jernej; Abdelazim, Mahmoud M; Aldosari, Saleh A; Aldawood, Abdulrahman S; Pain, Arnab

    2016-01-22

    The Red Palm Weevil (RPW) Rhynchophorus ferrugineus (Oliver) is one of the most damaging invasive insect species in the world. This weevil is highly specialized to thrive in adverse desert climates, and it causes major economic losses due to its effects on palm trees around the world. RPWs locate palm trees by means of plant volatile cues and use an aggregation pheromone to coordinate a mass-attack. Here we report on the high throughput sequencing of the RPW antennal transcriptome and present a description of the highly expressed chemosensory gene families. Deep sequencing and assembly of the RPW antennal transcriptome yielded 35,667 transcripts with an average length of 857 bp and identified a large number of highly expressed transcripts of odorant binding proteins (OBPs), chemosensory proteins (CSPs), odorant receptors/co-receptors (ORs/Orcos), sensory neuron membrane proteins (SNMPs), gustatory receptors (GRs) and ionotropic receptors (IRs). In total, 38 OBPs, 12 CSPs, 76 ORs, 1 Orco, 6 SNMPs, 15 GRs and 10 IRs were annotated in the R. ferrugineus antennal transcriptome. A comparative transcriptome analysis with the bark beetle showed that 25% of the blast hits were unique to R. ferrugineus, indicating a higher, more complete transcript coverage for R. ferrugineus. We categorized the RPW ORs into seven subfamilies of coleopteran ORs and predicted two new subfamilies of ORs. The OR protein sequences were compared with those of the flour beetle, the cerambycid beetle and the bark beetle, and we identified coleopteran-specific, highly conserved ORs as well as unique ORs that are putatively involved in RPW aggregation pheromone detection. We identified 26 Minus-C OBPs and 8 Plus-C OBPs and grouped R. ferrugineus OBPs into different OBP-subfamilies according to phylogeny, which indicated significant species-specific expansion and divergence in R. ferrugineus. We also identified a diverse family of CSP proteins, as well as a coleopteran-specific CSP lineage that

  11. Identification of the genes involved in odorant reception and detection in the palm weevil Rhynchophorus ferrugineus, an important quarantine pest, by antennal transcriptome analysis

    KAUST Repository

    Antony, Binu

    2016-01-22

    Background The Red Palm Weevil (RPW) Rhynchophorus ferrugineus (Oliver) is one of the most damaging invasive insect species in the world. This weevil is highly specialized to thrive in adverse desert climates, and it causes major economic losses due to its effects on palm trees around the world. RPWs locate palm trees by means of plant volatile cues and use an aggregation pheromone to coordinate a mass-attack. Here we report on the high throughput sequencing of the RPW antennal transcriptome and present a description of the highly expressed chemosensory gene families. Results Deep sequencing and assembly of the RPW antennal transcriptome yielded 35,667 transcripts with an average length of 857 bp and identified a large number of highly expressed transcripts of odorant binding proteins (OBPs), chemosensory proteins (CSPs), odorant receptors/co-receptors (ORs/Orcos), sensory neuron membrane proteins (SNMPs), gustatory receptors (GRs) and ionotropic receptors (IRs). In total, 38 OBPs, 12 CSPs, 76 ORs, 1 Orco, 6 SNMPs, 15 GRs and 10 IRs were annotated in the R. ferrugineus antennal transcriptome. A comparative transcriptome analysis with the bark beetle showed that 25 % of the blast hits were unique to R. ferrugineus, indicating a higher, more complete transcript coverage for R. ferrugineus. We categorized the RPW ORs into seven subfamilies of coleopteran ORs and predicted two new subfamilies of ORs. The OR protein sequences were compared with those of the flour beetle, the cerambycid beetle and the bark beetle, and we identified coleopteran-specific, highly conserved ORs as well as unique ORs that are putatively involved in RPW aggregation pheromone detection. We identified 26 Minus-C OBPs and 8 Plus-C OBPs and grouped R. ferrugineus OBPs into different OBP-subfamilies according to phylogeny, which indicated significant species-specific expansion and divergence in R. ferrugineus. We also identified a diverse family of CSP proteins, as well as a coleopteran

  12. Serum cytokine profiling and enrichment analysis reveal the involvement of immunological and inflammatory pathways in stable patients with chronic obstructive pulmonary disease

    Directory of Open Access Journals (Sweden)

    Bade G

    2014-08-01

    Full Text Available Geetanjali Bade,1 Meraj Alam Khan,2 Akhilesh Kumar Srivastava,1 Parul Khare,1 Krishna Kumar Solaiappan,1 Randeep Guleria,3 Nades Palaniyar,2 Anjana Talwar1 1Department of Physiology, All India Institute of Medical Sciences, New Delhi, India; 2Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Department of Laboratory Medicine and Pathobiology, and Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; 3Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India Abstract: Chronic obstructive pulmonary disease (COPD is a major global health problem. It results from chronic inflammation and causes irreversible airway damage. Levels of different serum cytokines could be surrogate biomarkers for inflammation and lung function in COPD. We aimed to determine the serum levels of different biomarkers in COPD patients, the association between cytokine levels and various prognostic parameters, and the key pathways/networks involved in stable COPD. In this study, serum levels of 48 cytokines were examined by multiplex assays in 30 subjects (control, n=9; COPD, n=21. Relationships between serum biomarkers and forced expiratory volume in 1 second, peak oxygen uptake, body mass index, dyspnea score, and smoking were assessed. Enrichment pathways and networks analyses were implemented, using a list of cytokines showing differential expression between healthy controls and patients with COPD by Cytoscape and GeneGo Metacore™ softwares (Thomson-Reuters Corporation, New York, NY, USA. Concentrations of cutaneous T-cell attracting chemokine, eotaxin, hepatocyte growth factor, interleukin 6 (IL-6, IL-16, and stem cell factor are significantly higher in COPD patients compared with in control patients. Notably, this study identifies stem cell factor as a biomarker for COPD. Multiple regression analysis predicts that cutaneous T

  13. De novo sequencing and analysis of the cranberry fruit transcriptome to identify putative genes involved in flavonoid biosynthesis, transport and regulation.

    Science.gov (United States)

    Sun, Haiyue; Liu, Yushan; Gai, Yuzhuo; Geng, Jinman; Chen, Li; Liu, Hongdi; Kang, Limin; Tian, Youwen; Li, Yadong

    2015-09-02

    Cranberries (Vaccinium macrocarpon Ait.), renowned for their excellent health benefits, are an important berry crop. Here, we performed transcriptome sequencing of one cranberry cultivar, from fruits at two different developmental stages, on the Illumina HiSeq 2000 platform. Our main goals were to identify putative genes for major metabolic pathways of bioactive compounds and compare the expression patterns between white fruit (W) and red fruit (R) in cranberry. In this study, two cDNA libraries of W and R were constructed. Approximately 119 million raw sequencing reads were generated and assembled de novo, yielding 57,331 high quality unigenes with an average length of 739 bp. Using BLASTx, 38,460 unigenes were identified as putative homologs of annotated sequences in public protein databases, including NCBI NR, NT, Swiss-Prot, KEGG, COG and GO. Of these, 21,898 unigenes mapped to 128 KEGG pathways, with the metabolic pathways, secondary metabolites, glycerophospholipid metabolism, ether lipid metabolism, starch and sucrose metabolism, purine metabolism, and pyrimidine metabolism being well represented. Among them, many candidate genes were involved in flavonoid biosynthesis, transport and regulation. Furthermore, digital gene expression (DEG) analysis identified 3,257 unigenes that were differentially expressed between the two fruit developmental stages. In addition, 14,473 simple sequence repeats (SSRs) were detected. Our results present comprehensive gene expression information about the cranberry fruit transcriptome that could facilitate our understanding of the molecular mechanisms of fruit development in cranberries. Although it will be necessary to validate the functions carried out by these genes, these results could be used to improve the quality of breeding programs for the cranberry and related species.

  14. Comparative transcriptome analysis of isonuclear-alloplasmic lines unmask key transcription factor genes and metabolic pathways involved in sterility of maize CMS-C

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    Chuan Li

    2017-05-01

    Full Text Available Although C-type cytoplasmic male sterility (CMS-C is one of the most attractive tools for maize hybrid seed production, the detailed regulation network of the male sterility remains unclear. In order to identify the CMS-C sterility associated genes and/or pathways, the comparison of the transcriptomes between the CMS-C line C48-2 and its isonuclear-alloplasmic maintainer line N48-2 at pollen mother cell stage (PS, an early development stage of microspore, and mononuclear stage (MS, an abortive stage of microspore, were analyzed. 2,069 differentially expressed genes (DEGs between the two stages were detected and thought to be essential for the spikelet development of N48-2. 453 of the 2,069 DEGs were differentially expressed at MS stage between the two lines and thought to be participated in the process or the causes of microspore abortion. Among the 453 DEGs, 385 (84.99% genes were down-regulated and only 68 (15.01% genes were up-regulated in C48-2 at MS stage. The dramatic decreased expression of the four DEGs encoding MYB transcription factors and the DEGs involved in “polyamine metabolic process”, “Cutin, suberine and wax biosynthesis”, “Fatty acid elongation”, “Biosynthesis of unsaturated fatty acids” and “Proline metabolism” might play an important role in the sterility of C48-2. This study will point out some directions for detailed molecular analysis and better understanding of sterility of CMS-C in maize.

  15. Comparative Proteomic Analysis Provides insight into the Key Proteins as Possible Targets Involved in Aspirin Inhibiting Biofilm Formation of Staphylococcus xylosus

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    Chang-Geng Xu

    2017-08-01

    Full Text Available Staphylococcus xylosus is an opportunistic pathogen that causes infection in humans and cow mastitis. And S. xylosus possesses a strong ability to form biofilms in vitro. As biofilm formation facilitates resistance to antimicrobial agents, the discovery of new medicinal properties for classic drugs is highly desired. Aspirin, which is the most common active component of non-steroidal anti-inflammatory compounds, affects the biofilm-forming capacity of various bacterial species. We have found that aspirin effectively inhibits biofilm formation of S. xylosus by Crystal violet (CV staining and scanning electron microscopy analyses. The present study sought to elucidate possible targets of aspirin in suppressing S. xylosus biofilm formation. Based on an isobaric tag for relative and absolute quantitation (iTRAQ fold-change of >1.2 or <0.8 (P-value < 0.05, 178 differentially expressed proteins, 111 down-regulated and 67 up-regulated, were identified after application of aspirin to cells at a 1/2 minimal inhibitory concentration. Gene ontology analysis indicated enrichment in metabolic processes for the majority of the differentially expressed proteins. We then used the Kyoto Encyclopedia of Genes and Genomes (KEGG pathway database to analyze a large number of differentially expressed proteins and identified genes involved in biosynthesis of amino acids pathway, carbon metabolism (pentose phosphate and glycolytic pathways, tricarboxylic acid cycle and nitrogen metabolism (histidine metabolism. These novel proteins represent candidate targets in aspirin-mediated inhibition of S. xylosus biofilm formation at sub-MIC levels. The findings lay the foundation for further studies to identify potential aspirin targets.

  16. Transcriptome analysis and discovery of genes involved in immune pathways in large yellow croaker (Larimichthys crocea) under high stocking density stress.

    Science.gov (United States)

    Sun, Peng; Bao, Peibo; Tang, Baojun

    2017-09-01

    The large yellow croaker, Larimichthys crocea, is an economically important maricultured species in southeast China. Owing to the importance of stocking densities in commercial fish production, it is crucial to establish the physiological responses and molecular mechanisms that govern adaptation to crowding in order to optimize welfare and health. In the present study, an extensive immunity-related analysis was performed at the transcriptome level in L. crocea in response to crowding stress. Over 145 million high-quality reads were generated and de novo assembled into a final set of 40,123 unigenes. Gene Ontology and genome analyses revealed that molecular function, biological process, intracellular, ion binding, and cell process were the most highly enriched pathways among genes that were differentially expressed under stress. Among all of the pathways involved, 16 pathways were related to the immune system, among which the complement and coagulation cascades pathway was the most enriched for differentially expressed immunity-related genes, followed by the chemokine signaling pathway, toll-like receptor signaling pathway, and leukocyte transendothelial migration pathway. The consistently high expression of immune-related genes in the complement and coagulation cascades pathway (from 24 to 96 h after being subjected to stress) suggested its importance in both response to stress and resistance against bacterial invasion at an early stage. These results also demonstrated that crowding can significantly induce immunological responses in fish. However, long-term exposure to stress eventually impairs the defense capability in fish. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Involvement of organic acids and amino acids in ameliorating Ni(II) toxicity induced cell cycle dysregulation in Caulobacter crescentus: a metabolomics analysis.

    Science.gov (United States)

    Jain, Abhishek; Chen, Wei Ning

    2018-04-03

    Nickel (Ni(II)) toxicity is addressed by many different bacteria, but bacterial responses to nickel stress are still unclear. Therefore, we studied the effect of Ni(II) toxicity on cell proliferation of α-proteobacterium Caulobacter crescentus. Next, we showed the mechanism that allows C. crescentus to survive in Ni(II) stress condition. Our results revealed that the growth of C. crescentus is severely affected when the bacterium was exposed to different Ni(II) concentrations, 0.003 mM slightly affected the growth, 0.008 mM reduced the growth by 50%, and growth was completely inhibited at 0.015 mM. It was further shown that Ni(II) toxicity induced mislocalization of major regulatory proteins such as MipZ, FtsZ, ParB, and MreB, resulting in dysregulation of the cell cycle. GC-MS metabolomics analysis of Ni(II) stressed C. crescentus showed an increased level of nine important metabolites including TCA cycle intermediates and amino acids. This indicates that changes in central carbon metabolism and nitrogen metabolism are linked with the disruption of cell division process. Addition of malic acid, citric acid, alanine, proline, and glutamine to 0.015 mM Ni(II)-treated C. crescentus restored its growth. Thus, the present work shows a protective effect of these organic acids and amino acids on Ni(II) toxicity. Metabolic stimulation through the PutA/GlnA pathway, accelerated degradation of CtrA, and Ni-chelation by organic acids or amino acids are some of the possible mechanisms suggested to be involved in enhancing C. crescentus's tolerance. Our results shed light on the mechanism of increased Ni(II) tolerance in C. crescentus which may be useful in bioremediation strategies and synthetic biology applications such as the development of whole cell biosensor.

  18. Transcriptomic analysis of chicken cochleae after gentamicin damage and the involvement of four signaling pathways (Notch, FGF, Wnt and BMP) in hair cell regeneration.

    Science.gov (United States)

    Jiang, Lingling; Xu, Jincao; Jin, Ran; Bai, Huanju; Zhang, Meiguang; Yang, Siyuan; Zhang, Xuebo; Zhang, Xinwen; Han, Zhongming; Zeng, Shaoju

    2018-04-01

    Unlike mammalian hair cells, which are essentially unable to regenerate after damage, avian hair cells have a robust capacity for regeneration. The prerequisite for understanding the above difference is knowing the genetic programming of avian hair cell regeneration. Although the major processes have been known, the precise molecular signaling that induces regeneration remains unclear. To address this issue, we performed a high-throughput transcriptomic analysis of gene expression during hair cell regeneration in the chick cochlea after antibiotic injury in vivo. A total of 16,588 genes were found to be expressed in the cochlea, of which about 1000 genes were differentially expressed among the four groups studied, i.e., 2 days (d) or 3 d post-treatment with gentamicin or physiological saline. The differentially expressed genes were distributed across approximately one hundred signaling pathways, including the Notch, MAPK (FGF), Wnt and TGF-β (BMP) pathways that have been shown to play important roles in embryonic development. Some differentially expressed genes (2-3 in each pathway) were further verified by qRT-PCR. After blocking Notch, FGF or BMP signaling, the number of regenerating hair cells and mitotic supporting cells increased. However, the opposite effect was observed after suppressing the Wnt pathway or enhancing BMP signaling. To our knowledge, the present study provided a relatively complete dataset of candidate genes and signaling pathways most likely involved in hair cell regeneration and should be a useful start in deciphering the genetic circuitry for inducing hair cell regeneration in the chick cochlea. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. De Novo Assembly and Analysis of Tartary Buckwheat (Fagopyrum tataricum Garetn. Transcriptome Discloses Key Regulators Involved in Salt-Stress Response

    Directory of Open Access Journals (Sweden)

    Qi Wu

    2017-10-01

    Full Text Available Soil salinization has been a tremendous obstacle for agriculture production. The regulatory networks underlying salinity adaption in model plants have been extensively explored. However, limited understanding of the salt response mechanisms has hindered the planting and production in Fagopyrum tataricum, an economic and health-beneficial plant mainly distributing in southwest China. In this study, we performed physiological analysis and found that salt stress of 200 mM NaCl solution significantly affected the relative water content (RWC, electrolyte leakage (EL, malondialdehyde (MDA content, peroxidase (POD and superoxide dismutase (SOD activities in tartary buckwheat seedlings. Further, we conducted transcriptome comparison between control and salt treatment to identify potential regulatory components involved in F. tataricum salt responses. A total of 53.15 million clean reads from control and salt-treated libraries were produced via an Illumina sequencing approach. Then we de novo assembled these reads into a transcriptome dataset containing 57,921 unigenes with N50 length of 1400 bp and total length of 44.5 Mb. A total of 36,688 unigenes could find matches in public databases. GO, KEGG and KOG classification suggested the enrichment of these unigenes in 56 sub-categories, 25 KOG, and 273 pathways, respectively. Comparison of the transcriptome expression patterns between control and salt treatment unveiled 455 differentially expressed genes (DEGs. Further, we found the genes encoding for protein kinases, phosphatases, heat shock proteins (HSPs, ATP-binding cassette (ABC transporters, glutathione S-transferases (GSTs, abiotic-related transcription factors and circadian clock might be relevant to the salinity adaption of this species. Thus, this study offers an insight into salt tolerance mechanisms, and will serve as useful genetic information for tolerant elite breeding programs in future.

