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Sample records for determining phenotypic severity

  1. Voxel-based analysis in neuroferritinopathy expands the phenotype and determines radiological correlates of disease severity.

    PubMed

    Keogh, M J; Aribisala, B S; He, J; Tulip, E; Butteriss, D; Morris, C; Gorman, G; Horvath, R; Chinnery, P F; Blamire, Andrew M

    2015-10-01

    Neuroferritinopathy is an autosomal dominant adult-onset movement disorder which occurs due to mutations in the ferritin light chain gene (FTL). Extensive iron deposition and cavitation are observed post-mortem in the basal ganglia, but whether more widespread pathological changes occur, and whether they correlate with disease severity is unknown. 3D-T1w and quantitative T2 whole brain MRI scans were performed in 10 clinically symptomatic patients with the 460InsA FTL mutation and 10 age-matched controls. Voxel-based morphometry (VBM) and voxel-based relaxometry (VBR) were subsequently performed. Clinical assessment using the Unified Dystonia Rating Scale (UDRS) and Unified Huntington's Disease Rating Scale (UHDRS) was undertaken in all patients. VBM detected significant tissue changes within the substantia nigra, midbrain and dentate together with significant cerebellar atrophy in patients (FWE, p < 0.05). Iron deposition in the caudate head and cavitation in the lateral globus pallidus correlated with UDRS score (p < 0.001). There were no differences between groups with VBR. Our data show that progressive iron accumulation in the caudate nucleus, and cavitation of the globus pallidus correlate with disease severity in neuroferritinopathy. We also confirm sub-clinical cerebellar atrophy as a feature of the disease. We suggest that VBM is an effective technique to detect regions of iron deposition and cavitation, with potential wider utility to determine radiological markers of disease severity for all NBIA disorders. PMID:26142024

  2. Cyclic Neutropenia and Severe Congenital Neutropenia in Patients with a Shared ELANE Mutation and Paternal Haplotype: Evidence for Phenotype Determination by Modifying Genes

    PubMed Central

    Newburger, Peter E.; Pindyck, Talia N.; Zhu, Zhiqing; Bolyard, Audrey Anna; Aprikyan, Andrew A. G.; Dale, David C.; Smith, Gary D.; Boxer, Laurence A.

    2010-01-01

    Background Cyclic neutropenia (CN) and severe congenital neutropenia (SCN) are disorders of neutrophil production that differ markedly in disease severity. Mutations of the ELANE gene (the symbol recently replacing ELA2) are considered largely responsible for most cases of CN and SCN, but specific mutations are typically associated with one or the other Procedure We performed ELANE genotyping on all individuals and paternal sperm in an SCN kindred with 8 SCN progeny of a sperm donor and 6 different mothers. Results One patient with CN had the same S97L ELANE mutation as seven patients with the SCN phenotype. The mutant allele was detected in the donor’s spermatozoa, representing 18% of the ELANE gene pool, but not in DNA from his lymphocytes, neutrophils, or buccal mucosa, indicating gonadal mosaicism. Conclusions The coexistence of CN and SCN phenotypes in this kindred with a shared paternal haplotype strongly suggests both a role for modifying genes in determination of congenital neutropenia disease phenotypes, and the classification of CN and SCN within a spectrum of phenotypes expressing varying degrees of the same disease process. PMID:20582973

  3. Somatic-cell selection is a major determinant of the blood-cell phenotype in heterozygotes for glucose-6-phosphate dehydrogenase mutations causing severe enzyme deficiency.

    PubMed Central

    Filosa, S.; Giacometti, N.; Wangwei, C.; De Mattia, D.; Pagnini, D.; Alfinito, F.; Schettini, F.; Luzzatto, L.; Martini, G.

    1996-01-01

    X-chromosome inactivation in mammals is regarded as an essentially random process, but the resulting somatic-cell mosaicism creates the opportunity for cell selection. In most people with red-blood-cell glucose-6-phosphate dehydrogenase (G6PD) deficiency, the enzyme-deficient phenotype is only moderately expressed in nucleated cells. However, in a small subset of hemizygous males who suffer from chronic nonspherocytic hemolytic anemia, the underlying mutations (designated class I) cause more-severe G6PD deficiency, and this might provide an opportunity for selection in heterozygous females during development. In order to test this possibility we have analyzed four heterozygotes for class I G6PD mutations: two with G6PD Portici (1178G-->A) and two with G6PD Bari (1187C-->T). We found that in fractionated blood cell types (including erythroid, myeloid, and lymphoid cell lineages) there was a significant excess of G6PD-normal cells. The significant concordance that we have observed in the degree of imbalance in the different blood-cell lineages indicates that a selective mechanism is likely to operate at the level of pluripotent blood stem cells. Thus, it appears that severe G6PD deficiency affects adversely the proliferation or the survival of nucleated blood cells and that this phenotypic characteristic is critical during hematopoiesis. Images Figure 1 Figure 3 Figure 4 Figure 5 Figure 6 PMID:8808605

  4. Somatic-cell selection is a major determinant of the blood-cell phenotype in heterozygotes for glucose-6-phosphate dehydrogenase mutations causing severe enzyme deficiency

    SciTech Connect

    Filosa, S.; Giacometti, N.; Wangwei, C.; Martini, G.

    1996-10-01

    X-chromosome inactivation in mammals is regarded as an essentially random process, but the resulting somatic-cell mosaicism creates the opportunity for cell selection. In most people with red-blood-cell glucose-6-phosphate dehydrogenase (G6PD) deficiency, the enzyme-deficient phenotype is only moderately expressed in nucleated cells. However, in a small subset of hemizygous males who suffer from chronic nonspherocytic hemolytic anemia, the underlying mutations (designated class I) cause more-severe G6PD deficiency, and this might provide an opportunity for selection in heterozygous females during development. In order to test this possibility we have analyzed four heterozygotes for class I G6PD mutations: two with G6PD Portici (1178G{r_arrow}A) and two with G6PD Bari (1187C{r_arrow}T). We found that in fractionated blood cell types (including erythroid, myeloid, and lymphoid cell lineages) there was a significant excess of G6PD-normal cells. The significant concordance that we have observed in the degree of imbalance in the different blood-cell lineages indicates that a selective mechanism is likely to operate at the level of pluripotent blood stem cells. Thus, it appears that severe G6PD deficiency affects adversely the proliferation or the survival of nucleated blood cells and that this phenotypic characteristic is critical during hematopoiesis. 65 refs., 6 figs., 3 tabs.

  5. Identifying neurobiological phenotypes associated with alcohol use disorder severity.

    PubMed

    Claus, Eric D; Ewing, Sarah W Feldstein; Filbey, Francesca M; Sabbineni, Amithrupa; Hutchison, Kent E

    2011-09-01

    Although numerous studies provide general support for the importance of genetic factors in the risk for alcohol use disorders (AUDs), candidate gene and genome-wide studies have yet to identify a set of genetic variations that explain a significant portion of the variance in AUDs. One reason is that alcohol-related phenotypes used in genetic studies are typically based on highly heterogeneous diagnostic categories. Therefore, identifying neurobiological phenotypes related to neuroadaptations that drive the development of AUDs is critical for the future success of genetic and epigenetic studies. One such neurobiological phenotype is the degree to which exposure to alcohol taste cues recruits the basal ganglia, prefrontal cortex, and motor areas, all of which have been shown to have a critical role in addictive behaviors in animal studies. To that end, this study was designed to examine whether cue-elicited responses of these structures are associated with AUD severity in a large sample (n=326) using voxelwise and functional connectivity measures. Results suggested that alcohol cues significantly activated dorsal striatum, insula/orbitofrontal cortex, anterior cingulate cortex, and ventral tegmental area. AUD severity was moderately correlated with regions involved in incentive salience such as the nucleus accumbens and amygdala, and stronger relationships with precuneus, insula, and dorsal striatum. The findings indicate that AUDs are related to neuroadaptations in these regions and that these measures may represent important neurobiological phenotypes for subsequent genetic studies. PMID:21677649

  6. Determining which phenotypes underlie a pleiotropic signal

    PubMed Central

    Majumdar, Arunabha; Haldar, Tanushree; Witte, John S.

    2016-01-01

    Discovering pleiotropic loci is important to understand the biological basis of seemingly distinct phenotypes. Most methods for assessing pleiotropy only test for the overall association between genetic variants and multiple phenotypes. To determine which specific traits are pleiotropic, we evaluate via simulation and application three different strategies. The first is model selection techniques based on the inverse regression of genotype on phenotypes. The second is a subset-based meta-analysis ASSET [Bhattacharjee et al., 2012], which provides an optimal subset of non-null traits. And the third is a modified Benjamini-Hochberg (B-H) procedure of controlling the expected false discovery rate [Benjamini and Hochberg, 1995] in the framework of phenome-wide association study. From our simulations we see that an inverse regression based approach MultiPhen [O’Reilly et al., 2012] is more powerful than ASSET for detecting overall pleiotropic association, except for when all the phenotypes are associated and have genetic effects in the same direction. For determining which specific traits are pleiotropic, the modified B-H procedure performs consistently better than the other two methods. The inverse regression based selection methods perform competitively with the modified B-H procedure only when the phenotypes are weakly correlated. The efficiency of ASSET is observed to lie below and in between the efficiency of the other two methods when the traits are weakly and strongly correlated, respectively. In our application to a large GWAS, we find that the modified B-H procedure also performs well, indicating that this may be an optimal approach for determining the traits underlying a pleiotropic signal. PMID:27238845

  7. Determining Which Phenotypes Underlie a Pleiotropic Signal.

    PubMed

    Majumdar, Arunabha; Haldar, Tanushree; Witte, John S

    2016-07-01

    Discovering pleiotropic loci is important to understand the biological basis of seemingly distinct phenotypes. Most methods for assessing pleiotropy only test for the overall association between genetic variants and multiple phenotypes. To determine which specific traits are pleiotropic, we evaluate via simulation and application three different strategies. The first is model selection techniques based on the inverse regression of genotype on phenotypes. The second is a subset-based meta analysis ASSET [Bhattacharjee et al., ], which provides an optimal subset of nonnull traits. And the third is a modified Benjamini-Hochberg (B-H) procedure of controlling the expected false discovery rate [Benjamini and Hochberg, ] in the framework of phenome-wide association study. From our simulations we see that an inverse regression-based approach MultiPhen [O'Reilly et al., ] is more powerful than ASSET for detecting overall pleiotropic association, except for when all the phenotypes are associated and have genetic effects in the same direction. For determining which specific traits are pleiotropic, the modified B-H procedure performs consistently better than the other two methods. The inverse regression-based selection methods perform competitively with the modified B-H procedure only when the phenotypes are weakly correlated. The efficiency of ASSET is observed to lie below and in between the efficiency of the other two methods when the traits are weakly and strongly correlated, respectively. In our application to a large GWAS, we find that the modified B-H procedure also performs well, indicating that this may be an optimal approach for determining the traits underlying a pleiotropic signal. PMID:27238845

  8. MECP2 duplication: possible cause of severe phenotype in females.

    PubMed

    Scott Schwoerer, Jessica; Laffin, Jennifer; Haun, Joanne; Raca, Gordana; Friez, Michael J; Giampietro, Philip F

    2014-04-01

    MECP2 duplication syndrome, originally described in 2005, is an X-linked neurodevelopmental disorder comprising infantile hypotonia, severe to profound intellectual disability, autism or autistic-like features, spasticity, along with a variety of additional features that are not always clinically apparent. The syndrome is due to a duplication (or triplication) of the gene methyl CpG binding protein 2 (MECP2). To date, the disorder has been described almost exclusively in males. Female carriers of the duplication are thought to have no or mild phenotypic features. Recently, a phenotype for females began emerging. We describe a family with ∼290 kb duplication of Xq28 region that includes the MECP2 gene where the proposita and affected family members are female. Twin sisters, presumed identical, presented early with developmental delay, and seizures. Evaluation of the proposita at 25 years of age included microarray comparative genomic hybridization (aCGH) which revealed the MECP2 gene duplication. The same duplication was found in the proposita's sister, who is more severely affected, and the proband's mother who has mild intellectual disability and depression. X-chromosome inactivation studies showed significant skewing in the mother, but was uninformative in the twin sisters. We propose that the MECP2 duplication caused for the phenotype of the proband and her sister. These findings support evidence for varied severity in some females with MECP2 duplications. PMID:24458799

  9. Mast Cell Phenotype, Location, and Activation in Severe Asthma

    PubMed Central

    Balzar, Silvana; Fajt, Merritt L.; Comhair, Suzy A. A.; Erzurum, Serpil C.; Bleecker, Eugene; Busse, William W.; Castro, Mario; Gaston, Benjamin; Israel, Elliot; Schwartz, Lawrence B.; Curran-Everett, Douglas; Moore, Charity G.; Wenzel, Sally E.

    2011-01-01

    Rationale: Severe asthma (SA) remains poorly understood. Mast cells (MC) are implicated in asthma pathogenesis, but it remains unknown how their phenotype, location, and activation relate to asthma severity. Objectives: To compare MC-related markers measured in bronchoscopically obtained samples with clinically relevant parameters between normal subjects and subjects with asthma to clarify their pathobiologic importance. Methods: Endobronchial biopsies, epithelial brushings, and bronchoalveolar lavage were obtained from subjects with asthma and normal subjects from the Severe Asthma Research Program (N = 199). Tryptase, chymase, and carboxypeptidase A (CPA)3 were used to identify total MC (MCTot) and the MCTC subset (MCs positive for both tryptase and chymase) using immunostaining and quantitative real-time polymerase chain reaction. Lavage was analyzed for tryptase and prostaglandin D2 (PGD2) by ELISA. Measurements and Main Results: Submucosal MCTot (tryptase-positive by immunostaining) numbers were highest in “mild asthma/no inhaled corticosteroid (ICS) therapy” subjects and decreased with greater asthma severity (P = 0.002). In contrast, MCTC (chymase-positive by immunostaining) were the predominant (MCTC/MCTot > 50%) MC phenotype in SA (overall P = 0.005). Epithelial MCTot were also highest in mild asthma/no ICS, but were not lower in SA. Instead, they persisted and were predominantly MCTC. Epithelial CPA3 and tryptase mRNA supported the immunostaining data (overall P = 0.008 and P = 0.02, respectively). Lavage PGD2 was higher in SA than in other steroid-treated groups (overall P = 0.02), whereas tryptase did not differentiate the groups. In statistical models, PGD2 and MCTC/MCTot predicted SA. Conclusions: Severe asthma is associated with a predominance of MCTC in the airway submucosa and epithelium. Activation of those MCTC may contribute to the increases in PGD2 levels. The data suggest an altered and active MC population contributes to SA pathology

  10. The Molecular Phenotype of Severe Asthma in Children

    PubMed Central

    Fitzpatrick, Anne M.; Higgins, Melinda; Holguin, Fernando; Brown, Lou Ann S.; Teague, W. Gerald

    2010-01-01

    Background Although the clinical attributes of severe asthma in children have been well described, the differentiating features of the lower airway inflammatory response. Objectives We sought to discriminate severe from moderate asthma in children by applying linear discriminant analysis, a supervised method of high-dimensional data reduction, to cytokines and chemokines measured in the bronchoalveolar lavage (BAL) fluid and alveolar macrophage (AM) lysate. Methods BAL fluid was available from 53 asthmatic children (severe asthma, n = 31) undergoing bronchoscopy for clinical indications and 30 non-smoking adults. 23 cytokines and chemokines were measured using bead-based multiplex assays. Linear discriminant analyses of the BAL fluid and AM analytes were performed to develop predictive models of severe asthma in children. Results Although univariate analysis of single analytes did not differentiate severe from moderate asthma in children, linear discriminant analyses allowed for near complete separation of the moderate and severe asthmatic groups. Significant correlations were also noted between several of the AM and BAL analytes measured. In the BAL fluid, IL-13 and IL-6 differentiated asthmatics from controls, whereas GRO (CXCL1), RANTES (CCL5), IL-12, IFNγ, and IL-10 best characterized severe versus moderate asthma in children. In the AM lysate, IL-6 was the strongest discriminator of all the groups. Conclusions Severe asthma in children is characterized by a distinct airway molecular phenotype that does not have a clear Th1 or Th2 pattern. Improved classification of children with severe asthma may assist with the development of targeted therapeutics for this group of children who are difficult to treat. PMID:20371397

  11. Neutrophilic and Pauci-immune Phenotypes in Severe Asthma.

    PubMed

    Panettieri, Reynold A

    2016-08-01

    Although 2 T-helper type 2 inflammation evokes airway hyperresponsiveness and narrowing, neutrophilic or pauci-immune asthma accounts for significant asthma morbidity. Viruses, toxicants, environmental tobacco smoke exposure, and bacterial infections induce asthma exacerbations mediated by neutrophilic inflammation or by structural cell (pauci-immune) mechanisms. Therapeutic challenges exist in the management of neutrophilic and pauci-immune phenotypes because both syndromes manifest steroid insensitivity. The recognition that neutrophil subsets exist and their functions are unique poses exciting opportunities to develop precise therapies. The conventional thought to target neutrophil activation or migration globally may explain why current drug development in neutrophilic asthma remains challenging. PMID:27401627

  12. Airway Microbiota in Severe Asthma and Relationship to Asthma Severity and Phenotypes

    PubMed Central

    Liang, Zhike; Brinkmann, Folke; Cardenas, Paul A; Duff, Rachael; Bhavsar, Pankaj; Cookson, William; Moffatt, Miriam; Chung, Kian Fan

    2016-01-01

    Background The lower airways harbor a community of bacterial species which is altered in asthma. Objectives We examined whether the lower airway microbiota were related to measures of asthma severity. Methods We prospectively recruited 26 severe asthma, 18 non-severe asthma and 12 healthy subjects. DNA was extracted from induced sputum and PCR amplification of the V3-V5 region of bacterial 16S rRNA gene was performed. Results We obtained 138,218 high quality sequences which were rarefied at 133 sequences/sample. Twenty OTUs had sequences ≥1% of total. There were marked differences in the distribution of Phyla between groups (P = 2.8x10-118). Bacteroidetes and Fusobacteria were reduced in non-severe and severe asthmatic groups. Proteobacteria were more common in non-severe asthmatics compared to controls (OR = 2.26; 95% CI = 1.94–2.64) and Firmicutes were increased in severe asthmatics compared to controls (OR = 2.15; 95%CI = 1.89–2.45). Streptococcal OTUs amongst the Firmicutes were associated with recent onset asthma, rhinosinusitis and sputum eosinophilia. Conclusions Sputum microbiota in severe asthma differs from healthy controls and non-severe asthmatics, and is characterized by the presence of Streptococcus spp with eosinophilia. Whether these organisms are causative for the pathophysiology of asthma remains to be determined. PMID:27078029

  13. The determinants of fishing vessel accident severity.

    PubMed

    Jin, Di

    2014-05-01

    The study examines the determinants of fishing vessel accident severity in the Northeastern United States using vessel accident data from the U.S. Coast Guard for 2001-2008. Vessel damage and crew injury severity equations were estimated separately utilizing the ordered probit model. The results suggest that fishing vessel accident severity is significantly affected by several types of accidents. Vessel damage severity is positively associated with loss of stability, sinking, daytime wind speed, vessel age, and distance to shore. Vessel damage severity is negatively associated with vessel size and daytime sea level pressure. Crew injury severity is also positively related to the loss of vessel stability and sinking. PMID:24473412

  14. The physical basis of how prion conformations determine strain phenotypes

    NASA Astrophysics Data System (ADS)

    Tanaka, Motomasa; Collins, Sean R.; Toyama, Brandon H.; Weissman, Jonathan S.

    2006-08-01

    A principle that has emerged from studies of protein aggregation is that proteins typically can misfold into a range of different aggregated forms. Moreover, the phenotypic and pathological consequences of protein aggregation depend critically on the specific misfolded form. A striking example of this is the prion strain phenomenon, in which prion particles composed of the same protein cause distinct heritable states. Accumulating evidence from yeast prions such as [PSI+] and mammalian prions argues that differences in the prion conformation underlie prion strain variants. Nonetheless, it remains poorly understood why changes in the conformation of misfolded proteins alter their physiological effects. Here we present and experimentally validate an analytical model describing how [PSI+] strain phenotypes arise from the dynamic interaction among the effects of prion dilution, competition for a limited pool of soluble protein, and conformation-dependent differences in prion growth and division rates. Analysis of three distinct prion conformations of yeast Sup35 (the [PSI+] protein determinant) and their in vivo phenotypes reveals that the Sup35 amyloid causing the strongest phenotype surprisingly shows the slowest growth. This slow growth, however, is more than compensated for by an increased brittleness that promotes prion division. The propensity of aggregates to undergo breakage, thereby generating new seeds, probably represents a key determinant of their physiological impact for both infectious (prion) and non-infectious amyloids.

  15. Understanding the Anatomy of Dystonia: Determinants of Penetrance and Phenotype

    PubMed Central

    Lerner, Renata P; Niethammer, Martin; Eidelberg, David

    2013-01-01

    The dystonias comprise a group of syndromes characterized by prolonged involuntary muscle contractions resulting in repetitive movements and abnormal postures. Primary dystonia has been associated with over 14 different genotypes, most of which follow an autosomal dominant inheritance pattern with reduced penetrance. Independent of etiology, the disease is characterized by extensive variability in disease phenotype and clinical severity. Recent neuroimaging studies investigating this phenomenon in manifesting and non-manifesting genetic carriers of dystonia have discovered microstructural integrity differences in the cerebello-thalamo-cortical tract in both groups related to disease penetrance. Further study suggests these differences to be specific to subrolandic white matter regions somatotopically related to clinical phenotype. Clinical severity was correlated to the degree of microstructural change. These findings suggest a mechanism for the penetrance and clinical variability observed in dystonia and may represent a novel therapeutic target for patients with refractory limb symptoms. PMID:24114145

  16. Severe asthma in school-age children: evaluation and phenotypic advances.

    PubMed

    Coverstone, Andrea; Bacharier, Leonard B; Fitzpatrick, Anne M

    2015-05-01

    Although the majority of children with asthma have a favorable clinical response to treatment with low to moderate doses of inhaled corticosteroids (ICS), a small subset of children have "severe" asthma characterized by ongoing symptoms and airway inflammation despite treatment with high doses of ICS and even oral corticosteroids. Although there is symptom heterogeneity in the affected children, children with severe asthma share the risk for adverse outcomes, including recurrent and potentially life-threatening exacerbations, which contribute to substantial economic burden. This article reviews current knowledge of severe asthma in school-age children (age 6-17 years) with a focus on recent literature published after January 2012. Clinical management approaches for children with severe asthma are discussed as well as current phenotyping efforts and emerging phenotypic-directed therapies that may be of benefit for subpopulations of children with severe asthma in the future. PMID:26134431

  17. Using Image Processing to Determine Emphysema Severity

    NASA Astrophysics Data System (ADS)

    McKenzie, Alexander; Sadun, Alberto

    2010-10-01

    Currently X-rays and computerized tomography (CT) scans are used to detect emphysema, but other tests are required to accurately quantify the amount of lung that has been affected by the disease. These images clearly show if a patient has emphysema, but are unable by visual scan alone, to quantify the degree of the disease, as it presents as subtle, dark spots on the lung. Our goal is to use these CT scans to accurately diagnose and determine emphysema severity levels in patients. This will be accomplished by performing several different analyses of CT scan images of several patients representing a wide range of severity of the disease. In addition to analyzing the original CT data, this process will convert the data to one and two bit images and will then examine the deviation from a normal distribution curve to determine skewness. Our preliminary results show that this method of assessment appears to be more accurate and robust than the currently utilized methods, which involve looking at percentages of radiodensities in the air passages of the lung.

  18. Deficient transcription of XIST from tiny ring X chromosomes in females with severe phenotypes.

    PubMed Central

    Migeon, B R; Luo, S; Stasiowski, B A; Jani, M; Axelman, J; Van Dyke, D L; Weiss, L; Jacobs, P A; Yang-Feng, T L; Wiley, J E

    1993-01-01

    The severe phenotype of human females whose karyotype includes tiny ring X chromosomes has been attributed to the inability of the small ring X chromosome to inactivate. The XIST locus is expressed only from the inactive X chromosome, resides at the putative X inactivation center, and is considered a prime player in the initiation of mammalian X dosage compensation. Using PCR, Southern blot analysis, and in situ hybridization, we have looked for the presence of the XIST locus in tiny ring X chromosomes from eight females who have multiple congenital malformations and severe mental retardation. Our studies reveal heterogeneity within this group; some rings lack the XIST locus, while others have sequences homologous to probes for XIST. However, in the latter, the locus is either not expressed or negligibly expressed, based on reverse transcription-PCR analysis. Therefore, what these tiny ring chromosomes have in common is a level of XIST transcription comparable to an active X. As XIST transcription is an indicator of X chromosome inactivity, the absence of XIST transcription strongly suggests that tiny ring X chromosomes in females with severe phenotypes are mutants in the X chromosome inactivation pathway and that the inability of these rings to inactivate is responsible for the severe phenotypes. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:8265665

  19. Acampomelic campomelic dysplasia with de novo 5q;17q reciprocal translocation and severe phenotype.

    PubMed Central

    Savarirayan, R; Bankier, A

    1998-01-01

    Campomelic dysplasia (CD) is a rare skeletal malformation syndrome caused by mutations in the SRY related gene SOX9, mapped to 17q24.3-q25.1. A small proportion of cases are associated with structural rearrangements involving 17q and it has been proposed that this subgroup have a milder phenotype and better prognosis compared to those with mutations in the SOX9 gene. We report a severely affected infant with the acampomelic form of campomelic dysplasia, who died at 11 days and was found to have a de novo reciprocal translocation, 46,XX,t(5;17)(q15;q25.1). This is the second reported case of severe campomelic dysplasia associated with a structural rearrangement involving 17q and suggests that this subgroup of patients may not significantly differ from those without chromosomal rearrangements with regards to phenotype or prognosis. Images PMID:9678706

  20. Severity of mutant phenotype in a series of chlorophyll-deficient wheat mutants depends on light intensity and the severity of the block in chlorophyll synthesis.

    PubMed Central

    Falbel, T G; Meehl, J B; Staehelin, L A

    1996-01-01

    Analyses of a series of allelic chlorina mutants of wheat (Triticum aestivum L.), which have partial blocks in chlorophyll (Chl) synthesis and, therefore, a limited Chl supply, reinforce the principle that Chl is required for the stable accumulation of Chl-binding proteins and that only reaction centers accumulate when the supply of Chl is severely limited. Depending on the rate of Chl accumulation (determined by the severity of the mutation) and on the rate of turnover of Chl and its precursors (determined by the environment in which the plant is grown), the mutants each reach an equilibrium of Chl synthesis and degradation. Together these mutants generate a spectrum of phenotypes. Under the harshest conditions (high illumination), plants with moderate blocks in Chl synthesis have membranes with very little Chl and Chl-proteins and membrane stacks resembling the thylakoids of the lethal xantha mutants of barely grown at low to medium light intensities (which have more severe blocks). In contrast, when grown under low-light conditions the same plants with moderate blocks have thylakoids resembling those of the wild type. The wide range of phenotypes of Chl b-deficient mutants has historically produced more confusion than enlightenment, but incomparable growth conditions can now explain the discrepancies reported in the literature. PMID:8883392

  1. Identification of Asthma Phenotypes Using Cluster Analysis in the Severe Asthma Research Program

    PubMed Central

    Moore, Wendy C.; Meyers, Deborah A.; Wenzel, Sally E.; Teague, W. Gerald; Li, Huashi; Li, Xingnan; D'Agostino, Ralph; Castro, Mario; Curran-Everett, Douglas; Fitzpatrick, Anne M.; Gaston, Benjamin; Jarjour, Nizar N.; Sorkness, Ronald; Calhoun, William J.; Chung, Kian Fan; Comhair, Suzy A. A.; Dweik, Raed A.; Israel, Elliot; Peters, Stephen P.; Busse, William W.; Erzurum, Serpil C.; Bleecker, Eugene R.

    2010-01-01

    Rationale: The Severe Asthma Research Program cohort includes subjects with persistent asthma who have undergone detailed phenotypic characterization. Previous univariate methods compared features of mild, moderate, and severe asthma. Objectives: To identify novel asthma phenotypes using an unsupervised hierarchical cluster analysis. Methods: Reduction of the initial 628 variables to 34 core variables was achieved by elimination of redundant data and transformation of categorical variables into ranked ordinal composite variables. Cluster analysis was performed on 726 subjects. Measurements and Main Results: Five groups were identified. Subjects in Cluster 1 (n = 110) have early onset atopic asthma with normal lung function treated with two or fewer controller medications (82%) and minimal health care utilization. Cluster 2 (n = 321) consists of subjects with early-onset atopic asthma and preserved lung function but increased medication requirements (29% on three or more medications) and health care utilization. Cluster 3 (n = 59) is a unique group of mostly older obese women with late-onset nonatopic asthma, moderate reductions in FEV1, and frequent oral corticosteroid use to manage exacerbations. Subjects in Clusters 4 (n = 120) and 5 (n = 116) have severe airflow obstruction with bronchodilator responsiveness but differ in to their ability to attain normal lung function, age of asthma onset, atopic status, and use of oral corticosteroids. Conclusions: Five distinct clinical phenotypes of asthma have been identified using unsupervised hierarchical cluster analysis. All clusters contain subjects who meet the American Thoracic Society definition of severe asthma, which supports clinical heterogeneity in asthma and the need for new approaches for the classification of disease severity in asthma. PMID:19892860

  2. T cell genetic background determines default T helper phenotype development in vitro

    PubMed Central

    1995-01-01

    A host's ability to resist certain pathogens such as Leishmania major can depend upon the phenotype of T helper (Th) subset that develops. Different murine genetic backgrounds are known to significantly alter the direction of Th subset development, although the cellular basis of this influence is poorly understood. To examine the basis of this effect we used an in vitro alpha/beta-T cell receptor (TCR) transgenic system for analysis of Th phenotype development. To control for TCR usage, we derived the DO11.10 alpha/beta-TCR transgene in several genetic backgrounds. Our findings suggest that the effects of genetic background on Th phenotype development reside within the T cell, and not the antigen-presenting cell compartment. Transgenic T cells from both the B10.D2 and BALB/c backgrounds showed development toward either the Th1 or Th2 phenotype under the strong directing influence of interleukin (IL) 12 and IL4, respectively. However, when T cells were activated in vitro under neutral conditions in which exogenous cytokines were not added, B10.D2-derived T cells acquired a significantly stronger Th1 phenotype than T cells from the BALB/c background, correspondent with in vivo Th responses to Leishmania in these strains. Importantly, these cytokine differences resulted in distinct functional properties, because B10.D2- but not BALB/c-derived T cells could induce macrophage production of nitric oxide, an important antimicrobial factor. Thus, the genetically determined default Th phenotype development observed in vitro may correspond to in vivo Th subset responses for pathogens such as Leishmania which do not initiate strong Th phenotype-directing signals. PMID:7836924

  3. Deletion of Dystrophin In-Frame Exon 5 Leads to a Severe Phenotype: Guidance for Exon Skipping Strategies

    PubMed Central

    Toh, Zhi Yon Charles; Thandar Aung-Htut, May; Pinniger, Gavin; Adams, Abbie M.; Krishnaswarmy, Sudarsan; Wong, Brenda L.; Fletcher, Sue; Wilton, Steve D.