  20. Functional analysis of a tyrosinase gene involved in early larval shell biogenesis in Crassostrea angulata and its response to ocean acidification.

    Science.gov (United States)

    Yang, Bingye; Pu, Fei; Li, Lingling; You, Weiwei; Ke, Caihuan; Feng, Danqing

    2017-04-01

    The formation of the primary shell is a vital process in marine bivalves. Ocean acidification largely influences shell formation. It has been reported that enzymes involved in phenol oxidation, such as tyrosinase and phenoloxidases, participate in the formation of the periostracum. In the present study, we cloned a tyrosinase gene from Crassostrea angulata named Ca-tyrA1, and its potential function in early larval shell biogenesis was investigated. The Ca-tyrA1 gene has a full-length cDNA of 2430bp in size, with an open reading frame of 1896bp in size, which encodes a 631-amino acid protein that includes a 24-amino acid putative signal peptide. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed that Ca-tyrA1 transcription mainly occurs at the trochophore stage, and the Ca-tyrA1 mRNA levels in the 3000ppm treatment group were significantly upregulated in the early D-veliger larvae. WMISH and electron scanning microscopy analyses showed that the expression of Ca-tyrA1 occurs at the gastrula stage, thereby sustaining the early D-veliger larvae, and the shape of its signal is saddle-like, similar to that observed under an electron scanning microscope. Furthermore, the RNA interference has shown that the treatment group has a higher deformity rate than that of the control, thereby indicating that Ca-tyrA1 participates in the biogenesis of the primary shell. In conclusion, and our results indicate that Ca-tyrA1 plays a vital role in the formation of the larval shell and participates in the response to larval shell damages in Crassostrea angulata that were induced by ocean acidification. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Comparative transcriptome analysis of genes involved in anthocyanin biosynthesis in the red and yellow fruits of sweet cherry (Prunus avium L..

    Directory of Open Access Journals (Sweden)

    Hairong Wei

    Full Text Available Fruit color is one of the most important economic traits of the sweet cherry (Prunus avium L.. The red coloration of sweet cherry fruit is mainly attributed to anthocyanins. However, limited information is available regarding the molecular mechanisms underlying anthocyanin biosynthesis and its regulation in sweet cherry.In this study, a reference transcriptome of P. avium L. was sequenced and annotated to identify the transcriptional determinants of fruit color. Normalized cDNA libraries from red and yellow fruits were sequenced using the next-generation Illumina/Solexa sequencing platform and de novo assembly. Over 66 million high-quality reads were assembled into 43,128 unigenes using a combined assembly strategy. Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database. Furthermore, transcriptome differences between the four stages of fruit ripening were analyzed using Illumina digital gene expression (DGE profiling. Biological pathway analysis revealed that 72 unigenes were involved in anthocyanin biosynthesis. The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL, 4-coumarate-CoA ligase (4CL, chalcone synthase (CHS, chalcone isomerase (CHI, flavanone 3-hydroxylase (F3H, flavanone 3'-hydroxylase (F3'H, dihydroflavonol 4-reductase (DFR, anthocyanidin synthase (ANS and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT during fruit ripening differed between red and yellow fruit. In addition, we identified some transcription factor families (such as MYB, bHLH and WD40 that may control anthocyanin biosynthesis. We confirmed the altered expression levels of eighteen unigenes that encode anthocyanin biosynthetic enzymes and transcription factors using quantitative real-time PCR (qRT-PCR.The obtained sweet cherry transcriptome and DGE profiling data provide comprehensive gene expression information that lends insights

  2. Comparative transcriptome analysis of genes involved in anthocyanin biosynthesis in the red and yellow fruits of sweet cherry (Prunus avium L.).

    Science.gov (United States)

    Wei, Hairong; Chen, Xin; Zong, Xiaojuan; Shu, Huairui; Gao, Dongsheng; Liu, Qingzhong

    2015-01-01

    Fruit color is one of the most important economic traits of the sweet cherry (Prunus avium L.). The red coloration of sweet cherry fruit is mainly attributed to anthocyanins. However, limited information is available regarding the molecular mechanisms underlying anthocyanin biosynthesis and its regulation in sweet cherry. In this study, a reference transcriptome of P. avium L. was sequenced and annotated to identify the transcriptional determinants of fruit color. Normalized cDNA libraries from red and yellow fruits were sequenced using the next-generation Illumina/Solexa sequencing platform and de novo assembly. Over 66 million high-quality reads were assembled into 43,128 unigenes using a combined assembly strategy. Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database. Furthermore, transcriptome differences between the four stages of fruit ripening were analyzed using Illumina digital gene expression (DGE) profiling. Biological pathway analysis revealed that 72 unigenes were involved in anthocyanin biosynthesis. The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavanone 3'-hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT) during fruit ripening differed between red and yellow fruit. In addition, we identified some transcription factor families (such as MYB, bHLH and WD40) that may control anthocyanin biosynthesis. We confirmed the altered expression levels of eighteen unigenes that encode anthocyanin biosynthetic enzymes and transcription factors using quantitative real-time PCR (qRT-PCR). The obtained sweet cherry transcriptome and DGE profiling data provide comprehensive gene expression information that lends insights into

  3. Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus.

    Science.gov (United States)

    Kariuki, S N; Ghodke-Puranik, Y; Dorschner, J M; Chrabot, B S; Kelly, J A; Tsao, B P; Kimberly, R P; Alarcón-Riquelme, M E; Jacob, C O; Criswell, L A; Sivils, K L; Langefeld, C D; Harley, J B; Skol, A D; Niewold, T B

    2015-01-01

    Systemic lupus erythematosus (SLE) is a chronic autoimmune disorder characterized by inflammation of multiple organ systems and dysregulated interferon responses. SLE is both genetically and phenotypically heterogeneous, greatly reducing the power of case-control studies in SLE. Elevated circulating interferon-alpha (IFN-α) is a stable, heritable trait in SLE, which has been implicated in primary disease pathogenesis. About 40-50% of patients have high IFN-α, and high levels correspond with clinical differences. To study genetic heterogeneity in SLE, we performed a case-case study comparing patients with high vs low IFN-α in over 1550 SLE cases, including genome-wide association study and replication cohorts. In meta-analysis, the top associations in European ancestry were protein kinase, cyclic GMP-dependent, type I (PRKG1) rs7897633 (P(Meta) = 2.75 × 10(-8)) and purine nucleoside phosphorylase (PNP) rs1049564 (P(Meta) = 1.24 × 10(-7)). We also found evidence for cross-ancestral background associations with the ankyrin repeat domain 44 (ANKRD44) and pleckstrin homology domain containing, family F member 2 gene (PLEKHF2) loci. These loci have not been previously identified in case-control SLE genetic studies. Bioinformatic analyses implicated these loci functionally in dendritic cells and natural killer cells, both of which are involved in IFN-α production in SLE. As case-control studies of heterogeneous diseases reach a limit of feasibility with respect to subject number and detectable effect size, the study of informative pathogenic sub-phenotypes becomes an attractive strategy for genetic discovery in complex disease.

  4. Analysis of the impact of professional involvement in evidence generation for the HTA Process, subproject "cochlear implants": methodology, results and recommendations.

    Science.gov (United States)

    Berrettini, S; Arslan, E; Baggiani, A; Burdo, S; Cassandro, E; Cuda, D; Filipo, R; Rossi, P Giorgi; Mancini, P; Martini, A; Quaranta, A; Quaranta, N; Turchetti, G; Forli, F

    2011-10-01

    The aim of Health Technology Assessment (HTA) is to provide decision-makers, distributors and recipients with information on the effectiveness, cost and impact of health technologies. The present study constitutes a subproject within the wider project "Analysis of the impact of professional involvement in evidence generation for the HTA process", which is part of the strategic programme "Transfer of the results of the research in clinical practice and organisation of healthcare services", coordinated by Laziosanità - Agency of Public Healthcare of the Lazio Region and AgeNaS (National Agency for Regional Healthcare Services). The objectives of the present subproject (cochlear implants) are as follows: a) to produce a report regarding the health impact of cochlear implants (CI) on their recipients, through a systematic review of literature and extensive selection of relative studies, combining the outcomes with metanalytical techniques. Output: report on the indications of usage in the groups of population for which benefits are controversial; b) to create a registry of patients using cochlear implants. The registry should contain a selection of anagraphic and clinical information relative to patient follow-up in order to assess factors associated with safety and impact on cochlear implant users. This source of information is essential for future observational studies. This was divided into 4 phases: 1(st) phase: definition of key participants in the assessment process; 2(nd) phase: definition of methods and timing of "Aims" (definition of the objective); 3(rd) phase: definition of the methods and times of the "assessment process", 4(th) phase: production of the final report. From the analysis of systematic reviews and italian and international guidelines, the Working Group members approved recommendations on the following topics: results after CI in children in relation to age at implantation, bilateral CI in children, CI in deaf children with associated

  5. The influence of sensation-seeking and parental and peer influences in early adolescence on risk involvement through middle adolescence: A structural equation modeling analysis.

    Science.gov (United States)

    Wang, Bo; Deveaux, Lynette; Lunn, Sonja; Dinaj-Koci, Veronica; Li, Xiaoming; Stanton, Bonita

    2016-03-01

    This study examined the relationships between youth and parental sensation-seeking, peer influence, parental monitoring and youth risk involvement in adolescence using structural equation modeling. Beginning in grade-six, longitudinal data were collected from 543 students over three years. Youth sensation-seeking in grade six contributed to risk involvement in early adolescence (grades six and seven) indirectly through increased peer risk influence and decreased parental monitoring but did not have a direct contribution. It contributed directly and indirectly to risk involvement in middle adolescence (grades eight and nine). Parent sensation-seeking at baseline was positively associated with peer risk influence and negatively associated with parental monitoring; it had no direct effect on adolescent risk involvement. Parental monitoring buffers negative peer influence on adolescent risk involvement. Results highlight the need for intervention efforts to provide normative feedback about adolescent risky behaviors and to vary among families in which parents and/or youth have high sensation-seeking propensities.

  6. Associations of Omega-3 Fatty Acid Supplement Use With Cardiovascular Disease Risks: Meta-analysis of 10 Trials Involving 77 917 Individuals.

    Science.gov (United States)

    Aung, Theingi; Halsey, Jim; Kromhout, Daan; Gerstein, Hertzel C; Marchioli, Roberto; Tavazzi, Luigi; Geleijnse, Johanna M; Rauch, Bernhard; Ness, Andrew; Galan, Pilar; Chew, Emily Y; Bosch, Jackie; Collins, Rory; Lewington, Sarah; Armitage, Jane; Clarke, Robert

    2018-03-01

    Current guidelines advocate the use of marine-derived omega-3 fatty acids supplements for the prevention of coronary heart disease and major vascular events in people with prior coronary heart disease, but large trials of omega-3 fatty acids have produced conflicting results. To conduct a meta-analysis of all large trials assessing the associations of omega-3 fatty acid supplements with the risk of fatal and nonfatal coronary heart disease and major vascular events in the full study population and prespecified subgroups. This meta-analysis included randomized trials that involved at least 500 participants and a treatment duration of at least 1 year and that assessed associations of omega-3 fatty acids with the risk of vascular events. Aggregated study-level data were obtained from 10 large randomized clinical trials. Rate ratios for each trial were synthesized using observed minus expected statistics and variances. Summary rate ratios were estimated by a fixed-effects meta-analysis using 95% confidence intervals for major diseases and 99% confidence intervals for all subgroups. The main outcomes included fatal coronary heart disease, nonfatal myocardial infarction, stroke, major vascular events, and all-cause mortality, as well as major vascular events in study population subgroups. Of the 77 917 high-risk individuals participating in the 10 trials, 47 803 (61.4%) were men, and the mean age at entry was 64.0 years; the trials lasted a mean of 4.4 years. The associations of treatment with outcomes were assessed on 6273 coronary heart disease events (2695 coronary heart disease deaths and 2276 nonfatal myocardial infarctions) and 12 001 major vascular events. Randomization to omega-3 fatty acid supplementation (eicosapentaenoic acid dose range, 226-1800 mg/d) had no significant associations with coronary heart disease death (rate ratio [RR], 0.93; 99% CI, 0.83-1.03; P = .05), nonfatal myocardial infarction (RR, 0.97; 99% CI, 0.87-1.08; P = .43) or any

  7. Eye Involvement in TSC

    Science.gov (United States)

    ... Privacy Policy Sitemap Learn Engage Donate About TSC Eyes Campbell (1905) first described the eye involvement in ... some form of eye involvement. Nonretinal and Retinal Eye Findings Facial angiofibromas may involve the eyelids of ...

  8. Analysis of the Radio-Ecological State of Units and Installations Involved in Nuclear Submarine Decommissioning in the Northwest Region of Russia

    National Research Council Canada - National Science Library

    Sarkissov, A

    2003-01-01

    .... in the first section of the report, all nuclear-powered units and installations involved in the process of nuclear submarine utilization in the northwest region of Russia are listed and considered in detail...

  9. Analysis of General Accounting Office, Armed Services Board of Contract Appeals and Federal Court of Claims Decisions on Protests Disputes Involving Performance Specifications

    National Research Council Canada - National Science Library

    Murphy-Sweet, Philip

    2002-01-01

    ... involving Performance Specifications. Performance Specifications generally leave the contractor open to decide the best means to accomplish the work of a contract and deliver the product called for in the contract...

  10. Analysis of General Accounting Office, Armed Services Board of Contract Appeals and Federal Court of Claims Decisions on Protests Disputes Involving Performance Specifications

    National Research Council Canada - National Science Library

    Murphy-Sweet, Philip

    2002-01-01

    ... involving Performance Specifications. Performance Specifications generally leave the contractor open to decide the best means to accomplish the work of a contract and deliver the product called for in the...

  11. Quantitative analysis of the dynamic signaling pathway involved in the cAMP mediated induction of l-carnitine biosynthesis in E. coli cultures.

    Science.gov (United States)

    Hormiga, José; González-Alcón, Carlos; Sevilla, Angel; Cánovas, Manuel; Torres, Néstor V

    2010-04-01

    L-(-)-carnitine can be synthesized from waste bioprecursors in the form of crotonobetaine. Such biotransformation is carried out in E. coli by the enzymes encoded by operons regulated by the cAMP receptor proteins. Non-phosphorylated sugars, such as glycerol are used as energy and carbon source since glucose inhibits cAMP synthesis. Until now little attention has been paid to the regulatory signaling structure that operates during the transition from a glucose-consuming, non-l-carnitine producing steady state, to a glycerol-consuming l-carnitine producing steady state. In this work we aim to elucidate and quantify the underlying regulatory mechanisms operating in the abolition of the glucose inhibiting effect. For this purpose we make use of the systemic approach by integrating the available information and our own experimentally generated data to construct a mathematical model. The model is built using power-law representation and is used as a platform to make predictive simulations and to assess the consistency of the regulatory structure of the overall process. The model is subsequently checked for quality through stability and a special, dynamic sensitivity analysis. The results show that the model is able to deal with the observed system transient phase. The model is multi-hierarchical, comprising the metabolic, gene expression, signaling and bioreactor levels. It involves variables and parameters of a very different nature that develop in different time scales and orders of magnitude. Some of the most relevant conclusions obtained are: (i) the regulatory interactions among glucose, glycerol and cAMP metabolism are far stronger than those present in the l-carnitine transport, production and degradation processes; (ii) carnitine biosynthesis is very sensitive to the cAMP signaling system since it reacts at very low cAMP receptor concentrations, and (iii) ATP is a critical factor in the transient dynamics. All these model-derived observations have been

  12. Transcriptome Analysis of Salicylic Acid Treatment in Rehmannia glutinosa Hairy Roots Using RNA-seq Technique for Identification of Genes Involved in Acteoside Biosynthesis

    Directory of Open Access Journals (Sweden)

    Fengqing Wang

    2017-05-01

    Full Text Available Rehmannia glutinosa is a common bulk medicinal material that has been widely used in China due to its active ingredients. Acteoside, one of the ingredients, has antioxidant, antinephritic, anti-inflammatory, hepatoprotective, immunomodulatory, and neuroprotective effects, is usually selected as a quality-control component for R. glutinosa herb in the Chinese Pharmacopeia. The acteoside biosynthesis pathway in R. glutinosa has not yet been clearly established. Herein, we describe the establishment of a genetic transformation system for R. glutinosa mediated by Agrobacterium rhizogenes. We screened the optimal elicitors that markedly increased acteoside accumulation in R. glutinosa hairy roots. We found that acteoside accumulation dramatically increased with the addition of salicylic acid (SA; the optimal SA dose was 25 μmol/L for hairy roots. RNA-seq was applied to analyze the transcriptomic changes in hairy roots treated with SA for 24 h in comparison with an untreated control. A total of 3,716, 4,018, and 2,715 differentially expressed transcripts (DETs were identified in 0 h-vs.-12 h, 0 h-vs.-24 h, and 12 h-vs.-24 h libraries, respectively. KEGG pathway-based analysis revealed that 127 DETs were enriched in “phenylpropanoid biosynthesis.” Of 219 putative unigenes involved in acteoside biosynthesis, 54 were found to be up-regulated at at least one of the time points after SA treatment. Selected candidate genes were analyzed by quantitative real-time PCR (qRT-PCR in hairy roots with SA, methyl jasmonate (MeJA, AgNO3 (Ag+, and putrescine (Put treatment. All genes investigated were up-regulated by SA treatment, and most candidate genes were weakly increased by MeJA to some degree. Furthermore, transcription abundance of eight candidate genes in tuberous roots of the high-acteoside-content (HA cultivar QH were higher than those of the low-acteoside-content (LA cultivar Wen 85-5. These results will pave the way for understanding the molecular

  13. The influence of sensation-seeking and parental and peer influences in early adolescence on risk involvement through middle adolescence: A structural equation modeling analysis

    Science.gov (United States)

    Wang, Bo; Deveaux, Lynette; Lunn, Sonja; Dinaj-Koci, Veronica; Li, Xiaoming; Stanton, Bonita

    2014-01-01

    This study examined the relationships between youth and parental sensation-seeking, peer influence, parental monitoring and youth risk involvement in adolescence using structural equation modeling. Beginning in grade-six, longitudinal data were collected from 543 students over three years. Youth sensation-seeking in grade six contributed to risk involvement in early adolescence (grades six and seven) indirectly through increased peer risk influence and decreased parental monitoring but did not have a direct contribution. It contributed directly and indirectly to risk involvement in middle adolescence (grades eight and nine). Parent sensation-seeking at baseline was positively associated with peer risk influence and negatively associated with parental monitoring; it had no direct effect on adolescent risk involvement. Parental monitoring buffers negative peer influence on adolescent risk involvement. Results highlight the need for intervention efforts to provide normative feedback about adolescent risky behaviors and to vary among families in which parents and/or youth have high sensation-seeking propensities. PMID:27030784

  14. Analysis of Parental Involvement and Self-Esteem on Secondary School Students in Kieni West Sub-County, Nyeri County, Kenya

    Science.gov (United States)

    Wairimu, Mburu Josephine; Macharia, Susan M.; Muiru, Ann

    2016-01-01

    This study investigated the relationship between parental involvement and the self-esteem among adolescents in secondary school students in Kieni West District in Nyeri County. It was guided by Self Determination Theory (SDT) by James William and Baumrind Theory of Parenting Styles by Diana Blumberg Baumrind. Some of the gaps identified in the…

  15. Biochemical characterization and bioinformatic analysis of two large multi-domain enzymes from Microbacterium aurum B8.A involved in native starch degradation

    NARCIS (Netherlands)

    Valk, Vincent

    2017-01-01

    Microbacterium aurum B8.A is a unique bacterium with the ability to degrade starch granules through pore formation. In this study two enzymes (MaAmyA and MaAmyB) which are involved in granular starch degradation and were specific for the M. aurum B8.A strain, have been characterized in detail. Both

  16. Organizing Patient Involvement

    DEFF Research Database (Denmark)

    Brehm Johansen, Mette

    Patient involvement has become a part of the political agenda in Danish healthcare. Patients are to be involved not only in questions and decisions relating to their own treatment and care – to involve patients in quality improvement has also become a political expectation of quality work in Danish...... hospitals. During the last 25 years, patient involvement and quality improvement have become connected in Danish healthcare policy. However, the ideal of involving patients in quality improvement is described in very general terms and with only few specific expectations of how it is to be carried out...... in practice, as I show in the thesis. In the patient involvement literature, the difficulties of getting patient involvement in quality improvement to have in an impact on the planning and development of healthcare services is, for example, ascribed to conceptual vagueness of patient involvement, differences...

  17. Involvement of Pinus taeda MYB1 and MYB8 in phenylpropanoid metabolism and secondary cell wall biogenesis: a comparative in planta analysis.

    Science.gov (United States)

    Bomal, Claude; Bedon, Frank; Caron, Sébastien; Mansfield, Shawn D; Levasseur, Caroline; Cooke, Janice E K; Blais, Sylvie; Tremblay, Laurence; Morency, Marie-Josée; Pavy, Nathalie; Grima-Pettenati, Jacqueline; Séguin, Armand; Mackay, John

    2008-01-01

    The involvement of two R2R3-MYB genes from Pinus taeda L., PtMYB1 and PtMYB8, in phenylpropanoid metabolism and secondary cell wall biogenesis was investigated in planta. These pine MYBs were constitutively overexpressed (OE) in Picea glauca (Moench) Voss, used as a heterologous conifer expression system. Morphological, histological, chemical (lignin and soluble phenols), and transcriptional analyses, i.e. microarray and reverse transcription quantitative PCR (RT-qPCR) were used for extensive phenotyping of MYB-overexpressing spruce plantlets. Upon germination of somatic embryos, root growth was reduced in both transgenics. Enhanced lignin deposition was also a common feature but ectopic secondary cell wall deposition was more strongly associated with PtMYB8-OE. Microarray and RT-qPCR data showed that overexpression of each MYB led to an overlapping up-regulation of many genes encoding phenylpropanoid enzymes involved in lignin monomer synthesis, while misregulation of several cell wall-related genes and other MYB transcription factors was specifically associated with PtMYB8-OE. Together, the results suggest that MYB1 and MYB8 may be part of a conserved transcriptional network involved in secondary cell wall deposition in conifers.

  18. The effect of trainee involvement on procedure and list times: A statistical analysis with discussion of current issues affecting orthopaedic training in UK.

    Science.gov (United States)

    Wilson, T; Sahu, A; Johnson, D S; Turner, P G

    2010-02-01

    Training surgeons adds time to the duration of procedures and operation lists. This is not accounted for in the finance received to perform the operation by the hospital in the Payment by Results (PbR) system. To find out: 1. The effect on the duration of a procedure and the number of procedures performed on the list when a trainee is involved. 2. The percentage of orthopaedic cases with trainee involvement. 3. The effect of European working time directive (EWTD) on the trainee involvement in cases from theatre data in 2008 versus logbook data from 2004 - 2008. Data was taken from two different sources. Firstly, the Operating Room Information System (ORMIS) and patient operation notes. The second source was a consultant's logbook comprising 227 primary total knee replacements performed between 2004 and 2008. The data produced trends suggesting trainees took longer to perform procedures than consultants. In orthopaedic operations, 92% of cases had trainees present and of these 17% of cases were performed by trainees in 2008. Before the implementation of the EWTD, trainees performed more procedures when compared with current logbook data (38% versus 17% cases). Time taken by a trainee to perform the procedure under direct consultant supervision was significantly higher in comparison to procedures performed by a consultant alone (P = < 0.0001). Analysing the ORMIS and logbook data gave similar conclusions. Hospitals should be given financial recognition for training. In this debate, we should remain focused on the provision of quality training for the next generation of surgeons.

  19. Comparative efficacy and safety of anticoagulant strategies for acute coronary syndromes. Comprehensive network meta-analysis of 42 randomised trials involving 117,353 patients

    NARCIS (Netherlands)

    Navarese, Eliano Pio; Andreotti, Felicita; Kołodziejczak, Michalina; Schulze, Volker; Wolff, Georg; Dias, Sofia; Claessen, Bimmer; Brouwer, Marc; Tarantini, Giuseppe; Iliceto, Sabino; Brockmeyer, Maximilian; Kowalewski, Mariusz; Lin, Yingfeng; Eikelboom, John; Musumeci, Giuseppe; Lee, Leong; Lip, Gregory Y. H.; Valgimigli, Marco; Berti, Sergio; Kelm, Malte

    2015-01-01

    International guidelines differ in strengths of recommendation for anticoagulation strategies in acute coronary syndromes (ACS). We performed a comprehensive network meta-analysis (NMA) of randomised controlled trials (RCTs) to investigate the comparative efficacy and safety of parenteral

  20. Molecular analysis of the graviperception signal transduction in the flagellate Euglena gracilis: Involvement of a transient receptor potential-like channel and a calmodulin

    Science.gov (United States)

    Häder, Donat-Peter; Richter, Peter R.; Schuster, Martin; Daiker, Viktor; Lebert, Michael

    2009-04-01

    Euglena gracilis, a unicellular, photosynthetic flagellate is a model system for environmentally controlled behavior responses. The organism shows pronounced negative gravitaxis. This movement is based on physiological mechanisms, which in the past had been only indirectly assessed. It was shown that mechano-sensitive calcium channels are involved in the gravitaxis response. Recent studies have demonstrated that members of the transient receptor potential (TRP) family function as mechano-sensitive channels in several different cell types. We have sequenced part of a TRP gene in Euglena and applied RNA interference (RNAi) to confirm that these channels are involved in graviperception. It was found that RNAi against the putative TRP channel abolished gravitaxis. The genes of three calmodulins were sequences in Euglena, one of which was previously known in its protein structure (cal 1). The other two were unknown (cal 2 and cal 3). Cal 2 has been analyzed in detail. The biosynthesis of the corresponding proteins of cal 1 and cal 2 was inhibited by means of RNA interference to see whether this blockage impairs gravitaxis. RNAi of cal 1 leads to a long-term loss of free swimming in the cells (while euglenoid movement persists). It induced pronounced cell form aberrations and the division of cells was hampered. After recovery from RNAi the cell showed precise negative gravitaxis again. Thus cal 1 does not seem to be involved in gravitaxis. In contrast, the blockage of cal 2 has no pronounced influence on motility and cell form but leads to a complete loss of gravitactic orientation for more than 30 days showing that this calmodulin is an element in the signal transduction chain. The data are discussed in the context of the current model of the gravitaxis signal transduction chain in Euglena gracilis.

  1. Identification of Genes Putatively Involved in Chitin Metabolism and Insecticide Detoxification in the Rice Leaf Folder (Cnaphalocrocis medinalis) Larvae through Transcriptomic Analysis.

    Science.gov (United States)

    Yu, Hai-Zhong; Wen, De-Fu; Wang, Wan-Lin; Geng, Lei; Zhang, Yan; Xu, Jia-Ping

    2015-09-10

    The rice leaf roller (Cnaphalocrocis medinalis) is one of the most destructive agricultural pests. Due to its migratory behavior, it is difficult to control worldwide. To date, little is known about major genes of C. medinalis involved in chitin metabolism and insecticide detoxification. In order to obtain a comprehensive genome dataset of C. medinalis, we conducted de novo transcriptome sequencing which focused on the major feeding stage of fourth-instar larvae, and our work revealed useful information on chitin metabolism and insecticide detoxification and target genes of C. medinalis. We acquired 29,367,797 Illumina reads and assembled these reads into 63,174 unigenes with an average length of 753 bp. Among these unigenes, 31,810 were annotated against the National Center for Biotechnology Information non-redundant (NCBI nr) protein database, resulting in 24,246, 8669 and 18,176 assigned to Swiss-Prot, clusters of orthologous group (COG), and gene ontology (GO), respectively. We were able to map 10,043 unigenes into 285 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Specifically, 16 genes, including five chitin deacetylases, two chitin synthases, five chitinases and four other related enzymes, were identified to be putatively involved in chitin biosynthesis and degradation, whereas 360 genes, including cytochrome P450s, glutathione S-transferases, esterases, and acetylcholinesterases, were found to be potentially involved in insecticide detoxification or as insecticide targets. The reliability of the transcriptome data was determined by reverse transcription quantitative PCR (RT-qPCR) for the selected genes. Our data serves as a new and valuable sequence resource for genomic studies on C. medinalis. The findings should improve our understanding of C. medinalis genetics and contribute to management of this important agricultural pest.

  2. Identification of Genes Putatively Involved in Chitin Metabolism and Insecticide Detoxification in the Rice Leaf Folder (Cnaphalocrocis medinalis Larvae through Transcriptomic Analysis

    Directory of Open Access Journals (Sweden)

    Hai-Zhong Yu

    2015-09-01

    Full Text Available The rice leaf roller (Cnaphalocrocis medinalis is one of the most destructive agricultural pests. Due to its migratory behavior, it is difficult to control worldwide. To date, little is known about major genes of C. medinalis involved in chitin metabolism and insecticide detoxification. In order to obtain a comprehensive genome dataset of C. medinalis, we conducted de novo transcriptome sequencing which focused on the major feeding stage of fourth-instar larvae, and our work revealed useful information on chitin metabolism and insecticide detoxification and target genes of C. medinalis. We acquired 29,367,797 Illumina reads and assembled these reads into 63,174 unigenes with an average length of 753 bp. Among these unigenes, 31,810 were annotated against the National Center for Biotechnology Information non-redundant (NCBI nr protein database, resulting in 24,246, 8669 and 18,176 assigned to Swiss-Prot, clusters of orthologous group (COG, and gene ontology (GO, respectively. We were able to map 10,043 unigenes into 285 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG. Specifically, 16 genes, including five chitin deacetylases, two chitin synthases, five chitinases and four other related enzymes, were identified to be putatively involved in chitin biosynthesis and degradation, whereas 360 genes, including cytochrome P450s, glutathione S-transferases, esterases, and acetylcholinesterases, were found to be potentially involved in insecticide detoxification or as insecticide targets. The reliability of the transcriptome data was determined by reverse transcription quantitative PCR (RT-qPCR for the selected genes. Our data serves as a new and valuable sequence resource for genomic studies on C. medinalis. The findings should improve our understanding of C. medinalis genetics and contribute to management of this important agricultural pest.

  3. Apparent involvement of purines in the control of expression of Salmonella typhimurium pyr genes: analysis of a leaky guaB mutant resistant to pyrimidine analogs

    DEFF Research Database (Denmark)

    Jensen, Kaj Frank

    1979-01-01

    A leaky guaB mutant of Salmonella typhimurium LT-2 was obtained during a selection for mutants resistant to a combination of the two pyrimidine analogs, 5-fluorouracil and 5-fluorouridine. In the absence of exogenous guanine compounds, the growth rate of this mutant is limited by the endogenous s......%, respectively. The pyrimidine metabolism of the guaB mutant is restored completely by addition of guanine (or xanthine) to the growth medium. The data indicate purine nucleotide involvement in the regulation of expression of the pyr genes of S. typhimurium....

  4. High Ki-67 Immunohistochemical Reactivity Correlates With Poor Prognosis in Bladder Carcinoma: A Comprehensive Meta-Analysis with 13,053 Patients Involved.

    Science.gov (United States)

    Luo, Yihuan; Zhang, Xin; Mo, Meile; Tan, Zhong; Huang, Lanshan; Zhou, Hong; Wang, Chunqin; Wei, Fanglin; Qiu, Xiaohui; He, Rongquan; Chen, Gang

    2016-04-01

    Ki-67 is considered as one of prime biomarkers to reflect cell proliferation and immunohistochemical Ki-67 staining has been widely applied in clinical pathology. To solve the widespread controversy whether Ki-67 reactivity significantly predicts clinical prognosis of bladder carcinoma (BC), we performed a comprehensive meta-analysis by combining results from different literature. A comprehensive search was conducted in the Chinese databases of WanFang, China National Knowledge Infrastructure and Chinese VIP as well as English databases of PubMed, ISI web of science, EMBASE, Science Direct, and Wiley online library. Independent studies linking Ki-67 to cancer-specific survival (CSS), disease-free survival (DFS), overall survival (OS), progression-free survival (PFS), and recurrence-free survival (RFS) were included in our meta-analysis. With the cut-off values literature provided, hazard ratio (HR) values between the survival distributions were extracted and later combined with STATA 12.0. In total, 76 studies (n = 13,053 patients) were eligible for the meta-analysis. It was indicated in either univariate or multivariate analysis for survival that high Ki-67 reactivity significantly predicted poor prognosis. In the univariate analysis, the combined HR for CSS, DFS, OS, PFS, and RFS were 2.588 (95% confidence interval [CI]: 1.623-4.127, P Asian and European-American patients (P Asian patients, for CSS, DFS, PFS, and RFS in European-American patients (P literature with low cut-off value (<20%) demonstrated that high Ki-67 reactivity predicted shorter DFS, PFS, and RFS in BC patients (P < 0.05). In the subgroup analysis of high cut-off value (≥20%), our meta-analysis indicated that high Ki-67 reactivity, in either univariate or multivariate analysis, significantly correlated with all five clinical outcomes in BC patients (P < 0.05). The meta-analysis indicates that high Ki-67 reactivity significantly correlates with deteriorated clinical outcomes

  5. Breast cancer detected in screening mammography: a comparative analysis of the cases involving women aged 40 to 49 years and 50 to 64 years

    International Nuclear Information System (INIS)

    Echevarria, J.J.; Lopez, J.A.; Segovia, M.C.; Rodriguez, M.; Zabalza, I.; Garcia, M.

    1998-01-01

    To determine and compare the prognostic criteria (tumor, size, lymph node involvement, clinical staging and histological type and grade) for breast neoplasms detected at screening mammography in women 40 to 49 and 50 to 64 years of age. We review a total of 216 unelected cases of breast carcinoma diagnosed in our hospital, 109 discovered at screening mammography (45 in women aged 40 to 40 years and 64 in women aged 50 to 64 years). We found no statistically significant differences between the two age groups with respect to tumor size, lymph node involvement or clinical staging. In all, 64.4% and 61.6% of the carcinomas detected in 40 to 49-year-old women and in 50 to 64-year-old women, respectively, corresponded to clinical stages 0 and 1. Nor did we observe significant differences with respect to the histological type or grade. Given the similarity in the major prognostic criteria for the neoplasms diagnosed in both age groups, we consider that the performance of screening mammography in women aged 40 to 49 years allows the detection of breast carcinomas at stages as early as those in which these lesions are detected in women aged 50 to 64 years. (Author) 24 refs

  6. In situ analysis of Bacillus licheniformis biofilms: amyloid-like polymers and eDNA are involved in the adherence and aggregation of the extracellular matrix.

    Science.gov (United States)

    Randrianjatovo-Gbalou, I; Rouquette, P; Lefebvre, D; Girbal-Neuhauser, E; Marcato-Romain, C-E

    2017-05-01

    This study attempts to determine which of the exopolymeric substances are involved in the adherence and aggregation of a Bacillus licheniformis biofilm. The involvement of extracellular proteins and eDNA were particularly investigated using DNase and proteinase K treatment. The permeability of the biofilms increased fivefold after DNase I treatment. The quantification of the matrix components showed that, irrespective to the enzyme tested, eDNA and amyloid-like polymers were removed simultaneously. Size-exclusion chromatography analyses supported these observations and revealed the presence of associated nucleic acid and protein complexes in the biofilm lysates. These data suggest that some extracellular DNA and amyloid-like proteins were closely interlaced within the matrix. Finally, confocal laser scanning microscopy imaging gave supplementary clues about the 3D organization of the biofilms, confirming that eDNA and exoproteins were essentially layered under and around the bacterial cells, whereas the amyloid-like fractions were homogeneously distributed within the matrix. These results confirm that some DNA-amyloid complexes play a key role in the modulation of the mechanical resistance of B. licheniformis biofilms. The study highlights the need to consider the whole structure of biofilms and to target the interactions between matrix components. A better understanding of B. licheniformis biofilm physiology and the structural organization of the matrix will strengthen strategies of biofilm control. © 2017 The Society for Applied Microbiology.