    2016-01-01

    Duchenne and Becker muscular dystrophy severity depends upon the nature and location of the DMD gene lesion and generally correlates with the dystrophin open reading frame. However, there are striking exceptions where an in-frame genomic deletion leads to severe pathology or protein-truncating mutations (nonsense or frame-shifting indels) manifest as mild disease. Exceptions to the dystrophin reading frame rule are usually resolved after molecular diagnosis on muscle RNA. We report a moderate/severe Becker muscular dystrophy patient with an in-frame genomic deletion of DMD exon 5. This mutation has been reported by others as resulting in Duchenne or Intermediate muscular dystrophy, and the loss of this in-frame exon in one patient led to multiple splicing events, including omission of exon 6, that disrupts the open reading frame and is consistent with a severe phenotype. The patient described has a deletion of dystrophin exon 5 that does not compromise recognition of exon 6, and although the deletion does not disrupt the reading frame, his clinical presentation is more severe than would be expected for classical Becker muscular dystrophy. We suggest that the dystrophin isoform lacking the actin-binding sequence encoded by exon 5 is compromised, reflected by the phenotype resulting from induction of this dystrophin isoform in mouse muscle in vivo. Hence, exon skipping to address DMD-causing mutations within DMD exon 5 may not yield an isoform that confers marked clinical benefit. Additional studies will be required to determine whether multi-exon skipping strategies could yield more functional dystrophin isoforms, since some BMD patients with larger in-frame deletions in this region have been reported with mild phenotypes. PMID:26745801

  4. Deletion of Dystrophin In-Frame Exon 5 Leads to a Severe Phenotype: Guidance for Exon Skipping Strategies.

    PubMed

    Toh, Zhi Yon Charles; Thandar Aung-Htut, May; Pinniger, Gavin; Adams, Abbie M; Krishnaswarmy, Sudarsan; Wong, Brenda L; Fletcher, Sue; Wilton, Steve D

    2016-01-01

    Duchenne and Becker muscular dystrophy severity depends upon the nature and location of the DMD gene lesion and generally correlates with the dystrophin open reading frame. However, there are striking exceptions where an in-frame genomic deletion leads to severe pathology or protein-truncating mutations (nonsense or frame-shifting indels) manifest as mild disease. Exceptions to the dystrophin reading frame rule are usually resolved after molecular diagnosis on muscle RNA. We report a moderate/severe Becker muscular dystrophy patient with an in-frame genomic deletion of DMD exon 5. This mutation has been reported by others as resulting in Duchenne or Intermediate muscular dystrophy, and the loss of this in-frame exon in one patient led to multiple splicing events, including omission of exon 6, that disrupts the open reading frame and is consistent with a severe phenotype. The patient described has a deletion of dystrophin exon 5 that does not compromise recognition of exon 6, and although the deletion does not disrupt the reading frame, his clinical presentation is more severe than would be expected for classical Becker muscular dystrophy. We suggest that the dystrophin isoform lacking the actin-binding sequence encoded by exon 5 is compromised, reflected by the phenotype resulting from induction of this dystrophin isoform in mouse muscle in vivo. Hence, exon skipping to address DMD-causing mutations within DMD exon 5 may not yield an isoform that confers marked clinical benefit. Additional studies will be required to determine whether multi-exon skipping strategies could yield more functional dystrophin isoforms, since some BMD patients with larger in-frame deletions in this region have been reported with mild phenotypes. PMID:26745801

  5. Combined influences of Gm and HLA phenotypes upon multiple sclerosis susceptibility and severity.

    PubMed Central

    Salier, J P; Sesboüé, R; Martin-Mondière, C; Daveau, M; Cesaro, P; Cavelier, B; Coquerel, A; Legrand, L; Goust, J M; Degos, J D

    1986-01-01

    In some Caucasian populations, multiple sclerosis (MS) susceptibility has been independently related to given alleles of HLA or Gm systems that respectively code for major histocompatibility complex class I and II antigens or immunoglobulin G heavy chains. Whether given combinations of alleles at both series of loci simultaneously influence MS susceptibility and/or severity was investigated by comparing 147 French MS patients and 226 geographically-matched healthy controls. The G2m(-23)/HLA-B35 phenotype and G1m(-1)/HLA-B7(-)/HLA-DR2 phenotype were respectively associated with significant protection against (relative risk = 0.05) and susceptibility to (relative risk = 4.3) MS. When considering MS severity, the presence of HLA-B7 antigen correlated with a more severe disease in Gm1/Gm3 heterozygous patients, but not in Gm3/Gm3 homozygous patients. Conversely, an HLA-B12-associated milder disease was restricted to Gm3/Gm3 homozygotes. These results demonstrate the combined influence on MS of genetic loci that are unlinked but immune response-associated. Combined Gm and HLA typing is very likely able to serve as a prognostic indicator in this disease. PMID:3461005

  6. Combined influences of Gm and HLA phenotypes upon multiple sclerosis susceptibility and severity.

    PubMed

    Salier, J P; Sesboüé, R; Martin-Mondière, C; Daveau, M; Cesaro, P; Cavelier, B; Coquerel, A; Legrand, L; Goust, J M; Degos, J D

    1986-08-01

    In some Caucasian populations, multiple sclerosis (MS) susceptibility has been independently related to given alleles of HLA or Gm systems that respectively code for major histocompatibility complex class I and II antigens or immunoglobulin G heavy chains. Whether given combinations of alleles at both series of loci simultaneously influence MS susceptibility and/or severity was investigated by comparing 147 French MS patients and 226 geographically-matched healthy controls. The G2m(-23)/HLA-B35 phenotype and G1m(-1)/HLA-B7(-)/HLA-DR2 phenotype were respectively associated with significant protection against (relative risk = 0.05) and susceptibility to (relative risk = 4.3) MS. When considering MS severity, the presence of HLA-B7 antigen correlated with a more severe disease in Gm1/Gm3 heterozygous patients, but not in Gm3/Gm3 homozygous patients. Conversely, an HLA-B12-associated milder disease was restricted to Gm3/Gm3 homozygotes. These results demonstrate the combined influence on MS of genetic loci that are unlinked but immune response-associated. Combined Gm and HLA typing is very likely able to serve as a prognostic indicator in this disease. PMID:3461005

  7. Microvesicle phenotypes are associated with transfusion requirements and mortality in subjects with severe injuries

    PubMed Central

    Matijevic, Nena; Wang, Yao-Wei W.; Holcomb, John B.; Kozar, Rosemary; Cardenas, Jessica C.; Wade, Charles E.

    2015-01-01

    Background Severe injury often results in substantial bleeding and mortality. Injury provokes cellular activation and release of extracellular vesicles. Circulating microvesicles (MVs) are predominantly platelet-derived and highly procoagulant. They support hemostasis and vascular function. The roles of MVs in survival after severe injury are largely unknown. We hypothesized that altered MV phenotypes would be associated with transfusion requirements and poor outcomes. Methods This single-centre study was approved by the Institutional Review Board. The study cohort consisted of patients with major trauma requiring blood product transfusion and 26 healthy controls. Plasma samples for MVs were collected upon admission to the emergency department (n=169) and post-resuscitation (n=42), and analysed by flow cytometry for MV counts and cellular origin: platelet (PMV), erythrocyte (RMV), leukocyte (LMV), endothelial (EMV), tissue factor (TFMV), and annexin V (AVMV). Twenty-four hour mortality is the outcome measurement used to classify survivors versus non-survivors. Data were compared over time and analysed with demographic and clinical data. Results The median age was 34 (IQR 23, 51), 72% were male, Injury Severity Score was 29 (IQR 19, 36), and 24 h mortality was 13%. MV levels and phenotypes differed between patients and controls. Elevated admission EMVs were found both in survivors (409/µL) and non-survivors (393/µL) compared to controls (23/µL, p<0.001) and persisted over time. Admission levels of PMV, AVMV, RMV, and TFMV were significantly lower in patients who died compared to survivors, but were not independently associated with the 24 h mortality rate. Patients with low MV levels at admission received the most blood products within the first 24 h. AVMV and PMV levels either increased over time or stabilized in survivors but decreased in non-survivors, resulting in significantly lower levels at intensive care unit admission in non-survivors (1,048 vs. 1

  8. The molecular basis of variable phenotypic severity among common missense mutations causing Rett syndrome.

    PubMed

    Brown, Kyla; Selfridge, Jim; Lagger, Sabine; Connelly, John; De Sousa, Dina; Kerr, Alastair; Webb, Shaun; Guy, Jacky; Merusi, Cara; Koerner, Martha V; Bird, Adrian

    2016-02-01

    Rett syndrome is caused by mutations in the X-linked MECP2 gene, which encodes a chromosomal protein that binds to methylated DNA. Mouse models mirror the human disorder and therefore allow investigation of phenotypes at a molecular level. We describe an Mecp2 allelic series representing the three most common missense Rett syndrome (RTT) mutations, including first reports of Mecp2[R133C] and Mecp2[T158M] knock-in mice, in addition to Mecp2[R306C] mutant mice. Together these three alleles comprise ∼25% of all RTT mutations in humans, but they vary significantly in average severity. This spectrum is mimicked in the mouse models; R133C being least severe, T158M most severe and R306C of intermediate severity. Both R133C and T158M mutations cause compound phenotypes at the molecular level, combining compromised DNA binding with reduced stability, the destabilizing effect of T158M being more severe. Our findings contradict the hypothesis that the R133C mutation exclusively abolishes binding to hydroxymethylated DNA, as interactions with DNA containing methyl-CG, methyl-CA and hydroxymethyl-CA are all reduced in vivo. We find that MeCP2[T158M] is significantly less stable than MeCP2[R133C], which may account for the divergent clinical impact of the mutations. Overall, this allelic series recapitulates human RTT severity, reveals compound molecular aetiologies and provides a valuable resource in the search for personalized therapeutic interventions. PMID:26647311

  9. Severe phenotypes in a Charcot-Marie-Tooth 1A patient with PMP22 triplication.

    PubMed

    Kim, Sung Min; Lee, Jinho; Yoon, Bo Ram; Kim, Ye Jin; Choi, Byung-Ok; Chung, Ki Wha

    2015-02-01

    Charcot-Marie-Tooth disease (CMT) is a genetically and clinically heterogeneous hereditary motor and sensory neuropathy signified by a distal symmetric polyneuropathy. The most frequent subtype is type 1A (CMT1A) caused by duplication in chromosome 17p12 that includes PMP22. This study reports a woman with a family history of CMT1A due to PMP22 duplication. However, she presented with a more severe phenotype than her sibling or ancestors and was found to have a PMP22 triplication instead of the duplication. This was caused by de novo mutation on her affected mother's duplication chromosome. Her lower limb magnetic resonance imaging revealed severe diffused atrophy and fatty replacement. However, her affected sister with typical PMP22 duplication showed almost intact lower limb. Triplication patient's median motor nerve conduction velocity was far lower compared with her sister. Her onset age was faster (8 years) than her sister (42 years). CMT1A triplication might be generated by a female-specific chromosomal rearrangement mechanism that is different from the frequent paternal-originated CMT1A duplication. It also suggests that the wide phenotypic variation of CMT1A might be partly caused by unstable genomic rearrangement, including PMP22 triplication. PMID:25500726

  10. Osteogenesis imperfecta caused by PPIB mutation with severe phenotype and congenital hearing loss

    PubMed Central

    Rush, Eric T.; Caldwell, Kathleen S.; Kreikemeier, Rose M.; Lutz, Richard E.; Esposito, Paul W.

    2014-01-01

    Osteogenesis imperfecta (OI) is an inherited disorder of connective tissue typically caused by defects in either COL1A1 or COL1A2. A number of other genes causative of this disorder have been found, including PPIB, which forms one subunit of the prolyl 3-hydroxylase enzyme complex. Patients with homozygous or compound heterozygous mutations in this gene have OI with a trend toward lethal or severe phenotype. We present a Native American female with prenatal diagnosis of OI. Long bones were shortened with significant rhizomelia. At birth, fractures were present in ribs, humerii, and femurs. She had significant respiratory disease at birth, and required oxygen throughout her life. She also had recurrent pneumonias, one of which ultimately caused her death at age 16 mo. She also had significant bilateral sensorineural hearing loss. Molecular testing showed that the patient was homozygous for a single nucleotide substitution in PPIB (c. 136-2A>G). Patients with OI caused by PPIB mutations have had variable disease, but with majority of either with perinatal lethality or progressively deforming severe disease. Patients with OI due to PPIB mutation have shown some differences in phenotype. There appears to be a trend toward rhizomelic shortening and less severe bowing of the extremities, as compared to patients with comparably severe OI caused by COL1A1 or COL1A2 mutation. Congenital hearing loss may be an inconsistent feature of this condition, or may have co-occurred in our patient for unrelated reasons. Still, patients with OI caused by PPIB mutation should have appropriate early and regular management of their hearing.

  11. Physiological determinants and impacts of the adipocyte phenotype.

    PubMed

    Tchernof, A; Richard, D

    2015-08-01

    The properties of adipose tissues accumulating in various compartments and ectopic sites around the body represent critical determinants of the relationship between obesity and metabolic disease. The increasingly recognized plasticity of the adipose cell phenotype led to many articles on the cellular characteristics and origins on brown, white and also of 'beige' or 'brite' adipocytes in recent years. This overview is a summary of manuscripts that were prepared by speakers at the 16th International Symposium of the Laval University Research Chair in Obesity. The data reviewed herein suggest that brown adipose tissue-inducing therapies may also modulate skeletal status through their effects on bone morphology and structure. Moreover, recently identified beige-like properties of epicardial fat in humans could eventually be considered for the management of coronary heart disease in humans. The regulation of brown adipose tissue activation through sympathetic nervous system innervation or non-sympathetic activators is also a complex phenomenon that needs further investigation. Scientific work aimed at better understanding the characteristics and regulation of metabolic homeostasis in each adipose compartment is an important aspect of our progression toward preventive or even curative approaches for obesity. PMID:27152170

  12. COPD phenotypes on computed tomography and its correlation with selected lung function variables in severe patients

    PubMed Central

    da Silva, Silvia Maria Doria; Paschoal, Ilma Aparecida; De Capitani, Eduardo Mello; Moreira, Marcos Mello; Palhares, Luciana Campanatti; Pereira, Mônica Corso

    2016-01-01

    Background Computed tomography (CT) phenotypic characterization helps in understanding the clinical diversity of chronic obstructive pulmonary disease (COPD) patients, but its clinical relevance and its relationship with functional features are not clarified. Volumetric capnography (VC) uses the principle of gas washout and analyzes the pattern of CO2 elimination as a function of expired volume. The main variables analyzed were end-tidal concentration of carbon dioxide (ETCO2), Slope of phase 2 (Slp2), and Slope of phase 3 (Slp3) of capnogram, the curve which represents the total amount of CO2 eliminated by the lungs during each breath. Objective To investigate, in a group of patients with severe COPD, if the phenotypic analysis by CT could identify different subsets of patients, and if there was an association of CT findings and functional variables. Subjects and methods Sixty-five patients with COPD Gold III–IV were admitted for clinical evaluation, high-resolution CT, and functional evaluation (spirometry, 6-minute walk test [6MWT], and VC). The presence and profusion of tomography findings were evaluated, and later, the patients were identified as having emphysema (EMP) or airway disease (AWD) phenotype. EMP and AWD groups were compared; tomography findings scores were evaluated versus spirometric, 6MWT, and VC variables. Results Bronchiectasis was found in 33.8% and peribronchial thickening in 69.2% of the 65 patients. Structural findings of airways had no significant correlation with spirometric variables. Air trapping and EMP were strongly correlated with VC variables, but in opposite directions. There was some overlap between the EMP and AWD groups, but EMP patients had signicantly lower body mass index, worse obstruction, and shorter walked distance on 6MWT. Concerning VC, EMP patients had signicantly lower ETCO2, Slp2 and Slp3. Increases in Slp3 characterize heterogeneous involvement of the distal air spaces, as in AWD. Conclusion Visual assessment and

  13. A severe phenotype of Gitelman syndrome with increased prostaglandin excretion and favorable response to indomethacin

    PubMed Central

    Larkins, Nicholas; Wallis, Mathew; McGillivray, Barbara; Mammen, Cherry

    2014-01-01

    Our understanding of Gitelman syndrome (GS) and Bartter syndrome has continued to evolve with the use of genetic testing to more precisely define the tubular defects responsible. GS is caused by mutations in the SLC12A3 gene encoding the Na+–Cl− co-transporter of the distal convoluted tubule (NCCT) and tends to be associated with a milder salt-losing phenotype. We describe two female siblings presenting in infancy with a severe salt-losing tubulopathy and failure to thrive due to compound heterozygous mutations in the SLC12A3 gene encoding the NCCT. Both children were treated with indomethacin resulting in improved linear growth and polyuria. Some atypical biochemical findings in our cases are discussed including raised urinary prostaglandin (PGE2) excretion that normalized with intravenous fluid repletion. PMID:25852896

  14. Adult nephron-specific MR-deficient mice develop a severe renal PHA-1 phenotype.

    PubMed

    Canonica, Jérémie; Sergi, Chloé; Maillard, Marc; Klusonova, Petra; Odermatt, Alex; Koesters, Robert; Loffing-Cueni, Dominique; Loffing, Johannes; Rossier, Bernard; Frateschi, Simona; Hummler, Edith

    2016-05-01

    Aldosterone is the main mineralocorticoid hormone controlling sodium balance, fluid homeostasis, and blood pressure by regulating sodium reabsorption in the aldosterone-sensitive distal nephron (ASDN). Germline loss-of-function mutations of the mineralocorticoid receptor (MR) in humans and in mice lead to the "renal" form of type 1 pseudohypoaldosteronism (PHA-1), a case of aldosterone resistance characterized by salt wasting, dehydration, failure to thrive, hyperkalemia, and metabolic acidosis. To investigate the importance of MR in adult epithelial cells, we generated nephron-specific MR knockout mice (MR(Pax8/LC1)) using a doxycycline-inducible system. Under standard diet, MR(Pax8/LC1) mice exhibit inability to gain weight and significant weight loss compared to control mice. Interestingly, despite failure to thrive, MR(Pax8/LC1) mice survive but develop a severe PHA-1 phenotype with higher urinary Na(+) levels, decreased plasma Na(+), hyperkalemia, and higher levels of plasma aldosterone. This phenotype further worsens and becomes lethal under a sodium-deficient diet. Na(+)/Cl(-) co-transporter (NCC) protein expression and its phosphorylated form are downregulated in the MR(Pax8/LC1) knockouts, as well as the αENaC protein expression level, whereas the expression of glucocorticoid receptor (GR) is increased. A diet rich in Na(+) and low in K(+) does not restore plasma aldosterone to control levels but is sufficient to restore body weight, plasma, and urinary electrolytes. In conclusion, MR deletion along the nephron fully recapitulates the features of severe human PHA-1. ENaC protein expression is dependent on MR activity. Suppression of NCC under hyperkalemia predominates in a hypovolemic state. PMID:26762397

  15. Expression of Caytaxin Protein in Cayman Ataxia Mouse Models Correlates with Phenotype Severity

    PubMed Central

    Sikora, Kristine M.; Nosavanh, LaGina M.; Kantheti, Prameela; Burmeister, Margit; Hortsch, Michael

    2012-01-01

    Caytaxin is a highly-conserved protein, which is encoded by the Atcay/ATCAY gene. Mutations in Atcay/ATCAY have been identified as causative of cerebellar disorders such as the rare hereditary disease Cayman ataxia in humans, generalized dystonia in the dystonic (dt) rat, and marked motor defects in three ataxic mouse lines. While several lines of evidence suggest that Caytaxin plays a critical role in maintaining nervous system processes, the physiological function of Caytaxin has not been fully characterized. In the study presented here, we generated novel specific monoclonal antibodies against full-length Caytaxin to examine endogenous Caytaxin expression in wild type and Atcay mutant mouse lines. Caytaxin protein is absent from brain tissues in the two severely ataxic Atcayjit (jittery) and Atcayswd (sidewinder) mutant lines, and markedly decreased in the mildly ataxic/dystonic Atcayji-hes (hesitant) line, indicating a correlation between Caytaxin expression and disease severity. As the expression of wild type human Caytaxin in mutant sidewinder and jittery mice rescues the ataxic phenotype, Caytaxin’s physiological function appears to be conserved between the human and mouse orthologs. Across multiple species and in several neuronal cell lines Caytaxin is expressed as several protein isoforms, the two largest of which are caused by the usage of conserved methionine translation start sites. The work described in this manuscript presents an initial characterization of the Caytaxin protein and its expression in wild type and several mutant mouse models. Utilizing these animal models of human Cayman Ataxia will now allow an in-depth analysis to elucidate Caytaxin’s role in maintaining normal neuronal function. PMID:23226316

  16. Successful Phenotype Improvement following Gene Therapy for Severe Hemophilia A in Privately Owned Dogs

    PubMed Central

    Callan, Mary Beth; Haskins, Mark E.; Wang, Ping; Zhou, Shangzhen; High, Katherine A.; Arruda, Valder R.

    2016-01-01

    Severe hemophilia A (HA) is an inherited bleeding disorder characterized by <1% of residual factor VIII (FVIII) clotting activity. The disease affects several mammals including dogs, and, like humans, is associated with high morbidity and mortality. In gene therapy using adeno-associated viral (AAV) vectors, the canine model has been one of the best predictors of the therapeutic dose tested in clinical trials for hemophilia B (factor IX deficiency) and other genetic diseases, such as congenital blindness. Here we report our experience with liver gene therapy with AAV-FVIII in two outbred, privately owned dogs with severe HA that resulted in sustained expression of 1–2% of normal FVIII levels and prevented 90% of expected bleeding episodes. A Thr62Met mutation in the F8 gene was identified in one dog. These data recapitulate the improvement of the disease phenotype in research animals, and in humans, with AAV liver gene therapy for hemophilia B. Our experience is a novel example of the benefits of a relevant preclinical canine model to facilitate both translational studies in humans and improved welfare of privately owned dogs. PMID:27011017

  17. Successful Phenotype Improvement following Gene Therapy for Severe Hemophilia A in Privately Owned Dogs.

    PubMed

    Callan, Mary Beth; Haskins, Mark E; Wang, Ping; Zhou, Shangzhen; High, Katherine A; Arruda, Valder R

    2016-01-01

    Severe hemophilia A (HA) is an inherited bleeding disorder characterized by <1% of residual factor VIII (FVIII) clotting activity. The disease affects several mammals including dogs, and, like humans, is associated with high morbidity and mortality. In gene therapy using adeno-associated viral (AAV) vectors, the canine model has been one of the best predictors of the therapeutic dose tested in clinical trials for hemophilia B (factor IX deficiency) and other genetic diseases, such as congenital blindness. Here we report our experience with liver gene therapy with AAV-FVIII in two outbred, privately owned dogs with severe HA that resulted in sustained expression of 1-2% of normal FVIII levels and prevented 90% of expected bleeding episodes. A Thr62Met mutation in the F8 gene was identified in one dog. These data recapitulate the improvement of the disease phenotype in research animals, and in humans, with AAV liver gene therapy for hemophilia B. Our experience is a novel example of the benefits of a relevant preclinical canine model to facilitate both translational studies in humans and improved welfare of privately owned dogs. PMID:27011017

  18. Molecular modeling indicates distinct classes of missense variants with mild and severe XLRS phenotypes

    PubMed Central

    Sergeev, Yuri V.; Vitale, Susan; Sieving, Paul A.; Vincent, Ajoy; Robson, Anthony G.; Moore, Anthony T.; Webster, Andrew R.; Holder, Graham E.

    2013-01-01

    X-linked retinoschisis (XLRS) is a vitreo-retinal degeneration caused by mutations in the RS1 gene which encodes the protein retinoschisin (RS1), required for the structural and functional integrity of the retina. Data are presented from a group of 38 XLRS patients from Moorfields Eye Hospital (London, UK) who had one of 18 missense mutations in RS1. Patients were grouped based on mutation severity predicted by molecular modeling: mild (class I), moderate (intermediate) and severe (class II). Most patients had an electronegative scotopic bright flash electroretinogram  (ERG) (reduced b/a-wave ratio) in keeping with predominant inner retinal dysfunction. An association between the type of structural RS1 alterations and the severity of b/a-wave reduction was found in all but the oldest group of patients, significant in patients aged 15–30 years. Severe RS1 missense changes were associated with a lower ERG b/a ratio than were mild changes, suggesting that the extent of inner retinal dysfunction is influenced by the effect of the mutations on protein structure. The majority of class I mutations showed no changes involving cysteine residues. Class II mutations caused severe perturbations due to the removal or insertion of cysteine residues or due to changes in the hydrophobic core. The ERG b/a ratio in intermediate cases was abnormal but showed significant variability, possibly related to the role of proline or arginine residues. We also conducted a second study, using a completely independent cohort, to indicate a genotype–ERG phenotype correlation. PMID:23847049

  19. Can genotype determine the sports phenotype? A paradigm shift in sports medicine.

    PubMed

    Ghosh, Amit; Mahajan, Preetam B

    2016-06-01

    In last two decades, there has been an evolution in sports medicine. Several researchers have worked on different domains of sports medicine, like strength, endurance, sports injury, and psychology. Besides this, several groups have explored the changes at cellular and molecular levels during exercise, which has led to the development of the new domain in sports science known as genetic medicine. Genetic medicine deals with the genotypic basis of sports phenotype. In this article, we try to provide an up-to-date review on genetic determinants of sports performance, which will be like a journey from the nostalgic past towards the traditional present and the romantic future of sports medicine. Endurance and power performance are two important domains of athletes. They vary in individuals, even among trained athletes. Researches indicate that the genetic makeup of sportsmen play a vital role in their performance. Several genetic factors are reported to be responsible for endurance, power, susceptibility to injury, and even psychology of the individual. Besides this, proper training, nutrition, and environment are also important in shaping their potential. The aim of this discussion is to understand the influence of the environment and the genetic makeup on the performance of the athletes. There is sufficient evidence to suggest that genotype determines the sports phenotype in an athlete. Choosing the right sports activity based on genetic endowment is the key for achieving excellence in sports. PMID:26812785

  20. Characterizing the hoarding phenotype in individuals with OCD: associations with comorbidity, severity and gender.

    PubMed

    Wheaton, Michael; Timpano, Kiara R; Lasalle-Ricci, V Holland; Murphy, Dennis

    2008-01-01

    Hoarding frequently occurs in obsessive-compulsive disorder (OCD), and some evidence suggests that it constitutes a distinct OCD subtype, with genetic contributions. This study investigated differences between OCD patients with and without hoarding symptoms. Of the 473 OCD patients studied, 24% were classified as hoarders according to combined interviewer and self-ratings, which were validated with the Savings Inventory-Revised in a subsample. Hoarders suffered from significantly more severe OCD symptoms, (especially compulsions) and had greater impairment and dysphoria. Hoarders also had more comorbid psychiatric disorders. Further study revealed that many of these differences were attributable to the female subjects: Compared to female non-hoarders, female hoarders were more likely to suffer from bipolar I, substance abuse, panic disorder, binge-eating disorder, and had greater OCD severity. Male hoarders had an increased prevalence of social phobia compared to non-hoarding males. These results suggest that there are gender-specific differences in the hoarding sub-phenotype of OCD. PMID:17339096

  1. Power Analysis and Sample Size Determination in Metabolic Phenotyping.

    PubMed

    Blaise, Benjamin J; Correia, Gonçalo; Tin, Adrienne; Young, J Hunter; Vergnaud, Anne-Claire; Lewis, Matthew; Pearce, Jake T M; Elliott, Paul; Nicholson, Jeremy K; Holmes, Elaine; Ebbels, Timothy M D

    2016-05-17

    Estimation of statistical power and sample size is a key aspect of experimental design. However, in metabolic phenotyping, there is currently no accepted approach for these tasks, in large part due to the unknown nature of the expected effect. In such hypothesis free science, neither the number or class of important analytes nor the effect size are known a priori. We introduce a new approach, based on multivariate simulation, which deals effectively with the highly correlated structure and high-dimensionality of metabolic phenotyping data. First, a large data set is simulated based on the characteristics of a pilot study investigating a given biomedical issue. An effect of a given size, corresponding either to a discrete (classification) or continuous (regression) outcome is then added. Different sample sizes are modeled by randomly selecting data sets of various sizes from the simulated data. We investigate different methods for effect detection, including univariate and multivariate techniques. Our framework allows us to investigate the complex relationship between sample size, power, and effect size for real multivariate data sets. For instance, we demonstrate for an example pilot data set that certain features achieve a power of 0.8 for a sample size of 20 samples or that a cross-validated predictivity QY(2) of 0.8 is reached with an effect size of 0.2 and 200 samples. We exemplify the approach for both nuclear magnetic resonance and liquid chromatography-mass spectrometry data from humans and the model organism C. elegans. PMID:27116637

  2. Concordance between two phenotypic assays and ultradeep pyrosequencing for determining HIV-1 tropism.

    PubMed

    Saliou, Adrien; Delobel, Pierre; Dubois, Martine; Nicot, Florence; Raymond, Stéphanie; Calvez, Vincent; Masquelier, Bernard; Izopet, Jacques

    2011-06-01

    There have been few studies on the concordance between phenotypic assays for predicting human immunodeficiency virus type 1 (HIV-1) coreceptor usage. The sensitivity of ultradeep pyrosequencing combined with genotyping tools is similar to that of phenotypic assays for detecting minor CXCR4-using variants. We evaluated the agreement between two phenotypic assays, the Toulouse tropism test (TTT) and the Trofile assay, and ultradeep pyrosequencing for determining the tropism of HIV-1 quasispecies. The concordance between the TTT and Trofile assays was assessed for 181 samples successfully phenotyped by both assays. The TTT was 86% concordant with the standard Trofile assay and 91.7% with its enhanced-sensitivity version. The concordance between phenotypic characterization of HIV-1 tropism and ultradeep pyrosequencing genotypic prediction was further studied in selected samples. The HIV-1 tropism inferred from ultradeep pyrosequencing of 11 samples phenotyped as X4 and dualtropic and 12 phenotyped as R5-tropic agreed closely with the results of phenotyping. However, ultradeep pyrosequencing detected minor CXCR4-using variants in 3 of 12 samples phenotyped as R5-tropic. Ultradeep pyrosequencing also detected minor CXCR4-using variants that had been missed by direct sequencing in 6 of 9 samples phenotyped as X4-tropic but genotyped as R5-tropic by direct sequencing. Ultradeep pyrosequencing was 87% concordant with the Trofile and TTT phenotypic assays and was in the same range of sensitivity (0.4%) than these two phenotypic assays (0.3 to 0.5%) for detecting minor CXCR4-using variants. Ultradeep pyrosequencing provides a new way to improve the performance of genotypic prediction of HIV-1 tropism to match that of the phenotypic assays. PMID:21464245

  3. Concordance between Two Phenotypic Assays and Ultradeep Pyrosequencing for Determining HIV-1 Tropism▿†

    PubMed Central

    Saliou, Adrien; Delobel, Pierre; Dubois, Martine; Nicot, Florence; Raymond, Stéphanie; Calvez, Vincent; Masquelier, Bernard; Izopet, Jacques

    2011-01-01

    There have been few studies on the concordance between phenotypic assays for predicting human immunodeficiency virus type 1 (HIV-1) coreceptor usage. The sensitivity of ultradeep pyrosequencing combined with genotyping tools is similar to that of phenotypic assays for detecting minor CXCR4-using variants. We evaluated the agreement between two phenotypic assays, the Toulouse tropism test (TTT) and the Trofile assay, and ultradeep pyrosequencing for determining the tropism of HIV-1 quasispecies. The concordance between the TTT and Trofile assays was assessed for 181 samples successfully phenotyped by both assays. The TTT was 86% concordant with the standard Trofile assay and 91.7% with its enhanced-sensitivity version. The concordance between phenotypic characterization of HIV-1 tropism and ultradeep pyrosequencing genotypic prediction was further studied in selected samples. The HIV-1 tropism inferred from ultradeep pyrosequencing of 11 samples phenotyped as X4 and dualtropic and 12 phenotyped as R5-tropic agreed closely with the results of phenotyping. However, ultradeep pyrosequencing detected minor CXCR4-using variants in 3 of 12 samples phenotyped as R5-tropic. Ultradeep pyrosequencing also detected minor CXCR4-using variants that had been missed by direct sequencing in 6 of 9 samples phenotyped as X4-tropic but genotyped as R5-tropic by direct sequencing. Ultradeep pyrosequencing was 87% concordant with the Trofile and TTT phenotypic assays and was in the same range of sensitivity (0.4%) than these two phenotypic assays (0.3 to 0.5%) for detecting minor CXCR4-using variants. Ultradeep pyrosequencing provides a new way to improve the performance of genotypic prediction of HIV-1 tropism to match that of the phenotypic assays. PMID:21464245

  4. Severe ocular phenotypes in Rbp4-deficient mice in the C57BL/6 genetic background.

    PubMed

    Shen, Jingling; Shi, Dan; Suzuki, Tomohiro; Xia, Zunping; Zhang, Hanli; Araki, Kimi; Wakana, Shigeharu; Takeda, Naoki; Yamamura, Ken-Ichi; Jin, Shoude; Li, Zhenghua

    2016-06-01

    Retinol-binding protein 4 (RBP4) is a specific carrier for retinol in the blood. In hepatocytes, newly synthesized RBP4 associates with retinol and transthyretin and is secreted into the blood. The ternary transthyretin-RBP4-retinol complex transports retinol in the circulation and delivers it to target tissues. Rbp4-deficient mice in a mixed genetic background (129xC57BL/6J) have decreased sensitivity to light in the b-wave amplitude on electroretinogram. Sensitivity progressively improves and approaches that of wild-type mice at 24 weeks of age. In the present study, we produced Rbp4-deficient mice in the C57BL/6 genetic background. These mice displayed more severe phenotypes. They had decreased a- and b-wave amplitudes on electroretinograms. In accordance with these abnormalities, we found structural changes in these mice, such as loss of the peripheral choroid and photoreceptor layer in the peripheral retinas. In the central retinas, the distance between the inner limiting membrane and the outer plexiform layer was much shorter with fewer ganglion cells and fewer synapses in the inner plexiform layer. Furthermore, ocular developmental defects of retinal depigmentation, optic disc abnormality, and persistent hyaloid artery were also observed. All these abnormalities had not recovered even at 40 weeks of age. Our Rbp4-deficient mice accumulated retinol in the liver but it was undetectable in the serum, indicating an inverse relation between serum and liver retinol levels. Our results suggest that RBP4 is critical for the mobilization of retinol from hepatic storage pools, and that such mobilization is necessary for ocular development and visual function. PMID:26974396

  5. Biallelic Mutations in TMEM126B Cause Severe Complex I Deficiency with a Variable Clinical Phenotype.

    PubMed

    Alston, Charlotte L; Compton, Alison G; Formosa, Luke E; Strecker, Valentina; Oláhová, Monika; Haack, Tobias B; Smet, Joél; Stouffs, Katrien; Diakumis, Peter; Ciara, Elżbieta; Cassiman, David; Romain, Nadine; Yarham, John W; He, Langping; De Paepe, Boel; Vanlander, Arnaud V; Seneca, Sara; Feichtinger, René G; Płoski, Rafal; Rokicki, Dariusz; Pronicka, Ewa; Haller, Ronald G; Van Hove, Johan L K; Bahlo, Melanie; Mayr, Johannes A; Van Coster, Rudy; Prokisch, Holger; Wittig, Ilka; Ryan, Michael T; Thorburn, David R; Taylor, Robert W

    2016-07-01

    Complex I deficiency is the most common biochemical phenotype observed in individuals with mitochondrial disease. With 44 structural subunits and over 10 assembly factors, it is unsurprising that complex I deficiency is associated with clinical and genetic heterogeneity. Massively parallel sequencing (MPS) technologies including custom, targeted gene panels or unbiased whole-exome sequencing (WES) are hugely powerful in identifying the underlying genetic defect in a clinical diagnostic setting, yet many individuals remain without a genetic diagnosis. These individuals might harbor mutations in poorly understood or uncharacterized genes, and their diagnosis relies upon characterization of these orphan genes. Complexome profiling recently identified TMEM126B as a component of the mitochondrial complex I assembly complex alongside proteins ACAD9, ECSIT, NDUFAF1, and TIMMDC1. Here, we describe the clinical, biochemical, and molecular findings in six cases of mitochondrial disease from four unrelated families affected by biallelic (c.635G>T [p.Gly212Val] and/or c.401delA [p.Asn134Ilefs(∗)2]) TMEM126B variants. We provide functional evidence to support the pathogenicity of these TMEM126B variants, including evidence of founder effects for both variants, and establish defects within this gene as a cause of complex I deficiency in association with either pure myopathy in adulthood or, in one individual, a severe multisystem presentation (chronic renal failure and cardiomyopathy) in infancy. Functional experimentation including viral rescue and complexome profiling of subject cell lines has confirmed TMEM126B as the tenth complex I assembly factor associated with human disease and validates the importance of both genome-wide sequencing and proteomic approaches in characterizing disease-associated genes whose physiological roles have been previously undetermined. PMID:27374774

  6. Characterization of a “high” TNF-α phenotype in moderate-to-severe asthmatic children

    PubMed Central

    Brown, Sheena D.; Brown, Lou Ann; Stephenson, Susan; Dodds, Jennifer C.; Douglas, Shaneka L.; Qu, Hongyan; Fitzpatrick, Anne M.

    2015-01-01

    Summary Systemic TNF-α expression is increased in a subset of children with moderate-to-severe asthma despite aggressive corticosteroid treatment and is associated with poor asthma control. Phenotypic-directed TNF-α inhibition may be of benefit in some asthmatic children. PMID:25725987

  7. Phenotypic Diversity in Caucasian Adults with Moderate to Severe Class II Malocclusion

    PubMed Central

    Moreno Uribe, Lina M.; Howe, Sara C.; Kummet, Colleen; Vela, Kaci C.; Dawson, Deborah V.; Southard, Thomas E.

    2014-01-01

    INTRODUCTION Class II malocclusion affects about 15 % of the US population and is characterized by a convex profile and occlusion disharmonies. The specific etiological mechanisms resulting in the range of Class II dento-skeletal combinations observed is not yet understood. Most studies describing the class II phenotypic diversity have utilized moderate sample sizes or have focused on younger individuals that later in life may outgrow their class II discrepancies; such a focus may also preclude the visualization of adult class II features. The majority have utilized simple correlation methods resulting in phenotypes that may not be generalizable to different samples and thus may not be suitable for studies of malocclusion etiology. The purpose of this study is to address these knowledge gaps by capturing the maximum phenotypic variation present in a large Caucasian sample of class II individuals selected with strict eligibility criteria and rigorously standardized multivariate reduction analyses. METHODS Sixty-three lateral cephalometric variables were measured from pre-treatment records of 309 Class II Caucasian adults (82 males, 227 females; ages 16–60 years). Principal component analysis (PCA) and cluster analysis were used to generate comprehensive phenotypes in an effort to identify the most homogeneous groups of individuals reducing heterogeneity and improving the power of future malocclusion etiology studies. RESULTS PCA resulted in 7 principal components that accounted for 81% of the variation. The first three components represented variation on mandibular rotation, upper incisor angulation and mandibular length, respectively. The cluster analysis identified 5 distinct Class II phenotypes. CONCLUSIONS A comprehensive spectrum of Class II phenotypic definitions was obtained that could be generalized to other samples advancing our efforts to the identification of etiological factors underlying Class II malocclusion. PMID:24582022

  8. Phenotypic Diversity in Caucasian Adults with Moderate to Severe Class III Malocclusion

    PubMed Central

    Moreno Uribe, Lina M.; Vela, Kaci C.; Kummet, Colleen; Dawson, Deborah V.; Southard, Thomas E.

    2014-01-01

    INTRODUCTION Class III malocclusion is characterized by a composite of dento-skeletal patterns that lead to the forward positioning of the mandibular teeth in relation to the maxillary teeth and a concave profile. Environmental and genetic factors are associated with this condition, which affects 1% of the US population and imposes significant esthetic and functional burdens on affected individuals. The purpose of this study was to capture the phenotypic variation present in a large sample of white adults with Class III malocclusion by using multivariate reduction methods. METHODS Sixty-three lateral cephalometric variables were measured from pre-treatment records of 292 Class II Caucasian adults (126 males, 166 females; ages 16-57 years). Principal component analysis and cluster analysis were used to capture the phenotypic variation and identify the most homogeneous groups of individuals to reduce genetic heterogeneity. RESULTS Principal component analysis resulted in 6 principal components that accounted for 81.2% of the variation. The first three components represented variations in mandibular horizontal and vertical position, maxillary horizontal position, and mandibular incisor angulation, respectively. The cluster model identified 5 distinct subphenotypes of Class III malocclusion. CONCLUSIONS A spectrum of phenotypic definitions was obtained replicating results of previous studies and supporting the validity of these phenotypic measures in future research of genetic and environmental etiology of Class III malocclusion. PMID:23810043

  9. In silico analyses of missense mutations in coagulation factor VIII: identification of severity determinants of haemophilia A.

    PubMed

    Sengupta, M; Sarkar, D; Ganguly, K; Sengupta, D; Bhaskar, S; Ray, K

    2015-09-01

    Factor VIII (FVIII) mutations cause haemophilia A (HA), an X-linked recessive coagulation disorder. Over 1000 missense mutations in FVIII are known and they lead to variable clinical phenotypes (severe, moderate and mild). The exact molecular basis of this phenotypic heterogeneity by FVIII missense mutations is elusive to date. In this study, we aimed to identify the severity determinants that cause phenotypic heterogeneity of HA. We compiled and curated a data set of 766 missense mutations from the repertoire of missense mutations in FVIII. We analysed these mutations by computational programs (e.g. Swiss-PdbViewer) and different mutation analysis servers (e.g. SIFT, PROVEAN, CUPSAT, PolyPhen2, MutPred); and various sequence- and structure-based parameters were assessed for any significant distribution bias among different HA phenotypes. Our analyses suggest that 'mutations in evolutionary conserved residues', 'mutations in buried residues', mutation-induced 'steric clash' and 'surface electrostatic potential alteration' act as risk factors towards severe HA. We have developed a grading system for FVIII mutations combining the severity determinants, and the grading pattern correlates with HA phenotype. This study will help to correctly associate the HA phenotype with a mutation and aid early characterization of novel variants. PMID:25854144

  10. Intractable epileptic spasms in a patient with Pontocerebellar hypoplasia: Severe phenotype of type 2 or another subtype?

    PubMed Central

    Samanta, Debopam; Willis, Erin

    2016-01-01

    Introduction: Pontocerebellar hypoplasia (PCH) involves a diverse range of etiologies including a group of single gene disorders. Mutations in the tRNA splicing endonuclease complex (TSEN) 54 gene can be responsible for PCH type 2, 4 and 5. The more common and less severe PCH 2 phenotype is caused by homozygosity for the common missense mutation A307S, while the severe phenotype seen in type 4 and 5 is caused by compound heterozygosity of the A307S mutation along with a nonsense or splice site mutation. Report: We report a 4- month-old girl who presented with epileptic spasms that remained intractable to several antiepileptic medications. Magnetic Resonance Imaging (MRI) brain showed fairly severe hypoplasia with superimposed atrophy of the cerebellum and brainstem with prominent extra-axial fluid spaces. Extensive metabolic testing was negative. Commercial testing for PCH via TSEN54 gene revealed missense mutation of Ala307Ser. A novel sequence variant, designated c.17_40 del, was also found and was predictive of an in-frame deletion of eight amino acids. Follow-up over 2 years revealed intractable epileptic spasms, progressive microcephaly and development of prominent choreoathetosis. Conclusion: This case report describes a rare case of PCH with overlapping features of the less severe PCH2 and the more severe PCH4/5 phenotype. It also adds another new entity in the list of genetic conditions where West syndrome and pontocerebellar hypoplasia can be seen together, emphasizing the need for further investigations of the genotype-phenotype correlation of mutations in order to advance our understanding of the pathophysiologic mechanism in these rare conditions. PMID:27570394

  11. Genetic contributions to circadian activity rhythm and sleep pattern phenotypes in pedigrees segregating for severe bipolar disorder.

    PubMed

    Pagani, Lucia; St Clair, Patricia A; Teshiba, Terri M; Service, Susan K; Fears, Scott C; Araya, Carmen; Araya, Xinia; Bejarano, Julio; Ramirez, Margarita; Castrillón, Gabriel; Gomez-Makhinson, Juliana; Lopez, Maria C; Montoya, Gabriel; Montoya, Claudia P; Aldana, Ileana; Navarro, Linda; Freimer, Daniel G; Safaie, Brian; Keung, Lap-Woon; Greenspan, Kiefer; Chou, Katty; Escobar, Javier I; Ospina-Duque, Jorge; Kremeyer, Barbara; Ruiz-Linares, Andres; Cantor, Rita M; Lopez-Jaramillo, Carlos; Macaya, Gabriel; Molina, Julio; Reus, Victor I; Sabatti, Chiara; Bearden, Carrie E; Takahashi, Joseph S; Freimer, Nelson B

    2016-02-01

    Abnormalities in sleep and circadian rhythms are central features of bipolar disorder (BP), often persisting between episodes. We report here, to our knowledge, the first systematic analysis of circadian rhythm activity in pedigrees segregating severe BP (BP-I). By analyzing actigraphy data obtained from members of 26 Costa Rican and Colombian pedigrees [136 euthymic (i.e., interepisode) BP-I individuals and 422 non-BP-I relatives], we delineated 73 phenotypes, of which 49 demonstrated significant heritability and 13 showed significant trait-like association with BP-I. All BP-I-associated traits related to activity level, with BP-I individuals consistently demonstrating lower activity levels than their non-BP-I relatives. We analyzed all 49 heritable phenotypes using genetic linkage analysis, with special emphasis on phenotypes judged to have the strongest impact on the biology underlying BP. We identified a locus for interdaily stability of activity, at a threshold exceeding genome-wide significance, on chromosome 12pter, a region that also showed pleiotropic linkage to two additional activity phenotypes. PMID:26712028

  12. Genetic contributions to circadian activity rhythm and sleep pattern phenotypes in pedigrees segregating for severe bipolar disorder

    PubMed Central

    Pagani, Lucia; St. Clair, Patricia A.; Teshiba, Terri M.; Service, Susan K.; Fears, Scott C.; Araya, Carmen; Araya, Xinia; Bejarano, Julio; Ramirez, Margarita; Castrillón, Gabriel; Gomez-Makhinson, Juliana; Lopez, Maria C.; Montoya, Gabriel; Montoya, Claudia P.; Aldana, Ileana; Navarro, Linda; Freimer, Daniel G.; Safaie, Brian; Keung, Lap-Woon; Greenspan, Kiefer; Chou, Katty; Escobar, Javier I.; Ospina-Duque, Jorge; Kremeyer, Barbara; Ruiz-Linares, Andres; Cantor, Rita M.; Lopez-Jaramillo, Carlos; Macaya, Gabriel; Molina, Julio; Reus, Victor I.; Sabatti, Chiara; Bearden, Carrie E.; Takahashi, Joseph S.; Freimer, Nelson B.

    2016-01-01

    Abnormalities in sleep and circadian rhythms are central features of bipolar disorder (BP), often persisting between episodes. We report here, to our knowledge, the first systematic analysis of circadian rhythm activity in pedigrees segregating severe BP (BP-I). By analyzing actigraphy data obtained from members of 26 Costa Rican and Colombian pedigrees [136 euthymic (i.e., interepisode) BP-I individuals and 422 non–BP-I relatives], we delineated 73 phenotypes, of which 49 demonstrated significant heritability and 13 showed significant trait-like association with BP-I. All BP-I–associated traits related to activity level, with BP-I individuals consistently demonstrating lower activity levels than their non–BP-I relatives. We analyzed all 49 heritable phenotypes using genetic linkage analysis, with special emphasis on phenotypes judged to have the strongest impact on the biology underlying BP. We identified a locus for interdaily stability of activity, at a threshold exceeding genome-wide significance, on chromosome 12pter, a region that also showed pleiotropic linkage to two additional activity phenotypes. PMID:26712028

  13. The Splicing Efficiency of Activating HRAS Mutations Can Determine Costello Syndrome Phenotype and Frequency in Cancer.

    PubMed

    Hartung, Anne-Mette; Swensen, Jeff; Uriz, Inaki E; Lapin, Morten; Kristjansdottir, Karen; Petersen, Ulrika S S; Bang, Jeanne Mari V; Guerra, Barbara; Andersen, Henriette Skovgaard; Dobrowolski, Steven F; Carey, John C; Yu, Ping; Vaughn, Cecily; Calhoun, Amy; Larsen, Martin R; Dyrskjøt, Lars; Stevenson, David A; Andresen, Brage S

    2016-05-01

    Costello syndrome (CS) may be caused by activating mutations in codon 12/13 of the HRAS proto-oncogene. HRAS p.Gly12Val mutations have the highest transforming activity, are very frequent in cancers, but very rare in CS, where they are reported to cause a severe, early lethal, phenotype. We identified an unusual, new germline p.Gly12Val mutation, c.35_36GC>TG, in a 12-year-old boy with attenuated CS. Analysis of his HRAS cDNA showed high levels of exon 2 skipping. Using wild type and mutant HRAS minigenes, we confirmed that c.35_36GC>TG results in exon 2 skipping by simultaneously disrupting the function of a critical Exonic Splicing Enhancer (ESE) and creation of an Exonic Splicing Silencer (ESS). We show that this vulnerability of HRAS exon 2 is caused by a weak 3' splice site, which makes exon 2 inclusion dependent on binding of splicing stimulatory proteins, like SRSF2, to the critical ESE. Because the majority of cancer- and CS- causing mutations are located here, they affect splicing differently. Therefore, our results also demonstrate that the phenotype in CS and somatic cancers is not only determined by the different transforming potentials of mutant HRAS proteins, but also by the efficiency of exon 2 inclusion resulting from the different HRAS mutations. Finally, we show that a splice switching oligonucleotide (SSO) that blocks access to the critical ESE causes exon 2 skipping and halts proliferation of cancer cells. This unravels a potential for development of new anti-cancer therapies based on SSO-mediated HRAS exon 2 skipping. PMID:27195699

  14. The Splicing Efficiency of Activating HRAS Mutations Can Determine Costello Syndrome Phenotype and Frequency in Cancer

    PubMed Central

    Kristjansdottir, Karen; Petersen, Ulrika S. S.; Bang, Jeanne Mari V.; Guerra, Barbara; Andersen, Henriette Skovgaard; Dobrowolski, Steven F.; Carey, John C.; Yu, Ping; Calhoun, Amy; Larsen, Martin R.; Dyrskjøt, Lars; Stevenson, David A.; Andresen, Brage S.

    2016-01-01

    Costello syndrome (CS) may be caused by activating mutations in codon 12/13 of the HRAS proto-oncogene. HRAS p.Gly12Val mutations have the highest transforming activity, are very frequent in cancers, but very rare in CS, where they are reported to cause a severe, early lethal, phenotype. We identified an unusual, new germline p.Gly12Val mutation, c.35_36GC>TG, in a 12-year-old boy with attenuated CS. Analysis of his HRAS cDNA showed high levels of exon 2 skipping. Using wild type and mutant HRAS minigenes, we confirmed that c.35_36GC>TG results in exon 2 skipping by simultaneously disrupting the function of a critical Exonic Splicing Enhancer (ESE) and creation of an Exonic Splicing Silencer (ESS). We show that this vulnerability of HRAS exon 2 is caused by a weak 3’ splice site, which makes exon 2 inclusion dependent on binding of splicing stimulatory proteins, like SRSF2, to the critical ESE. Because the majority of cancer- and CS- causing mutations are located here, they affect splicing differently. Therefore, our results also demonstrate that the phenotype in CS and somatic cancers is not only determined by the different transforming potentials of mutant HRAS proteins, but also by the efficiency of exon 2 inclusion resulting from the different HRAS mutations. Finally, we show that a splice switching oligonucleotide (SSO) that blocks access to the critical ESE causes exon 2 skipping and halts proliferation of cancer cells. This unravels a potential for development of new anti-cancer therapies based on SSO-mediated HRAS exon 2 skipping. PMID:27195699

  15. Plant defense phenotypes determine the consequences of volatile emission for individuals and neighbors

    PubMed Central

    Schuman, Meredith C; Allmann, Silke; Baldwin, Ian T

    2015-01-01

    Plants are at the trophic base of terrestrial ecosystems, and the diversity of plant species in an ecosystem is a principle determinant of community structure. This may arise from diverse functional traits among species. In fact, genetic diversity within species can have similarly large effects. However, studies of intraspecific genetic diversity have used genotypes varying in several complex traits, obscuring the specific phenotypic variation responsible for community-level effects. Using lines of the wild tobacco Nicotiana attenuata genetically altered in specific well-characterized defense traits and planted into experimental populations in their native habitat, we investigated community-level effects of trait diversity in populations of otherwise isogenic plants. We conclude that the frequency of defense traits in a population can determine the outcomes of these traits for individuals. Furthermore, our results suggest that some ecosystem-level services afforded by genetically diverse plant populations could be recaptured in intensive monocultures engineered to be functionally diverse. DOI: http://dx.doi.org/10.7554/eLife.04490.001 PMID:25873033

  16. An enzyme linked immunosorbent assay (ELISA) for the determination of the human haptoglobin phenotype

    PubMed Central

    Levy, Nina S.; Vardi, Moshe; Blum, Shany; Miller-Lotan, Rachel; Afinbinder, Yefim; Cleary, Patricia A.; Paterson, Andrew D.; Bharaj, Bhupinder; Snell-Bergeon, Janet K.; Rewers, Marian J.; Lache, Orit; Levy, Andrew P.

    2013-01-01

    Background Haptoglobin (Hp) is an abundant serum protein which binds extracorpuscular hemoglobin (Hb). Two alleles exist in humans for the Hp gene, denoted 1 and 2. Diabetic individuals with the Hp 2-2 genotype are at increased risk of developing vascular complications including heart attack, stroke, and kidney disease. Recent evidence shows that treatment with vitamin E can reduce the risk of diabetic vascular complications by as much as 50% in Hp 2-2 individuals. We sought to develop a rapid and accurate test for Hp phenotype (which is 100% concordant with the three major Hp genotypes) to facilitate widespread diagnostic testing as well as prospective clinical trials. Methods A monoclonal antibody raised against human Hp was shown to distinguish between the three Hp phenotypes in an enzyme linked immunosorbent assay (ELISA). Hp phenotypes obtained in over 8000 patient samples using this ELISA method were compared with those obtained by polyacrylamide gel electrophoresis or the TaqMan PCR method. Results Our analysis showed that the sensitivity and specificity of the ELISA test for Hp 2-2 phenotype is 99.0% and 98.1%, respectively. The positive predictive value and the negative predictive value for Hp 2-2 phenotype is 97.5% and 99.3%, respectively. Similar results were obtained for Hp 2-1 and Hp 1-1 phenotypes. In addition, the ELISA was determined to be more sensitive and specific than the TaqMan method. Conclusions The Hp ELISA represents a user-friendly, rapid and highly accurate diagnostic tool for determining Hp phenotypes. This test will greatly facilitate the typing of thousands of samples in ongoing clinical studies. PMID:23492570

  17. Genetic and metabolic determinants of nutritional phenotype in an insect-bacterial symbiosis.

    PubMed

    MacDonald, S J; Thomas, G H; Douglas, A E

    2011-05-01

    The pervasive influence of resident microorganisms on the phenotype of their hosts is exemplified by the intracellular bacterium Buchnera aphidicola, which provides its aphid partner with essential amino acids (EAAs). We investigated variation in the dietary requirement for EAAs among four pea aphid (Acyrthosiphon pisum) clones. Buchnera-derived nitrogen contributed to the synthesis of all EAAs for which aphid clones required a dietary supply, and to none of the EAAs for which all four clones had no dietary requirement, suggesting that low total dietary nitrogen may select for reduced synthesis of certain EAAs in some aphid clones. The sequenced Buchnera genomes showed that the EAA nutritional phenotype (i.e. the profile of dietary EAAs required by the aphid) cannot be attributed to sequence variation of Buchnera genes coding EAA biosynthetic enzymes. Metabolic modelling by flux balance analysis demonstrated that EAA output from Buchnera can be determined precisely by the flux of host metabolic precursors to Buchnera. Specifically, the four EAA nutritional phenotypes could be reproduced by metabolic models with unique profiles of host inputs, dominated by variation in supply of aspartate, homocysteine and glutamate. This suggests that the nutritional phenotype of the symbiosis is determined principally by host metabolism and transporter genes that regulate nutrient supply to Buchnera. Intraspecific variation in the nutritional phenotype of symbioses is expected to mediate partitioning of plant resources among aphid genotypes, potentially promoting the genetic subdivision of aphid populations. In this way, microbial symbioses may play an important role in the evolutionary diversification of phytophagous insects. PMID:21392141

  18. COMPARISON OF SEVERAL TECHNIQUES FOR DETERMINING DRY DEPOSITION FLUX

    EPA Science Inventory

    Over the period from 1/22/81 through 5/4/82, measurements were conducted to permit comparison of several techniques for determining dry deposition flux of nitrates and sulfates. Direct flux estimates were made by using actual leaf surfaces and foliar wash and by exposing and wash...