  7. Sequence analysis and identification of the pyrKDbF operon from Lactococcus lactis including a novel gene, pyrK, involved in pyrimidine biosynthesis

    DEFF Research Database (Denmark)

    Andersen, Paal Skytt; Martinussen, Jan; Hammer, Karin

    1996-01-01

    Three genes encoding enzymes involved in the biosynthesis of pyrimidines have been found to constitute an operon in Lactococcus lactis. Two of the genes are the well-known pyr genes pyrDb and pyrF, encoding dihydroorotate dehydrogenase and orotidine monophosphate decarboxylase, respectively....... The third gene encodes a protein which was shown to be necessary for the activity of the pyrDb-encoded dihydroorotate dehydrogenase; we propose to name the gene pyrK. The pyrK-encoded protein is homologous to a number of proteins which are involved in electron transfer. The lactococcal pyrKDbF operon...... is highly homologous to the corresponding part of the much-larger pyr operon of Bacillus subtilis. orf2, the pyrK homolog in B. subtilis, has also been shown to be necessary for pyrimidine biosynthesis (A.E. Kahler and R.L. Switzer, J. Bacteriol. 178:5013-5016, 1996). Four genes adjacent to the operon, i...

  8. Involvement of Wingless/Armadillo signaling in the posterior sequential segmentation in the cricket, Gryllus bimaculatus (Orthoptera), as revealed by RNAi analysis.

    Science.gov (United States)

    Miyawaki, Katsuyuki; Mito, Taro; Sarashina, Isao; Zhang, Hongjie; Shinmyo, Yohei; Ohuchi, Hideyo; Noji, Sumihare

    2004-02-01

    In insects, there are two different modes of segmentation. In the higher dipteran insects (like Drosophila), their segmentation takes place almost simultaneously in the syncytial blastoderm. By contrast, in the orthopteran insects (like Schistocerca (grasshopper)), the anterior segments form almost simultaneously in the cellular blastoderm and then the remaining posterior part elongates to form segments sequentially from the posterior proliferative zone. Although most of their orthologues of the Drosophila segmentation genes may be involved in their segmentation, little is known about their roles. We have investigated segmentation processes of Gryllus bimaculatus, focusing on its orthologues of the Drosophila segment-polarity genes, G. bimaculatus wingless (Gbwg), armadillo (Gbarm) and hedgehog (Gbhh). Gbhh and Gbwg were observed to be expressed in the each anterior segment and the posterior proliferative zone. In order to know their roles, we used RNA interference (RNAi). We could not observed any significant effects of RNAi for Gbwg and Gbhh on segmentation, probably due to functional replacement by another member of the corresponding gene families. Embryos obtained by RNAi for Gbarm exhibited abnormal anterior segments and lack of the abdomen. Our results suggest that GbWg/GbArm signaling is involved in the posterior sequential segmentation in the G. bimaculatus embryos, while Gbwg, Gbarm and Gbhh are likely to act as the segment-polarity genes in the anterior segmentation similarly as in Drosophila.

  9. In silico analysis of expression data for identification of genes involved in spatial accumulation of calcium in developing seeds of rice.

    Science.gov (United States)

    Goel, Anshita; Gaur, Vikram S; Arora, Sandeep; Gupta, Sanjay; Kumar, Anil

    2012-01-01

    The calcium (Ca(2+)) transporters, like Ca(2+) channels, Ca(2+) ATPases, and Ca(2+) exchangers, are instrumental for signaling and transport. However, the mechanism by which they orchestrate the accumulation of Ca(2+) in grain filling has not yet been investigated. Hence the present study was designed to identify the potential calcium transporter genes that may be responsible for the spatial accumulation of calcium during grain filling. In silico expression analyses were performed to identify Ca(2+) transporters that predominantly express during the different developmental stages of Oryza sativa. A total of 13 unique calcium transporters (7 from massively parallel signature sequencing [MPSS] data analysis, and 9 from microarray analysis) were identified. Analysis of variance (ANOVA) revealed differential expression of the transporters across tissues, and principal component analysis (PCA) exhibited their seed-specific distinctive expression profile. Interestingly, Ca(2+) exchanger genes are highly expressed in the initial stages, whereas some Ca(2+) ATPase genes are highly expressed throughout seed development. Furthermore, analysis of the cis-elements located in the promoter region of the subset of 13 genes suggested that D of proteins play essential roles in regulating the expression of Ca(2+) transporter genes during rice seed development. Based on these results, we developed a hypothetical model explaining the transport and tissue specific distribution of calcium in developing cereal seeds. The model may be extrapolated to understand the mechanism behind the exceptionally high level of calcium accumulation seen in grains like finger millet.

  10. Fatal poisonings involving propoxyphene before and after voluntary withdrawal from the United States' market: An analysis from the state of Florida.

    Science.gov (United States)

    Delcher, Chris; Chen, Guanming; Wang, Yanning; Slavova, Svetla; Goldberger, Bruce A

    2017-11-01

    The synthetic opioid propoxyphene was a schedule IV controlled substance with multiple reported health risks before the US Food and Drug Administration issued a request for voluntary market withdrawal in November 2010. The purpose of this study is to investigate the characteristics and occurrences of propoxyphene-related deaths in Florida before and after voluntary market removal. Decedent-level toxicology data from Florida's Medical Examiners Commission was used to compare the temporal, polysubstance use, sociodemographic, and geographic profiles associated with propoxyphene-involved deaths for a pre-withdrawal (November 2008-November 2010) and post-withdrawal (December 2010-December 2012) period. Sensitivity analyses using multiple data sources, including Florida's Prescription Drug Monitoring Program and other states' data, were conducted to examine potential reporting bias. Results showed that the number of propoxyphene-involved deaths declined by 84% from 580 deaths to 92 deaths after market withdrawal. The co-occurrence of other prevalent drugs, such as oxycodone (17.2% to 26.1%, p=0.0422) increased significantly in the post-withdrawal study period. A larger proportion of the propoxyphene-related deaths were reported from South Florida after the withdrawal (28.4% to 56.5%, pmarket withdrawal, as recently as 2016. Our findings are consistent with previous studies that propoxyphene was still available after removal from the US market. Continued surveillance is recommended after highly abused opioids are withdrawn from the market due to on-going safety risks. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Transcriptome sequence analysis of an ornamental plant, Ananas comosus var. bracteatus, revealed the potential unigenes involved in terpenoid and phenylpropanoid biosynthesis.

    Directory of Open Access Journals (Sweden)

    Jun Ma

    Full Text Available Ananas comosus var. bracteatus (Red Pineapple is an important ornamental plant for its colorful leaves and decorative red fruits. Because of its complex genome, it is difficult to understand the molecular mechanisms involved in the growth and development. Thus high-throughput transcriptome sequencing of Ananas comosus var. bracteatus is necessary to generate large quantities of transcript sequences for the purpose of gene discovery and functional genomic studies.The Ananas comosus var. bracteatus transcriptome was sequenced by the Illumina paired-end sequencing technology. We obtained a total of 23.5 million high quality sequencing reads, 1,555,808 contigs and 41,052 unigenes. In total 41,052 unigenes of Ananas comosus var. bracteatus, 23,275 unigenes were annotated in the NCBI non-redundant protein database and 23,134 unigenes were annotated in the Swiss-Port database. Out of these, 17,748 and 8,505 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Functional annotation against Kyoto Encyclopedia of Genes and Genomes Pathway database identified 5,825 unigenes which were mapped to 117 pathways. The assembly predicted many unigenes that were previously unknown. The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum. Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique. We predicted unigenes encoding enzymes involved in terpenoid and phenylpropanoid biosynthesis.The sequence data provide the most comprehensive transcriptomic resource currently available for Ananas comosus var. bracteatus. To our knowledge; this is the first report on the de novo transcriptome sequencing of the Ananas comosus var. bracteatus. Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus.

  12. Transcriptome sequence analysis of an ornamental plant, Ananas comosus var. bracteatus, revealed the potential unigenes involved in terpenoid and phenylpropanoid biosynthesis.

    Science.gov (United States)

    Ma, Jun; Kanakala, S; He, Yehua; Zhang, Junli; Zhong, Xiaolan

    2015-01-01

    Ananas comosus var. bracteatus (Red Pineapple) is an important ornamental plant for its colorful leaves and decorative red fruits. Because of its complex genome, it is difficult to understand the molecular mechanisms involved in the growth and development. Thus high-throughput transcriptome sequencing of Ananas comosus var. bracteatus is necessary to generate large quantities of transcript sequences for the purpose of gene discovery and functional genomic studies. The Ananas comosus var. bracteatus transcriptome was sequenced by the Illumina paired-end sequencing technology. We obtained a total of 23.5 million high quality sequencing reads, 1,555,808 contigs and 41,052 unigenes. In total 41,052 unigenes of Ananas comosus var. bracteatus, 23,275 unigenes were annotated in the NCBI non-redundant protein database and 23,134 unigenes were annotated in the Swiss-Port database. Out of these, 17,748 and 8,505 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Functional annotation against Kyoto Encyclopedia of Genes and Genomes Pathway database identified 5,825 unigenes which were mapped to 117 pathways. The assembly predicted many unigenes that were previously unknown. The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum. Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique. We predicted unigenes encoding enzymes involved in terpenoid and phenylpropanoid biosynthesis. The sequence data provide the most comprehensive transcriptomic resource currently available for Ananas comosus var. bracteatus. To our knowledge; this is the first report on the de novo transcriptome sequencing of the Ananas comosus var. bracteatus. Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus.

  13. Safety incidents involving confused and forgetful older patients in a specialised care setting--analysis of the safety incidents reported to the HaiPro reporting system.

    Science.gov (United States)

    Kinnunen-Luovi, Kaisa; Saarnio, Reetta; Isola, Arja

    2014-09-01

    To describe the safety incidents involving confused and forgetful older patients in a specialised care setting entered in the HaiPro reporting system. About 10% of patients experience a safety incident during hospitalisation, which causes or could cause them harm. The possibility of a safety incident during hospitalisation increases significantly with age. A mild or moderate memory disorder and acute confusion are often present in the safety incidents originating with an older patient. The design of the study was action research with this study using findings from one of the first-phase studies, which included qualitative and quantitative analysed data. Data were collected from the reporting system for safety incidents (HaiPro) in a university hospital in Finland. There were 672 reported safety incidents from four acute medical wards during the years 2009-2011, which were scrutinised. Seventy-five of them were linked to a confused patient and were analysed. The majority of the safety incidents analysed involved patient-related accidents. In addition to challenging behaviour, contributing factors included ward routines, shortage of nursing staff, environmental factors and staff knowledge and skills. Nurses tried to secure the patient safety in many different ways, but the modes of actions were insufficient. Nursing staff need evidence-based information on how to assess the cognitive status of a confused patient and how to encounter such patients. The number of nursing staff and ward routines should be examined critically and put in proportion to the care intensity demands caused by the patient's confused state. The findings can be used as a starting point in the prevention of safety incidents and in improving the care of older patients. © 2013 John Wiley & Sons Ltd.

  14. Rectal cancer: Local staging and assessment of lymph node involvement with endoluminal US, CT, and MR imaging - A meta-analysis

    NARCIS (Netherlands)

    Bipat, Shandra; Glas, Afina S.; Slors, Frederik J. M.; Zwinderman, Aeilko H.; Bossuyt, Patrick M. M.; Stoker, Jaap

    2004-01-01

    PURPOSE: To perform a meta-analysis to compare endoluminal ultrasonography (US), computed tomography (CT), and magnetic resonance (MR) imaging in rectal cancer staging. MATERIALS AND METHODS: Relevant articles published between 1985 and 2002 were included if more than 20 patients were studied,

  15. The cytochrome P450 genes of channel catfish: their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq datasets

    Science.gov (United States)

    Cytochrome P450s (CYPs) encode one of the most diverse enzyme superfamily in nature. They catalyze oxidative reactions of endogenous molecules and exogenous chemicals. Methods: We identifiedCYPs genes through in silico analysis using EST, RNA-Seq and genome databases of channel catfish.Phylogenetic ...

  16. Carbohydrate Analysis Experiment Involving Mono- and Disaccharides with a Twist of Glycobiology: Two New Tests for Distinguishing Pentoses and Glycosidic Bonds

    Science.gov (United States)

    Herdman, Chelsea; Diop, Lamine; Dickman, Michael

    2013-01-01

    Carbohydrate analysis is an excellent way to expose second-year biochemistry majors to the subtlety and nuance of sugar chemistry. In one, 3-h practical period, students must identify an unknown mono- or disaccharide from a collection of three hexoses (glucose, galactose, and mannose), two pentoses (ribose and arabinose), and three disaccharides…

  17. True microbiota involved in chronic lung infection of cystic fibrosis patients found by culturing and 16S rRNA gene analysis

    DEFF Research Database (Denmark)

    Rudkjøbing, Vibeke Børsholt; Thomsen, Trine R; Alhede, Morten

    2011-01-01

    Patients suffering from cystic fibrosis (CF) develop chronic lung infection. In this study, we investigated the microorganisms present in transplanted CF lungs (n = 5) by standard culturing and 16S rRNA gene analysis. A correspondence between culturing and the molecular methods was observed. In c...

  18. A novel complete-case analysis to determine statistical significance between treatments in an intention-to-treat population of randomized clinical trials involving missing data.

    Science.gov (United States)

    Liu, Wei; Ding, Jinhui

    2018-04-01

    The application of the principle of the intention-to-treat (ITT) to the analysis of clinical trials is challenged in the presence of missing outcome data. The consequences of stopping an assigned treatment in a withdrawn subject are unknown. It is difficult to make a single assumption about missing mechanisms for all clinical trials because there are complicated reactions in the human body to drugs due to the presence of complex biological networks, leading to data missing randomly or non-randomly. Currently there is no statistical method that can tell whether a difference between two treatments in the ITT population of a randomized clinical trial with missing data is significant at a pre-specified level. Making no assumptions about the missing mechanisms, we propose a generalized complete-case (GCC) analysis based on the data of completers. An evaluation of the impact of missing data on the ITT analysis reveals that a statistically significant GCC result implies a significant treatment effect in the ITT population at a pre-specified significance level unless, relative to the comparator, the test drug is poisonous to the non-completers as documented in their medical records. Applications of the GCC analysis are illustrated using literature data, and its properties and limits are discussed.

  19. Commericial Involvement in Intramurals.

    Science.gov (United States)

    Maas, Gerry

    Sport in general has long had ties with commercial interests, the most popular and widespread involving publicity. Intramural sports programs, however, have not cultivated many commercial involvements in publicity. The approach in intramural sports advertising is simple. A commercial interest pays for space or time in a given communication media…

  20. Conversational Involvement and Loneliness.

    Science.gov (United States)

    Bell, Robert A.

    1985-01-01

    Assessed the relationship of conversational involvement and loneliness among college students. Found that lonely participants in this study had lower rates of talkativeness, interruptions, and attention than the nonlonely; they were also perceived as less involved and less interpersonally attractive. (PD)

  1. Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways

    DEFF Research Database (Denmark)

    Ewald, David Adrian; Malajian, Dana; Krueger, James G.

    2015-01-01

    . This transcriptome enriches key AD pathways more than the individual studies, and associates AD with novel pathways, such as atherosclerosis signaling (IL-37, selectin E/SELE). We identified wide lipid abnormalities and, for the first time in vivo, correlated Th2 immune activation with downregulation of key......Atopic dermatitis (AD) is a common inflammatory skin disease with limited treatment options. Several microarray experiments have been conducted on lesional/LS and non-lesional/NL AD skin to develop a genomic disease phenotype. Although these experiments have shed light on disease pathology, inter-study...... comparisons reveal large differences in resulting sets of differentially expressed genes (DEGs), limiting the utility of direct comparisons across studies. We carried out a meta-analysis combining 4 published AD datasets to define a robust disease profile, termed meta-analysis derived AD (MADAD) transcriptome...

  2. Survivin protein expression is involved in the progression of non-small cell lung cancer in Asians: a meta-analysis

    International Nuclear Information System (INIS)

    Duan, Liang; Hu, Xuefei; Jin, Yuxing; Liu, Ruijun; You, Qingjun

    2016-01-01

    Surviving expression might serve as a prognostic biomarker predicting the clinical outcome of non-small cell lung cancer (NSCLC). The study was conducted to explore the potential correlation of survivin protein expression with NSCLC and its clinicopathologic characteristics. PubMed, Medline, Cochrane Library, CNKI and Wanfang database were searched through January 2016 with a set of inclusion and exclusion criteria. Data was extracted from these articles and all statistical analysis was conducted by using Stata 12.0. A total of 28 literatures (14 studies in Chinese and 14 studies in English) were enrolled in this meta-analysis, including 3206 NSCLC patients and 816 normal controls. The result of meta-analysis demonstrated a significant difference of survivin positive expression between NSCLC patients and normal controls (RR = 7.16, 95 % CI = 4.63-11.07, P < 0.001). To investigate the relationship of survivin expression and clinicopathologic characteristics, we performed a meta-analysis in NSCLC patients. Our results indicates survivin expression was associated with histological differentiation, tumor-node-metastasis (TNM) stage and lymph node metastasis (LNM) (RR = 0.80, 95 % CI = 0.73-0.87, P < 0.001; RR = 0.75, 95 % CI = 0.67-0.84, P < 0.001; RR = 1.14, 95 % CI = 1.01-1.29, P = 0.035, respectively), but not pathological type and tumor size. (RR = 1.00, 95 % CI = 0.93-1.07, P = 0.983; RR = 0.95, 95 % CI = 0.86-1.05, P = 0.336, respectively). Higher expression of survivin in NSCLC patients was found when compared to normal controls. Survivin expression was associated with the clinicopathologic characteristics of NSCLC and may serves as an important biomarker for NSCLC progression

  3. Structural analysis of natural killer cell receptor protein 1 (NKR-P1) extracellular domains suggests a conserved long loop region involved in ligand specificity

    Czech Academy of Sciences Publication Activity Database

    Sovová, Žofie; Kopecký, V.; Pazderka, T.; Hofbauerová, Kateřina; Rozbeský, Daniel; Vaněk, Ondřej; Bezouška, K.; Ettrich, Rüdiger

    2011-01-01

    Roč. 17, č. 6 (2011), s. 1353-1370 ISSN 1610-2940 R&D Projects: GA MŠk(CZ) LC06010; GA AV ČR KJB101120805 Institutional research plan: CEZ:AV0Z60870520; CEZ:AV0Z50200510 Keywords : cladogram * differential scanning calorimetry * FTIR * molecular dynamics * raman spectroscopy * RMSF * thermal dynamics * topology * two-dimensional correlation analysis Subject RIV: CE - Biochemistry Impact factor: 1.797, year: 2011

  4. Can a Boxer Engine Reduce Leg Injuries Among Motorcyclists? Analysis of Injury Distributions in Crashes Involving Different Motorcycles Fitted with Antilock Brakes (ABS).