  19. Properties of anaerobic fungi isolated from several habitats: complexity of phenotypes.

    PubMed

    Zelená, Viera; Birošová, Lucia; Olejníková, Petra; Polák, Martin; Lakatoš, Boris; Varečka, Ľudovít

    2016-01-01

    Isolates of anaerobic fungi from rumen, animal faeces and compost displayed morphological similarity with known anaerobic fungi. According to their ITS sequences, species were related to Neocallimastix and Piromyces. Rumen fungi tolerated exposure to an aerobic atmosphere for at least four days. Under anaerobic conditions, they could grow on both, defined or complex substrates. Growth in liquid media was monitored by the continuous measurement of metabolic gases (O2, CO2, H2, CO, H2S, CH4). Monitored metabolism was complex, showed that both CO2 and H2 were produced and subsequently consumed by yet unknown metabolic pathway(s). CO and H2S were evolved similarly, but not identically with the generation of CO2 and H2 suggesting their connection with energetic metabolism. Anaerobic fungi from snail faeces and compost produced concentrations of H2S, H2, CO near the lower limit of detection. The rumen isolates produced cellulases and xylanases with similar pH and temperature optima. Proteolytic enzymes were secreted as well. Activities of some enzymes of the main catabolic pathways were found in cell-free homogenates of mycelia. The results indicate the presence of the pentose cycle, the glyoxylate cycle and an incomplete citrate cycle in these fungi. Differences between isolates indicate phenotypic variability between anaerobic fungi. PMID:26612922

  20. Simultaneous Determination of Glass Transition Temperatures of Several Polymers

    PubMed Central

    He, Jiang; Liu, Wei; Huang, Yao-Xiong

    2016-01-01

    Aims A simple and easy optical method is proposed for the determination of glass transition temperature (Tg) of polymers. Methods & Results Tg was determined using the technique of microsphere imaging to monitor the variation of the refractive index of polymer microsphere as a function of temperature. It was demonstrated that the method can eliminate most thermal lag and has sensitivity about six fold higher than the conventional method in Tg determination. So the determined Tg is more accurate and varies less with cooling/heating rate than that obtained by conventional methods. The most attractive character of the method is that it can simultaneously determine the Tg of several polymers in a single experiment, so it can greatly save experimental time and heating energy. Conclusion The method is not only applicable for polymer microspheres, but also for the materials with arbitrary shapes. Therefore, it is expected to be broadly applied to different fundamental researches and practical applications of polymers. PMID:26985670

  1. Beyond the Central Dogma: Model-Based Learning of How Genes Determine Phenotypes

    ERIC Educational Resources Information Center

    Reinagel, Adam; Speth, Elena Bray

    2016-01-01

    In an introductory biology course, we implemented a learner-centered, model-based pedagogy that frequently engaged students in building conceptual models to explain how genes determine phenotypes. Model-building tasks were incorporated within case studies and aimed at eliciting students' understanding of 1) the origin of variation in a population…

  2. Differential secretion of the mutated protein is a major component affecting phenotypic severity in CRLF1-associated disorders

    PubMed Central

    Herholz, Jana; Meloni, Alessandra; Marongiu, Mara; Chiappe, Francesca; Deiana, Manila; Herrero, Carmen Roche; Zampino, Giuseppe; Hamamy, Hanan; Zalloum, Yusra; Waaler, Per Erik; Crisponi, Giangiorgio; Crisponi, Laura; Rutsch, Frank

    2011-01-01

    Crisponi syndrome (CS) and cold-induced sweating syndrome type 1 (CISS1) are disorders caused by mutations in CRLF1. The two syndromes share clinical characteristics, such as dysmorphic features, muscle contractions, scoliosis and cold-induced sweating, with CS patients showing a severe clinical course in infancy involving hyperthermia, associated with death in most cases in the first years of life. To evaluate a potential genotype/phenotype correlation and whether CS and CISS1 represent two allelic diseases or manifestations at different ages of the same disorder, we carried out a detailed clinical analysis of 19 patients carrying mutations in CRLF1. We studied the functional significance of the mutations found in CRLF1, providing evidence that phenotypic severity of the two disorders mainly depends on altered kinetics of secretion of the mutated CRLF1 protein. On the basis of these findings, we believe that the two syndromes, CS and CISS1, represent manifestations of the same disorder, with different degrees of severity. We suggest renaming the two genetic entities CS and CISS1 with the broader term of Sohar–Crisponi syndrome. PMID:21326283

  3. Cell-Envelope Remodeling as a Determinant of Phenotypic Antibacterial Tolerance in Mycobacterium tuberculosis

    PubMed Central

    2016-01-01

    The mechanisms that lead to phenotypic antibacterial tolerance in bacteria remain poorly understood. We investigate whether changes in NaCl concentration toward physiologically higher values affect antibacterial efficacy against Mycobacterium tuberculosis (Mtb), the causal agent of human tuberculosis. Indeed, multiclass phenotypic antibacterial tolerance is observed during Mtb growth in physiologic saline. This includes changes in sensitivity to ethionamide, ethambutol, d-cycloserine, several aminoglycosides, and quinolones. By employing organism-wide metabolomic and lipidomic approaches combined with phenotypic tests, we identified a time-dependent biphasic adaptive response after exposure of Mtb to physiological levels of NaCl. A first rapid, extensive, and reversible phase was associated with changes in core and amino acid metabolism. In a second phase, Mtb responded with a substantial remodelling of plasma membrane and outer lipid membrane composition. We demonstrate that phenotypic tolerance at physiological concentrations of NaCl is the result of changes in plasma and outer membrane lipid remodeling and not changes in core metabolism. Altogether, these results indicate that physiologic saline-induced antibacterial tolerance is kinetically coupled to cell envelope changes and demonstrate that metabolic changes and growth arrest are not the cause of phenotypic tolerance observed in Mtb exposed to physiologic concentrations of NaCl. Importantly, this work uncovers a role for bacterial cell envelope remodeling in antibacterial tolerance, alongside well-documented allterations in respiration, metabolism, and growth rate. PMID:27231718

  4. Severity grading of chronic obstructive pulmonary disease: the confounding effect of phenotype and thoracic gas compression.

    PubMed

    Pellegrino, Riccardo; Crimi, Emanuele; Gobbi, Alessandro; Torchio, Roberto; Antonelli, Andrea; Gulotta, Carlo; Baroffio, Michele; Papa, Giuseppe Francesco Sferrazza; Dellacà, Raffaele; Brusasco, Vito

    2015-04-01

    Current guidelines recommend severity of chronic obstructive pulmonary disease be graded by using forced expiratory volume in 1 s (FEV1). But this measurement is biased by thoracic gas compression depending on lung volume and airflow resistance. The aim of this study was to test the hypothesis that the effect of thoracic gas compression on FEV1 is greater in emphysema than chronic bronchitis because of larger lung volumes, and this influences severity classification and prognosis. FEV1 was simultaneously measured by spirometry and body plethysmography (FEV1-pl) in 47 subjects with dominant emphysema and 51 with dominant chronic bronchitis. Subjects with dominant emphysema had larger lung volumes, lower diffusion capacity, and lower FEV1 than those with dominant chronic bronchitis. However, FEV1-pl, patient-centered variables (dyspnea, quality of life, exercise tolerance, exacerbation frequency), arterial blood gases, and respiratory impedance were not significantly different between groups. Using FEV1-pl instead of FEV1 shifted severity distribution toward less severe classes in dominant emphysema more than chronic bronchitis. The body mass, obstruction, dyspnea, and exercise (BODE) index was significantly higher in dominant emphysema than chronic bronchitis, but this difference significantly decreased when FEV1-pl was substituted for FEV1. In conclusion, the FEV1 is biased by thoracic gas compression more in subjects with dominant emphysema than in those with chronic bronchitis. This variably and significantly affects the severity grading systems currently recommended. PMID:25414244

  5. Kenny Caffey syndrome with severe respiratory and gastrointestinal involvement: expanding the clinical phenotype

    PubMed Central

    Christodoulou, Loucas; Krishnaiah, Anil; Spyridou, Christina; Salpietro, Vincenzo; Hannan, Siobhan; Saggar, Anand; Mankad, Kshitij; Deep, Akash

    2015-01-01

    Kenny Caffey syndrome (KCS) is a rare syndrome reported almost exclusively in Middle Eastern populations. It is characterized by severe growth retardation—short stature, dysmorphic features, episodic hypocalcaemia, hypoparathyroidism, seizures, and medullary stenosis of long bones with thickened cortices. We report a 10-year-old boy with KCS with an unusually severe respiratory and gastrointestinal system involvement—features not previously described in the literature. He had severe psychomotor retardation and regressed developmentally from walking unaided to sitting with support. MRI brain showed bilateral hippocampal sclerosis, marked supra-tentorial volume loss and numerous calcifications. A 12 bp deletion of exon 2 of tubulin-specific chaperone E (TBCE) gene was identified and the diagnosis of KCS was confirmed. Hypercarbia following a sleep study warranted nocturnal continuous positive airway pressure (CPAP) when aged 6. When boy aged 8, persistent hypercarbia with increasing oxygen requirement and increased frequency and severity of lower respiratory tract infections led to progressive respiratory failure. He became fully dependent on non-invasive ventilation and by 9 years he had a tracheotomy and was established on long-term ventilation. He developed retching, vomiting and diarrhea. Chest CT showed changes consistent with chronic aspiration, but no interstitial pulmonary fibrosis. He died aged 10 from respiratory complications. PMID:26029652

  6. Kenny Caffey syndrome with severe respiratory and gastrointestinal involvement: expanding the clinical phenotype.

    PubMed

    Christodoulou, Loucas; Krishnaiah, Anil; Spyridou, Christina; Salpietro, Vincenzo; Hannan, Siobhan; Saggar, Anand; Mankad, Kshitij; Deep, Akash; Kinali, Maria

    2015-06-01

    Kenny Caffey syndrome (KCS) is a rare syndrome reported almost exclusively in Middle Eastern populations. It is characterized by severe growth retardation-short stature, dysmorphic features, episodic hypocalcaemia, hypoparathyroidism, seizures, and medullary stenosis of long bones with thickened cortices. We report a 10-year-old boy with KCS with an unusually severe respiratory and gastrointestinal system involvement-features not previously described in the literature. He had severe psychomotor retardation and regressed developmentally from walking unaided to sitting with support. MRI brain showed bilateral hippocampal sclerosis, marked supra-tentorial volume loss and numerous calcifications. A 12 bp deletion of exon 2 of tubulin-specific chaperone E (TBCE) gene was identified and the diagnosis of KCS was confirmed. Hypercarbia following a sleep study warranted nocturnal continuous positive airway pressure (CPAP) when aged 6. When boy aged 8, persistent hypercarbia with increasing oxygen requirement and increased frequency and severity of lower respiratory tract infections led to progressive respiratory failure. He became fully dependent on non-invasive ventilation and by 9 years he had a tracheotomy and was established on long-term ventilation. He developed retching, vomiting and diarrhea. Chest CT showed changes consistent with chronic aspiration, but no interstitial pulmonary fibrosis. He died aged 10 from respiratory complications. PMID:26029652

  7. Improving diagnosis and broadening the phenotypes in early-onset seizure and severe developmental delay disorders through gene panel analysis

    PubMed Central

    Trump, Natalie; McTague, Amy; Brittain, Helen; Papandreou, Apostolos; Meyer, Esther; Ngoh, Adeline; Palmer, Rodger; Morrogh, Deborah; Boustred, Christopher; Hurst, Jane A; Jenkins, Lucy; Kurian, Manju A; Scott, Richard H

    2016-01-01

    Background We sought to investigate the diagnostic yield and mutation spectrum in previously reported genes for early-onset epilepsy and disorders of severe developmental delay. Methods In 400 patients with these disorders with no known underlying aetiology and no major structural brain anomaly, we analysed 46 genes using a combination of targeted sequencing on an Illumina MiSeq platform and targeted, exon-level microarray copy number analysis. Results We identified causative mutations in 71/400 patients (18%). The diagnostic rate was highest among those with seizure onset within the first two months of life (39%), although overall it was similar in those with and without seizures. The most frequently mutated gene was SCN2A (11 patients, 3%). Other recurrently mutated genes included CDKL5, KCNQ2, SCN8A (six patients each), FOXG1, MECP2, SCN1A, STXBP1 (five patients each), KCNT1, PCDH19, TCF4 (three patients each) and ATP1A3, PRRT2 and SLC9A6 (two patients each). Mutations in EHMT1, GABRB3, LGI1, MBD5, PIGA, UBE3A and ZEB2 were each found in single patients. We found mutations in a number of genes in patients where either the electroclinical features or dysmorphic phenotypes were atypical for the identified gene. In only 11 cases (15%) had the clinician sufficient certainty to specify the mutated gene as the likely cause before testing. Conclusions Our data demonstrate the considerable utility of a gene panel approach in the diagnosis of patients with early-onset epilepsy and severe developmental delay disorders., They provide further insights into the phenotypic spectrum and genotype–phenotype correlations for a number of the causative genes and emphasise the value of exon-level copy number testing in their analysis. PMID:26993267

  8. Xq28 duplications including MECP2 in five females: Expanding the phenotype to severe mental retardation

    PubMed Central

    Bijlsma, E.K.; Collins, A.; Papa, F.T.; Tejada, M.I.; Wheeler, P.; Peeters, E.A.J.; Gijsbers, A.C.J.; van de Kamp, J.M.; Kriek, M.; Losekoot, M.; Broekma, A.J.; Crolla, J.A.; Pollazzon, M.; Mucciolo, M.; Katzaki, E.; Disciglio, V.; Ferreri, M.I.; Marozza, A.; Mencarelli, M.A.; Castagnini, C.; Dosa, L.; Ariani, F.; Mari, F.; Canitano, R.; Hayek, G.; Botella, M.P.; Gener, B.; Mínguez, M.; Renieri, A.; Ruivenkamp, C.A.L.

    2012-01-01

    Duplications leading to functional disomy of chromosome Xq28, including MECP2 as the critical dosage-sensitive gene, are associated with a distinct clinical phenotype in males, characterized by severe mental retardation, infantile hypotonia, progressive neurologic impairment, recurrent infections, bladder dysfunction, and absent speech. Female patients with Xq duplications including MECP2 are rare. Only recently submicroscopic duplications of this region on Xq28 have been recognized in four females, and a triplication in a fifth, all in combination with random X-chromosome inactivation (XCI). Based on this small series, it was concluded that in females with MECP2 duplication and random XCI, the typical symptoms of affected boys are not present. We present clinical and molecular data on a series of five females with an Xq28 duplication including the MECP2 gene, both isolated and as the result of a translocation, and compare them with the previously reported cases of small duplications in females. The collected data indicate that the associated phenotype in females is distinct from males with similar duplications, but the clinical effects may be as severe as seen in males. PMID:22522176

  9. Severe congenital neutropenia with neurological impairment due to a homozygous VPS45 p.E238K mutation: A case report suggesting a genotype-phenotype correlation.

    PubMed

    Meerschaut, Ilse; Bordon, Victoria; Dhooge, Catharina; Delbeke, Patricia; Vanlander, Arnaud V; Simon, Amos; Klein, Christoph; Kooy, R Frank; Somech, Raz; Callewaert, Bert

    2015-12-01

    VPS45 mutations cause severe congenital neutropenia (SCN). We report on a girl with SCN and neurological impairment harboring a homozygous p.E238K mutation in VPS45 (vacuolar sorting protein 45). She successfully underwent hematopoietic stem cell transplantation. Our findings delineate the phenotype and indicate a possible genotype-phenotype correlation for neurological involvement. PMID:26358756

  10. The Relationship between the Broader Autism Phenotype, Child Severity, and Stress and Depression in Parents of Children with Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Ingersoll, Brooke; Hambrick, David Z.

    2011-01-01

    This study examined the relationship between child symptom severity, parent broader autism phenotype (BAP), and stress and depression in parents of children with ASD. One hundred and forty-nine parents of children with ASD completed a survey of parenting stress, depression, broader autism phenotype, coping styles, perceived social support, and…

  11. The severe phenotype of females with tiny ring X chromosomes is associated with inability of these chromosomes to undergo X inactivation

    SciTech Connect

    Migeon, B.R.; Luo, S.; Jani, M.; Jeppesen, P.

    1994-09-01

    Mental retardation and a constellation of congenital malformations not usually associated with Turner syndrome are seen in some females with a mosaic 45,X/46,X,r(X) karyotype. Studies of these females show that the XIST locus on their tiny ring X chromosomes is either not present or not expressed. As XIST transcription is well correlated with inactivation of the X chromosome in female somatic cells and spermatogonia, nonexpression of the locus even if it is present suggests that these chromosomes are transcriptionally active. The authors examined the transcriptional activity of ring X chromosomes lacking XIST expression (XIST E{sup {minus}}), from three females with severe phenotypes. The two tiny ring X chromosomes studied with an antibody specific for the acetylated isoforms of histone H4 marking transcribed chromatin domains were labeled at a level consistent with their being active. The authors also examined two of the XIST E{sup {minus}} ring chromosomes to determine whether genes that are normally silent on an inactive X are expressed from these chromosomes. Analyses of hybrid cells show that TIMP, ZXDA, and ZCDB loci on the proximal short arm, and AR and PHKA1 loci on the long arm, are well expressed from the tiny ring X chromosome lacking XIST DNA. Studies of the ring chromosome that has XIST DNA but does not transcribe it show that its AR allele is transcribed along with the one on the normal X allele. These findings provide compelling evidence that (1) ring X chromosomes associated with severe phenotypes are unable to undergo X chromosome inactivation; (2) they represent chromosomal mutations affecting cis inactivation; and (3) the severe phenotype is due to functional disomy resulting from lack of dosage compensation for genes present within the ring chromosome. 31 refs., 5 figs., 1 tab.

  12. A novel missense mutation in POMT1 modulates the severe congenital muscular dystrophy phenotype associated with POMT1 nonsense mutations.

    PubMed

    Wallace, Stephanie E; Conta, Jessie H; Winder, Thomas L; Willer, Tobias; Eskuri, Jamie M; Haas, Richard; Patterson, Kathleen; Campbell, Kevin P; Moore, Steven A; Gospe, Sidney M

    2014-04-01

    Mutations in POMT1 lead to a group of neuromuscular conditions ranging in severity from Walker-Warburg syndrome to limb girdle muscular dystrophy. We report two male siblings, ages 19 and 14, and an unrelated 6-year old female with early onset muscular dystrophy and intellectual disability with minimal structural brain anomalies and no ocular abnormalities. Compound heterozygous mutations in POMT1 were identified including a previously reported nonsense mutation (c.2167dupG; p.Asp723Glyfs*8) associated with Walker-Warburg syndrome and a novel missense mutation in a highly conserved region of the protein O-mannosyltransferase 1 protein (c.1958C>T; p.Pro653Leu). This novel variant reduces the phenotypic severity compared to patients with homozygous c.2167dupG mutations or compound heterozygous patients with a c.2167dupG mutation and a wide range of other mutant POMT1 alleles. PMID:24491487

  13. A Novel Missense Mutation in POMT1 Modulates the Severe Congenital Muscular Dystrophy Phenotype Associated with POMT1 Nonsense Mutations

    PubMed Central

    Wallace, Stephanie E.; Conta, Jessie H.; Winder, Thomas L.; Willer, Tobias; Eskuri, Jamie M.; Haas, Richard; Patterson, Kathleen; Campbell, Kevin P.; Moore, Steven A.; Gospe, Sidney M.

    2014-01-01

    Mutations in POMT1 lead to a group of neuromuscular conditions ranging in severity from Walker-Warburg syndrome to limb girdle muscular dystrophy. We report two male siblings, ages 19 and 14, and an unrelated 6-year old female with early onset muscular dystrophy and intellectual disability with minimal structural brain anomalies and no ocular abnormalities. Compound heterozygous mutations in POMT1 were identified including a previously reported nonsense mutation (c.2167dupG; p.Asp723Glyfs*8) associated with Walker-Warburg syndrome and a novel missense mutation in a highly conserved region of the protein O-mannosyltransferase 1 protein (c.1958C>T; p.Pro653Leu). This novel variant reduces the phenotypic severity compared to patients with homozygous c.2167dupG mutations or compound heterozygous patients with a c.2167dupG mutation and a wide range of other mutant POMT1 alleles. PMID:24491487

  14. Beyond the Central Dogma: Model-Based Learning of How Genes Determine Phenotypes.

    PubMed

    Reinagel, Adam; Bray Speth, Elena

    2016-01-01

    In an introductory biology course, we implemented a learner-centered, model-based pedagogy that frequently engaged students in building conceptual models to explain how genes determine phenotypes. Model-building tasks were incorporated within case studies and aimed at eliciting students' understanding of 1) the origin of variation in a population and 2) how genes/alleles determine phenotypes. Guided by theory on hierarchical development of systems-thinking skills, we scaffolded instruction and assessment so that students would first focus on articulating isolated relationships between pairs of molecular genetics structures and then integrate these relationships into an explanatory network. We analyzed models students generated on two exams to assess whether students' learning of molecular genetics progressed along the theoretical hierarchical sequence of systems-thinking skills acquisition. With repeated practice, peer discussion, and instructor feedback over the course of the semester, students' models became more accurate, better contextualized, and more meaningful. At the end of the semester, however, more than 25% of students still struggled to describe phenotype as an output of protein function. We therefore recommend that 1) practices like modeling, which require connecting genes to phenotypes; and 2) well-developed case studies highlighting proteins and their functions, take center stage in molecular genetics instruction. PMID:26903496

  15. Beyond the Central Dogma: Model-Based Learning of How Genes Determine Phenotypes

    PubMed Central

    Reinagel, Adam; Bray Speth, Elena

    2016-01-01

    In an introductory biology course, we implemented a learner-centered, model-based pedagogy that frequently engaged students in building conceptual models to explain how genes determine phenotypes. Model-building tasks were incorporated within case studies and aimed at eliciting students’ understanding of 1) the origin of variation in a population and 2) how genes/alleles determine phenotypes. Guided by theory on hierarchical development of systems-thinking skills, we scaffolded instruction and assessment so that students would first focus on articulating isolated relationships between pairs of molecular genetics structures and then integrate these relationships into an explanatory network. We analyzed models students generated on two exams to assess whether students’ learning of molecular genetics progressed along the theoretical hierarchical sequence of systems-thinking skills acquisition. With repeated practice, peer discussion, and instructor feedback over the course of the semester, students’ models became more accurate, better contextualized, and more meaningful. At the end of the semester, however, more than 25% of students still struggled to describe phenotype as an output of protein function. We therefore recommend that 1) practices like modeling, which require connecting genes to phenotypes; and 2) well-developed case studies highlighting proteins and their functions, take center stage in molecular genetics instruction. PMID:26903496

  16. A proteome map of a quadruple photoreceptor mutant sustains its severe photosynthetic deficient phenotype.

    PubMed

    Fox, Ana Romina; Barberini, Maria Laura; Ploschuk, Edmundo Leonardo; Muschietti, Jorge Prometeo; Mazzella, Maria Agustina

    2015-08-01

    Light is the environmental factor that most affects plant growth and development through its impact on photomorphogenesis and photosynthesis. A quadruple photoreceptor mutant lacking four of the most important photoreceptors in plants, phytochromes A and B (phyA, phyB) and cryptochromes 1 and 2 (cry1, cry2), is severely affected in terms of growth and development. Previous studies have suggested that in addition to a photomorphogenic disorder, the phyA phyB cry1 cry2 quadruple mutant might have severe alterations in photosynthetic ability. Here, we investigated the photosynthetic processes altered in the quadruple mutant and performed a proteomic profiling approach to identify some of the proteins involved. The phyA phyB cry1 cry2 quadruple mutant showed reduced leaf area and total chlorophyll content. Photosynthetic rates at high irradiances were reduced approximately 65% compared to the wild type (WT). Light-saturated photosynthesis and the response of net CO2 exchange to low and high internal CO2 concentrations suggest that the levels or activity of the components of the Calvin cycle and electron transport might be reduced in the quadruple mutant. Most of the under-expressed proteins in the phyA phyB cry1 cry2 quadruple mutant consistently showed a chloroplastic localization, whereas components of the Calvin cycle and light reaction centers were overrepresented. Additionally, Rubisco expression was reduced threefold in the phyA phyB cry1 cry2 quadruple mutant. Together, these results highlight the importance of the phytochrome and cryptochrome families in proper autotrophy establishment in plants. They also suggest that an overall limitation in the chlorophyll levels, expression of Rubisco, and enzymes of the Calvin Cycle and electron transport that affect ribulose-1,5-biphosphate (RuBP) regeneration reduced photosynthetic capacity in the phyA phyB cry1 cry2 quadruple mutant. PMID:26264966

  17. Streptococcus pneumoniae capsule determines disease severity in experimental pneumococcal meningitis

    PubMed Central

    Grandgirard, Denis; Valente, Luca G.; Täuber, Martin G.; Leib, Stephen L.

    2016-01-01

    Streptococcus pneumoniae bacteria can be characterized into over 90 serotypes according to the composition of their polysaccharide capsules. Some serotypes are common in nasopharyngeal carriage whereas others are associated with invasive disease, but when carriage serotypes do invade disease is often particularly severe. It is unknown whether disease severity is due directly to the capsule type or to other virulence factors. Here, we used a clinical pneumococcal isolate and its capsule-switch mutants to determine the effect of capsule, in isolation from the genetic background, on severity of meningitis in an infant rat model. We found that possession of a capsule was essential for causing meningitis. Serotype 6B caused significantly more mortality than 7F and this correlated with increased capsule thickness in the cerebrospinal fluid (CSF), a stronger inflammatory cytokine response in the CSF and ultimately more cortical brain damage. We conclude that capsule type has a direct effect on meningitis severity. This is an important consideration in the current era of vaccination targeting a subset of capsule types that causes serotype replacement. PMID:27009189

  18. Streptococcus pneumoniae capsule determines disease severity in experimental pneumococcal meningitis.

    PubMed

    Hathaway, Lucy J; Grandgirard, Denis; Valente, Luca G; Täuber, Martin G; Leib, Stephen L

    2016-03-01

    Streptococcus pneumoniaebacteria can be characterized into over 90 serotypes according to the composition of their polysaccharide capsules. Some serotypes are common in nasopharyngeal carriage whereas others are associated with invasive disease, but when carriage serotypes do invade disease is often particularly severe. It is unknown whether disease severity is due directly to the capsule type or to other virulence factors. Here, we used a clinical pneumococcal isolate and its capsule-switch mutants to determine the effect of capsule, in isolation from the genetic background, on severity of meningitis in an infant rat model. We found that possession of a capsule was essential for causing meningitis. Serotype 6B caused significantly more mortality than 7F and this correlated with increased capsule thickness in the cerebrospinal fluid (CSF), a stronger inflammatory cytokine response in the CSF and ultimately more cortical brain damage. We conclude that capsule type has a direct effect on meningitis severity. This is an important consideration in the current era of vaccination targeting a subset of capsule types that causes serotype replacement. PMID:27009189

  19. Mechanism, Prevalence, and More Severe Neuropathy Phenotype of the Charcot-Marie-Tooth Type 1A Triplication

    PubMed Central

    Liu, Pengfei; Gelowani, Violet; Zhang, Feng; Drory, Vivian E.; Ben-Shachar, Shay; Roney, Erin; Medeiros, Adam C.; Moore, Rebecca J.; DiVincenzo, Christina; Burnette, William B.; Higgins, Joseph J.; Li, Jun; Orr-Urtreger, Avi; Lupski, James R.

    2014-01-01

    Copy-number variations cause genomic disorders. Triplications, unlike deletions and duplications, are poorly understood because of challenges in molecular identification, the choice of a proper model system for study, and awareness of their phenotypic consequences. We investigated the genomic disorder Charcot-Marie-Tooth disease type 1A (CMT1A), a dominant peripheral neuropathy caused by a 1.4 Mb recurrent duplication occurring by nonallelic homologous recombination. We identified CMT1A triplications in families in which the duplication segregates. The triplications arose de novo from maternally transmitted duplications and caused a more severe distal symmetric polyneuropathy phenotype. The recombination that generated the triplication occurred between sister chromatids on the duplication-bearing chromosome and could accompany gene conversions with the homologous chromosome. Diagnostic testing for CMT1A (n = 20,661 individuals) identified 13% (n = 2,752 individuals) with duplication and 0.024% (n = 5 individuals) with segmental tetrasomy, suggesting that triplications emerge from duplications at a rate as high as ∼1:550, which is more frequent than the rate of de novo duplication. We propose that individuals with duplications are predisposed to acquiring triplications and that the population prevalence of triplication is underascertained. PMID:24530202

  20. Succinic Semialdehyde Dehydrogenase Deficiency in a Chinese Boy: A Novel ALDH5A1 Mutation With Severe Phenotype.

    PubMed

    Tay, Chee Geap; Ariffin, Hany; Yap, Sufin; Rahmat, Kartini; Sthaneshwar, Pavai; Ong, Lai Choo

    2015-06-01

    Succinic semialdehyde dehydrogenase deficiency is a rare autosomal recessive disorder affecting catabolism of the neurotransmitter gamma-aminobutyric acid (GABA), with a wide range of clinical phenotype. We report a Malaysian Chinese boy with a severe early onset phenotype due to a previously unreported mutation. Urine organic acid chromatogram revealed elevated 4-hydroxybutyric acid. Magnetic resonance imaging (MRI) of the brain demonstrated cerebral atrophy with atypical putaminal involvement. Molecular genetic analysis showed a novel homozygous 3-bp deletion at the ALDH5A1 gene c.1501_1503del (p.Glu501del). Both parents were confirmed to be heterozygotes for the p.Glu501del mutation. The clinical course was complicated by the development of subdural hemorrhage probably as a result of rocking the child to sleep for erratic sleep-wake cycles. This case illustrates the need to recognize that trivial or unintentional shaking of such children, especially in the presence of cerebral atrophy, can lead to subdural hemorrhage. PMID:25122112

  1. The QDREC web server: determining dose–response characteristics of complex macroparasites in phenotypic drug screens

    PubMed Central

    Asarnow, Daniel; Rojo-Arreola, Liliana; Suzuki, Brian M.; Caffrey, Conor R.; Singh, Rahul

    2015-01-01

    Summary: Neglected tropical diseases (NTDs) caused by helminths constitute some of the most common infections of the world’s poorest people. The etiological agents are complex and recalcitrant to standard techniques of molecular biology. Drug screening against helminths has often been phenotypic and typically involves manual description of drug effect and efficacy. A key challenge is to develop automated, quantitative approaches to drug screening against helminth diseases. The quantal dose–response calculator (QDREC) constitutes a significant step in this direction. It can be used to automatically determine quantitative dose–response characteristics and half-maximal effective concentration (EC50) values using image-based readouts from phenotypic screens, thereby allowing rigorous comparisons of the efficacies of drug compounds. QDREC has been developed and validated in the context of drug screening for schistosomiasis, one of the most important NTDs. However, it is equally applicable to general phenotypic screening involving helminths and other complex parasites. Availability and implementation: QDREC is publically available at: http://haddock4.sfsu.edu/qdrec2/. Source code and datasets are at: http://tintin.sfsu.edu/projects/phenotypicAssays.html. Contact: rahul@sfsu.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25540182

  2. Heterogeneous Determinants of Quality of Life in Different Phenotypes of Parkinson’s Disease

    PubMed Central

    Fereshtehnejad, Seyed-Mohammad; Shafieesabet, Mahdiyeh; Farhadi, Farzaneh; Hadizadeh, Hasti; Rahmani, Arash; Naderi, Nader; Khaefpanah, Dena; Shahidi, Gholam Ali; Delbari, Ahmad; Lökk, Johan

    2015-01-01

    Objectives Health-related quality of life (HRQoL) is considered a very important outcome indicator in patients with Parkinson’s disease (PD). A broad list of motor and non-motor features have been shown to affect HRQoL in PD, however, there is a dearth of information about the complexity of interrelationships between determinants of HRQoL in different PD phenotypes. We aimed to find independent determinates and the best structural model for HRQoL, also to investigate the heterogeneity in HRQoL between PD patients with different phenotypes regarding onset-age, progression rate and dominant symptom. Methods A broad spectrum of demographic, motor and non-motor characteristics were collected in 157 idiopathic PD patients, namely comorbidity profile, nutritional status, UPDRS (total items), psychiatric symptoms (depression, anxiety), fatigue and psychosocial functioning through physical examination, validated questionnaires and scales. Structural equation model (SEM) and multivariate regressions were applied to find determinants of Parkinson’s disease summary index (PDSI) and different domains of HRQoL (PDQ-39). Results Female sex, anxiety, depression and UPDRS-part II scores were the significant independent determinants of PDSI. A structural model consisting of global motor, global non-motor and co-morbidity indicator as three main components was able to predict 89% of the variance in HRQoL. In older-onset and slow-progression phenotypes, the motor domain showed smaller contribution on HRQoL and the majority of its effects were mediated through non-motor features. Comorbidity component was a significant determinant of HRQoL only among older-onset and non-tremor-dominant PD patients. Fatigue was not a significant indicator of non-motor component to affect HRQoL in rapid-progression PD. Conclusions Our findings showed outstanding heterogeneities in the pattern and determinants of HRQoL among PD phenotypes. These factors should be considered during the assessments and

  3. Serine protease activity and residual LEKTI expression determine phenotype in Netherton syndrome.

    PubMed

    Hachem, Jean-Pierre; Wagberg, Fredrik; Schmuth, Matthias; Crumrine, Debra; Lissens, Willy; Jayakumar, Arumugam; Houben, Evi; Mauro, Theodora M; Leonardsson, Göran; Brattsand, Maria; Egelrud, Torbjorn; Roseeuw, Diane; Clayman, Gary L; Feingold, Kenneth R; Williams, Mary L; Elias, Peter M

    2006-07-01

    Mutations in the SPINK5 gene encoding the serine protease (SP) inhibitor, lymphoepithelial-Kazal-type 5 inhibitor (LEKTI), cause Netherton syndrome (NS), a life-threatening disease, owing to proteolysis of the stratum corneum (SC). We assessed here the basis for phenotypic variations in nine patients with "mild", "moderate", and "severe" NS. The magnitude of SP activation correlated with both the barrier defect and clinical severity, and inversely with residual LEKTI expression. LEKTI co-localizes within the SC with kallikreins 5 and 7 and inhibits both SP. The permeability barrier abnormality in NS was further linked to SC thinning and proteolysis of two lipid hydrolases (beta-glucocerebrosidase and acidic sphingomyelinase), with resultant disorganization of extracellular lamellar membranes. SC attenuation correlated with phenotype-dependent, SP activation, and loss of corneodesmosomes, owing to desmoglein (DSG)1 and desmocollin (DSC)1 degradation. Although excess SP activity extended into the nucleated layers in NS, degrading desmosomal mid-line structures with loss of DSG1/DSC1, the integrity of the nucleated epidermis appears to be maintained by compensatory upregulation of DSG3/DSC3. Maintenance of sufficient permeability barrier function for survival correlated with a compensatory acceleration of lamellar body secretion, providing a partial permeability barrier in NS. These studies provide a mechanistic basis for phenotypic variations in NS, and describe compensatory mechanisms that permit survival of NS patients in the face of unrelenting SP attack. PMID:16601670

  4. Severe Myoclonic Epilepsy in Infancy - Adult Phenotype with Bradykinesia, Hypomimia, and Perseverative Behavior: Report of Five Cases.