    Science.gov (United States)

    Rizzi, Matteo

    2015-01-01

    Several studies have shown that motorcycle antilock braking systems (ABS) reduce crashes and injuries. However, it has been suggested that the improved stability provided by ABS would make upright crashes more frequent, thus changing the injury distributions among motorcyclists and increasing the risk of leg injuries. The overall motorcycle design can vary across different categories and manufacturers. For instance, some motorcycles are equipped with boxer-twin engines; that is, with protruding cylinder heads. A previous study based on a limited material has suggested that these could provide some leg protection; therefore, the aim of this research was to analyze injury distributions in crashes involving ABS-equipped motorcycles with boxer-twin engines compared to similar ABS-equipped motorcycles with other engine configurations. Swedish hospital and police records from 2003-2014 were used. Crashes involving ABS-equipped motorcycles with boxer-twin engines (n = 55) were compared with similar ABS-equipped motorcycles with other engines configurations (n = 127). The distributions of Abbreviated Injury Scale (AIS) 1+ and AIS 2+ were compared. Each subject's injury scores were also converted to the risk for permanent medical impairment (RPMI), which shows the risk of different levels of permanent medical impairment given the severity and location and of injuries. To compare injury severity, the mean RPMI 1+ and RPMI 10+ were analyzed for each body region and in overall for each group of motorcyclists. It was found that AIS 1+, AIS 2+, and PMI 1+ leg injuries were reduced by approximately 50% among riders with boxer engines. These results were statistically significant. The number of injuries to the upper body did not increase; the mean RPMI to the head and upper body were similar across the 2 groups, suggesting that the severity of injuries did not increase either. Indications were found suggesting that the overall mean RPMI 1+ was lower among riders with boxer engines

  5. Dental skill mix: a cross-sectional analysis of delegation practices between dental and dental hygiene-therapy students involved in team training in the South of England.

    Science.gov (United States)

    Wanyonyi, Kristina L; Radford, David R; Gallagher, Jennifer E

    2014-11-18

    Research suggests that health professionals who have trained together have a better understanding of one another's scope of practice and are thus equipped for teamwork during their professional careers. Dental hygiene-therapists (DHTs) are mid-level providers that can deliver routine care working alongside dentists. This study examines patterns of delegation (selected tasks and patients) by dental students to DHT students training together in an integrated team. A retrospective sample of patient data (n = 2,063) was extracted from a patient management system showing the treatment activities of two student cohorts (dental and DHT) involved in team training in a primary care setting in the South of England over two academic years. The data extracted included key procedures delegated by dental students to DHT students coded by skill-mix of operator (e.g., fissure sealants, restorations, paediatric extractions) and patient demography. χ2 tests were conducted to investigate the relationship between delegation and patient age group, gender, smoking status, payment-exemption status, and social deprivation. A total of 2,063 patients managed during this period received treatments that could be undertaken by either student type; in total, they received 14,996 treatment procedures. The treatments most commonly delegated were fissure sealants (90%) and restorations (51%); whilst the least delegated were paediatric extractions (2%). Over half of these patients (55%) had at least one instance of delegation from a dental to a DHT student. Associations were found between delegation and patient age group and smoking status (P delegation (86%) compared with adults of working age (50%) and patients aged 65 years and over (56%). A higher proportion of smokers had been delegated compared with non-smokers (45% cf. 26%; P delegation of care to DHT students training as a team with dental students, involved significantly greater experience in treating children and adult smokers, and

  6. Drug involvement in fatal overdoses

    Directory of Open Access Journals (Sweden)

    Christopher J. Ruhm

    2017-12-01

    Full Text Available Death certificate data from the Multiple Cause of Death (MCOD files were analyzed to better understand the drug categories most responsible for the increase in fatal overdoses occurring between 1999 and 2014. Statistical adjustment methods were used to account for the understatement in reported drug involvement occurring because death certificates frequently do not specify which drugs were involved in the deaths. The frequency of combination drug use introduced additional uncertainty and so a distinction was made between any versus exclusive drug involvement. Many results were sensitive to the starting and ending years chosen for examination. Opioid analgesics played a major role in the increased drug deaths for analysis windows starting in 1999 but other drugs, particularly heroin, became more significant for recent time periods. Combination drug use was important for all time periods and needs to be accounted for when designing policies to slow or reverse the increase in overdose deaths.

  7. Investigation of cyclin D1 rs9344 G>A polymorphism in colorectal cancer: a meta-analysis involving 13,642 subjects

    Directory of Open Access Journals (Sweden)

    Qiu H

    2016-10-01

    Full Text Available Hao Qiu,1,* Chengguo Cheng,2,* Yafeng Wang,3 Mingqiang Kang,4 Weifeng Tang,4,5 Shuchen Chen,4 Haiyong Gu,6 Chao Liu,5 Yu Chen7,8 1Department of Immunology, School of Medicine, Jiangsu University, 2Department of Pulmonary Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, 3Department of Cardiology, The People’s Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, 4Department of Thoracic Surgery, Affiliated Union Hospital, Fujian Medical University, Fuzhou, 5Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 6Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 7Department of Medical Oncology, Fujian Provincial Cancer Hospital, Fujian Medical University Cancer Hospital, 8Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, People’s Republic of China *These authors contributed equally to this work Abstract: The relationship between cyclin D1 (CCND1 rs9344 G>A polymorphism and colorectal cancer (CRC risk is still ambiguous. To obtain a precise estimation of the relationship, we performed an extensive meta-analysis based on the eligible studies. Crude odds ratios with their 95% confidence intervals were harnessed to determine the strength of correlation between CCND1 rs9344 G>A polymorphism and CRC risk under the allele, the homozygote, the dominant, and the recessive genetic models, respectively (28 studies with 5,784 CRC cases and 7,858 controls. Our results indicated evidence of the association between CCND1 rs9344 G>A polymorphism and the increased risk of CRC in four genetic models: A vs G, AA vs GG, AA+GA vs GG, and AA vs GA+GG. In a stratified analysis by cancer type of CRC, there was an increased risk of sporadic CRC found in three genetic models: A vs G, AA vs GG, and AA+GA vs GG. In a stratified analysis by ethnicity, there was an increased CRC risk found among Asians in allele comparison

  8. Comparative proteomic analysis of oil palm leaves infected with Ganoderma boninense revealed changes in proteins involved in photosynthesis, carbohydrate metabolism, and immunity and defense.

    Science.gov (United States)

    Jeffery Daim, Leona Daniela; Ooi, Tony Eng Keong; Ithnin, Nalisha; Mohd Yusof, Hirzun; Kulaveerasingam, Harikrishna; Abdul Majid, Nazia; Karsani, Saiful Anuar

    2015-08-01

    The basidiomycete fungal pathogen Ganoderma boninense is the causative agent for the incurable basal stem rot (BSR) disease in oil palm. This disease causes significant annual crop losses in the oil palm industry. Currently, there is no effective method for disease control and elimination, nor is any molecular marker for early detection of the disease available. An understanding of how BSR affects protein expression in plants may help identify and/or assist in the development of an early detection protocol. Although the mode of infection of BSR disease is primarily via the root system, defense-related genes have been shown to be expressed in both the root and leafs. Thus, to provide an insight into the changes in the global protein expression profile in infected plants, comparative 2DE was performed on leaf tissues sampled from palms with and without artificial inoculation of the Ganoderma fungus. Comparative 2DE revealed that 54 protein spots changed in abundance. A total of 51 protein spots were successfully identified by LC-QTOF MS/MS. The majority of these proteins were those involved in photosynthesis, carbohydrate metabolism as well as immunity and defense. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Proteomic analysis of Fasciola hepatica excretory and secretory products (FhESPs) involved in interacting with host PBMCs and cytokines by shotgun LC-MS/MS.

    Science.gov (United States)

    Liu, Qing; Huang, Si-Yang; Yue, Dong-Mei; Wang, Jin-Lei; Wang, Yujian; Li, Xiangrui; Zhu, Xing-Quan

    2017-02-01

    Fasciola hepatica is a helminth parasite with a worldwide distribution, which can cause chronic liver disease, fasciolosis, leading to economic losses in the livestock and public health in many countries. Control is mostly reliant on the use of drugs, and as a result, drug resistance has now emerged. The identification of F. hepatica genes involved in interaction between the parasite and host immune system is utmost important to elucidate the evasion mechanisms of the parasite and develop more effective strategies against fasciolosis. In this study, we aimed to identify molecules in F. hepatica excretory and secretory products (FhESPs) interacting with the host peripheral blood mononuclear cells (PBMCs), Th1-like cytokines (IL2 and IFN-γ), and Th17-like cytokines (IL17) by Co-IP combined with tandem mass spectrometry. The results showed that 14, 16, and 9 proteins in FhESPs could bind with IL2, IL17, and IFN-γ, respectively, which indicated that adult F. hepatica may evade the host immune responses through directly interplaying with cytokines. In addition, nine proteins in FhESPs could adhere to PBMCs. Our findings provided potential targets as immuno-regulators, and will be helpful to elucidate the molecular basis of host-parasite interactions and search for new potential proteins as vaccine and drug target candidates.

  10. Differential involvement of Atg16L1 in Crohn disease and canonical autophagy: analysis of the organization of the Atg16L1 complex in fibroblasts.

    Science.gov (United States)

    Fujita, Naonobu; Saitoh, Tatsuya; Kageyama, Shun; Akira, Shizuo; Noda, Takeshi; Yoshimori, Tamotsu

    2009-11-20

    A single nucleotide polymorphism in Atg16L1, an autophagy-related gene (ATG), is a risk factor for Crohn disease, a major form of chronic inflammatory bowel disease. However, it is still unknown how the Atg16L1 variant contributes to disease development. The Atg16L1 protein possesses a C-terminal WD repeat domain whose function is entirely unknown, and the Crohn disease-associated mutation (T300A) is within this domain. To elucidate the function of the WD repeat domain, we established an experimental system in which a WD repeat domain mutant of Atg16L1 is stably expressed in Atg16L1-deficient mouse embryonic fibroblasts. Using the system, we show that the Atg16L1 complex forms a dimeric complex and that the total Atg16L1 protein level is strictly maintained, possibly by the ubiquitin proteasome system. Furthermore, we show that an Atg16L1 WD repeat domain deletion and the T300A mutant have little impact on canonical autophagy and autophagy against Salmonella enterica serovar Typhimurium. Therefore, we propose that Atg16L1 T300A is differentially involved in Crohn disease and canonical autophagy.

  11. Transcriptomic Analysis of Long Non-Coding RNAs and Coding Genes Uncovers a Complex Regulatory Network That Is Involved in Maize Seed Development

    Directory of Open Access Journals (Sweden)

    Ming Zhu

    2017-10-01

    Full Text Available Long non-coding RNAs (lncRNAs have been reported to be involved in the development of maize plant. However, few focused on seed development of maize. Here, we identified 753 lncRNA candidates in maize genome from six seed samples. Similar to the mRNAs, lncRNAs showed tissue developmental stage specific and differential expression, indicating their putative role in seed development. Increasing evidence shows that crosstalk among RNAs mediated by shared microRNAs (miRNAs represents a novel layer of gene regulation, which plays important roles in plant development. Functional roles and regulatory mechanisms of lncRNAs as competing endogenous RNAs (ceRNA in plants, particularly in maize seed development, are unclear. We combined analyses of consistently altered 17 lncRNAs, 840 mRNAs and known miRNA to genome-wide investigate potential lncRNA-mediated ceRNA based on “ceRNA hypothesis”. The results uncovered seven novel lncRNAs as potential functional ceRNAs. Functional analyses based on their competitive coding-gene partners by Gene Ontology (GO and KEGG biological pathway demonstrated that combined effects of multiple ceRNAs can have major impacts on general developmental and metabolic processes in maize seed. These findings provided a useful platform for uncovering novel mechanisms of maize seed development and may provide opportunities for the functional characterization of individual lncRNA in future studies.

  12. Doctors' involvement in torture.

    Science.gov (United States)

    Jesper, Sonntag

    2008-01-01

    Doctors from both non-democratic and democratic countries are involved in torture. The majority of doctors involved in torture are doctors at risk. Doctors at risk might compromise their ethical duty towards patients for the following possible reasons: individual factors (such as career, economic or ideological reasons), threats, orders from a higher ranking officer, political initiatives, working in atrocity-producing situations or dual loyalty. In dual loyalty conflicts, factors that might compromise doctors' ethical obligations towards detainees/patients are: ideological totalitarianism, moral disengagement, victim blame, patriotism, individual factors or threats. Another important reason why doctors are involved in torture is that not all doctors are trained in addressing human rights issues of detainees. Torture survivors report that they have experienced doctors' involvement in torture and doctors themselves report that they have been involved in torture. Testimonies from both torture survivors and doctors demonstrate that the most common way doctors are involved is in the diagnosis/medical examination of torture survivors/prisoners. And it is common before, during and after torture. Both torture survivors and doctors state that doctors are involved during torture by treatment and direct participation. Doctors also falsify journals, certificates and reports. When doctors are involved in torture it has devastating consequences for both torture survivors and doctors. The consequences for the survivors can be mistrust of doctors, avoidance of seeking doctors' help and nightmares involving doctors. Mistrust and avoidance of doctors could be especially fatal to the survivor, as it could mean a survivor who is ill may not seek medical attention. When the unambiguous role of the doctor as the protector and helper of people is questioned, it affects the medical profession all over the world.

  13. IDEA and Family Involvement

    Directory of Open Access Journals (Sweden)

    Mehmet Emin Öztürk

    2017-01-01

    Full Text Available Individuals with Disabilities Education Act (IDEA gives many rights to parents with special needs in terms of involvement and participation. Given the importance of family involvement in the special education process, and federal legislation that increasingly mandated and supported such involvement over time, considerable research has focused on the multiple ways that relationships between schools and families in the special education decision making process have played out. Educational professionals should create a positive climate for CLD families so that they feel more comfortable and therefore are able to participate more authentically and meaningfully.

  14. De novo transcriptome sequencing of black pepper (Piper nigrum L.) and an analysis of genes involved in phenylpropanoid metabolism in response to Phytophthora capsici.

    Science.gov (United States)

    Hao, Chaoyun; Xia, Zhiqiang; Fan, Rui; Tan, Lehe; Hu, Lisong; Wu, Baoduo; Wu, Huasong

    2016-10-21

    Piper nigrum L., or "black pepper", is an economically important spice crop in tropical regions. Black pepper production is markedly affected by foot rot disease caused by Phytophthora capsici, and genetic improvement of black pepper is essential for combating foot rot diseases. However, little is known about the mechanism of anti- P. capsici in black pepper. The molecular mechanisms underlying foot rot susceptibility were studied by comparing transcriptome analysis between resistant (Piper flaviflorum) and susceptible (Piper nigrum cv. Reyin-1) black pepper species. 116,432 unigenes were acquired from six libraries (three replicates of resistant and susceptible black pepper samples), which were integrated by applying BLAST similarity searches and noted by adopting Kyoto Encyclopaedia of Genes and Gene Ontology (GO) genome orthology identifiers. The reference transcriptome was mapped using two sets of digital gene expression data. Using GO enrichment analysis for the differentially expressed genes, the majority of the genes associated with the phenylpropanoid biosynthesis pathway were identified in P. flaviflorum. In addition, the expression of genes revealed that after susceptible and resistant species were inoculated with P. capsici, the majority of genes incorporated in the phenylpropanoid metabolism pathway were up-regulated in both species. Among various treatments and organs, all the genes were up-regulated to a relatively high degree in resistant species. Phenylalanine ammonia lyase and peroxidase enzyme activity increased in susceptible and resistant species after inoculation with P. capsici, and the resistant species increased faster. The resistant plants retain their vascular structure in lignin revealed by histochemical analysis. Our data provide critical information regarding target genes and a technological basis for future studies of black pepper genetic improvements, including transgenic breeding.

  15. A Scoping Analysis Of The Impact Of SiC Cladding On Late-Phase Accident Progression Involving Core–Concrete Interaction

    Energy Technology Data Exchange (ETDEWEB)

    Farmer, M. T. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-11-01

    The overall objective of the current work is to carry out a scoping analysis to determine the impact of ATF on late phase accident progression; in particular, the molten core-concrete interaction portion of the sequence that occurs after the core debris fails the reactor vessel and relocates into containment. This additional study augments previous work by including kinetic effects that govern chemical reaction rates during core-concrete interaction. The specific ATF considered as part of this study is SiC-clad UO2.

  16. Numerical stability of the Saul'yev finite difference algorithms for electrochemical kinetic simulations: Matrix stability analysis for an example problem involving mixed boundary conditions

    DEFF Research Database (Denmark)

    Bieniasz, Leslaw K.; Østerby, Ole; Britz, Dieter

    1995-01-01

    The stepwise numerical stability of the Saul'yev finite difference discretization of an example diffusional initial boundary value problem from electrochemical kinetics has been investigated using the matrix method of stability analysis. Special attention has been paid to the effect...... of unconditional stability of the Saul'yev algorithms, reported in the literature, the left-right variant of the Saul'yev algorithm becomes unstable for large values of the dimensionless diffusion parameter λ = δt/h2, under mixed boundary conditions. This limitation is not, however, severe for most practical...

  17. Gene Expression Meta-Analysis identifies Cytokine Pathways and 5q Aberrations involved in Metastasis of ERBB2 Amplified and Basal Breast Cancer

    DEFF Research Database (Denmark)

    Thomassen, Mads; Tan, Qihua; Burton, Mark

    2013-01-01

    mechanisms, aside from the subtypes, were identified in a training set of 1,239 tumors and confirmed by survival analysis in two independent validation datasets from the same type of platform and consisting of very comparable node-negative patients that did not receive adjuvant medical therapy. The results...... show that high expression of 5q14 genes and low levels of TNFR2 pathway genes were associated with poor survival in basal-like cancers. Furthermore, low expression of 5q33 genes and interleukin-12 pathway genes were associated with poor outcome exclusively in ERBB2-like tumors. Conclusion...

  18. Mother Involvement as an Influence on Father Involvement with Early Adolescents

    OpenAIRE

    Pleck, Joseph H.; Hofferth, Sandra L.

    2008-01-01

    This study hypothesized that father involvement is influenced by mothers' level of involvement as well as by marital conflict, mothers' work hours, and fathers' status as biological or step father. The analysis also tested hypotheses about mother involvement as a potential mediator of the effects of marital conflict and maternal work hours on father involvement, and hypotheses about factors influencing mother involvement. Children aged 10-14 from the NLSY79 who resided with their biological o...

  19. Transcriptome profiling and digital gene expression analysis of sweet potato for the identification of putative genes involved in the defense response against Fusarium oxysporum f. sp. batatas.

    Science.gov (United States)

    Lin, Yuli; Zou, Weikun; Lin, Shiqiang; Onofua, Dennis; Yang, Zhijian; Chen, Haizhou; Wang, Songliang; Chen, Xuanyang

    2017-01-01

    Sweet potato production is constrained by Fusarium wilt, which is caused by Fusarium oxysporum f. sp. batatas (Fob). The identification of genes related to disease resistance and the underlying mechanisms will contribute to improving disease resistance via sweet potato breeding programs. In the present study, we performed de novo transcriptome assembly and digital gene expression (DGE) profiling of sweet potato challenged with Fob using Illumina HiSeq technology. In total, 89,944,188 clean reads were generated from 12 samples and assembled into 101,988 unigenes with an average length of 666 bp; of these unigenes, 62,605 (61.38%) were functionally annotated in the NCBI non-redundant protein database by BLASTX with a cutoff E-value of 10-5. Clusters of Orthologous Groups (COG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were examined to explore the unigenes' functions. We constructed four DGE libraries for the sweet potato cultivars JinShan57 (JS57, highly resistant) and XinZhongHua (XZH, highly susceptible), which were challenged with pathogenic Fob. Genes that were differentially expressed in the four libraries were identified by comparing the transcriptomes. Various genes that were differentially expressed during defense, including chitin elicitor receptor kinase 1 (CERK), mitogen-activated protein kinase (MAPK), WRKY, NAC, MYB, and ethylene-responsive transcription factor (ERF), as well as resistance genes, pathogenesis-related genes, and genes involved in salicylic acid (SA) and jasmonic acid (JA) signaling pathways, were identified. These data represent a sequence resource for genetic and genomic studies of sweet potato that will enhance the understanding of the mechanism of disease resistance.

  20. The perturbation theory in the fundamental mode. Its application to the analysis of neutronic experiments involving small amounts of materials in fast neutron multiplying media

    International Nuclear Information System (INIS)

    Remsak, Stanislav.

    1975-01-01

    The formalism of the perturbation theory at the first order, is developed in its simplest form: diffusion theory in the fundamental mode and then the more complex formalism of the transport theory in the fundamental mode. A comparison shows the effect of the angular correlation between the fine structures of the flux and its adjoint function, the difference in the treatment of neutron leakage phenomena, and the existence of new terms in the perturbation formula, entailing a reactivity representation in the diffusion theory that is not quite exact. Problems of using the formalism developed are considered: application of the multigroup formalism, transients of the flux and its adjoint function, validity of the first order approximation etc. A detailed analysis allows the formulation of a criterion specifying the validity range. Transients occuring in the reference medium are also treated. A set of numerical tests for determining a method of elimination of transient effects is presented. Some differential experiments are then discussed: sodium blowdown in enriched uranium or plutonium cores, experiments utilizing some structural materials (iron and oxygen) and plutonium sample oscillations. The Cadarache version II program was systematically used but the analysis of the experiments of plutonium sample oscillation in Ermine required the Cadarache version III program [fr

  1. Trends involving monoclonal antibody (mAb) research and commercialization: A scientometric analysis of IMS Lifecycle R&D Focus Database (1980-2016).

    Science.gov (United States)

    Lai, Yunfeng; Suo, Sizhuo; Wang, Ruibing; Kong, Xiangjun; Hu, Yuanjia; Tang, Daisheng; Shi, Honghao; Chen, Shengqi; Hu, Hao

    2018-04-03

    This article aims to explore the trends of monoclonal antibodies (mAbs) research and commercialization, mainly to examine the development trajectories by a contrastive exploration of successful and unsuccessful mAb. This work is based on two sets of R&D project reports, consisting of 517 discontinued mAb project reports and 64 marketed mAb project reports, from IMS Lifecycle R&D Focus. The analysis of drug development processes will provide the basic evidences of mAb technology commercialization. We examined the mAb research and commercialization from three perspectives: (1) Countries with mAb research activity; (2) Organizations participating in mAb research and development; and (3) Clusters of keywords (indication and class description) regarding mAb. The technology factor, the market factor and the abilities of participating firms to pursue commercialization were analyzed. Through data analysis, we have discovered that the research and development on mAb has reached a mature and diversified stage.

  2. De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers.

    Science.gov (United States)

    Xanthopoulou, Aliki; Ganopoulos, Ioannis; Psomopoulos, Fotis; Manioudaki, Maria; Moysiadis, Theodoros; Kapazoglou, Aliki; Osathanunkul, Maslin; Michailidou, Sofia; Kalivas, Apostolos; Tsaftaris, Athanasios; Nianiou-Obeidat, Irini; Madesis, Panagiotis

    2017-07-30

    The genetic basis of fruit size and shape was investigated for the first time in Cucurbita species and genetic loci associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato (Solanum lycopersicum), cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), genomic databases for Cucurbita species are limited. Recently, our group reported the generation of pumpkin (Cucurbita pepo) transcriptome databases from two contrasting cultivars with extreme fruit sizes. In the current study we used these databases to perform comparative transcriptome analysis in order to identify genes with potential roles in fruit morphology and fruit size. Differential Gene Expression (DGE) analysis between cv. 'Munchkin' (small-fruit) and cv. 'Big Moose' (large-fruit) revealed a variety of candidate genes associated with fruit morphology with significant differences in gene expression between the two cultivars. In addition, we have set the framework for generating EST-SSR markers, which discriminate different C. pepo cultivars and show transferability to related Cucurbitaceae species. The results of the present study will contribute to both further understanding the molecular mechanisms regulating fruit morphology and furthermore identifying the factors that determine fruit size. Moreover, they may lead to the development of molecular marker tools for selecting genotypes with desired morphological traits. Copyright © 2017. Published by Elsevier B.V.

  3. Comparative Transcriptome Analysis of Mink (Neovison vison) Skin Reveals the Key Genes Involved in the Melanogenesis of Black and White Coat Colour.

    Science.gov (United States)

    Song, Xingchao; Xu, Chao; Liu, Zongyue; Yue, Zhigang; Liu, Linling; Yang, Tongao; Cong, Bo; Yang, Fuhe

    2017-09-29

    Farmed mink (Neovison vison) is one of the most important fur-bearing species worldwide, and coat colour is a crucial qualitative characteristic that contributes to the economic value of the fur. To identify additional genes that may play important roles in coat colour regulation, Illumina/Solexa high-throughput sequencing technology was used to catalogue the global gene expression profiles in mink skin with two different coat colours (black and white). RNA-seq analysis indicated that a total of 12,557 genes were differentially expressed in black versus white minks, with 3,530 genes up-regulated and 9,027 genes down-regulated in black minks. Significant differences were not observed in the expression of MC1R and TYR between the two different coat colours, and the expression of ASIP was not detected in the mink skin of either coat colour. The expression levels of KITLG, LEF1, DCT, TYRP1, PMEL, Myo5a, Rab27a and SLC7A11 were validated by qRT-PCR, and the results were consistent with RNA-seq analysis. This study provides several candidate genes that may be associated with the development of two coat colours in mink skin. These results will expand our understanding of the complex molecular mechanisms underlying skin physiology and melanogenesis in mink and will provide a foundation for future studies.

  4. Microarray gene expression analysis reveals major differences between Toxocara canis and Toxocara cati neurotoxocarosis and involvement of T. canis in lipid biosynthetic processes.

    Science.gov (United States)

    Janecek, Elisabeth; Wilk, Esther; Schughart, Klaus; Geffers, Robert; Strube, Christina

    2015-06-01

    Toxocara canis and Toxocara cati are globally occurring intestinal nematodes of dogs and cats with a high zoonotic potential. Migrating larvae in the CNS of paratenic hosts, including humans, may cause neurotoxocarosis resulting in a variety of neurological symptoms. Toxocara canis exhibits a stronger affinity to the CNS than T. cati, causing more severe neurological symptoms in the mouse model. Pathomechanisms of neurotoxocarosis as well as host responses towards the respective parasite are mostly unknown. Therefore, the aim of this study was to characterise the pathogenesis at a transcriptional level using whole genome microarray expression analysis and identify differences and similarities between T. canis- and T. cati-infected brains. Microarray analysis was conducted in cerebra and cerebella of infected C57Bl/6J mice 42daysp.i. revealing more differentially transcribed genes for T. canis- than T. cati-infected brains. In cerebra and cerebella of T. canis-infected mice, a total of 2304 and 1954 differentially transcribed genes, respectively, were identified whereas 113 and 760 differentially transcribed genes were determined in cerebra and cerebella of T. cati-infected mice. Functional annotation analysis revealed major differences in host responses in terms of significantly enriched biological modules. Up-regulated genes were mainly associated with the terms "immune and defence response", "sensory perception" as well as "behaviour/taxis" retrieved from the Gene Ontology database. These observations indicate a strong immune response in both infection groups with T. cati-infected brains revealing less severe reactions. Down-regulated genes in T. canis-infected cerebra and cerebella revealed a significant enrichment for the Gene Ontology term "lipid/cholesterol biosynthetic process". Cholesterol is a highly abundant and important component in the brain, representing several functions. Disturbances of synthesis as well as concentration changes may lead to

  5. The Gly482Ser genotype at the PPARGC1A gene and elevated blood pressure: a meta-analysis involving 13,949 individuals

    DEFF Research Database (Denmark)

    Vimaleswaran, Karani Santhanakrishnan; Luan, Jian'an; Andersen, Gitte

    2008-01-01

    inversely with blood pressure. We used conventional meta-analysis methods to assess the association between Gly482Ser and systolic (SBP) or diastolic blood pressures (DBP) or hypertension in 13,949 individuals from 17 studies, of which 6,042 were previously unpublished observations. The studies comprised...... the Ser482 allele and hypertension [odds ratio: 0.97, 95% CI = 0.87-1.08, P = 0.585]. These results were materially unchanged when analyses were focused on whites only. However, statistical evidence of gene-age interaction was apparent for DBP [Gly482Gly: 73.5 (72.8, 74.2), Gly482Ser: 77.0 (76.2, 77...

  6. In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli-mastitis

    DEFF Research Database (Denmark)

    Buitenhuis, Albert Johannes; Rontved, Christine M.; Edwards, Stefan McKinnon

    2011-01-01

    Background Bovine mastitis is one of the most costly and prevalent diseases affecting dairy cows worldwide. In order to develop new strategies to prevent Escherichia coli-induced mastitis, a detailed understanding of the molecular mechanisms underlying the host immune response to an E. coli...... infection is necessary. To this end, we performed a global gene-expression analysis of mammary gland tissue collected from dairy cows that had been exposed to a controlled E. coli infection. Biopsy samples of healthy and infected utter tissue were collected at T=24h post-infection (p.i.) and at T=192h p.......i. to represent the acute phase response (APR) and chronic stage, respectively. Differentially expressed (DE) genes for each stage were analyzed and the DE genes detected at T=24h were also compared to data collected from two previous E. coli mastitis studies that were carried out on post mortem tissue. Results...

  7. Improvement of soybean transformation via Agrobacterium tumefaciens methods involving α-aminooxyacetic acid and sonication treatments enlightened by gene expression profile analysis.

    Science.gov (United States)

    Zhang, Yan-Min; Liu, Zi-Hui; Yang, Rui-Juan; Li, Guo-Liang; Guo, Xiu-Lin; Zhang, Hua-Ning; Zhang, Hong-Mei; Di, Rui; Zhao, Qing-Song; Zhang, Meng-Chen

    2016-06-01

    Antagonists and sonication treatment relieved the structural barriers of Agrobacterium entering into cells; hindered signal perception and transmission; alleviated defense responses and increased cell susceptibility to Agrobacterium infection. Soybean gene expression analysis was performed to elucidate the general response of soybean plant to Agrobacterium at an early stage of infection. Agrobacterium infection stimulated the PAMPs-triggered immunity (BRI1, BAK1, BZR1, FLS2 and EFR) and effector-triggered immunity (RPM1, RPS2, RPS5, RIN4, and PBS1); up-regulated the transcript factors (WRKY25, WRKY29, MEKK1P, MKK4/5P and MYC2) in MAPK pathway; strengthened the biosynthesis of flavonoid and isoflavonoid in the second metabolism; finally led to a fierce defense response of soybean to Agrobacterium infection and thereby lower transformation efficiency. To overcome it, antagonist α-aminooxyacetic acid (AOA) and sonication treatment along with Agrobacterium infection were applied. This novel method dramatically decreased the expression of genes coding for F3'H, HCT, β-glucosidase and IF7GT, etc., which are important for isoflavone biosynthesis or the interconversion of aglycones and glycon; genes coding for peroxidase, FLS2, PBS1 and transcription factor MYC2, etc., which are important components in plant-pathogen interaction; and genes coding for GPAT and α-L-fucosidase, which are important in polyesters formation in cell membrane and the degradation of fucose-containing glycoproteins and glycolipids on the external surface of cell membrane, respectively. This analysis implied that AOA and sonication treatment not only relieved the structural membrane barriers of Agrobacterium entering into cells, but also hindered the perception of 'invasion' signal on cell membrane and intercellular signal transmission, thus effectively alleviated the defense responses and increased the cell susceptibility to Agrobacterium infection. All these factors benefit the transformation

  8. Identification of a Key Gene Involved in Branched-Chain Short Fatty Acids Formation in Natto by Transcriptional Analysis and Enzymatic Characterization in Bacillus subtilis.

    Science.gov (United States)

    Hong, Chenlu; Chen, Yangyang; Li, Lu; Chen, Shouwen; Wei, Xuetuan

    2017-03-01

    Natto as a fermented soybean product has many health benefits for human due to its rich nutritional and functional components. However, the unpleasant odor of natto, caused by the formation of branched-chain short fatty acids (BCFAs), prohibits the wide acceptance of natto products. This work is to identify the key gene of BCFAs formation and develop the guidance to reduce natto odor. Transcriptional analysis of BCFAs synthesis pathway genes was conducted in two Bacillus subtilis strains with obvious different BCFAs synthesis abilities. The transcriptional levels of bcd, bkdAA, and ptb in B. subtilis H-9 were 2.7-fold, 0.7-fold, and 8.9-fold higher than that of B. subtilis H-4, respectively. Therefore, the ptb gene with the highest transcriptional change was considered as the key gene in BCFAs synthesis. The ptb encoded enzyme Ptb was further characterized by inducible expression in Escherichia coli. The recombinant Ptb protein (about 32 kDa) was verified by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis analysis. The catalysis functions of Ptb were confirmed on substrates of isovaleryl-CoA and isobutyryl-CoA, and the higher catalysis efficiency of Ptb on isovaleryl-CoA explained the higher level of isovaleric acid in natto. The optimal activities of Ptb were observed at 50 °C and pH 8.0, and the enzymatic activity was inhibited by Ca 2+ , Zn 2+ , Ba 2+ , Mn 2+ , Cu 2+ , SDS, and EDTA. Collectively, this study reports a key gene responsible for BCFAs formation in natto fermentation and provides potential strategies to solve the odor problem.

  9. Analysis of transcription factors, microRNAs and cytokines involved in T lymphocyte differentiation in patients with tuberculosis after directly observed treatment short-course.

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    Corral-Fernández, Nancy Elizabeth; Cortes-García, Juan Diego; Bruno, Rivas-Santiago; Romano-Moreno, Silvia; Medellín-Garibay, Susanna E; Magaña-Aquino, Martín; Salazar-González, Raúl A; González-Amaro, Roberto; Portales-Pérez, Diana Patricia

    2017-07-01

    Tuberculosis (Tb) is an infectious disease in which the immune system plays an important role. MicroRNAs are involved in the development and maintenance of CD4 + T lymphocyte subpopulations. miR-326 regulates the differentiation to Th17 cells and miR-29 correlates with the Th1 response. The aim of this study was to determine the role of microRNAs, Transcription Factors, and cytokines in Th differentiation before and after the directly observed treatment short-course (DOTS). Peripheral blood mononuclear cells and serum from Tb patients were collected at times 0 (before therapy), 2 (after the intensive phase), and 6 months (after the holding phase). The cells were cultivated in presence or absence of ESAT-6 (10 μg/ml) and CFP-10 (10 μg/ml). Transcription Factor and microRNA expressions were analyzed by qPCR and cytokine production in both serum and culture supernatant using ELISA. A decrease in Th1 response with a diminishing in the relative expression of TBET and miR-29a at 2 and 6 months after the anti-Tb therapy (p < 0.01) were found. The miR-326 levels decreased after the intensive phase of the DOTS scheme. However, subdivision of the Tb patients according to gender, showed increased levels of miR-29a and miR-155 in females after the intensive phase of the therapeutic treatment when compared to time 0 and similar increased levels of miR-326 at time 6 versus time 0. In contrast, we observed a decrease in miR-326 levels in males at 6 months when compared to before therapy (time 0). In addition, high production of IL-17 in the culture supernatant was found at 2 and 6 months (p < 0.05) while in serum IL-17 was decreased. A positive correlation between IL-17 and RORC2 at time 6 was detected (p = 0.0202, r = 0.7880). In conclusion, these data suggest a reduction in Th1 and an induction of Th17 response after the anti-Tb therapy. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Selection and validation of reference genes for qRT-PCR expression analysis of candidate genes involved in olfactory communication in the butterfly Bicyclus anynana.