    PubMed

    Martin, P; Rautenstrauβ, B; Abicht, A; Fahrbach, J; Koster, S

    2010-01-01

    Dravet syndrome or severe myoclonic epilepsy in infancy (SMEI) is an epileptic syndrome characterised by refractory epilepsy and intellectual disability, typically presenting with febrile and afebrile generalised and unilateral clonic/tonic-clonic seizures in the first year of life and other types of seizures appearing later in the course of the disease. Five adult patients with SMEI and SCN1A mutations are reported, in which motor and behavioural abnormalities were outstanding symptoms. Bradykinesia, responding with latency, slow speaking with a thin voice, midface hypomimia and perseveration were distinctive features in all cases. These symptoms may be fit to define the adult phenotype of SMEI beyond seizure/epilepsy criteria. The motor and behavioural symptoms are discussed in the context of a possibly underlying frontal lobe/mesofrontal and cerebellar dysfunction. PMID:22140375

  5. Severity and Frequency of Proximal Tubule Injury Determines Renal Prognosis.

    PubMed

    Takaori, Koji; Nakamura, Jin; Yamamoto, Shinya; Nakata, Hirosuke; Sato, Yuki; Takase, Masayuki; Nameta, Masaaki; Yamamoto, Tadashi; Economides, Aris N; Kohno, Kenji; Haga, Hironori; Sharma, Kumar; Yanagita, Motoko

    2016-08-01

    AKI increases the risk of developing CKD, but the mechanisms linking AKI to CKD remain unclear. Because proximal tubule injury is the mainstay of AKI, we postulated that proximal tubule injury triggers features of CKD. We generated a novel mouse model to induce proximal tubule-specific adjustable injury by inducing the expression of diphtheria toxin (DT) receptor with variable prevalence in proximal tubules. Administration of high-dose DT in mice expressing the DT receptor consistently caused severe proximal tubule-specific injury associated with interstitial fibrosis and reduction of erythropoietin production. Mild proximal tubule injury from a single injection of low-dose DT triggered reversible fibrosis, whereas repeated mild injuries caused sustained interstitial fibrosis, inflammation, glomerulosclerosis, and atubular glomeruli. DT-induced proximal tubule-specific injury also triggered distal tubule injury. Furthermore, injured tubular cells cocultured with fibroblasts stimulated induction of extracellular matrix and inflammatory genes. These results support the existence of proximal-distal tubule crosstalk and crosstalk between tubular cells and fibroblasts. Overall, our data provide evidence that proximal tubule injury triggers several features of CKD and that the severity and frequency of proximal tubule injury determines the progression to CKD. PMID:26701981

  6. Type of mutation in the neurofibromatosis type 2 gene (NF2) frequently determines severity of disease.

    PubMed Central

    Ruttledge, M. H.; Andermann, A. A.; Phelan, C. M.; Claudio, J. O.; Han, F. Y.; Chretien, N.; Rangaratnam, S.; MacCollin, M.; Short, P.; Parry, D.; Michels, V.; Riccardi, V. M.; Weksberg, R.; Kitamura, K.; Bradburn, J. M.; Hall, B. D.; Propping, P.; Rouleau, G. A.

    1996-01-01

    The gene predisposing to neurofibromatosis type 2 (NF2) on human chromosome 22 has revealed a wide variety of different mutations in NF2 individuals. These patients display a marked variability in clinical presentation, ranging from very severe disease with numerous tumors at a young age to a relatively mild condition much later in life. To investigate whether this phenotypic heterogeneity is determined by the type of mutation in NF2, we have collected clinical information on 111 NF2 cases from 73 different families on whom we have performed mutation screening in this gene. Sixty-seven individuals (56.2%) from 41 of these kindreds revealed 36 different putative disease-causing mutations. These include 26 proposed protein-truncating alterations (frameshift deletions/insertions and nonsense mutations), 6 splice-site mutations, 2 missense mutations, 1 base substitution in the 3' UTR of the NF2 cDNA, and a single 3-bp in-frame insertion. Seventeen of these mutations are novel, whereas the remaining 19 have been described previously in other NF2 individuals or sporadic tumors. When individuals harboring protein-truncating mutations are compared with cases with single codon alterations, a significant correlation (P < .001) with clinical outcome is observed. Twenty-four of 28 patients with mutations that cause premature truncation of the NF2 protein, schwannomin, present with severe phenotypes. In contrast, all 16 cases from three families with mutations that affect only a single amino acid have mild NF2. These data provide conclusive evidence that a phenotype/genotype correlation exists for certain NF2 mutations. PMID:8755919

  7. Gender as a Modifying Factor Influencing Myotonic Dystrophy Type 1 Phenotype Severity and Mortality: A Nationwide Multiple Databases Cross-Sectional Observational Study

    PubMed Central

    Hamroun, Dalil; Varet, Hugo; Fabbro, Marianne; Rougier, Felix; Amarof, Khadija; Arne Bes, Marie-Christine; Bedat-Millet, Anne-Laure; Behin, Anthony; Bellance, Remi; Bouhour, Françoise; Boutte, Celia; Boyer, François; Campana-Salort, Emmanuelle; Chapon, Françoise; Cintas, Pascal; Desnuelle, Claude; Deschamps, Romain; Drouin-Garraud, Valerie; Ferrer, Xavier; Gervais-Bernard, Helene; Ghorab, Karima; Laforet, Pascal; Magot, Armelle; Magy, Laurent; Menard, Dominique; Minot, Marie-Christine; Nadaj-Pakleza, Aleksandra; Pellieux, Sybille; Pereon, Yann; Preudhomme, Marguerite; Pouget, Jean; Sacconi, Sabrina; Sole, Guilhem; Stojkovich, Tanya; Tiffreau, Vincent; Urtizberea, Andoni; Vial, Christophe; Zagnoli, Fabien; Caranhac, Gilbert; Bourlier, Claude; Riviere, Gerard; Geille, Alain; Gherardi, Romain K.; Eymard, Bruno; Puymirat, Jack; Katsahian, Sandrine; Bassez, Guillaume

    2016-01-01

    Background Myotonic Dystrophy type 1 (DM1) is one of the most heterogeneous hereditary disease in terms of age of onset, clinical manifestations, and severity, challenging both medical management and clinical trials. The CTG expansion size is the main factor determining the age of onset although no factor can finely predict phenotype and prognosis. Differences between males and females have not been specifically reported. Our aim is to study gender impact on DM1 phenotype and severity. Methods We first performed cross-sectional analysis of main multiorgan clinical parameters in 1409 adult DM1 patients (>18y) from the DM-Scope nationwide registry and observed different patterns in males and females. Then, we assessed gender impact on social and economic domains using the AFM-Téléthon DM1 survey (n = 970), and morbidity and mortality using the French National Health Service Database (n = 3301). Results Men more frequently had (1) severe muscular disability with marked myotonia, muscle weakness, cardiac, and respiratory involvement; (2) developmental abnormalities with facial dysmorphism and cognitive impairment inferred from low educational levels and work in specialized environments; and (3) lonely life. Alternatively, women more frequently had cataracts, dysphagia, digestive tract dysfunction, incontinence, thyroid disorder and obesity. Most differences were out of proportion to those observed in the general population. Compared to women, males were more affected in their social and economic life. In addition, they were more frequently hospitalized for cardiac problems, and had a higher mortality rate. Conclusion Gender is a previously unrecognized factor influencing DM1 clinical profile and severity of the disease, with worse socio-economic consequences of the disease and higher morbidity and mortality in males. Gender should be considered in the design of both stratified medical management and clinical trials. PMID:26849574

  8. Accurate determination of cobalt traces in several biological reference materials.

    PubMed

    Dybczyński, R; Danko, B

    1994-01-01

    A newly devised, very accurate ("definitive") method for the determination of trace amounts of cobalt in biological materials was validated by the analysis of several certified reference materials. The method is based on a combination of neutron activation and selective and quantitative postirradiation isolation of radiocobalt from practically all other radionuclides by ion-exchange and extraction chromatography followed by gamma-ray spectrometric measurement. The significance of criteria that should be fulfilled in order to accept a given result as obtained by the "definitive method" is emphasized. In view of the demonstrated very good accuracy of the method, it is suggested that our values for cobalt content in those reference materials in which it was originally not certified (SRM 1570 spinach, SRM 1571 orchard leaves, SRM 1577 bovine liver, and Czechoslovak bovine liver 12-02-01) might be used as provisional certified values. PMID:7710879

  9. Determinants of Skeletal Muscle Catabolism After Severe Burn

    PubMed Central

    Hart, David W.; Wolf, Steven E.; Chinkes, David L.; Gore, Dennis C.; Mlcak, Ronald P.; Beauford, Robert B.; Obeng, Michael K.; Lal, Sophia; Gold, Warren F.; Wolfe, Robert R.; Herndon, David N.

    2000-01-01

    Objective To determine which patient factors affect the degree of catabolism after severe burn. Summary Background Data Catabolism is associated with severe burn and leads to erosion of lean mass, impaired wound healing, and delayed rehabilitation. Methods From 1996 to 1999, 151 stable-isotope protein kinetic studies were performed in 102 pediatric and 21 adult subjects burned over 20–99.5% of their total body surface area (TBSA). Patient demographics, burn characteristics, and hospital course variables were correlated with the net balance of skeletal muscle protein synthesis and breakdown across the leg. Data were analyzed sequentially and cumulatively through univariate and cross-sectional multiple regression. Results Increasing age, weight, and delay in definitive surgical treatment predict increased catabolism (P < .05). Body surface area burned increased catabolism until 40% TBSA was reached; catabolism did not consistently increase thereafter. Resting energy expenditure and sepsis were also strong predictors of net protein catabolism. Among factors that did not significantly correlate were burn type, pneumonia, wound contamination, and time after burn. From these results, the authors also infer that gross muscle mass correlates independently with protein wasting after burn. Conclusions Heavier, more muscular subjects, and subjects whose definitive surgical treatment is delayed are at the greatest risk for excess catabolism after burn. Sepsis and excessive hypermetabolism are also associated with protein catabolism. PMID:10998644

  10. A novel splicing mutation in the IQSEC2 gene that modulates the phenotype severity in a family with intellectual disability.

    PubMed

    Madrigal, Irene; Alvarez-Mora, Maria Isabel; Rosell, Jordi; Rodríguez-Revenga, Laia; Karlberg, Olof; Sauer, Sascha; Syvänen, Ann-Christine; Mila, Montserrat

    2016-08-01

    The IQSEC2 gene is located on chromosome Xp11.22 and encodes a guanine nucleotide exchange factor for the ADP-ribosylation factor family of small GTPases. This gene is known to have a significant role in cytoskeletal organization, dendritic spine morphology and synaptic organization. Variants in IQSEC2 cause moderate to severe intellectual disability in males and a variable phenotype in females because this gene escapes from X-chromosome inactivation. Here we report on the first splicing variant in IQSEC2 (g.88032_88033del; NG_021296.1) that co-segregates in a family diagnosed with an X-linked form of ID. In a percentage of the cells, the variant activates an intraexonic splice acceptor site that abolishes 26 amino acids from the highly conserved PH domain of IQSEC2 and creates a premature stop codon 36 amino acids later in exon 13. Interestingly, the percentage of aberrant splicing seems to correlate with the severity of the disease in each patient. The impact of this variant in the target tissue is unknown, but we can hypothesize that these differences may be related to the amount of abnormal IQSEC2 transcript. To our knowledge, we are reporting a novel mechanism of IQSEC2 involvement in ID. Variants that affect splicing are related to many genetic diseases and the understanding of their role in disease expands potential opportunities for gene therapy. Modulation of aberrant splicing transcripts can become a potent therapeutic approach for many of these diseases. PMID:26733290

  11. Seven novel mutations in the methylenetetrahydrofolate reductase gene and genotype/phenotype correlations in severe methylenetetrahydrofolate reductase deficiency

    SciTech Connect

    Goyette, P.; Frosst, P.; Rosenblatt, D.S.; Rozen. R.

    1995-05-01

    5-Methyltetrahydrofolate, the major form of folate in plasma, is a carbon donor for the remethylation of homocysteine to methionine. This form of folate is generated from 5,10-methylenetetrahydrofolate through the action of 5,10-methylenetetrahydrofolate reductase (MTHFR), a cytosolic flavoprotein. Patients with an autosomal recessive severe deficiency of MTHFR have homocystinuria and a wide range of neurological and vascular disturbances. We have recently described the isolation of a cDNA for MTHFR and the identification of two mutations in patients with severe MTHFR deficiency. We report here the characterization of seven novel mutations in this gene: six missense mutations and a 5{prime} splice-site defect that activates a cryptic splice in the coding sequence. We also present a preliminary analysis of the relationship between genotype and phenotype for all nine mutations identified thus far in this gene. A nonsense mutation and two missense mutations (proline to leucine and threonine to methionine) in the homozygous state are associated with extremely low activity (0%-3%) and onset of symptoms within the 1st year of age. Other missense mutations (arginine to cysteine and arginine to glutamine) are associated with higher enzyme activity and later onset of symptoms. 19 refs., 4 figs., 2 tabs.

  12. Natural Variation in MAM Within and Between Populations of Arabidopsis lyrata Determines Glucosinolate Phenotype

    PubMed Central

    Heidel, Andrew J.; Clauss, Maria J.; Kroymann, Juergen; Savolainen, Outi; Mitchell-Olds, Thomas

    2006-01-01

    The genetic variation that underlies the glucosinolate phenotype of Arabidopsis lyrata ssp. petraea was investigated between and within populations. A candidate glucosinolate biosynthetic locus (MAM, containing methylthioalkylmalate synthase genes) was mapped in A. lyrata to a location on linkage group 6 corresponding to the homologous location for MAM in A. thaliana. In A. thaliana MAM is responsible for side chain elongation in aliphatic glucosinolates, and the MAM phenotype can be characterized by the ratios of long- to short-chain glucosinolates. A quantitative trait loci (QTL) analysis of glucosinolate ratios in an A. lyrata interpopulation cross found one QTL at MAM. Additional QTL were identified for total indolic glucosinolates and for the ratio of aliphatic to indolic glucosinolates. MAM was then used as the candidate gene for a within-population cosegregation analysis in a natural A. lyrata population from Germany. Extensive variation in microsatellite markers at MAM was found and this variation cosegregated with the same glucosinolate ratios as in the QTL study. The combined results indicate that both between- and within-population genetic variation in the MAM region determines phenotypic variation in glucosinolate side chains in A. lyrata. PMID:16702431

  13. NIPBL expression levels in CdLS probands as a predictor of mutation type and phenotypic severity.

    PubMed

    Kaur, Maninder; Mehta, Devanshi; Noon, Sarah E; Deardorff, Matthew A; Zhang, Zhe; Krantz, Ian D

    2016-06-01

    Cornelia de Lange syndrome (CdLS) is a rare, genetically heterogeneous multisystem developmental disorder with a high degree of variability in its clinical presentation. Approximately 65% of probands harbor mutations in genes that encode core components (SMC1A, SMC3, and RAD21) or regulators (NIPBL, HDAC8) of the cohesin complex, of which mutations in NIPBL are the most common. Cohesin plays a canonical role in sister chromatid cohesion during cell division and non-canonical roles in DNA repair, stem cell maintenance and differentiation, and regulation of gene expression. Disruption of the latter role seems to be the major contributor to the underlying molecular pathogenesis of CdLS. NIPBL is required for loading and unloading the cohesin complex onto chromosomes. The expression levels of NIPBL itself appear to be tightly regulated and highly evolutionarily conserved. Droplet digital PCR was used to quantify NIPBL mRNA expression levels with high precision from a cohort of 37 samples (NIPBL, SMC1A, SMC3, and HDAC8 mutation positive probands and negative control). Probands with severe forms of CdLS or severe mutation types were found to have lower levels of NIPBL in comparison to phenotypically milder patients and controls. Levels of NIPBL also correlated with the presence of mutations in different CdLS-causing genes. The data suggests that NIPBL levels are closely correlated with the severity of CdLS and with specific causative genes and types of mutations. ddPCR may provide a tool to assist in diagnostic approaches to CdLS, for genetic counseling and prognosis, and for monitoring potential therapeutic modalities in the future. © 2016 Wiley Periodicals, Inc. PMID:27125329

  14. Ablation of RIC8A function in mouse neurons leads to a severe neuromuscular phenotype and postnatal death.

    PubMed

    Ruisu, Katrin; Kask, Keiu; Meier, Riho; Saare, Merly; Raid, Raivo; Veraksitš, Alar; Karis, Alar; Tõnissoo, Tambet; Pooga, Margus

    2013-01-01

    Resistance to inhibitors of cholinesterase 8 (RIC8) is a guanine nucleotide exchange factor required for the intracellular regulation of G protein signalling. RIC8 activates different Gα subunits via non-canonical pathway, thereby amplifying and prolonging the G protein mediated signal. In order to circumvent the embryonic lethality associated with the absence of RIC8A and to study its role in the nervous system, we constructed Ric8a conditional knockout mice using Cre/loxP technology. Introduction of a synapsin I promoter driven Cre transgenic mouse strain (SynCre) into the floxed Ric8a (Ric8a (F/F) ) background ablated RIC8A function in most differentiated neuron populations. Mutant SynCre (+/-) Ric8 (lacZ/F) mice were born at expected Mendelian ratio, but they died in early postnatal age (P4-P6). The mutants exhibited major developmental defects, like growth retardation and muscular weakness, impaired coordination and balance, muscular spasms and abnormal heart beat. Histological analysis revealed that the deficiency of RIC8A in neurons caused skeletal muscle atrophy and heart muscle hypoplasia, in addition, the sinoatrial node was misplaced and its size reduced. However, we did not observe gross morphological changes in brains of SynCre (+/-) Ric8a (lacZ/F) mutants. Our results demonstrate that in mice the activity of RIC8A in neurons is essential for survival and its deficiency causes a severe neuromuscular phenotype. PMID:23977396

  15. Human haptoglobin phenotypes and concentration determination by nanogold-enhanced electrochemical impedance spectroscopy

    NASA Astrophysics Data System (ADS)

    Cheng, Tsai-Mu; Lee, Tzu-Cheng; Tseng, Shin-Hua; Chu, Hsueh-Liang; Pan, Ju-Pin; Chang, Chia-Ching

    2011-06-01

    Haptoglobin (Hp) is an acute phase protein that binds free hemoglobin (Hb), preventing Hb-induced oxidative damage in the vascular system. There are three phenotypes in human Hp, whose heterogeneous polymorphic structures and varying concentrations in plasma have been attributed to the cause of diseases and outcome of clinical treatments. Different phenotypes of Hp may be composed of the same subunits but different copy numbers, rendering their determination difficult by a single procedure. In this study, we have developed a simple, fast, reliable and sensitive method, using label-free nanogold-modified bioprobes coupled with self-development electrochemical impedance spectroscopy (EIS). By this method, probe surface charge transfer resistance is detected. The relative charge transfer resistance ratios for Hp 1-1, Hp 2-1 and Hp 2-2 were characterized. We were able to determine protein size difference within 3 nm, and the linear region of the calibration curve for Hp levels in the range of 90 pg ml - 1 and 90 µg ml - 1 (~1 fM to 1 pM). We surmise that similar approaches can be used to investigate protein polymorphism and altered protein-protein interaction associated with diseases.

  16. Accurate Cytotoxicity and Proliferation Determination: Advantages of a High-Throughput Phenotypic Approach Over ATP Luminescence Assays.

    PubMed

    Hammerstein, Anne F; Wylie, Paul G

    2016-09-01

    Cell viability and proliferation assays are a fundamental tool in the drug discovery process and are used to evaluate both the antiproliferative potency and toxicity of compounds. Some lead discovery groups generate cell viability data for up to two million compounds per screen, so any method used to assess these parameters needs to deliver not only on data quality but also on throughput and assay cost per well. Most methods used to determine cell viability cannot deliver on all three of these requirements, so compromises have to be made. Here we show the development and implementation of a cost-effective, no-wash phenotypic assay to simultaneously report the number of cells, percentage of live cells, and cell cycle phase distribution as markers of proliferation and viability. We demonstrate that this assay can be applied to high-density plate formats and be imaged and analyzed in 8 min per plate on a laser scanning imaging cytometer. By comparing the drug-responses of several well-characterized anticancer drugs on HeLa cells, we highlight the key differences between the phenotypic assay and a commercial ATP luminescence detection system. PMID:27504922

  17. Molecular determination of RhD phenotype by DNA typing: clinical applications.

    PubMed

    Cotorruelo, C; Biondi, C; Borrás, S G; Galizzi, S; Di Mónaco, R; Racca, A

    2000-11-01

    Rhesus D (RhD) typing is performed by agglutination methods; however, in clinical situations where these techniques cannot be performed, RhD DNA typing is an alternative approach. The Rh antigens are encoded by the RHD and RHCE genes. In RhD-negative individuals the RHD gene is absent or grossly deleted, but variations in the arrangement of the RH locus in different populations are emerging. The aim of this study was to analyse the gross organization of the RH genes in our population using a previously described multiplex polymerase chain reaction (PCR) method with some modifications. We studied 253 DNA samples from Argentinian blood donors, 15 samples with a reduced expression of the D antigen and 1 Dc- phenotype. We evaluated the clinical utility of this method to ascertain the RhD antigen in 10 patients with warm-type autoimmune haemolytic anaemia (AIHA) and 14 samples of amniotic fluids. All Rh phenotypes were properly characterized and no discrepancies with serological typing were found. Analyses performed in the Dc- phenotype suggest the presence of a hybrid RHCE-RHD gene. DNA typing confirmed the RhD-negative type of one AIHA sample in which serological tests were inconclusive. Foetal DNA typing correctly indicated the RhD in every foetus. VNTR (variable number of tandem repeats) and STR (short tandem repeats) analysis detected maternal contamination in two amniocentesis samples and confirmed the foetal origin of 12. This multiplex PCR strategy is suitable for RhD determination in clinical situations in which serological typing cannot be accomplished with its usual ease. PMID:11085623

  18. Sphingomyelinase-Like Phosphodiesterase 3b Expression Levels Determine Podocyte Injury Phenotypes in Glomerular Disease

    PubMed Central

    Yoo, Tae-Hyun; Pedigo, Christopher E.; Guzman, Johanna; Correa-Medina, Mayrin; Wei, Changli; Villarreal, Rodrigo; Mitrofanova, Alla; Leclercq, Farah; Faul, Christian; Li, Jing; Kretzler, Matthias; Nelson, Robert G.; Lehto, Markku; Forsblom, Carol; Groop, Per-Henrik; Reiser, Jochen; Burke, George William

    2015-01-01

    Diabetic kidney disease (DKD) is the most common cause of ESRD in the United States. Podocyte injury is an important feature of DKD that is likely to be caused by circulating factors other than glucose. Soluble urokinase plasminogen activator receptor (suPAR) is a circulating factor found to be elevated in the serum of patients with FSGS and causes podocyte αVβ3 integrin-dependent migration in vitro. Furthermore, αVβ3 integrin activation occurs in association with decreased podocyte-specific expression of acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3b) in kidney biopsy specimens from patients with FSGS. However, whether suPAR-dependent αVβ3 integrin activation occurs in diseases other than FSGS and whether there is a direct link between circulating suPAR levels and SMPDL3b expression in podocytes remain to be established. Our data indicate that serum suPAR levels are also elevated in patients with DKD. However, unlike in FSGS, SMPDL3b expression was increased in glomeruli from patients with DKD and DKD sera-treated human podocytes, where it prevented αVβ3 integrin activation by its interaction with suPAR and led to increased RhoA activity, rendering podocytes more susceptible to apoptosis. In vivo, inhibition of acid sphingomyelinase reduced proteinuria in experimental DKD but not FSGS, indicating that SMPDL3b expression levels determined the podocyte injury phenotype. These observations suggest that SMPDL3b may be an important modulator of podocyte function by shifting suPAR-mediated podocyte injury from a migratory phenotype to an apoptotic phenotype and that it represents a novel therapeutic glomerular disease target. PMID:24925721

  19. Sphingomyelinase-like phosphodiesterase 3b expression levels determine podocyte injury phenotypes in glomerular disease.