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    Alok Arun

    Full Text Available Real-time quantitative reverse transcription PCR (qRT-PCR is a technique widely used to quantify the transcriptional expression level of candidate genes. qRT-PCR requires the selection of one or several suitable reference genes, whose expression profiles remain stable across conditions, to normalize the qRT-PCR expression profiles of candidate genes. Although several butterfly species (Lepidoptera have become important models in molecular evolutionary ecology, so far no study aimed at identifying reference genes for accurate data normalization for any butterfly is available. The African bush brown butterfly Bicyclus anynana has drawn considerable attention owing to its suitability as a model for evolutionary ecology, and we here provide a maiden extensive study to identify suitable reference gene in this species. We monitored the expression profile of twelve reference genes: eEF-1α, FK506, UBQL40, RpS8, RpS18, HSP, GAPDH, VATPase, ACT3, TBP, eIF2 and G6PD. We tested the stability of their expression profiles in three different tissues (wings, brains, antennae, two developmental stages (pupal and adult and two sexes (male and female, all of which were subjected to two food treatments (food stress and control feeding ad libitum. The expression stability and ranking of twelve reference genes was assessed using two algorithm-based methods, NormFinder and geNorm. Both methods identified RpS8 as the best suitable reference gene for expression data normalization. We also showed that the use of two reference genes is sufficient to effectively normalize the qRT-PCR data under varying tissues and experimental conditions that we used in B. anynana. Finally, we tested the effect of choosing reference genes with different stability on the normalization of the transcript abundance of a candidate gene involved in olfactory communication in B. anynana, the Fatty Acyl Reductase 2, and we confirmed that using an unstable reference gene can drastically alter the

  11. Elevated homocysteine level and folate deficiency associated with increased overall risk of carcinogenesis: meta-analysis of 83 case-control studies involving 35,758 individuals.

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    Donghong Zhang

    Full Text Available Results of the association of folate metabolism and carcinogenesis are conflicting. We performed a meta-analysis to examine the effect of the interaction of serum concentration of homocysteine (Hcy, folate, and vitamin B12 and 5,10-methylenetetrahydrofolate reductase (MTHFR polymorphism on risk of cancer overall.Two reviewers independently searched for all published studies of Hcy and cancer in PubMed, EMBASE-MEDLINE and Chinese databases. Pooled results were reported as odds ratios (ORs and mean differences and presented with 95% confidence intervals (95% CIs and 2-sided probability values.We identified 83 eligible studies of 15,046 cases and 20,712 controls. High level of Hcy but low level of folate was associated with risk of cancer overall, with little effect by type of cancer or ethnicity. Vitamin B12 level was inversely associated with only urinary-system and gastrointestinal carcinomas and for Asian and Middle Eastern patients. As well, MTHFR C677T, A1298C and G1793A polymorphisms were related to elevated serum level of Hcy, and folate and vitamin B12 deficiency. However, only MTHFR C677T homogeneity/wild-type (TT/CC polymorphism was positively associated with overall risk of cancer.Elevated serum Hcy level and folate deficiency are associated with increased overall risk of cancer.

  12. A standardized fold change method for microarray differential expression analysis used to reveal genes involved in acute rejection in murine allograft models.

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    Zhou, Weichen; Wang, Yi; Fujino, Masayuki; Shi, Leming; Jin, Li; Li, Xiao-Kang; Wang, Jiucun

    2018-03-01

    Murine transplantation models are used extensively to research immunological rejection and tolerance. Here we studied both murine heart and liver allograft models using microarray technology. We had difficulty in identifying genes related to acute rejections expressed in both heart and liver transplantation models using two standard methodologies: Student's t test and linear models for microarray data (Limma). Here we describe a new method, standardized fold change (SFC), for differential analysis of microarray data. We estimated the performance of SFC, the t test and Limma by generating simulated microarray data 100 times. SFC performed better than the t test and showed a higher sensitivity than Limma where there is a larger value for fold change of expression. SFC gave better reproducibility than Limma and the t test with real experimental data from the MicroArray Quality Control platform and expression data from a mouse cardiac allograft. Eventually, a group of significant overlapping genes was detected by SFC in the expression data of mouse cardiac and hepatic allografts and further validated with the quantitative RT-PCR assay. The group included genes for important reactions of transplantation rejection and revealed functional changes of the immune system in both heart and liver of the mouse model. We suggest that SFC can be utilized to stably and effectively detect differential gene expression and to explore microarray data in further studies.

  13. Involvement of clip-domain serine protease in the anti-Vibrio immune response of abalone (Haliotis discus hannai)-Molecular cloning, characterization and functional analysis.

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    Hu, Jian-Jian; Chen, Yu-Lei; Duan, Xue-Kun; Jin, Teng-Chuan; Li, Yue; Zhang, Ling-Jing; Liu, Guang-Ming; Cao, Min-Jie

    2018-01-01

    Vibrio parahemolyticus (V. parahemolyticus) is a major pathogen for abalone, an important economical shellfish in coastal area of China. There is little known about the abalone innate immune system against pathogen infection. Clip-domain serine proteases (cSPs) are increasingly recognized to play important roles in host immune defense in invertebrates. In this study, we cloned a cSP (Hdh-cSP) from abalone (Haliotis discus hannai). We found out that Hdh-cSP was widely expressed in multiple tissues of abalone, with highest level in the immune-like organ, hepatopancreas. V. parahemolyticus infection induced significantly elevated expression of Hdh-cSP in addition to better-characterized innate immune component genes including Rel/NF-κB, allograft inflammatory factor (ALInFa), macrophage expressed protein (MEP) and caspase-8. Importantly, the silencing of Hdh-cSP reduced the expression of these genes, suggesting that Hdh-cSP was an upstream regulatory factor in V. parahemolyticus infection. Further analysis showed that apoptosis of hemocytes was inhibited when the transcription of Hdh-cSP was knocked down, suggesting that Hdh-cSP participated in cell apoptosis by regulation of caspase 8 expression in V. parahemolyticus infection. Therefore, our study established an important role of cSP in the innate immunity against V. parahemolyticus infection in abalone. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis.

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    Suzana Tiemi Ivamoto

    Full Text Available Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are produced. To understand the molecular aspects related to coffee fruit and grain development, we report a large-scale transcriptome analysis of leaf, flower and perisperm fruit tissue development. Illumina sequencing yielded 41,881,572 high-quality filtered reads. De novo assembly generated 65,364 unigenes with an average length of 1,264 bp. A total of 24,548 unigenes were annotated as protein coding genes, including 12,560 full-length sequences. In the annotation process, we identified nine candidate genes related to the biosynthesis of raffinose family oligossacarides (RFOs. These sugars confer osmoprotection and are accumulated during initial fruit development. Four genes from this pathway had their transcriptional pattern validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR. Furthermore, we identified ~24,000 putative target sites for microRNAs (miRNAs and 134 putative transcriptionally active transposable elements (TE sequences in our dataset. This C. arabica transcriptomic atlas provides an important step for identifying candidate genes related to several coffee metabolic pathways, especially those related to fruit chemical composition and therefore beverage quality. Our results are the starting point for enhancing our knowledge about the coffee genes that are transcribed during the flowering and initial fruit development stages.

  15. The role of the referee and his involvement in the promotion of fair play. Analysis and proposals of intervention in the context of University sport

    Directory of Open Access Journals (Sweden)

    María Prat Grau

    2013-07-01

    Full Text Available The figure of referees and their role in sports competitions have been the object of numerous studies, but few have analysed the role of referees from a more training based perspective. This article analyses the function of the referee in the area of university sports, based on the idea that the intervention of referees can help with the development of sportsmanship and fair play. The study examines the internal 7-a-side football league played by the Physical Activity Service (SAF at the Universidad Autónoma de Barcelona (UAB, and the research objectives are focused on analyzing the current reality of this group, detecting possible problems, and generating proposals for improvement aimed at seeking more educational refereeing. The instruments used are interviews, observation and document analysis. The results obtained reveal the need for referees to be trained pedagogically in the university environment; the establishment of ethical commitments that enable compliance with possible decalogues and codes of conduct; and the introduction of women to the refereeing collective.

  16. [Pulmonary involvements of sarcoidosis].

    Science.gov (United States)

    Ohmichi, M; Hiraga, Y; Hirasawa, M

    1990-01-01

    We reported about intrathoracic changes and prognosis of 686 patients with sarcoidosis diagnosed in our hospital between 1963 and 1988. We evaluated CT findings in 135 patients with sarcoidosis and found pulmonary involvements in 81. We analyzed CT findings according to the classification by Tuengerthal which classified radiographic findings combining ILO classification of pneumoconiosis and characteristic findings of bronchovascular sheath with sarcoidosis. The CT findings were as follows: small opacities (44 out of 81 cases, 54.3%), large opacities (37 cases, 46.7%). Additional findings were as follows: peribronchial marking (42 cases, 51.9%), contraction (17 cases, 21.0%), pleural involvement (9 cases, 11.1%), bulla (5 cases, 6.2%). The characteristic CT findings of serious sarcoidosis were extasis of bronchus, thickening of the bronchial wall, unclearness of vascular shadow, atelectasis and thickening of pleura. Concerning the prognosis of pulmonary involvement, according to age, patients younger than 30 years old at initial diagnosis were better than those of 30 years and over in terms of disappearance of pulmonary involvements. According to stage, patients of stage I and stage II were better than those of stage III. Among the patients we were able to observe chest X-ray findings during five years according to the character of shadow, ill-defined shadow of small opacities and rounded shadows of large opacities had a higher disappearance rate of pulmonary involvements than irregular shadows of large opacities, atelectasis and contraction.

  17. Functional analysis of endo-1,4-β-glucanases in response to Botrytis cinerea and Pseudomonas syringae reveals their involvement in plant-pathogen interactions.

    Science.gov (United States)

    Finiti, I; Leyva, M O; López-Cruz, J; Calderan Rodrigues, B; Vicedo, B; Angulo, C; Bennett, A B; Grant, M; García-Agustín, P; González-Bosch, C

    2013-09-01

    Plant cell wall modification is a critical component in stress responses. Endo-1,4-β-glucanases (EGs) take part in cell wall editing processes, e.g. elongation, ripening and abscission. Here we studied the infection response of Solanum lycopersicum and Arabidopsis thaliana with impaired EGs. Transgenic TomCel1 and TomCel2 tomato antisense plants challenged with Pseudomonas syringae showed higher susceptibility, callose priming and increased jasmonic acid pathway marker gene expression. These two EGs could be resistance factors and may act as negative regulators of callose deposition, probably by interfering with the defence-signalling network. A study of a set of Arabidopsis EG T-DNA insertion mutants challenged with P. syringae and Botrytis cinerea revealed that the lack of other EGs interferes with infection phenotype, callose deposition, expression of signalling pathway marker genes and hormonal balance. We conclude that a lack of EGs could alter plant response to pathogens by modifying the properties of the cell wall and/or interfering with signalling pathways, contributing to generate the appropriate signalling outcomes. Analysis of microarray data demonstrates that EGs are differentially expressed upon many different plant-pathogen challenges, hormone treatments and many abiotic stresses. We found some Arabidopsis EG mutants with increased tolerance to osmotic and salt stress. Our results show that impairing EGs can alter plant-pathogen interactions and may contribute to appropriate signalling outcomes in many different biotic and abiotic plant stress responses. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

  18. Literature-Informed Analysis of a Genome-Wide Association Study of Gestational Age in Norwegian Women and Children Suggests Involvement of Inflammatory Pathways

    Science.gov (United States)

    Bacelis, Jonas; Juodakis, Julius; Sengpiel, Verena; Zhang, Ge; Myhre, Ronny; Muglia, Louis J.; Nilsson, Staffan; Jacobsson, Bo

    2016-01-01

    Background Five-to-eighteen percent of pregnancies worldwide end in preterm birth, which is the major cause of neonatal death and morbidity. Approximately 30% of the variation in gestational age at birth can be attributed to genetic factors. Genome-wide association studies (GWAS) have not shown robust evidence of association with genomic loci yet. Methods We separately investigated 1921 Norwegian mothers and 1199 children from pregnancies with spontaneous onset of delivery. Individuals were further divided based on the onset of delivery: initiated by labor or prelabor rupture of membranes. Genetic association with ultrasound-dated gestational age was evaluated using three genetic models and adaptive permutations. The top-ranked loci were tested for enrichment in 12 candidate gene-sets generated by text-mining PubMed abstracts containing pregnancy-related keywords. Results The six GWAS did not reveal significant associations, with the most extreme empirical p = 5.1 × 10−7. The top loci from maternal GWAS with deliveries initiated by labor showed significant enrichment in 10 PubMed gene-sets, e.g., p = 0.001 and 0.005 for keywords "uterus" and "preterm" respectively. Enrichment signals were mainly caused by infection/inflammation-related genes TLR4, NFKB1, ABCA1, MMP9. Literature-informed analysis of top loci revealed further immunity genes: IL1A, IL1B, CAMP, TREM1, TFRC, NFKBIA, MEFV, IRF8, WNT5A. Conclusion Our analyses support the role of inflammatory pathways in determining pregnancy duration and provide a list of 32 candidate genes for a follow-up work. We observed that the top regions from GWAS in mothers with labor-initiated deliveries significantly more often overlap with pregnancy-related genes than would be expected by chance, suggesting that increased sample size would benefit similar studies. PMID:27490719

  19. GC/TOFMS analysis of metabolites in serum and urine reveals metabolic perturbation of TCA cycle in db/db mice involved in diabetic nephropathy.

    Science.gov (United States)

    Li, Mengjie; Wang, Xufang; Aa, Jiye; Qin, Weisong; Zha, Weibin; Ge, Yongchun; Liu, Linsheng; Zheng, Tian; Cao, Bei; Shi, Jian; Zhao, Chunyan; Wang, Xinwen; Yu, Xiaoyi; Wang, Guangji; Liu, Zhihong

    2013-06-01

    Early diagnosis of diabetic nephropathy (DN) is difficult although it is of crucial importance to prevent its development. To probe potential markers and the underlying mechanism of DN, an animal model of DN, the db/db mice, was used and serum and urine metabolites were profiled using gas chromatography/time-of-flight mass spectrometry. Metabolic patterns were evaluated based on serum and urine data. Principal component analysis of the data revealed an obvious metabonomic difference between db/db mice and controls, and db/db mice showed distinctly different metabolic patterns during the progression from diabetes to early, medium, and later DN. The identified metabolites discriminating between db/db mice and controls suggested that db/db mice have perturbations in the tricarboxylic acid cycle (TCA, citrate, malate, succinate, and aconitate), lipid metabolism, glycolysis, and amino acid turnover. The db/db mice were characterized by acidic urine, high TCA intermediates in serum at week 6 and a sharp decline thereafter, and gradual elevation of free fatty acids in the serum. The sharp drop of serum TCA intermediates from week 6 to 8 indicated the downregulated glycolysis and insulin resistance. However, urinary TCA intermediates did not decrease in parallel with those in the serum from week 6 to 10, and an increased portion of TCA intermediates in the serum was excreted into the urine at 8, 10, and 12 wk than at 6 wk, indicating kidney dysfunction occurred. The relative abundances of TCA intermediates in urine relative to those in serum were suggested as an index of renal damage.

  20. Enhancing 18F-FDG-PET/CT analysis in lung cancer patients. Is CT-CT image fusion helpful in predicting pleural involvement? A pilot study.

    Science.gov (United States)

    Kapfhammer, A; Winkens, T; Lesser, T; Reissig, A; Steinert, M; Freesmeyer, M

    2015-01-01

    To retrospectively evaluate the feasibility and value of CT-CT image fusion to assess the shift of peripheral lung cancers with/-out chest wall infiltration, comparing computed tomography acquisitions in shallow-breathing (SB-CT) and deep-inspiration breath-hold (DIBH-CT) in patients undergoing FDG-PET/CT for lung cancer staging. Image fusion of SB-CT and DIBH-CT was performed with a multimodal workstation used for nuclear medicine fusion imaging. The distance of intrathoracic landmarks and the positional shift of tumours were measured using semi-transparent overlay of both CT series. Statistical analyses were adjusted for confounders of tumour infiltration. Cutoff levels were calculated for prediction of no-/infiltration. Lateral pleural recessus and diaphragm showed the largest respiratory excursions. Infiltrating lung cancers showed more limited respiratory shifts than non-infiltrating tumours. A large respiratory tumour-motility accurately predicted non-infiltration. However, the tumour shifts were limited and variable, limiting the accuracy of prediction. This pilot fusion study proved feasible and allowed a simple analysis of the respiratory shifts of peripheral lung tumours using CT-CT image fusion in a PET/CT setting. The calculated cutoffs were useful in predicting the exclusion of chest wall infiltration but did not accurately predict tumour infiltration. This method can provide additional qualitative information in patients with lung cancers with contact to the chest wall but unclear CT evidence of infiltration undergoing PET/CT without the need of additional investigations. Considering the small sample size investigated, further studies are necessary to verify the obtained results.

  1. Systematic Identification, Evolution and Expression Analysis of the Zea mays PHT1 Gene Family Reveals Several New Members Involved in Root Colonization by Arbuscular Mycorrhizal Fungi.