    PubMed

    Yoo, Tae-Hyun; Pedigo, Christopher E; Guzman, Johanna; Correa-Medina, Mayrin; Wei, Changli; Villarreal, Rodrigo; Mitrofanova, Alla; Leclercq, Farah; Faul, Christian; Li, Jing; Kretzler, Matthias; Nelson, Robert G; Lehto, Markku; Forsblom, Carol; Groop, Per-Henrik; Reiser, Jochen; Burke, George William; Fornoni, Alessia; Merscher, Sandra

    2015-01-01

    Diabetic kidney disease (DKD) is the most common cause of ESRD in the United States. Podocyte injury is an important feature of DKD that is likely to be caused by circulating factors other than glucose. Soluble urokinase plasminogen activator receptor (suPAR) is a circulating factor found to be elevated in the serum of patients with FSGS and causes podocyte αVβ3 integrin-dependent migration in vitro. Furthermore, αVβ3 integrin activation occurs in association with decreased podocyte-specific expression of acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3b) in kidney biopsy specimens from patients with FSGS. However, whether suPAR-dependent αVβ3 integrin activation occurs in diseases other than FSGS and whether there is a direct link between circulating suPAR levels and SMPDL3b expression in podocytes remain to be established. Our data indicate that serum suPAR levels are also elevated in patients with DKD. However, unlike in FSGS, SMPDL3b expression was increased in glomeruli from patients with DKD and DKD sera-treated human podocytes, where it prevented αVβ3 integrin activation by its interaction with suPAR and led to increased RhoA activity, rendering podocytes more susceptible to apoptosis. In vivo, inhibition of acid sphingomyelinase reduced proteinuria in experimental DKD but not FSGS, indicating that SMPDL3b expression levels determined the podocyte injury phenotype. These observations suggest that SMPDL3b may be an important modulator of podocyte function by shifting suPAR-mediated podocyte injury from a migratory phenotype to an apoptotic phenotype and that it represents a novel therapeutic glomerular disease target. PMID:24925721

  20. Analysis of Detailed Phenotype Profiles Reveals CHRNA5-CHRNA3-CHRNB4 Gene Cluster Association With Several Nicotine Dependence Traits

    PubMed Central

    Broms, Ulla; Wedenoja, Juho; Largeau, Marine R.; Korhonen, Tellervo; Pitkäniemi, Janne; Keskitalo-Vuokko, Kaisu; Häppölä, Anja; Heikkilä, Katri H.; Heikkilä, Kauko; Ripatti, Samuli; Sarin, Antti-Pekka; Salminen, Outi; Paunio, Tiina; Pergadia, Michele L.; Madden, Pamela A. F.; Kaprio, Jaakko

    2012-01-01

    Introduction: The role of the nicotinic acetylcholine receptor gene cluster on chromosome 15q24-25 in the etiology of nicotine dependence (ND) is still being defined. In this study, we included all 15 tagging single nucleotide polymorphisms (SNPs) within the CHRNA5-CHRNA3-CHRNB4 cluster and tested associations with 30 smoking-related phenotypes. Methods: The study sample was ascertained from the Finnish Twin Cohort study. Twin pairs born 1938–1957 and concordant for a history of cigarette smoking were recruited along with their family members (mainly siblings), as part of the Nicotine Addiction Genetics consortium. The study sample consisted of 1,428 individuals (59% males) from 735 families, with mean age 55.6 years. Results: We detected multiple novel associations for ND. DSM-IV ND symptoms associated significantly with the proxy SNP Locus 1 (rs2036527, p = .000009) and Locus 2 (rs578776, p = .0001) and tolerance factor of the Nicotine Dependence Syndrome Scale (NDSS) showed suggestive association to rs11636753 (p = .0059), rs11634351 (p = .0069), and rs1948 (p = .0071) in CHRNB4. Furthermore, we report significant association with DSM-IV ND diagnosis (rs2036527, p = .0003) for the first time in a Caucasian population. Several SNPs indicated suggestive association for traits related to ages at smoking initiation. Also, rs11636753 in CHRNB4 showed suggestive association with regular drinking (p = .0029) and the comorbidity of depression and ND (p = .0034). Conclusions: We demonstrate novel associations of DSM-IV ND symptoms and the NDSS tolerance subscale. Our results confirm and extend association findings for other ND measures. We show pleiotropic effects of this gene cluster on multiple measures of ND and also regular drinking and the comorbidity of ND and depression. PMID:22241830

  1. Factors that determine the severity of experimental myasthenia gravis.

    PubMed

    Drachman, D B; McIntosh, K R; Yang, B

    1998-05-13

    R antibody production than T cells with specificity for other Torpedo AChR epitopes. This results in production of greater amounts of AChR antibodies, including a critical subset that cross-reacts with autologous mouse AChR. The higher autoantibody levels contribute to the greater susceptibility to EAMG and to the greater severity of manifestations in the B6 strain compared with the bm12 strain. (4) There is a bias in B6 mice toward the production of AChR antibodies of IgG2b isotype. We suggest that T cells specific for alpha 146-162 may contribute to this isotype bias. The IgG2b antibodies appear to have particularly potent "myasthenogenic" effects in rats and mice. (5) Finally, it should be emphasized that these differences in immunological and clinical aspects of EAMG in B6 and bm12 mice are relative rather than absolute. T cells that respond to AChR epitopes other than alpha 146-162 can also provide help for AChR antibody production, albeit less potent. In a sense, this model represents a special case of molecular mimicry. In this case, the source of the foreign antigenic molecule is injection rather than the more usual route of infection. The antigen (Torpedo AChR) is one that these mice would never naturally encounter, and the critical amino acid (lysine 155) of the key epitope (alpha 146-162) is present only in the AChR of electric organs of electric fish and not in the AChR of mice, chickens, cows, or humans. The important point is that a detail of the structure of the foreign antigen--that is, a particular peptide of Torpedo AChR--can determine the severity of an antibody-mediated autoimmune disease, depending on how it interacts with a detail of the structure of the MHC Class II molecule and, in turn, on how the peptide/MHC Class II complex interacts with the available T cell repertoire. (ABSTRACT TRUNCATED) PMID:9668247

  2. Genotype-Phenotype Correlations in Multiple Sclerosis: "HLA" Genes Influence Disease Severity Inferred by [superscript 1]HMR Spectroscopy and MRI Measures

    ERIC Educational Resources Information Center

    Okuda, D. T.; Srinivasan, R.; Oksenberg, J. R.; Goodin, D. S.; Baranzini, S. E.; Beheshtian, A.; Waubant, E.; Zamvil, S. S.; Leppert, D.; Qualley, P.; Lincoln, R.; Gomez, R.; Caillier, S.; George, M.; Wang, J.; Nelson, S. J.; Cree, B. A. C.; Hauser, S. L.; Pelletier, D.

    2009-01-01

    Genetic susceptibility to multiple sclerosis (MS) is associated with the human leukocyte antigen (HLA) "DRB1*1501" allele. Here we show a clear association between DRB1*1501 carrier status and four domains of disease severity in an investigation of genotype-phenotype associations in 505 robust, clinically well characterized MS patients evaluated…

  3. A phenotypic in vitro model for the main determinants of human whole heart function.

    PubMed

    Stancescu, Maria; Molnar, Peter; McAleer, Christopher W; McLamb, William; Long, Christopher J; Oleaga, Carlota; Prot, Jean-Matthieu; Hickman, James J

    2015-08-01

    This article details the construction and testing of a phenotypic assay system that models in vivo cardiac function in a parallel in vitro environment with human stem cell derived cardiomyocytes. The major determinants of human whole-heart function were experimentally modeled by integrating separate 2D cellular systems with BioMicroelectromechanical Systems (BioMEMS) constructs. The model features a serum-free defined medium to enable both acute and chronic evaluation of drugs and toxins. The integration of data from both systems produced biologically relevant predictions of cardiac function in response to varying concentrations of selected drugs. Sotalol, norepinephrine and verapamil were shown to affect the measured parameters according to their specific mechanism of action, in agreement with clinical data. This system is applicable for cardiac side effect assessment, general toxicology, efficacy studies, and evaluation of in vitro cellular disease models in body-on-a-chip systems. PMID:25978005

  4. A phenotypic in vitro model for the main determinants of human whole heart function

    PubMed Central

    Stancescu, Maria; Molnar, Peter; McAleer, Christopher W.; McLamb, William; Long, Christopher J.; Oleaga, Carlota; Prot, Jean-Matthieu; Hickman, James J.

    2015-01-01

    This article details the construction and testing of a phenotypic assay system that models in vivo cardiac function in a parallel in vitro environment with human stem cell derived cardiomyocytes. The major determinants of human whole-heart function were experimentally modeled by integrating separate 2D cellular systems with BioMicroelectromechanical Systems (BioMEMS) constructs. The model featured a serum-free defined medium to enable both acute and chronic evaluation of drugs and toxins. The integration of data from both systems produced biologically relevant predictions of cardiac function in response to varying concentrations of selected drugs. Sotalol, norepinephrine and verapamil were shown to affect the measured parameters according to their specific mechanism of action, in agreement with clinical data. This system is applicable for cardiac side effect assessment, general toxicology, efficacy studies, and evaluation of in vitro cellular disease models in body-on-a-chip systems. PMID:25978005

  5. Genetic Determinants of Risk, Severity, and Outcome in Intracerebral Hemorrhage.

    PubMed

    Falcone, Guido J; Rosand, Jonathan

    2016-06-01

    Spontaneous, nontraumatic intracerebral hemorrhage (ICH) is the most severe manifestation of common forms of cerebral small vessel disease. Although ICH represents only 15% of all strokes, it accounts for a large proportion of stroke-related costs and mortality. Preventive and acute treatments remain limited. Because genetic variation contributes substantially to ICH, genomic analyses constitute a powerful tool to identify new biological mechanisms involved in its occurrence. Through translational research efforts, these newly identified mechanisms can become targets for innovative therapeutic interventions. Here, the authors summarize the most recent genetic discoveries for ICH. They also introduce the Platform for Accelerating Genetic Discovery for Cerebrovascular Disease, a newly created resource that aims to create a common workspace for genetic analyses that will bring together 100,000 stroke cases and suitable controls from numerous institutions in several countries. PMID:27214705

  6. Aging is a weak but relentless determinant of dementia severity

    PubMed Central

    Royall, Donald R.; Palmer, Raymond F.

    2016-01-01

    Structural Equation Models (SEM) can explicitly distinguish “dementia-relevant” variance in cognitive task performance (i.e., “δ” for dementia). In prior work, δ appears to uniquely account for dementia severity regardless of the cognitive measures used to construct it. In this study, we test δ as a mediator of age's prospective association with future cognitive performance and dementia severity in a large, ethnically diverse longitudinal cohort, the Texas Alzheimer's Research and Care Consortium (TARCC). Age had adverse effects on future cognition, and these were largely mediated through δ, independently of education, ethnicity, gender, depression ratings, serum homo-cysteine levels, hemoglobin A1c, and apolipoprotein e4 status. Age explained 4% of variance in δ, and through it, 11-18% of variance in future cognitive performance. Our findings suggest that normative aging is a dementing condition (i.e., a “senility”). While the majority of variance in dementia severity must be independent of age, age's specific effect is likely to accumulate over the lifespan. Our findings also constrain age's dementing effects on cognition to the age-related fraction of “general intelligence” (Spearman's “g”). That has broad biological and pathophysiological implications. PMID:26930722

  7. Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling.

    PubMed

    Ceapa, Corina; Lambert, Jolanda; van Limpt, Kees; Wels, Michiel; Smokvina, Tamara; Knol, Jan; Kleerebezem, Michiel

    2015-08-15

    Lactobacillus rhamnosus is a bacterial species commonly colonizing the gastrointestinal (GI) tract of humans and also frequently used in food products. While some strains have been studied extensively, physiological variability among isolates of the species found in healthy humans or their diet is largely unexplored. The aim of this study was to characterize the diversity of carbohydrate utilization capabilities of human isolates and food-derived strains of L. rhamnosus in relation to their niche of isolation and genotype. We investigated the genotypic and phenotypic diversity of 25 out of 65 L. rhamnosus strains from various niches, mainly human feces and fermented dairy products. Genetic fingerprinting of the strains by amplified fragment length polymorphism (AFLP) identified 11 distinct subgroups at 70% similarity and suggested niche enrichment within particular genetic clades. High-resolution carbohydrate utilization profiling (OmniLog) identified 14 carbon sources that could be used by all of the strains tested for growth, while the utilization of 58 carbon sources differed significantly between strains, enabling the stratification of L. rhamnosus strains into three metabolic clusters that partially correlate with the genotypic clades but appear uncorrelated with the strain's origin of isolation. Draft genome sequences of 8 strains were generated and employed in a gene-trait matching (GTM) analysis together with the publicly available genomes of L. rhamnosus GG (ATCC 53103) and HN001 for several carbohydrates that were distinct for the different metabolic clusters: l-rhamnose, cellobiose, l-sorbose, and α-methyl-d-glucoside. From the analysis, candidate genes were identified that correlate with l-sorbose and α-methyl-d-glucoside utilization, and the proposed function of these genes could be confirmed by heterologous expression in a strain lacking the genes. This study expands our insight into the phenotypic and genotypic diversity of the species L. rhamnosus

  8. Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling

    PubMed Central

    Lambert, Jolanda; van Limpt, Kees; Wels, Michiel; Smokvina, Tamara; Knol, Jan; Kleerebezem, Michiel

    2015-01-01

    Lactobacillus rhamnosus is a bacterial species commonly colonizing the gastrointestinal (GI) tract of humans and also frequently used in food products. While some strains have been studied extensively, physiological variability among isolates of the species found in healthy humans or their diet is largely unexplored. The aim of this study was to characterize the diversity of carbohydrate utilization capabilities of human isolates and food-derived strains of L. rhamnosus in relation to their niche of isolation and genotype. We investigated the genotypic and phenotypic diversity of 25 out of 65 L. rhamnosus strains from various niches, mainly human feces and fermented dairy products. Genetic fingerprinting of the strains by amplified fragment length polymorphism (AFLP) identified 11 distinct subgroups at 70% similarity and suggested niche enrichment within particular genetic clades. High-resolution carbohydrate utilization profiling (OmniLog) identified 14 carbon sources that could be used by all of the strains tested for growth, while the utilization of 58 carbon sources differed significantly between strains, enabling the stratification of L. rhamnosus strains into three metabolic clusters that partially correlate with the genotypic clades but appear uncorrelated with the strain's origin of isolation. Draft genome sequences of 8 strains were generated and employed in a gene-trait matching (GTM) analysis together with the publicly available genomes of L. rhamnosus GG (ATCC 53103) and HN001 for several carbohydrates that were distinct for the different metabolic clusters: l-rhamnose, cellobiose, l-sorbose, and α-methyl-d-glucoside. From the analysis, candidate genes were identified that correlate with l-sorbose and α-methyl-d-glucoside utilization, and the proposed function of these genes could be confirmed by heterologous expression in a strain lacking the genes. This study expands our insight into the phenotypic and genotypic diversity of the species L. rhamnosus

  9. Daily rhythms of radiosensitivity of animals and several determining causes

    NASA Technical Reports Server (NTRS)

    Druzhinin, Y. P.; Malyutina, T. S.; Seraya, V. M.; Rodina, G. P.; Vatsek, A.; Rakova, A.

    1974-01-01

    Daily rhythms of radiosensitivity in rats and mice were determined by survival rates after acute total radiation at the same dosage at different times of the day. Radiosensitivity differed in animals of different species and varieties. Inbred mice exhibited one or two increases in radiosensitivity during the dark, active period of the day. These effects were attributed to periodic changes in the state of stem hematopoietic cells.

  10. Determining otitis media severity from middle ear fluid analysis.

    PubMed

    Juhn, S K; Garvis, W J; Lees, C J; Le, C T; Kim, C S

    1994-05-01

    Otitis media has a complex multifactorial pathogenesis, and the middle ear inflammatory response is typified by the accumulation of cellular and chemical mediators in middle ear effusion. However, specific biochemical and immunochemical factors that may be responsible for the severity or chronicity of otitis media have not been identified. Identification of factors involved in chronicity appears to be an essential step in the treatment and ultimate prevention of chronic otitis media. We analyzed 70 effusion samples from patients 1 to 10 years of age who had chronic otitis media with effusion for two cytokines (interleukin-1 beta and tumor necrosis factor alpha) and total collagenase. The highest concentrations of all three inflammatory mediators were found in purulent otitis media, and concentrations were higher in younger than in older patients. Mediator concentrations were similar in samples obtained from patients having their first myringotomy for otitis media with effusion and in those who had had multiple previous myringotomies. The multiresponse star, which incorporates several biochemical parameters in one graphic illustration, may best characterize the complex nature of middle ear inflammation. PMID:8179269

  11. CREBH Determines the Severity of Sulpyrine-Induced Fatal Shock

    PubMed Central

    Saiga, Hiroyuki; Ma, Ji Su; Ohshima, Jun; Machimura, Sakaaki; Sasai, Miwa; Kimura, Taishi; Ueda, Yoshiyasu; Kayama, Hisako; Takeda, Kiyoshi

    2013-01-01

    Although the pyrazolone derivative sulpyrine is widely used as an antipyretic analgesic drug, side effects, including fatal shock, have been reported. However, the molecular mechanism underlying such a severe side effect is largely unclear. Here, we report that the transcription factor CREBH that is highly expressed in the liver plays an important role in fatal shock induced by sulpyrine in mice. CREBH-deficient mice were resistant to experimental fatal sulpyrine shock. We found that sulpyrine-induced expression of cytochrome P450 2B (CYP2B) family genes, which are involved in sulpyrine metabolism, in the liver was severely impaired in CREBH-deficient mice. Moreover, introduction of CYP2B in CREBH-deficient liver restored susceptibility to sulpyrine. Furthermore, ectopic expression of CREBH up-regulated CYP2B10 promoter activity, and in vivo knockdown of CREBH in wild-type mice conferred a significant resistance to fatal sulpyrine shock. These data demonstrate that CREBH is a positive regulator of CYP2B in response to sulpyrine administration, which possibly results in fatal shock. PMID:23409047

  12. Litter Size Variation in Hypothalamic Gene Expression Determines Adult Metabolic Phenotype in Brandt's Voles (Lasiopodomys brandtii)

    PubMed Central

    Zhang, Xue-Ying; Zhang, Qiang; Wang, De-Hua

    2011-01-01

    Background Early postnatal environments may have long-term and potentially irreversible consequences on hypothalamic neurons involved in energy homeostasis. Litter size is an important life history trait and negatively correlated with milk intake in small mammals, and thus has been regarded as a naturally varying feature of the early developmental environment. Here we investigated the long-term effects of litter size on metabolic phenotype and hypothalamic neuropeptide mRNA expression involved in the regulation of energy homeostasis, using the offspring reared from large (10–12) and small (3–4) litter sizes, of Brandt's voles (Lasiopodomys brandtii), a rodent species from Inner Mongolia grassland in China. Methodology/Principal Findings Hypothalamic leptin signaling and neuropeptides were measured by Real-Time PCR. We showed that offspring reared from small litters were heavier at weaning and also in adulthood than offspring from large litters, accompanied by increased food intake during development. There were no significant differences in serum leptin levels or leptin receptor (OB-Rb) mRNA in the hypothalamus at weaning or in adulthood, however, hypothalamic suppressor of cytokine signaling 3 (SOCS3) mRNA in adulthood increased in small litters compared to that in large litters. As a result, the agouti-related peptide (AgRP) mRNA increased in the offspring from small litters. Conclusions/Significance These findings support our hypothesis that natural litter size has a permanent effect on offspring metabolic phenotype and hypothalamic neuropeptide expression, and suggest central leptin resistance and the resultant increase in AgRP expression may be a fundamental mechanism underlying hyperphagia and the increased risk of overweight in pups of small litters. Thus, we conclude that litter size may be an important and central determinant of metabolic fitness in adulthood. PMID:21637839

  13. Nucleus pulposus phenotypic markers to determine stem cell differentiation: fact or fiction?

    PubMed Central

    Thorpe, Abbey A.; Binch, Abbie L.A.; Creemers, Laura B.; Sammon, Christopher; Le Maitre, Christine L.

    2016-01-01

    Progress in mesenchymal stem cell (MSC) based therapies for nucleus pulposus (NP) regeneration are hampered by a lack of understanding and consensus of the normal NP cell phenotype. Despite the recent consensus paper on NP markers, there is still a need to further validate proposed markers. This study aimed to determine whether an NP phenotypic profile could be identified within a large population of mature NP samples. qRT-PCR was conducted to assess mRNA expression of 13 genes within human non-degenerate articular chondrocytes (AC) (n=10) and NP cells extracted from patients across a spectrum of histological degeneration grades (n=71). qRT-PCR results were used to select NP marker candidates for protein expression analysis. Differential expression at mRNA between AC and non-degenerate NP cells was only observed for Paired Box Protein 1 (PAX1) and Forkhead box F1 (FOXF1). In contrast no other previously suggested markers displayed differential expression between non-degenerate NP and AC at mRNA level. PAX1 and FOXF1 protein expression was significantly higher in the NP compared to annulus fibrosus (AF), cartilaginous endplate (CEP) and AC. In contrast Laminin-5 (LAM-332), Keratin-19 (KRT-19) and Hypoxia Inducible Factor 1 alpha (HIF1α) showed no differential expression in NP cells compared with AC cells. A marker which exclusively differentiates NP cells from AF and AC cells remains to be identified, raising the question: is the NP a heterogeneous population of cells? Or does the natural biological variation during IVD development, degeneration state and even the life cycle of cells make finding one definitive marker impossible? PMID:26735178

  14. The drag characteristics of several airships determined by deceleration tests

    NASA Technical Reports Server (NTRS)

    Thompson, F L; Kirschbaum, H W

    1932-01-01

    This report presents the results of deceleration tests conducted for the purpose of determining the drag characteristics of six airships. The tests were made with airships of various shapes and sizes belonging to the Army, the Navy, and the Goodyear-Zeppelin Corporation. Drag coefficients for the following airships are shown: Army TC-6, TC-10, and TE-2; Navy Los Angeles and ZMC-2; Goodyear Puritan. The coefficients vary from about 0.045 for the small blunt airships to 0.023 for the relatively large slender Los Angeles. This variation may be due to a combination of effects, but the most important of these is probably the effect of length-diameter ratio.

  15. Determining Factors of Lipophilic Micronutrient Bioaccessibility in Several Leafy Vegetables.

    PubMed

    Sriwichai, Wichien; Berger, Jacques; Picq, Christian; Avallone, Sylvie

    2016-03-01

    Micronutrient deficiencies are still a public health issue in least developed countries. Promoting diet diversification is a promising strategy. Numerous fruits and vegetables are rich in micronutrients, but some of these compounds are poorly bioaccessible. The objective of this study was to identify the biochemical determinants of the micronutrient bioaccessibility in leaves. The contents in cell walls, pectins, tannins, and proteins of the leafy vegetables were assessed, and correlations with the micronutrient bioaccessibitity were explored. The leafy vegetables have interesting nutritional profiles with noticeable amounts in protein, provitamin A (β-carotene), and α-tocopherol for some species. Their cell wall contents greatly varied from 3.4 to 8.7 g/100 g as well as their pectin percentages. Only the perilla and drumstick leaves contained condensed tannins. In fresh leaves, the contents in bioaccessible carotenoids were low. The correlation study highlighted that the carotenoid bioaccessibility was negatively correlated to the pectin contents of the leaves. PMID:26844382

  16. Impulsive Action but Not Impulsive Choice Determines Problem Gambling Severity

    PubMed Central

    Brevers, Damien; Cleeremans, Axel; Verbruggen, Frederick; Bechara, Antoine; Kornreich, Charles; Verbanck, Paul; Noël, Xavier

    2012-01-01

    Background Impulsivity is a hallmark of problem gambling. However, impulsivity is not a unitary construct and this study investigated the relationship between problem gambling severity and two facets of impulsivity: impulsive action (impaired ability to withhold a motor response) and impulsive choice (abnormal aversion for the delay of reward). Methods The recruitment includes 65 problem gamblers and 35 normal control participants. On the basis of DSM-IV-TR criteria, two groups of gamblers were distinguished: problem gamblers (n = 38) and pathological gamblers (n = 27) with similar durations of gambling practice. Impulsive action was assessed using a response inhibition task (the stop-signal task). Impulsive choice was estimated with the delay-discounting task. Possible confounds (e.g., IQ, mood, ADHD symptoms) were recorded. Results Both problem and pathological gamblers discounted reward at a higher rate than their controls, but only pathological gamblers showed abnormally low performance on the most demanding condition of the stop-signal task. None of the potential confounds covaried with these results. Conclusions These results suggest that, whereas abnormal impulsive choice characterizes all problem gamblers, pathological gamblers' impairments in impulsive action may represent an important developmental pathway of pathological gambling. PMID:23209796

  17. Environmental determinants of severity in sickle cell disease.

    PubMed

    Tewari, Sanjay; Brousse, Valentine; Piel, Frédéric B; Menzel, Stephan; Rees, David C

    2015-09-01

    Sickle cell disease causes acute and chronic illness, and median life expectancy is reduced by at least 30 years in all countries, with greater reductions in low-income countries. There is a wide spectrum of severity, with some patients having no symptoms and others suffering frequent, life-changing complications. Much of this variability is unexplained, despite increasingly sophisticated genetic studies. Environmental factors, including climate, air quality, socio-economics, exercise and infection, are likely to be important, as demonstrated by the stark differences in outcomes between patients in Africa and USA/Europe. The effects of weather vary with geography, although most studies show that exposure to cold or wind increases hospital attendance with acute pain. Most of the different air pollutants are closely intercorrelated, and increasing overall levels seem to correlate with increased hospital attendance, although higher concentrations of atmospheric carbon monoxide may offer some benefit for patients with sickle cell disease. Exercise causes some adverse physiological changes, although this may be off-set by improvements in cardiovascular health. Most sickle cell disease patients live in low-income countries and socioeconomic factors are undoubtedly important, but little studied beyond documenting that sickle cell disease is associated with decreases in some measures of social status. Infections cause many of the differences in outcomes seen across the world, but again these effects are relatively poorly understood. All the above factors are likely to account for much of the pathology and variability of sickle cell disease, and large prospective studies are needed to understand these effects better. PMID:26341524

  18. Environmental determinants of severity in sickle cell disease

    PubMed Central

    Tewari, Sanjay; Brousse, Valentine; Piel, Frédéric B.; Menzel, Stephan; Rees, David C.

    2015-01-01

    Sickle cell disease causes acute and chronic illness, and median life expectancy is reduced by at least 30 years in all countries, with greater reductions in low-income countries. There is a wide spectrum of severity, with some patients having no symptoms and others suffering frequent, life-changing complications. Much of this variability is unexplained, despite increasingly sophisticated genetic studies. Environmental factors, including climate, air quality, socio-economics, exercise and infection, are likely to be important, as demonstrated by the stark differences in outcomes between patients in Africa and USA/Europe. The effects of weather vary with geography, although most studies show that exposure to cold or wind increases hospital attendance with acute pain. Most of the different air pollutants are closely intercorrelated, and increasing overall levels seem to correlate with increased hospital attendance, although higher concentrations of atmospheric carbon monoxide may offer some benefit for patients with sickle cell disease. Exercise causes some adverse physiological changes, although this may be off-set by improvements in cardiovascular health. Most sickle cell disease patients live in low-income countries and socioeconomic factors are undoubtedly important, but little studied beyond documenting that sickle cell disease is associated with decreases in some measures of social status. Infections cause many of the differences in outcomes seen across the world, but again these effects are relatively poorly understood. All the above factors are likely to account for much of the pathology and variability of sickle cell disease, and large prospective studies are needed to understand these effects better. PMID:26341524

  19. Several methods to determine heavy metals in the human brain

    NASA Astrophysics Data System (ADS)

    Andrási, Erzsébet; Igaz, Sarolta; Szoboszlai, Norbert; Farkas, Éva; Ajtony, Zsolt

    1999-05-01

    The determination of naturally occurring heavy metals in various parts of the human brain is discussed. The patients had no diseases in their central nervous systems (five individuals, mean age 70 years). Twenty brain parts were selected from both hemispheres. The analysis was carried out by graphite furnace atomic absorption spectrometry, inductively coupled plasma atomic emission spectrometry and instrumental neutron activation analysis methods. Accuracy and precision of the applied techniques were tested by using standard reference materials. Two digestion methods were used to dissolve the brain samples for ICP-AES and GF-AAS. One was performed in a Parr-bomb and the second in a microwave oven. The present results show a non-homogeneous distribution of the essential elements (Cu, Fe, Mn, Zn) in normal human brain. Corresponding regions in both hemispheres showed an almost identical concentration of these elements. In the case of toxic elements (Pb, Cd) an average value in different brain regions can not be established because of the high variability of individual data. This study indicates that beside differences in Pb and Cd intake with foods or cigarette smoke inhalation, the main factors of the high inter-individual variability of these element concentrations in human brain parts may be a marked difference in individual elimination or accumulation capabilities.

  20. FISH diagnosis of partial trisomy 13 and tetrasomy 13 in a patient with severe trigonocephaly (C) phenotype

    SciTech Connect

    Chu, T.W.; Teebi, A.S.; Gibson, L.; Breg, W.R.; Yang-Feng, T.L.

    1994-08-01

    An infant girl with manifestations resembling Opitz trigonocephaly (C) syndrome who died at age 6 days was found to have a complex chromosome abnormality with t(13;18)(q22;q23) and a recombinant chromosome 13 involving duplicated segments of 13q. Precise characterization was possible with the application of fluorescence in situ hybridization (FISH) using chromosome specific probes. The patient`s phenotype is compared to that of other syndromes involving trigonocephaly. 20 refs., 3 figs., 3 tabs.

  1. Cloud Altitude Determination of Overshooting Tops in Severe Thunderstorms

    NASA Astrophysics Data System (ADS)

    Goldberg, R.; Magee, N. B.

    2011-12-01

    observation spot to the cloud top was measured and the geographic position of the cloud was determined using MODIS images and Google Earth. After cataloging about 125 A-Train intersects of deep convection from January 1 to July 1 of 2011, the maximum convective cloud altitudes were collected from CALIPSO, CloudSat, radar, and modeling data. Our results confirm previous findings that CALIPSO consistently detects cloud tops at a higher altitude than CloudSat. It was also found that CALIPSO cloud tops were consistently higher than Doppler-radar echo tops or NAM cloud tops. However, CALIPSO altitudes were very consistent with altitudes determined by direct sighting. Doppler radar and modeling data often closely matched satellite observations, but on occasion they showed large differences. Careful analysis of the limitations and the biases of these data could improve our understanding of convective cloud-top dynamics and improve in-flight routing decisions for commercial aviation.

  2. A point mutation in AgrC determines cytotoxic or colonizing properties associated with phenotypic variants of ST22 MRSA strains.