    Science.gov (United States)

    Liu, Fang; Xu, Yunjian; Jiang, Huanhuan; Jiang, Chaosheng; Du, Yibin; Gong, Cheng; Wang, Wei; Zhu, Suwen; Han, Guomin; Cheng, Beijiu

    2016-06-13

    The Phosphate Transporter1 (PHT1) family of genes plays pivotal roles in the uptake of inorganic phosphate from soils. However, there is no comprehensive report on the PHT1 family in Zea mays based on the whole genome. In the present study, a total of 13 putative PHT1 genes (ZmPHT1;1 to 13) were identified in the inbred line B73 genome by bioinformatics methods. Then, their function was investigated by a yeast PHO84 mutant complementary experiment and qRT-PCR. Thirteen ZmPHT1 genes distributed on six chromosomes (1, 2, 5, 7, 8 and 10) were divided into two paralogues (Class A and Class B). ZmPHT1;1/ZmPHT1;9 and ZmPHT1;9/ZmPHT1;13 are produced from recent segmental duplication events. ZmPHT1;1/ZmPHT1;13 and ZmPHT1;8/ZmPHT1;10 are produced from early segmental duplication events. All 13 putative ZmPHT1s can completely or partly complement the yeast Pi-uptake mutant, and they were obviously induced in maize under low Pi conditions, except for ZmPHT1;1 (p mycorrhizal fungi (AMF), implying that these genes might participate in mediating Pi absorption and/or transport. Analysis of the promoters revealed that the MYCS and P1BS element are widely distributed on the region of different AMF-inducible ZmPHT1 promoters. In light of the above results, five of 13 ZmPHT1 genes were newly-identified AMF-inducible high-affinity phosphate transporters in the maize genome. Our results will lay a foundation for better understanding the PHT1 family evolution and the molecular mechanisms of inorganic phosphate transport under AMF inoculation.

  2. Drug-facilitated sexual assault (DFSA) involving 4-methylethcathinone (4-MEC), 3,4-Methylenedioxypyrovalerone (MDPV) and doxylamine highlighted by hair analysis.

    Science.gov (United States)

    Larabi, Islam Amine; Martin, Marie; Etting, Isabelle; Penot, Pauline; Fabresse, Nicolas; Alvarez, Jean Claude

    2018-03-10

    Recently, the emergence of new psychoactive substances (NPS) has led to their wide use among clubbers and men who have sex with men (MSM) for their stimulant effects. However, their use in drug facilitated sexual assault (DFSA) has rarely been described. Herein we report a case of a 44 years-old man who was assaulted after a party. Due to late reporting of the offense, only hair (black) was sampled 15 days later and a segmental analysis was achieved to look for most DFSA agents and NPS. Twenty mg of each segment (A:0-1cm, B:1-3cm and C:3-5cm) were incubated in phosphate buffer pH 5.0. After alkaline liquid extraction and chromatographic separation on 1.9 μm Hypersil GOLD PFP column, compounds were detected by a TSQ Vantage mass spectrometer with electrospray ionization in positive mode with MRM acquisition. 4-methylethcathinone (4-MEC), methylenedioxypyrovalerone (MDPV) and doxylamine were found in proximal segment at very low concentrations (3, 5 and 9 pg/mg, respectively) which is in agreement with a single exposure in the previous month corresponding to the alleged facts. These substances were not detected in segments B and C showing a lack of repetitive exposure before the alleged event. Thus, the results do not contradict the patient's claim of being assaulted. Doxylamine has already been encountered in such cases but no publications referring to 4-MEC or MDPV use have ever been documented. Our case reports the unusual administration of cathinones to achieve a sexual assault and stresses the interest of seeking for designer drugs when dealing with DFSA cases. This article is protected by copyright. All rights reserved.

  3. Transcriptome analysis of a new peanut seed coat mutant for the physiological regulatory mechanism involved in seed coat cracking and pigmentation

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    Liyun Wan

    2016-10-01

    Full Text Available Seed-coat cracking and undesirable color of seed coat highly affects external appearance and commercial value of peanuts (Arachis hypogaea L.. With an objective to find genetic solution to the above problems, a peanut mutant with cracking and brown colored seed coat (testa was identified from an EMS treated mutant population and designated as peanut seed coat crack and brown color mutant line (pscb. The seed coat weight of the mutant was almost twice of the wild type, and the germination time was significantly lower than wild type. Further, the mutant had lower level of lignin, anthocyanin, proanthocyandin content and highly increased level of melanin content as compared to wild type. Using RNA-Seq, we examined the seed coat transcriptome in three stages of seed development in the wild type and the pscb mutant. The RNA-Seq analysis revealed presence of highly differentially expressed phenylpropanoid and flavonoid pathway genes in all the three seed development stages, especially at 40 days after flowering (DAF40. Also, the expression of polyphenol oxidases and peroxidase were found to be activated significantly especially in the late seed developmental stage. The genome-wide comparative study of the expression profiles revealed 62 differentially expressed genes common across all the three stages. By analyzing the expression patterns and the sequences of the common differentially expressed genes of the three stages, three candidate genes namely c36498_g1 (CCoAOMT1, c40902_g2 (kinesin and c33560_g1 (MYB3 were identified responsible for seed-coat cracking and brown color phenotype. Therefore, this study not only provided candidate genes but also provided greater insights and molecular genetic control of peanut seed-coat cracking and color variation. The information generated in this study will facilitate further identification of causal gene and diagnostic markers for breeding improved peanut varieties with smooth and desirable seed coat color.

  4. Genotyping analysis of protein S-Tokushima (K196E) and the involvement of protein S antigen and activity in patients with recurrent pregnancy loss.

    Science.gov (United States)

    Matsukawa, Yasushi; Asano, Eriko; Tsuda, Tomohide; Kuma, Hiroyuki; Kitaori, Tamao; Katano, Kinue; Ozaki, Yasuhiko; Sugiura-Ogasawara, Mayumi

    2017-04-01

    Preston et al. indicated that Protein S (PS) deficiency was associated with stillbirths but not miscarriages. The PS-Tokushima missense variant was reported to serve as a genetic risk factor for deep vein thrombosis in the Japanese population. A previous cross-sectional study showed no increase in the prevalence of PS-Tokushima in patients with recurrent early pregnancy loss or in patients with intra uterine fetal death and/or fetal growth restriction. There has been limited number of prospective studies examining the pregnancy outcome in patients with both a PS deficiency and recurrent pregnancy loss (RPL). We examined the association between PS deficiency, PS-Tokushima and RPL. The study group consisted of 355 Japanese women with two or more consecutive pregnancy losses and 101 parous women. The frequency of PS-Tokushima and the subsequent live birth rate in relation to a PS deficiency defined as low PS-specific activity (total PS activity/total PS antigen) and the carriage of PS-Tokushima were examined. There was no significant difference in the frequency of PS-Tokushima between patients and controls. The 8 patients carriers of PS-Tokushima variant were capable of a subsequent live birth without the use of heparin. There was no significant difference in subsequent live birth rates between patients with low or normal PS-specific activity/PS activity without heparin prophylaxis after excluding miscarriages caused by an abnormal embryonic karyotype using multivariate logistic regression analysis. There was no association between PS-Tokushima and RPL and a PS deficiency or low PS activity was shown not to serve as a reliable clinical predictor of subsequent miscarriage. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. iTRAQ-based quantitative proteomic analysis reveals the distinct early embryo myofiber type characteristics involved in landrace and miniature pig.

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    Zhang, Xumeng; Chen, Yaosheng; Pan, Jinchun; Liu, Xiaohong; Chen, Hu; Zhou, Xingyu; Yuan, Zhuning; Wang, Xilong; Mo, Delin

    2016-02-25

    Pig (Sus scrofa) is a major source of dietary proteins for human consumption and is becoming a valuable model in agricultural and biomedical research. The recently developed isobaric tag for relative and absolute quantitation (iTRAQ) method allows sensitive and accurate protein quantification. Here, we performed the first iTRAQ-based quantitative proteomic analyses of Landrace (LR) and Wuzhishan (WZS) pig longissimus dorsi muscle tissues during early embryonic development. The iTRAQ-based early embryonic longissimus dorsi muscle study of LR and WZS ranging from 21 to 42 days post coitus (dpc) identified a total of 4431 proteins from 17,214 peptides, which were matched with 36,4025 spectra at a false discovery rate of 5%. In both WZS and LR, the largest amount of differentially expressed proteins (DEPs) were found between 28 and 35 dpc. 252 breed-DEPs were selected by GO analysis, including 8 myofibrillar proteins. Only MYHCI/IIA mRNA were detected due to early embryonic stages, and significantly higher expression of them were found in WZS during these 4 stages. MYHCI was first found in WZS at 28 dpc and expressed in both breeds at later stages, while MYHCII protein was not detected until 35 dpc in both breeds. Thus, 33 myogenic breed-DEPs selected from last two stages were analyzed by STRING, which showed that some myofibrillar proteins (MYH1, TPM4, MYH10, etc.) and functional proteins (CSRP2, CASQ2, OTC, etc.), together with candidate myogenic proteins (H3F3A, HDGFRP2, etc.), probably participate in the regulatory network of myofiber formation. Our iTRAQ-based early embryonic longissimus dorsi muscle study of LR and WZS provides new data on the in vivo muscle development distinctions during early embryonic development, which contributes to the improved understanding in the regulation mechanism of early myogenesis in agricultural animals.

  6. De Novo Transcriptome Analysis of the Common New Zealand Stick Insect Clitarchus hookeri (Phasmatodea Reveals Genes Involved in Olfaction, Digestion and Sexual Reproduction.

    Directory of Open Access Journals (Sweden)

    Chen Wu

    Full Text Available Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White. The female olfactory gene repertoire revealed ten odorant binding proteins with three recently duplicated, 12 chemosensory proteins, 16 odorant receptors, and 17 ionotropic receptors. The majority of these olfactory genes were over-expressed in female antennae and have the inferred function of odorant reception. Others that were predominantly expressed in male terminalia (n = 3 and female midgut (n = 1 suggest they have a role in sexual reproduction and digestion, respectively. Over-represented transcripts in the midgut were enriched with digestive enzyme gene families. Clitarchus hookeri is likely to harbour nine members of an endogenous cellulase family (glycoside hydrolase family 9, two of which appear to be specific to the C. hookeri lineage. All of these cellulase sequences fall into four main phasmid clades and show gene duplication events occurred early in the diversification of Phasmatodea. In addition, C. hookeri genome is likely to express γ-proteobacteria pectinase transcripts that have recently been shown to be the result of horizontal transfer. We also predicted 711 male terminalia-enriched transcripts that are candidate accessory gland proteins, 28 of which were annotated to have molecular functions of peptidase activity and peptidase inhibitor activity, two groups being widely reported to regulate female reproduction through proteolytic cascades. Our study has yielded new insights into the genetic basis of odour detection, nutrient digestion

  7. Use of risk assessment instruments to predict violence and antisocial behaviour in 73 samples involving 24 827 people: systematic review and meta-analysis.

    Science.gov (United States)

    Fazel, Seena; Singh, Jay P; Doll, Helen; Grann, Martin

    2012-07-24

    To investigate the predictive validity of tools commonly used to assess the risk of violence, sexual, and criminal behaviour. Systematic review and tabular meta-analysis of replication studies following PRISMA guidelines. PsycINFO, Embase, Medline, and United States Criminal Justice Reference Service Abstracts. We included replication studies from 1 January 1995 to 1 January 2011 if they provided contingency data for the offending outcome that the tools were designed to predict. We calculated the diagnostic odds ratio, sensitivity, specificity, area under the curve, positive predictive value, negative predictive value, the number needed to detain to prevent one offence, as well as a novel performance indicator-the number safely discharged. We investigated potential sources of heterogeneity using metaregression and subgroup analyses. Risk assessments were conducted on 73 samples comprising 24,847 participants from 13 countries, of whom 5879 (23.7%) offended over an average of 49.6 months. When used to predict violent offending, risk assessment tools produced low to moderate positive predictive values (median 41%, interquartile range 27-60%) and higher negative predictive values (91%, 81-95%), and a corresponding median number needed to detain of 2 (2-4) and number safely discharged of 10 (4-18). Instruments designed to predict violent offending performed better than those aimed at predicting sexual or general crime. Although risk assessment tools are widely used in clinical and criminal justice settings, their predictive accuracy varies depending on how they are used. They seem to identify low risk individuals with high levels of accuracy, but their use as sole determinants of detention, sentencing, and release is not supported by the current evidence. Further research is needed to examine their contribution to treatment and management.

  8. Gene expression analysis of enzymes of the carotenoid biosynthesis pathway involved in β-cryptoxanthin accumulation in wild raspberry, Rubus palmatus.

    Science.gov (United States)

    Mizuno, Kouichi; Tokiwano, Tetsuo; Yoshizawa, Yuko

    2017-03-18

    β-cryptoxanthin (β-Cry), a xanthophyll, is unlike other abundant carotenoids, such as α-carotene, β-carotene, lycopene, lutein, and zeaxanthin. It is not found in most fruits or vegetables but is found only in specific fruits, such as hot chili pepper, persimmon, and citrus fruits. Because recent reports suggest that β-Cry intake is beneficial to human health, the xanthophyll requires further investigation. Although β-Cry accumulates in the fruit of wild raspberry, Rubus palmatus, it is not present in cultivated raspberry. In the present study, two wild raspberry species were studied-R. palmatus, which accumulates β-Cry in the fruit, and R. crataegifolius, which does not accumulate β-Cry. Four carotenoid biosynthetic enzymes derived from these two species were analyzed-phytoene synthase (PSY), lycopene β-cyclase (LCYb), β-carotene hydroxylase (HYb), and zeaxanthin epoxidase (ZEP). Expression levels of their genes were also assessed to elucidate mechanism underlying β-Cry accumulation. Partial gene sequences of RubPSY, RubLCYb, RubHYb, and RubZEP, isolated from immature raspberry fruits of R. palmatus, were used as probes for Northern blot analysis. RubZEP expression ceased as the fruits matured, possibly because of reduced production of zeaxanthin. β-Cry is considered to be an intermediate compound that accumulates in the mature fruits of R. palmatus. High expression of RubPSY was detectable in the mature fruits of R. crataegifolius, and the expression of RubLCYb, RubHYb, and RubZEP was detectable during all stages of fruit maturation. In contrast, β-Cry was absent in the mature fruits of R. crataegifolius. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. SU-F-P-52: A Meta-Analysis of Controlled Clinical Trials Comparing Elective Nodal Irradiation with Involved-Field Irradiation for Conformal Or Intensity-Modulated Radiotherapy in Patients with Esophageal Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Bai, W; Zhang, R; Zhou, Z; Qiao, X [The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei (China)

    2016-06-15

    Purpose: To compare elective nodal irradiation with involved-field irradiation for three-dimensional conformal radiotherapy or intensity-modulated radiotherapy in patients with esophageal cancer by a metaanalysis. Methods: Wanfang, CNKI, VIP, CBM databases, PubMed, Embase and Cochrane Library were searched to identify the controlled clinical trials of elective nodal irradiation with involved-field irradiation for three-dimensional conformal radiotherapy or intensity-modulated radiotherapy in patients with esophageal cancer. The obtained data were analyzed using Stata 11.0. The difference between two groups was estimated by calculating the odds ratio (OR) with 95% confidence interval (95% CI). Results: A total of 12 controlled clinical trials involving 1095 esophageal cancer patients, which were selected according to inclusion and exclusion criteria, were included in this meta-analysis. The meta-analysis showed that the elective nodal irradiation group reduced the rates of out-field failure comparing with involved-field irradiation group (OR=3.727, P=0.007). However, the rates of ≥grades 3 acute radiation pneumonitis and esophagitis were significantly higher in the elective nodal irradiation group than in the involved-field irradiation group (OR=0.348, P=0.001, OR=0.385, P=0.000). 1-, 2-, 3-year local control rates (OR=0.966, P=0.837, OR=0.946, P=0.781; OR=0.732P=0.098) and 1-, 3-, 5-year survival rates were similar in the two groups ( OR=0.966, P=0.837; OR=0.946, P=0.781; OR=0.732, P=0.098; OR=0.952, P=0.756; OR=1.149, P=0.422; OR=0.768, P=0.120). It is the same with the rates of distant metastasis (OR=0.986, P=0.937). Conclusion: Compared with involved-field irradiation, the elective nodal irradiation can reduce the rates of out-field failure for three-dimensional conformal radiotherapy or intensity-modulated radiotherapy in patients with esophageal cancer. However, its advantage of local control and survival rates is not obvious and it increases the incidence

  10. Cardiovascular involvement in myositis

    DEFF Research Database (Denmark)

    Diederichsen, Louise P

    2017-01-01

    PURPOSE OF REVIEW: The purpose of this review is to provide an update on cardiovascular involvement in idiopathic inflammatory myopathy (IIM). Studies from the past 18 months are identified and reviewed. Finally, the clinical impact of these findings is discussed. RECENT FINDINGS: Epidemiological...... on cardiac magnetic resonance (CMR) imaging suggests that CMR should be considered as a potentially viable diagnostic tool to evaluate the possibility of silent myocardial inflammation in IIM with normal routine noninvasive evaluation. SUMMARY: Updated literature on cardiovascular involvement in IIM has...... identified an increased risk for subclinical and clinical cardiovascular disease in these rare inflammatory muscle diseases....

  11. Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair.

    Science.gov (United States)

    Liu, Fan; Chen, Yan; Zhu, Gu; Hysi, Pirro G; Wu, Sijie; Adhikari, Kaustubh; Breslin, Krystal; Pospiech, Ewelina; Hamer, Merel A; Peng, Fuduan; Muralidharan, Charanya; Acuna-Alonzo, Victor; Canizales-Quinteros, Samuel; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Rothhammer, Francisco; Bortolini, Maria Catira; Gonzalez-Jose, Rolando; Zeng, Changqing; Xu, Shuhua; Jin, Li; Uitterlinden, André G; Ikram, M Arfan; van Duijn, Cornelia M; Nijsten, Tamar; Walsh, Susan; Branicki, Wojc