    PubMed

    Mairpady Shambat, Srikanth; Siemens, Nikolai; Monk, Ian R; Mohan, Disha B; Mukundan, Santhosh; Krishnan, Karthickeyan Chella; Prabhakara, Sushma; Snäll, Johanna; Kearns, Angela; Vandenesch, Francois; Svensson, Mattias; Kotb, Malak; Gopal, Balasubramanian; Arakere, Gayathri; Norrby-Teglund, Anna

    2016-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of skin and soft tissue infections. One of the highly successful and rapidly disseminating clones is MRSA ST22 commonly associated with skin tropism. Here we show that a naturally occurring single amino acid substitution (tyrosine to cysteine) at position 223 of AgrC determines starkly different ST22 S. aureus virulence phenotypes, e.g. cytotoxic or colonizing, as evident in both in vitro and in vivo skin infections. Y223C amino acid substitution destabilizes AgrC-AgrA interaction leading to a colonizing phenotype characterized by upregulation of bacterial surface proteins. The colonizing phenotype strains cause less severe skin tissue damage, show decreased susceptibility towards the antimicrobial LL-37 and induce autophagy. In contrast, cytotoxic strains with tyrosine at position 223 of AgrC cause infections characterized by inflammasome activation and severe skin tissue pathology. Taken together, the study demonstrates how a single amino acid substitution in the histidine kinase receptor AgrC of ST22 strains determines virulence properties and infection outcome. PMID:27511873

  3. A point mutation in AgrC determines cytotoxic or colonizing properties associated with phenotypic variants of ST22 MRSA strains

    PubMed Central

    Mairpady Shambat, Srikanth; Siemens, Nikolai; Monk, Ian R.; Mohan, Disha B.; Mukundan, Santhosh; Krishnan, Karthickeyan Chella; Prabhakara, Sushma; Snäll, Johanna; Kearns, Angela; Vandenesch, Francois; Svensson, Mattias; Kotb, Malak; Gopal, Balasubramanian; Arakere, Gayathri; Norrby-Teglund, Anna

    2016-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of skin and soft tissue infections. One of the highly successful and rapidly disseminating clones is MRSA ST22 commonly associated with skin tropism. Here we show that a naturally occurring single amino acid substitution (tyrosine to cysteine) at position 223 of AgrC determines starkly different ST22 S. aureus virulence phenotypes, e.g. cytotoxic or colonizing, as evident in both in vitro and in vivo skin infections. Y223C amino acid substitution destabilizes AgrC-AgrA interaction leading to a colonizing phenotype characterized by upregulation of bacterial surface proteins. The colonizing phenotype strains cause less severe skin tissue damage, show decreased susceptibility towards the antimicrobial LL-37 and induce autophagy. In contrast, cytotoxic strains with tyrosine at position 223 of AgrC cause infections characterized by inflammasome activation and severe skin tissue pathology. Taken together, the study demonstrates how a single amino acid substitution in the histidine kinase receptor AgrC of ST22 strains determines virulence properties and infection outcome. PMID:27511873

  4. Genetic Determinants of Cardio-Metabolic Risk: A Proposed Model for Phenotype Association and Interaction

    PubMed Central

    Blackett, Piers R; Sanghera, Dharambir K

    2012-01-01

    This review provides a translational and unifying summary of metabolic syndrome genetics and highlights evidence that genetic studies are starting to unravel and untangle origins of the complex and challenging cluster of disease phenotypes. The associated genes effectively express in the brain, liver, kidney, arterial endothelium, adipocytes, myocytes and β cells. Progression of syndrome traits has been associated with ectopic lipid accumulation in the arterial wall, visceral adipocytes, myocytes, and liver. Thus it follows that the genetics of dyslipidemia, obesity, and non-alcoholic fatty liver (NAFLD) disease are central in triggering progression of the syndrome to overt expression of disease traits, and have become a key focus of interest for early detection and for designing prevention and treatments. To support the “birds’ eye view” approach we provide a road-map depicting commonality and interrelationships between the traits and their genetic and environmental determinants based on known risk factors, metabolic pathways, pharmacological targets, treatment responses, gene networks, pleiotropy, and association with circadian rhythm. Although only a small portion of the known heritability is accounted for and there is insufficient support for clinical application of gene-based prediction models, there is direction and encouraging progress in a rapidly moving field that is beginning to show clinical relevance. PMID:23351585

  5. Phenotype Similarity Regression for Identifying the Genetic Determinants of Rare Diseases

    PubMed Central

    Greene, Daniel; Richardson, Sylvia; Turro, Ernest

    2016-01-01

    Rare genetic disorders, which can now be studied systematically with affordable genome sequencing, are often caused by high-penetrance rare variants. Such disorders are often heterogeneous and characterized by abnormalities spanning multiple organ systems ascertained with variable clinical precision. Existing methods for identifying genes with variants responsible for rare diseases summarize phenotypes with unstructured binary or quantitative variables. The Human Phenotype Ontology (HPO) allows composite phenotypes to be represented systematically but association methods accounting for the ontological relationship between HPO terms do not exist. We present a Bayesian method to model the association between an HPO-coded patient phenotype and genotype. Our method estimates the probability of an association together with an HPO-coded phenotype characteristic of the disease. We thus formalize a clinical approach to phenotyping that is lacking in standard regression techniques for rare disease research. We demonstrate the power of our method by uncovering a number of true associations in a large collection of genome-sequenced and HPO-coded cases with rare diseases. PMID:26924528

  6. Phenotype Similarity Regression for Identifying the Genetic Determinants of Rare Diseases.

    PubMed

    Greene, Daniel; Richardson, Sylvia; Turro, Ernest

    2016-03-01

    Rare genetic disorders, which can now be studied systematically with affordable genome sequencing, are often caused by high-penetrance rare variants. Such disorders are often heterogeneous and characterized by abnormalities spanning multiple organ systems ascertained with variable clinical precision. Existing methods for identifying genes with variants responsible for rare diseases summarize phenotypes with unstructured binary or quantitative variables. The Human Phenotype Ontology (HPO) allows composite phenotypes to be represented systematically but association methods accounting for the ontological relationship between HPO terms do not exist. We present a Bayesian method to model the association between an HPO-coded patient phenotype and genotype. Our method estimates the probability of an association together with an HPO-coded phenotype characteristic of the disease. We thus formalize a clinical approach to phenotyping that is lacking in standard regression techniques for rare disease research. We demonstrate the power of our method by uncovering a number of true associations in a large collection of genome-sequenced and HPO-coded cases with rare diseases. PMID:26924528

  7. Identification of a premature stop codon mutation in the PHGDH gene in severe Neu-Laxova syndrome-evidence for phenotypic variability.

    PubMed

    Mattos, Eduardo P; Silva, André Anjos da; Magalhães, José Antônio A; Leite, Júlio César L; Leistner-Segal, Sandra; Gus-Kessler, Rejane; Perez, Juliano Adams; Vedolin, Leonardo M; Torreblanca-Zanca, Albertina; Lapunzina, Pablo; Ruiz-Perez, Victor L; Sanseverino, Maria Teresa V

    2015-06-01

    In some cases Neu-Laxova syndrome (NLS) is linked to serine deficiency due to mutations in the phosphoglycerate dehydrogenase (PHGDH) gene. We describe the prenatal and postnatal findings in a fetus with one of the most severe NLS phenotypes described so far, caused by a homozygous nonsense mutation of PHGDH. Serial ultrasound (US) and pre- and postnatal magnetic resonance imaging (MRI) evaluations were performed. Prenatally, serial US evaluations suggested symmetric growth restriction, microcephaly, hypoplasia of the cerebellar vermis, micrognathia, hydrops, shortened limbs, arthrogryposis, and talipes equinovarus. The prenatal MRI confirmed these findings prompting a diagnosis of NLS. After birth, radiological imaging did not detect any gross bone abnormalities. DNA was extracted from fetal and parental peripheral blood, all coding exons of PHGDH were PCR-amplified and subjected to Sanger sequencing. Sequencing of PHGDH identified a homozygous premature stop codon mutation (c.1297C>T; p.Gln433*) in fetal DNA, both parents (first-cousins) being heterozygotes. Based on previous associations of mutations in this gene with a milder NLS phenotype, as well as cases of serine deficiency, these observations lend further support to a genotype-phenotype correlation between the degree of PHGDH inactivation and disease severity. PMID:25913727

  8. Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study

    PubMed Central

    Cleynen, Isabelle; Boucher, Gabrielle; Jostins, Luke; Schumm, L Philip; Zeissig, Sebastian; Ahmad, Tariq; Andersen, Vibeke; Andrews, Jane M; Annese, Vito; Brand, Stephan; Brant, Steven R; Cho, Judy H; Daly, Mark J; Dubinsky, Marla; Duerr, Richard H; Ferguson, Lynnette R; Franke, Andre; Gearry, Richard B; Goyette, Philippe; Hakonarson, Hakon; Halfvarson, Jonas; Hov, Johannes R; Huang, Hailang; Kennedy, Nicholas A; Kupcinskas, Limas; Lawrance, Ian C; Lee, James C; Satsangi, Jack; Schreiber, Stephan; Théâtre, Emilie; van der Meulen-de Jong, Andrea E; Weersma, Rinse K; Wilson, David C; Parkes, Miles; Vermeire, Severine; Rioux, John D; Mansfield, John; Silverberg, Mark S; Radford-Smith, Graham; McGovern, Dermot P B; Barrett, Jeffrey C; Lees, Charlie W

    2016-01-01

    Summary Background Crohn's disease and ulcerative colitis are the two major forms of inflammatory bowel disease; treatment strategies have historically been determined by this binary categorisation. Genetic studies have identified 163 susceptibility loci for inflammatory bowel disease, mostly shared between Crohn's disease and ulcerative colitis. We undertook the largest genotype association study, to date, in widely used clinical subphenotypes of inflammatory bowel disease with the goal of further understanding the biological relations between diseases. Methods This study included patients from 49 centres in 16 countries in Europe, North America, and Australasia. We applied the Montreal classification system of inflammatory bowel disease subphenotypes to 34 819 patients (19 713 with Crohn's disease, 14 683 with ulcerative colitis) genotyped on the Immunochip array. We tested for genotype–phenotype associations across 156 154 genetic variants. We generated genetic risk scores by combining information from all known inflammatory bowel disease associations to summarise the total load of genetic risk for a particular phenotype. We used these risk scores to test the hypothesis that colonic Crohn's disease, ileal Crohn's disease, and ulcerative colitis are all genetically distinct from each other, and to attempt to identify patients with a mismatch between clinical diagnosis and genetic risk profile. Findings After quality control, the primary analysis included 29 838 patients (16 902 with Crohn's disease, 12 597 with ulcerative colitis). Three loci (NOD2, MHC, and MST1 3p21) were associated with subphenotypes of inflammatory bowel disease, mainly disease location (essentially fixed over time; median follow-up of 10·5 years). Little or no genetic association with disease behaviour (which changed dramatically over time) remained after conditioning on disease location and age at onset. The genetic risk score representing all known risk alleles for

  9. New mitochondrial DNA mutations in tRNA associated with three severe encephalopamyopathic phenotypes: neonatal, infantile, and childhood onset.

    PubMed

    del Mar O'Callaghan, María; Emperador, Sonia; López-Gallardo, Ester; Jou, Cristina; Buján, Nuria; Montero, Raquel; Garcia-Cazorla, Angels; Gonzaga, Diana; Ferrer, Isidre; Briones, Paz; Ruiz-Pesini, Eduardo; Pineda, Mercè; Artuch, Rafael; Montoya, Julio

    2012-08-01

    The reported cases showed clinical, biochemical, histopathological, and molecular features lending support to the hypothesis of a pathogenic effect of the detected mutations. Case 1 was a neonatal presentation who showed multiple mitochondrial respiratory chain enzyme defects in muscle associated with a new homoplasmic m.5514A > G transition in the tRNA(Trp) gene. Case 2 was a late infantile presentation who also showed mitochondrial respiratory chain enzyme deficiencies in muscle together with a new m.1643A > G tRNA(Val) mutation in homoplasmy. Case 3 showed a MERRF phenotype presented in childhood associated with the once previously reported m.15923A > G mutation in heteroplasmy in all the tissues studied. PMID:22638997

  10. The proteasomal and apoptotic phenotype determine bortezomib sensitivity of non-small cell lung cancer cells

    PubMed Central

    Voortman, Jens; Chęcińska, Agnieszka; Giaccone, Giuseppe

    2007-01-01

    Bortezomib is a novel anti-cancer agent which has shown promising activity in non-small lung cancer (NSCLC) patients. However, only a subset of patients respond to this treatment. We show that NSCLC cell lines are differentially sensitive to bortezomib, IC50 values ranging from 5 to 83 nM. The apoptosis-inducing potential of bortezomib in NSCLC cells was found to be dependent not only on the apoptotic phenotype but also on the proteasomal phenotype of individual cell lines. Upon effective proteasome inhibition, H460 cells were more susceptible to apoptosis induction by bortezomib than SW1573 cells, indicating a different apoptotic phenotype. However, exposure to a low dose of bortezomib did only result in SW1573 cells, and not in H460 cells, in inhibition of proteasome activity and subsequent apoptosis. This suggests a different proteasomal phenotype as well. Additionally, overexpression of anti-apoptotic protein Bcl-2 in H460 cells did not affect the proteasomal phenotype of H460 cells but did result in decreased bortezomib-induced apoptosis. In conclusion, successful proteasome-inhibitor based treatment strategies in NSCLC face the challenge of having to overcome apoptosis resistance as well as proteasomal resistance of individual lung cancer cells. Further studies in NSCLC are warranted to elucidate underlying mechanisms. PMID:18021420

  11. Tumourigenic phenotypes of human melanoma cell lines in nude mice determined by an active antitumour mechanism.

    PubMed Central

    Jacubovich, R.; Cabrillat, H.; Gerlier, D.; Bailly, M.; Doré, J. F.

    1985-01-01

    Ten human melanoma cell lines (HMCL) were tested for their ability to grow subcutaneously in nude mice. Using a standard inoculum, the HMCL could be characterized by their highly, fairly or poorly xenografting phenotype. These phenotypes were stable and the phenotype of one HMCL was recovered within cell clones derived from it. The role of nude mice natural defences in the expression of HMCL xenografting phenotypes was studied. Sublethal whole body irradiation and silica pretreatment of recipients enabled poorly tumourigenic HMCL to grow in most animals without affecting their splenic NK activity. Admixture of BCG or MDP encapsulated in liposomes with highly tumourigenic HMCL resulted in the abrogation of tumour growth in naive nude mice. The long lasting abrogating of NK activity in vivo by treatment with anti-asialo-GM1 anti-serum did not enhance the growth of a poorly tumourigenic HMCL. The HMCL were found to be resistant to in vitro murine NK activity. These results showed that the expression of the HMCL xenografting phenotypes could be controlled by the nude mice natural defences. NK cells did not seem to be largely involved whereas macrophages might be good candidates as anti-xenograft effectors. PMID:3882112

  12. Nile red fluorescence screening facilitating neutral lipid phenotype determination in budding yeast, Saccharomyces cerevisiae, and the fission yeast Schizosaccharomyces pombe.

    PubMed

    Rostron, Kerry A; Rolph, Carole E; Lawrence, Clare L

    2015-07-01

    Investigation of yeast neutral lipid accumulation is important for biotechnology and also for modelling aberrant lipid metabolism in human disease. The Nile red (NR) method has been extensively utilised to determine lipid phenotypes of yeast cells via microscopic means. NR assays have been used to differentiate lipid accumulation and relative amounts of lipid in oleaginous species but have not been thoroughly validated for phenotype determination arising from genetic modification. A modified NR assay, first described by Sitepu et al. (J Microbiol Methods 91:321-328, 2012), was able to detect neutral lipid changes in Saccharomyces cerevisiae deletion mutants with sensitivity similar to more advanced methodology. We have also be able to, for the first time, successfully apply the NR assay to the well characterised fission yeast Schizosaccharomyces pombe, an increasingly important organism in biotechnology. The described NR fluorescence assay is suitable for increased throughput and rapid screening of genetically modified strains in both the biotechnology industry and for modelling ectopic lipid production for a variety of human diseases. This ultimately negates the need for labour intensive and time consuming lipid analyses of samples that may not yield a desirable lipid phenotype, whilst genetic modifications impacting significantly on the cellular lipid phenotype can be further promoted for more in depth analyses. PMID:25948336

  13. Severe XLP Phenotype Caused by a Novel Intronic Mutation in the SH2D1A Gene.

    PubMed

    Tóth, B; Soltész, B; Gyimesi, E; Csorba, G; Veres, Á; Lányi, Á; Kovács, G; Maródi, L; Erdős, M

    2015-01-01

    We describe here a novel c.137 + 5G > A intronic mutation in the SH2D1A gene of the signaling lymphocyte activation molecule (SLAM)-associated protein (SAP) in association with Epstein-Barr virus (EBV)-induced fatal infectious mononucleosis (FIM) in an 8-year-old male patient and his 3-year-old step brother. The mother and the maternal grandmother of the boys are healthy and heterozygous for this sequence variant. Genetic sequencing of blood-cell-derived cDNA in the younger patient revealed a 22 bp deletion in the SH2D1A cDNA. Immunoblot and flow cytometry analysis performed in this younger patient showed the lack of SAP protein expression in peripheral blood lymphocytes. These data suggest that the novel c.137 + 5G > A mutation results in loss of function of SAP protein and leads to typical X-linked lymphoproliferative disease phenotype. We propose that intron 1 and the c.137 + 5G may be the most frequent intronic hot spot for SH2D1A splicing mutation. PMID:25491288

  14. Virulence plasmid (pYV)-associated expression of phenotypic virulent determinants in pathogenic Yersinia species: a convenient method for monitoring the presence of pYV under culture conditions and its application for....food

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In Yersinia pestis, Y. pseudotuberculosis, and Y, enterocolitica, phenotypic expression of several virulence plasmid (pYV: 70-kb)-associated genetic determinants may include low calcium response (Lcr, pin point colony, size = 0.36 mm), colony morphology (size = 1.13 mm), crystal violet (CV) binding...

  15. A Novel Splice Variant in the N-propeptide of COL5A1 Causes an EDS Phenotype with Severe Kyphoscoliosis and Eye Involvement

    PubMed Central

    Symoens, Sofie; Malfait, Fransiska; Vlummens, Philip; Hermanns-Lê, Trinh; Syx, Delfien; De Paepe, Anne

    2011-01-01

    Background The Ehlers-Danlos Syndrome (EDS) is a heritable connective tissue disorder characterized by hyperextensible skin, joint hypermobility and soft tissue fragility. The classic subtype of EDS is caused by mutations in one of the type V collagen genes (COL5A1 and COL5A2). Most mutations affect the type V collagen helical domain and lead to a diminished or structurally abnormal type V collagen protein. Remarkably, only two mutations were reported to affect the extended, highly conserved N-propeptide domain, which plays an important role in the regulation of the heterotypic collagen fibril diameter. We identified a novel COL5A1 N-propeptide mutation, resulting in an unusual but severe classic EDS phenotype and a remarkable splicing outcome. Methodology/Principal Findings We identified a novel COL5A1 N-propeptide acceptor-splice site mutation (IVS6-2A>G, NM_000093.3_c.925-2A>G) in a patient with cutaneous features of EDS, severe progressive scoliosis and eye involvement. Two mutant transcripts were identified, one with an exon 7 skip and one in which exon 7 and the upstream exon 6 are deleted. Both transcripts are expressed and secreted into the extracellular matrix, where they can participate in and perturb collagen fibrillogenesis, as illustrated by the presence of dermal collagen cauliflowers. Determination of the order of intron removal and computational analysis showed that simultaneous skipping of exons 6 and 7 is due to the combined effect of delayed splicing of intron 7, altered pre-mRNA secondary structure, low splice site strength and possibly disturbed binding of splicing factors. Conclusions/Significance We report a novel COL5A1 N-propeptide acceptor-splice site mutation in intron 6, which not only affects splicing of the adjacent exon 7, but also causes a splicing error of the upstream exon 6. Our findings add further insights into the COL5A1 splicing order and show for the first time that a single COL5A1 acceptor-splice site mutation can perturb

  16. 78 FR 70329 - Modification to the Scopes of Recognition of Several NRTLs; Final Determination

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-25

    ...In this notice, OSHA is making a final determination to delete specific test standards from the scopes of recognition of several Nationally Recognized Testing Laboratories (NRTLs), and to incorporate replacement test standards into the scopes of recognition of several...

  17. A novel mutation in DNAJB6, p.(Phe91Leu), in childhood-onset LGMD1D with a severe phenotype.

    PubMed

    Nam, Tai-Seung; Li, Wenting; Heo, Suk-Hee; Lee, Kyung-Hwa; Cho, Anna; Shin, Jin-Hong; Kim, Young Ok; Chae, Jong-Hee; Kim, Dae-Seong; Kim, Myeong-Kyu; Choi, Seok-Yong

    2015-11-01

    To identify and characterize genetic mutation in a Korean family with limb-girdle muscular dystrophy 1 (LGMD1), we analyzed in the affected family members clinical features, DNAJB6 by Sanger sequencing, muscle structures by magnetic resonance imaging (MRI), and functional consequences of the identified mutation using a zebrafish model. The clinical phenotypes along with identification of a novel c.271T > C (p.(Phe91Leu)) mutation in DNAJB6 led to the diagnosis of LGMD1D in the affected family members. This mutation presents unique clinical and radiological features compared with other DNAJB6 mutants. All affected members examined showed reduced pulmonary function, and had nasal voice and dysphagia except the two members who were thirteen and twelve years of age at the time of examination. Muscle phenotypes developed between 8 and 11 years of age and were more severe as compared to previously reported LGMD1D patients with mutant DNAJB6. Patients' MRI scans exhibited early involvement of the lateral head of gastrocnemius, in contrast to its late involvement in reported LGMD1D cases. Functional study using zebrafish embryos demonstrated that p.Phe91Leu elicits more severe muscle defects than the reported p.Phe93Leu and p.Pro96Arg mutations. We conclude that a novel p.(Phe91Leu) mutation in DNAJB6 is associated with severe childhood-onset LGMD1D. PMID:26371419

  18. Als2 mRNA splicing variants detected in KO mice rescue severe motor dysfunction phenotype in Als2 knock-down zebrafish.

    PubMed

    Gros-Louis, Francois; Kriz, Jasna; Kabashi, Edor; McDearmid, Jonathan; Millecamps, Stéphanie; Urushitani, Makoto; Lin, Li; Dion, Patrick; Zhu, Qinzhang; Drapeau, Pierre; Julien, Jean-Pierre; Rouleau, Guy A

    2008-09-01

    Recessive ALS2 mutations are linked to three related but slightly different neurodegenerative disorders: amyotrophic lateral sclerosis, hereditary spastic paraplegia and primary lateral sclerosis. To investigate the function of the ALS2 encoded protein, we generated Als2 knock-out (KO) mice and zAls2 knock-down zebrafish. The Als2(-/-) mice lacking exon 2 and part of exon 3 developed mild signs of neurodegeneration compatible with axonal transport deficiency. In contrast, zAls2 knock-down zebrafish had severe developmental abnormalities, swimming deficits and motor neuron perturbation. We identified, by RT-PCR, northern and western blotting novel Als2 transcripts in mouse central nervous system. These Als2 transcripts were present in Als2 null mice as well as in wild-type littermates and some rescued the zebrafish phenotype. Thus, we speculate that the newly identified Als2 mRNA species prevent the Als2 KO mice from developing severe neurodegenerative disease and might also regulate the severity of the motor neurons phenotype observed in ALS2 patients. PMID:18558633

  19. Rapid-Throughput Skeletal Phenotyping of 100 Knockout Mice Identifies 9 New Genes That Determine Bone Strength

    PubMed Central

    Gogakos, Apostolos; White, Jacqueline K.; Evans, Holly; Jacques, Richard M.; van der Spek, Anne H.; Ramirez-Solis, Ramiro; Ryder, Edward; Sunter, David; Boyde, Alan; Campbell, Michael J.

    2012-01-01

    Osteoporosis is a common polygenic disease and global healthcare priority but its genetic basis remains largely unknown. We report a high-throughput multi-parameter phenotype screen to identify functionally significant skeletal phenotypes in mice generated by the Wellcome Trust Sanger Institute Mouse Genetics Project and discover novel genes that may be involved in the pathogenesis of osteoporosis. The integrated use of primary phenotype data with quantitative x-ray microradiography, micro-computed tomography, statistical approaches and biomechanical testing in 100 unselected knockout mouse strains identified nine new genetic determinants of bone mass and strength. These nine new genes include five whose deletion results in low bone mass and four whose deletion results in high bone mass. None of the nine genes have been implicated previously in skeletal disorders and detailed analysis of the biomechanical consequences of their deletion revealed a novel functional classification of bone structure and strength. The organ-specific and disease-focused strategy described in this study can be applied to any biological system or tractable polygenic disease, thus providing a general basis to define gene function in a system-specific manner. Application of the approach to diseases affecting other physiological systems will help to realize the full potential of the International Mouse Phenotyping Consortium. PMID:22876197

  20. X-linked creatine transporter defect: A report on two unrelated boys with a severe clinical phenotype

    PubMed Central

    Anselm, I. M.; Alkuraya, F. S.; Salomons, G. S.; Jakobs, C.; Fulton, A. B.; Mazumdar, M.; Rivkin, M.; Frye, R.; Poussaint, T. Young; Marsden, D.

    2008-01-01

    Summary We report two unrelated boys with the X-linked creatine transporter defect (CRTR) and clinical features more severe than those previously described with this disorder. These two boys presented at ages 12 and 30 months with severe mental retardation, absent speech development, hypotonia, myopathy and extra-pyramidal movement disorder. One boy has seizures and some dysmorphic features; he also has evidence of an oxidative phosphorylation defect. They both had classical absence of creatine peak on brain magnetic resonance spectroscopy (MRS). In one, however, this critical finding was overlooked in the initial interpretation and was discovered upon subsequent review of the MRS. PMID:16601897

  1. Improved Survival and Reduced Phenotypic Severity Following AAV9/MECP2 Gene Transfer to Neonatal and Juvenile Male Mecp2 Knockout Mice

    PubMed Central

    Gadalla, Kamal KE; Bailey, Mark ES; Spike, Rosemary C; Ross, Paul D; Woodard, Kenton T; Kalburgi, Sahana Nagabhushan; Bachaboina, Lavanya; Deng, Jie V; West, Anne E; Samulski, R Jude; Gray, Steven J; Cobb, Stuart R

    2013-01-01

    Typical Rett syndrome (RTT) is a pediatric disorder caused by loss-of-function mutations in the methyl-CpG binding protein 2 (MECP2) gene. The demonstrated reversibility of RTT-like phenotypes in mice suggests that MECP2 gene replacement is a potential therapeutic option in patients. We report improvements in survival and phenotypic severity in Mecp2-null male mice after neonatal intracranial delivery of a single-stranded (ss) AAV9/chicken β-actin (CBA)-MECP2 vector. Median survival was 16.6 weeks for MECP2-treated versus 9.3 weeks for green fluorescent protein (GFP)-treated mice. ssAAV9/CBA-MECP2–treated mice also showed significant improvement in the phenotype severity score, in locomotor function, and in exploratory activity, as well as a normalization of neuronal nuclear volume in transduced cells. Wild-type (WT) mice receiving neonatal injections of the same ssAAV9/CBA-MECP2 vector did not show any significant deficits, suggesting a tolerance for modest MeCP2 overexpression. To test a MECP2 gene replacement approach in a manner more relevant for human translation, a self-complementary (sc) adeno-associated virus (AAV) vector designed to drive MeCP2 expression from a fragment of the Mecp2 promoter was injected intravenously (IV) into juvenile (4–5 weeks old) Mecp2-null mice. While the brain transduction efficiency in juvenile mice was low (~2–4% of neurons), modest improvements in survival were still observed. These results support the concept of MECP2 gene therapy for RTT. PMID:23011033

  2. Biomechanical activation of vascular endothelium as a determinant of its functional phenotype

    PubMed Central

    García-Cardeña, Guillermo; Comander, Jason; Anderson, Keith R.; Blackman, Brett R.; Gimbrone, Michael A.

    2001-01-01

    One of the striking features of vascular endothelium, the single-cell-thick lining of the cardiovascular system, is its phenotypic plasticity. Various pathophysiologic factors, such as cytokines, growth factors, hormones, and metabolic products, can modulate its functional phenotype in health and disease. In addition to these humoral stimuli, endothelial cells respond to their biomechanical environment, although the functional implications of this biomechanical paradigm of activation have not been fully explored. Here we describe a high-throughput genomic analysis of modulation of gene expression observed in cultured human endothelial cells exposed to two well defined biomechanical stimuli—a steady laminar shear stress and a turbulent shear stress of equivalent spatial and temporal average intensity. Comparison of the transcriptional activity of 11,397 unique genes revealed distinctive patterns of up- and down-regulation associated with each type of stimulus. Cluster analyses of transcriptional profiling data were coupled with other molecular and cell biological techniques to examine whether these global patterns of biomechanical activation are translated into distinct functional phenotypes. Confocal immunofluorescence microscopy of structural and contractile proteins revealed the formation of a complex apical cytoskeleton in response to laminar shear stress. Cell cycle analysis documented different effects of laminar and turbulent shear stresses on cell proliferation. Thus, endothelial cells have the capacity to discriminate among specific biomechanical forces and to translate these input stimuli into distinctive phenotypes. The demonstration that hemodynamically derived stimuli can be strong modulators of endothelial gene expression has important implications for our understanding of the mechanisms of vascular homeostasis and atherogenesis. PMID:11296290

  3. Vertically transmitted faecal IgA levels determine extra-chromosomal phenotypic variation.

    PubMed

    Moon, Clara; Baldridge, Megan T; Wallace, Meghan A; Burnham, Carey-Ann D; Virgin, Herbert W; Stappenbeck, Thaddeus S

    2015-05-01

    The proliferation of genetically modified mouse models has exposed phenotypic variation between investigators and institutions that has been challenging to control. In many cases, the microbiota is the presumed cause of the variation. Current solutions to account for phenotypic variability include littermate and maternal controls or defined microbial consortia in gnotobiotic mice. In conventionally raised mice, the microbiome is transmitted from the dam. Here we show that microbially driven dichotomous faecal immunoglobulin-A (IgA) levels in wild-type mice within the same facility mimic the effects of chromosomal mutations. We observe in multiple facilities that vertically transmissible bacteria in IgA-low mice dominantly lower faecal IgA levels in IgA-high mice after co-housing or faecal transplantation. In response to injury, IgA-low mice show increased damage that is transferable by faecal transplantation and driven by faecal IgA differences. We find that bacteria from IgA-low mice degrade the secretory component of secretory IgA as well as IgA itself. These data indicate that phenotypic comparisons between mice must take into account the non-chromosomal hereditary variation between different breeders. We propose faecal IgA as one marker of microbial variability and conclude that co-housing and/or faecal transplantation enables analysis of progeny from different dams. PMID:25686606

  4. A Toll-like receptor-1 variant and its characteristic cellular phenotype is associated with severe malaria in Papua New Guinean children.

    PubMed

    Manning, L; Cutts, J; Stanisic, D I; Laman, M; Carmagnac, A; Allen, S; O'Donnell, A; Karunajeewa, H; Rosanas-Urgell, A; Siba, P; Davis, T M E; Michon, P; Schofield, L; Rockett, K; Kwiatkowski, D; Mueller, I

    2016-01-01

    Genetic factors are likely to contribute to low severe malaria case fatality rates in Melanesian populations, but association studies can be underpowered and may not provide plausible mechanistic explanations if significant associations are detected. In preparation for a genome-wide association study, 29 candidate single-nucleotide polymorphisms (SNPs) with minor allele frequencies >5% were examined in a case-control study of 504 Papua New Guinean children with severe malaria. In parallel, an immunological substudy was performed on convalescent peripheral blood mononuclear cells (PBMCs) from cases and controls. Following stimulation with a Toll-like receptor (TLR) 1/2 agonist, effector cytokines and chemokines were assayed. The only significant genetic association observed involved a nonsynonymous SNP (TLR1rs4833095) in the TLR1 gene. A recessive (TT) genotype was associated with reduced odds of severe malaria of 0.52 (95% confidence interval (0.29-0.90), P=0.006). Concentrations of pro-inflammatory cytokines interleukin-1β and tumour necrosis factor α were significantly higher in severe malaria cases compared with healthy controls, but lower in children with the protective recessive (TT) genotype. A genetic variant in TLR1 may contribute to the low severe malaria case fatality rates in this region through a reduced pro-inflammatory cellular phenotype. PMID:26633000

  5. The type of variants at the COL3A1 gene associates with the phenotype and severity of vascular Ehlers-Danlos syndrome.

    PubMed

    Frank, Michael; Albuisson, Juliette; Ranque, Brigitte; Golmard, Lisa; Mazzella, Jean-Michael; Bal-Theoleyre, Laurence; Fauret, Anne-Laure; Mirault, Tristan; Denarié, Nicolas; Mousseaux, Elie; Boutouyrie, Pierre; Fiessinger, Jean-Noël; Emmerich, Joseph; Messas, Emmanuel; Jeunemaitre, Xavier

    2015-12-01

    Vascular Ehlers-Danlos syndrome (vEDS) is a rare and severe autosomal dominant disorder caused by variants at the COL3A1 gene. Clinical characteristics and course of disease of 215 molecularly proven patients (146 index cases and 69 relatives) were analysed. We found 126 distincts variants that were divided into five groups: (1) Glycine substitutions (n=71), (2) splice-site and in-frame insertions-deletions (n=36), (3) variants leading to haplo-insufficiency (n=7), (4) non-glycine missense variants within the triple helix (n=4 variants), and (5) non-glycine missense variants or in-frame insertions-deletions, in the N- or C-terminal part of the protein (n=8). Overall, our cohort confirmed the severity of the disease with a median age at first complication of 29 years (IQR 22-39), the most frequent being arterial (48%) and digestive (24%) ruptures. Groups 2 and 1 were significantly more severe than groups 3-5, with extreme median ages at first major complication of 23-47 years. Patients of groups 3-5 had a less typical phenotype and remarkably absence of digestive events. The distribution of glycine-replacing amino acids was strongly biased towards more destabilizing residues of the collagen assembly. Thus the natural course of vEDS and the clinical phenotype of patients are influenced by the type of COL3A1 variant. This study also confirms that patients with variants located in the C- and N-termini or leading to haplo-insufficiency have milder course of the disease and less prevalent diagnostic criteria. These findings may help refine diagnostic strategy, genetic counselling and clinical care. PMID:25758994

  6. Phenotypic Plasticity Determines Cancer Stem Cell Therapeutic Resistance in Oral Squamous Cell Carcinoma

    PubMed Central

    Biddle, Adrian; Gammon, Luke; Liang, Xiao; Costea, Daniela Elena; Mackenzie, Ian C.

    2016-01-01

    Cancer stem cells (CSCs) drive tumour spread and therapeutic resistance, and can undergo epithelial-to-mesenchymal transition (EMT) and mesenchymal-to-epithelial transition (MET) to switch between epithelial and post-EMT sub-populations. Examining oral squamous cell carcinoma (OSCC), we now show that increased phenotypic plasticity, the ability to undergo EMT/MET, underlies increased CSC therapeutic resistance within both the epithelial and post-EMT sub-populations. The post-EMT CSCs that possess plasticity exhibit particularly enhanced therapeutic resistance and are defined by a CD44highEpCAMlow/− CD24+ cell surface marker profile. Treatment with TGFβ and retinoic acid (RA) enabled enrichment of this sub-population for therapeutic testing, through which the endoplasmic reticulum (ER) stressor and autophagy inhibitor Thapsigargin was shown to selectively target these cells. Demonstration of the link between phenotypic plasticity and therapeutic resistance, and development of an in vitro method for enrichment of a highly resistant CSC sub-population, provides an opportunity for the development of improved chemotherapeutic agents that can eliminate CSCs. PMID:26981578

  7. Abnormal patterns of equine leucocyte differentiation antigen expression in severe combined immunodeficiency foals suggests the phenotype of normal equine natural killer cells.

    PubMed Central

    Lunn, D P; McClure, J T; Schobert, C S; Holmes, M A

    1995-01-01

    Severe combined immunodeficiency (SCID) is a fatal autosommal disease of Arabian horses that leads to failure of maturation of T- and B-lymphocyte populations, although natural killer (NK) cells are unaffected. Thymic and lymph node tissues from two foals suffering from SCID were examined in an immunohistological study using a panel of monoclonal antibodies recognising equine leucocyte differentiation antigens. In both foals, the majority of cells in lymphoid tissues had an EqCD3-EqCD4-EqCD8+ phenotype, although rare EqCD3+ cells were also detected. The EqCD3-EqCD4-EqCD8+ cells may represent an abnormal lymphocyte differentiation product resulting from the SCID defect, or alternatively may be a normal equine NK cell population. We suggest that the evidence favours the latter proposal, and that equine NK cells in normal horses therefore may be identified by an EqCD3-EqCD8+ phenotype. The implications for the nature of the equine SCID defect are discussed. Images Figure 1 PMID:7751035

  8. Moderation of phenotypic severity in dystrophic and junctional forms of epidermolysis bullosa through in-frame skipping of exons containing non-sense or frameshift mutations.

    PubMed

    McGrath, J A; Ashton, G H; Mellerio, J E; Salas-Alanis, J C; Swensson, O; McMillan, J R; Eady, R A

    1999-09-01

    Non-sense mutations on both alleles of either the type VII collagen gene (COL7A1) or the genes encoding laminin 5 (LAMA3, LAMB3, or LAMC2) usually result in clinically severe forms of recessive dystrophic or junctional epidermolysis bullosa, respectively. In this study we assessed two unrelated families whose mutations in genomic DNA predicted severe recessive dystrophic epidermolysis bullosa or junctional epidermolysis bullosa phenotypes but in whom the manifestations were milder than expected. The recessive dystrophic epidermolysis bullosa patients had a homozygous single base-pair frameshift mutation in exon 19 of COL7A1 (2470insG). Clinically, there was generalized blistering but only mild scarring. Skin biopsy revealed positive type VII collagen immunoreactivity and recognizable anchoring fibrils. The junctional epidermolysis bullosa patients were compound heterozygotes for a frameshift/non-sense combination of mutations in exons 3 and 17 of LAMB3 (29insC/Q834X). These patients did not have the lethal form of junctional epidermolysis bullosa but, as adults, displayed the milder generalized atrophic benign epidermolysis bullosa variant. There was undetectable laminin 5 staining at the dermal-epidermal junction using an antibody to the beta3 chain, but faintly positive alpha3 and gamma2 chain labeling, and there was variable hypoplasia of hemidesmosomes. To explain the milder recessive dystrophic epidermolysis bullosa and junctional epidermolysis bullosa phenotypes in these families, reverse transcription-polymerase chain reaction, using RNA extracted from frozen skin, was able to provide evidence for some rescue of mutant mRNA transcripts with restoration of the open- reading frame. In the recessive dystrophic epidermolysis bullosa patients, transcripts containing in-frame skipping of exon 19 of COL7A1 in the cDNA were detected, and in the junctional epidermolysis bullosa patients transcripts with in-frame skipping of exon 17 of LAMB3 were identified. The

  9. Toward automatic phenotyping of retinal images from genetically determined mono- and dizygotic twins using amplitude modulation-frequency modulation methods

    NASA Astrophysics Data System (ADS)

    Soliz, P.; Davis, B.; Murray, V.; Pattichis, M.; Barriga, S.; Russell, S.

    2010-03-01

    This paper presents an image processing technique for automatically categorize age-related macular degeneration (AMD) phenotypes from retinal images. Ultimately, an automated approach will be much more precise and consistent in phenotyping of retinal diseases, such as AMD. We have applied the automated phenotyping to retina images from a cohort of mono- and dizygotic twins. The application of this technology will allow one to perform more quantitative studies that will lead to a better understanding of the genetic and environmental factors associated with diseases such as AMD. A method for classifying retinal images based on features derived from the application of amplitude-modulation frequency-modulation (AM-FM) methods is presented. Retinal images from identical and fraternal twins who presented with AMD were processed to determine whether AM-FM could be used to differentiate between the two types of twins. Results of the automatic classifier agreed with the findings of other researchers in explaining the variation of the disease between the related twins. AM-FM features classified 72% of the twins correctly. Visual grading found that genetics could explain between 46% and 71% of the variance.

  10. Exopolysaccharide Production and Ropy Phenotype Are Determined by Two Gene Clusters in Putative Probiotic Strain Lactobacillus paraplantarum BGCG11

    PubMed Central

    Zivkovic, Milica; Miljkovic, Marija; Ruas-Madiedo, Patricia; Strahinic, Ivana; Tolinacki, Maja; Golic, Natasa

    2014-01-01

    Lactobacillus paraplantarum BGCG11, a putative probiotic strain isolated from a soft, white, artisanal cheese, produces a high-molecular-weight heteropolysaccharide, exopolysaccharide (EPS)-CG11, responsible for the ropy phenotype and immunomodulatory activity of the strain. In this study, a 26.4-kb region originating from the pCG1 plasmid, previously shown to be responsible for the production of EPS-CG11 and a ropy phenotype, was cloned, sequenced, and functionally characterized. In this region 16 putative open reading frames (ORFs), encoding enzymes for the production of EPS-CG11, were organized in specific loci involved in the biosynthesis of the repeat unit, polymerization, export, regulation, and chain length determination. Interestingly, downstream of the eps gene cluster, a putative transposase gene was identified, followed by an additional rfb gene cluster containing the rfbACBD genes, the ones most probably responsible for dTDP-l-rhamnose biosynthesis. The functional analysis showed that the production of the high-molecular-weight fraction of EPS-CG11 was absent in two knockout mutants, one in the eps and the other in the rfb gene cluster, as confirmed by size exclusion chromatography analysis. Therefore, both eps and rfb genes clusters are prerequisites for the production of high-molecular-weight EPS-CG11 and for the ropy phenotype of strain L. paraplantarum BGCG11. PMID:25527533

  11. Hepatic fat content is a determinant of metabolic phenotypes and increased carotid intima-media thickness in obese adults

    PubMed Central

    Zhang, Huijie; Ma, Zhimin; Pan, Lingling; Xu, Yanfang; Shao, Jin; Huang, Zhufeng; Chen, Zheng; Sun, Qian; Liu, Changqin; Lin, Mingzhu; Yang, Shuyu; Li, Xuejun

    2016-01-01

    Individuals with metabolically healthy obesity (MHO) are at relatively low risk for the development of metabolic abnormalities and subclinical atherosclerosis. This study aims to examine whether hepatic fat accumulation determines metabolic phenotype of obesity and associated with subclinical atherosclerosis. A total of 485 obese adults (aged 40–65 years) who received magnetic resonance spectroscopy were divided into metabolically abnormally obesity (MAO) and MHO groups according to metabolic status. MHO individuals had lower levels of intrahepatic triglyceride (IHTG) content and carotid intima-media thickness (CIMT) than MAO individuals. In multivariable linear regression analyses, IHTG content was independently associated with metabolic syndrome components and CIMT. Based on receiver operating characteristic curve analysis, the IHTG content displayed a higher area under the curve (AUC) for detecting the MAO phenotype (AUC = 0.70, 95%CI = 0.65–0.75) and increased CIMT (AUC = 0.60, 95%CI = 0.54–0.66) than BMI, waist circumference, and body fat percent. MHO individuals were 1.9 times (p < 0.001) more likely to have metabolic syndrome per 1 SD change in IHTG content in multivariable-adjusted models. Likewise, the risk for high CIMT increased 29% per 1 SD change in IHTG content [OR (95% CI):1.29(1.01–1.64)]. These findings suggest that hepatic fat is a potential predictor of metabolically unhealthy obesity phenotype and subclinical atherosclerosis. PMID:26902311

  12. Hepatic fat content is a determinant of metabolic phenotypes and increased carotid intima-media thickness in obese adults.

    PubMed

    Zhang, Huijie; Ma, Zhimin; Pan, Lingling; Xu, Yanfang; Shao, Jin; Huang, Zhufeng; Chen, Zheng; Sun, Qian; Liu, Changqin; Lin, Mingzhu; Yang, Shuyu; Li, Xuejun

    2016-01-01

    Individuals with metabolically healthy obesity (MHO) are at relatively low risk for the development of metabolic abnormalities and subclinical atherosclerosis. This study aims to examine whether hepatic fat accumulation determines metabolic phenotype of obesity and associated with subclinical atherosclerosis. A total of 485 obese adults (aged 40-65 years) who received magnetic resonance spectroscopy were divided into metabolically abnormally obesity (MAO) and MHO groups according to metabolic status. MHO individuals had lower levels of intrahepatic triglyceride (IHTG) content and carotid intima-media thickness (CIMT) than MAO individuals. In multivariable linear regression analyses, IHTG content was independently associated with metabolic syndrome components and CIMT. Based on receiver operating characteristic curve analysis, the IHTG content displayed a higher area under the curve (AUC) for detecting the MAO phenotype (AUC = 0.70, 95%CI = 0.65-0.75) and increased CIMT (AUC = 0.60, 95%CI = 0.54-0.66) than BMI, waist circumference, and body fat percent. MHO individuals were 1.9 times (p < 0.001) more likely to have metabolic syndrome per 1 SD change in IHTG content in multivariable-adjusted models. Likewise, the risk for high CIMT increased 29% per 1 SD change in IHTG content [OR (95% CI):1.29(1.01-1.64)]. These findings suggest that hepatic fat is a potential predictor of metabolically unhealthy obesity phenotype and subclinical atherosclerosis. PMID:26902311

  13. Acetylator phenotyping of tuberculosis patients using matrix isoniazid or sulphadimidine and its prognostic significance for treatment with several intermittent isoniazid-containing regimens.

    PubMed Central

    Ellard, G A; Gammon, P T

    1977-01-01

    1. The acetylator phenotype of over 600 pulmonary tuberculosis patients treated with intermittent isoniazid-containing regimens in two controlled clinical trials was determined using either sulphadimidine or a slow-release isoniazid formulation. 2. Both methods unequivocally classified over 99% of the patients as being either slow or rapid acetylators. 3. Rapid and slow acetylation did not differ in their ability of hydrolyse acetylisoniazid to isonicotonic acid plus monoacetylhydrazine, or to conjugate isonicotinic acid with glycine. 4. Rapid acetylators acetylated the monoacetylhydrazine liberated in vivo more rapidly than slow acetylators, demonstrating that this compound is also polymorphologically acetylated in man. 5. The acetylator phenotype of the patients was without prognostic significance when they were treated on a twice-weekly basis with isoniazid plus streptomycin plus pyraziniamide, or with isoniazid plus rifampicin. However, when patients were treated once every week for 12 months with isoniazid plus rifampicin, 5% of the rapid acetylators had an unsatisfactory response as contrasted to the complete success of the treatment in the slow acetylators. PMID:843424

  14. Rapid PCR-Based Method Which Can Determine Both Phenotype and Genotype of Lactococcus lactis Subspecies

    PubMed Central

    Nomura, Masaru; Kobayashi, Miho; Okamoto, Takashi

    2002-01-01

    A highly efficient, rapid, and reliable PCR-based method for distinguishing Lactococcus lactis subspecies (L. lactis subsp. lactis and L. lactis subsp. cremoris) is described. Primers complementary to positions in the glutamate decarboxylase gene have been constructed. PCR analysis with extracted DNA or with cells of different L. lactis strains resulted in specific fragments. The length polymorphism of the PCR fragments allowed a clear distinction of the L. lactis subspecies. The amplified fragment length polymorphism with the primers and the restriction fragment length polymorphism of the amplified products agreed perfectly with the identification based on genotypic and phenotypic analyses, respectively. Isolates from cheese starters were investigated by this method, and amplified fragments of genetic variants were found to be approximately 40 bp shorter than the typical L. lactis subsp. cremoris fragments. PMID:11976090

  15. Complement factor H gene (CFH) polymorphisms C-257T, G257A and haplotypes are associated with protection against severe dengue phenotype, possible related with high CFH expression.

    PubMed

    Pastor, André F; Rodrigues Moura, Laís; Neto, José W D; Nascimento, Eduardo J M; Calzavara-Silva, Carlos E; Gomes, Ana Lisa V; Silva, Ana Maria da; Cordeiro, Marli T; Braga-Neto, Ulisses; Crovella, Sergio; Gil, Laura H V G; Marques, Ernesto T A; Acioli-Santos, Bartolomeu

    2013-09-01

    Four genetic polymorphisms located at the promoter (C-257T) and coding regions of CFH gene (exon 2 G257A, exon 14 A2089G and exon 19 G2881T) were investigated in 121 dengue patients (DENV-3) in order to assess the relationship between allele/haplotypes variants and clinical outcomes. A statistical value was found between the CFH-257T allele (TT/TC genotypes) and reduced susceptibility to severe dengue (SD). Statistical associations indicate that individuals bearing a T allele presented significantly higher protein levels in plasma. The -257T variant is located within a NF-κB binding site, suggesting that this variant might have effect on the ability of the CFH gene to respond to signals via the NF-κB pathway. The G257A allelic variant showed significant protection against severe dengue. When CFH haplotypes effect was considered, the ancestral CG/CG promoter-exon 2 SNP genotype showed significant risk to SD either in a general comparison (ancestral × all variant genotypes), as well as in individual genotypes comparison (ancestral × each variant genotype), where the most prevalent effect was observed in the CG/CG × CA/TG comparison. These findings support the involvement of -257T, 257A allele variants and haplotypes on severe dengue phenotype protection, related with high basal CFH expression. PMID:23747994

  16. Prediction of Long-Term Benefits of Inhaled Steroids by Phenotypic Markers in Moderate-to-Severe COPD: A Randomized Controlled Trial

    PubMed Central

    Snoeck-Stroband, Jiska B.; Lapperre, Therese S.; Sterk, Peter J.; Hiemstra, Pieter S.; Thiadens, Henk A.; Boezen, H. Marike; ten Hacken, Nick H. T.; Kerstjens, Huib A. M.; Postma, Dirkje S.; Timens, Wim; Sont, Jacob K.

    2015-01-01

    Background The decline in lung function can be reduced by long-term inhaled corticosteroid (ICS) treatment in subsets of patients with chronic obstructive pulmonary disease (COPD). We aimed to identify which clinical, physiological and non-invasive inflammatory characteristics predict the benefits of ICS on lung function decline in COPD. Methods Analysis was performed in 50 steroid-naive compliant patients with moderate to severe COPD (postbronchodilator forced expiratory volume in one second (FEV1), 30–80% of predicted, compatible with GOLD stages II-III), age 45–75 years, >10 packyears smoking and without asthma. Patients were treated with fluticasone propionate (500 μg bid) or placebo for 2.5 years. Postbronchodilator FEV1, dyspnea and health status were measured every 3 months; lung volumes, airway hyperresponsiveness (PC20), and induced sputum at 0, 6 and 30 months. A linear mixed effect model was used for analysis of this hypothesis generating study. Results Significant predictors of attenuated FEV1-decline by fluticasone treatment compared to placebo were: fewer packyears smoking, preserved diffusion capacity, limited hyperinflation and lower inflammatory cell counts in induced sputum (p<0.04). Conclusions Long-term benefits of ICS on lung function decline in patients with moderate-to-severe COPD are most pronounced in patients with fewer packyears, and less severe emphysema and inflammation. These data generate novel hypotheses on phenotype-driven therapy in COPD. Trial Registration ClinicalTrials.gov NCT00158847 PMID:26659582

  17. Phenotypic and genetic variation in leptin as determinants of weight regain

    PubMed Central

    Rudich, A; Meiner, V; Schwarzfuchs, D; Sharon, N; Shpitzen, S; Blüher, M; Stumvoll, M; Thiery, J; Fiedler, GM; Friedlander, Y; Leiterstdorf, E; Shai, I

    2016-01-01

    Aims Over 75% of obese subjects fail to maintain their weight following weight loss interventions. We aimed to identify phenotypic and genetic markers associated with weight maintenance/regain following a dietary intervention. Subjects and methods In the 2-year Dietary Intervention Randomized Controlled Trial, we assessed potential predictors for weight changes during the ‘weight loss phase’ (0–6 months) and the ‘weight maintenance/regain phase’ (7–24 months). Genetic variation between study participants was studied using single-nucleotide polymorphisms in the leptin gene (LEP). Results Mean weight reduction was −5.5% after 6 months, with a mean weight regain of 1.2% of baseline weight during the subsequent 7–24 months. In a multivariate regression model, higher baseline high-molecular-weight adiponectin was the only biomarker predictor of greater success in 0- to 6-month weight loss (β = −0.222, P-value = 0.044). In a multivariate regression model adjusted for 6-month changes in weight and various biomarkers, 6-month plasma leptin reduction exhibited the strongest positive association with 6-month weight loss (β = 0.505, P-value<0.001). Conversely, 6-month plasma leptin reduction independently predicted weight regain during the following 18 months (β = −0.131, P-value<.013). Weight regain was higher among participants who had a greater (top tertiles) 6-month decrease in both weight and leptin (+ 3.4% (95% confidence interval 2.1–4.8)) as compared with those in the lowest combined tertiles (+ 0.2% (95% confidence interval −1.1 to 1.4)); P-value<0.001. Weight regain was further significantly and independently associated with genetic variations in LEP (P = 0.006 for both rs4731426 and rs2071045). Adding genetic data to the phenotypic multivariate model increased its predictive value for weight regain by 34%. Conclusion Although greater reduction in leptin concentrations during the initial phase of a dietary intervention is associated with

  18. Novel Meta-Analysis-Derived Type 2 Diabetes Risk Loci Do Not Determine Prediabetic Phenotypes

    PubMed Central

    Staiger, Harald; Machicao, Fausto; Kantartzis, Konstantinos; Schäfer, Silke A.; Kirchhoff, Kerstin; Guthoff, Martina; Silbernagel, Günther; Stefan, Norbert; Fritsche, Andreas; Häring, Hans-Ulrich

    2008-01-01

    Background Genome-wide association (GWA) studies identified a series of novel type 2 diabetes risk loci. Most of them were subsequently demonstrated to affect insulin secretion of pancreatic β-cells. Very recently, a meta-analysis of GWA data revealed nine additional risk loci with still undefined roles in the pathogenesis of type 2 diabetes. Using our thoroughly phenotyped cohort of subjects at an increased risk for type 2 diabetes, we assessed the association of the nine latest genetic variants with the predominant prediabetes traits, i.e., obesity, impaired insulin secretion, and insulin resistance. Methodology/Principal Findings One thousand five hundred and seventy-eight metabolically characterized non-diabetic German subjects were genotyped for the reported candidate single nucleotide polymorphisms (SNPs) JAZF1 rs864745, CDC123/CAMK1D rs12779790, TSPAN8/LGR5 rs7961581, THADA rs7578597, ADAMTS9 rs4607103, NOTCH2 rs10923931, DCD rs1153188, VEGFA rs9472138, and BCL11A rs10490072. Insulin sensitivity was derived from fasting glucose and insulin concentrations, oral glucose tolerance test (OGTT), and hyperinsulinemic-euglycemic clamp. Insulin secretion was estimated from OGTT data. After appropriate adjustment for confounding variables and Bonferroni correction for multiple comparisons (corrected α-level: p = 0.0014), none of the SNPs was reliably associated with adiposity, insulin sensitivity, or insulin secretion (all p≥0.0117, dominant inheritance model). The risk alleles of ADAMTS9 SNP rs4607103 and VEGFA SNP rs9472138 tended to associate with more than one measure of insulin sensitivity and insulin secretion, respectively, but did not reach formal statistical significance. The study was sufficiently powered (1-β = 0.8) to detect effect sizes of 0.19≤d≤0.25 (α = 0.0014) and 0.13≤d≤0.16 (α = 0.05). Conclusions/Significance In contrast to the first series of GWA-derived type 2 diabetes candidate SNPs, we could not detect reliable

  19. Self-Determination for Individuals with the Most Severe Disabilities: Moving beyond Chimera.

    ERIC Educational Resources Information Center

    Brown, Fredda; Gothelf, Carole R.; Guess, Doug; Lehr, Donna H.

    1998-01-01

    This article explores implications of people's interpretations of communicative efforts by people with severe disabilities. Recent initiatives to support and promote self-determination are critically assessed as possibly functioning to limit self-determination. Use of preference assessments and behavior supports is discussed as a key to…

  20. Tuberous sclerosis complex 1-mechanistic target of rapamycin complex 1 signaling determines brown-to-white adipocyte phenotypic switch.

    PubMed

    Xiang, Xinxin; Lan, He; Tang, Hong; Yuan, Fang; Xu, Yanhui; Zhao, Jing; Li, Yin; Zhang, Weizhen

    2015-02-01

    Interconversion of white and brown adipocytes occurs between anabolic and catabolic states. The molecular mechanism regulating this phenotypic switch remains largely unknown. This study explores the role of tuberous sclerosis complex 1 (TSC1)-mechanistic target of rapamycin (mTOR) signaling in the conversion of brown to white adipose tissue (WAT). A colony of Fabp4-Tsc1(-/-) mice, in which the Tsc1 gene was specifically deleted by the fatty acid binding protein 4 (FABP4)-Cre, was established. Western blotting and immunostaining demonstrated the absence of TSC1 and activation of ribosomal protein S6 kinase 1, the downstream target of mTOR complex 1 (mTORC1) signaling, in the brown adipose tissues (BATs) of Fabp4-Tsc1(-/-) mice. Accumulation of lipid droplets in BAT was significantly increased. Levels of brown adipocyte markers were markedly downregulated, while white adipocyte markers were upregulated. Rapamycin reversed the conversion from BAT to WAT in Fabp4-Tsc1(-/-) mice. Deletion of the Tsc1 gene in cultured brown preadipocytes significantly increased the conversion to white adipocytes. FoxC2 mRNA, the transcriptional factor for brown adipocyte determination, was significantly decreased, while mRNAs for retinoblastoma protein, p107 and RIP140, the transcriptional factors for white adipocyte determination, increased in the BAT of Fabp4-Tsc1(-/-) mice. Our study demonstrates that TSC1-mTORC1 signaling contributes to the brown-to-white adipocyte phenotypic switch. PMID:25213336

  1. The common occurrence of epistasis in the determination of human pigmentation and its impact on DNA-based pigmentation phenotype prediction.

    PubMed

    Pośpiech, Ewelina; Wojas-Pelc, Anna; Walsh, Susan; Liu, Fan; Maeda, Hitoshi; Ishikawa, Takaki; Skowron, Małgorzata; Kayser, Manfred; Branicki, Wojciech

    2014-07-01

    The role of epistatic effects in the determination of complex traits is often underlined but its significance in the prediction of pigmentation phenotypes has not been evaluated so far. The prediction of pigmentation from genetic data can be useful in forensic science to describe the physical appearance of an unknown offender, victim, or missing person who cannot be identified via conventional DNA profiling. Available forensic DNA prediction systems enable the reliable prediction of several eye and hair colour categories. However, there is still space for improvement. Here we verified the association of 38 candidate DNA polymorphisms from 13 genes and explored the extent to which interactions between them may be involved in human pigmentation and their impact on forensic DNA prediction in particular. The model-building set included 718 Polish samples and the model-verification set included 307 independent Polish samples and additional 72 samples from Japan. In total, 29 significant SNP-SNP interactions were found with 5 of them showing an effect on phenotype prediction. For predicting green eye colour, interactions between HERC2 rs12913832 and OCA2 rs1800407 as well as TYRP1 rs1408799 raised the prediction accuracy expressed by AUC from 0.667 to 0.697 and increased the prediction sensitivity by >3%. Interaction between MC1R 'R' variants and VDR rs731236 increased the sensitivity for light skin by >1% and by almost 3% for dark skin colour prediction. Interactions between VDR rs1544410 and TYR rs1042602 as well as between MC1R 'R' variants and HERC2 rs12913832 provided an increase in red/non-red hair prediction accuracy from an AUC of 0.902-0.930. Our results thus underline epistasis as a common phenomenon in human pigmentation genetics and demonstrate that considering SNP-SNP interactions in forensic DNA phenotyping has little impact on eye, hair and skin colour prediction. PMID:24681889

  2. Obtaining of pure transferrins D, M and R from equine serum and determination of transferrin level in relation to phenotype.

    PubMed

    Didkowski, S; Kaminski, M; Kerjan, P; Tomaszewska-Guszkiewicz, K; Zurkowski, M

    1984-01-01

    By the method of precipitation with Rivanol (2-ethoxy-6,9-diaminoacridine lactate) and ammonium sulphate followed by chromatography on DEAE cellulose three genetic variants of transferrin were purified from equine serum: D, M and R. Their molecular mass determined in this study was 80 000, and it was identical for all three variants, which differed slightly in their amino acid composition. The protein level was determined in the serum of 535 two-year-old thoroughbred English horses by the method of rocket immunoelectrophoresis using antibodies obtained against three transferrins. The individual variability of the protein level in horses of the same phenotype was fairly high (variability index 9-15%). No differences were observed in the transferrin level related to sex. It was found that the presence of D, F and H alleles was connected with a higher serum transferrin level, while O and R alleles were connected with a lower level. PMID:6545995

  3. Carnitine Deficiency in OCTN2−/− Newborn Mice Leads to a Severe Gut and Immune Phenotype with Widespread Atrophy, Apoptosis and a Pro-Inflammatory Response

    PubMed Central

    Sonne, Srinivas; Shekhawat, Prem S.; Matern, Dietrich; Ganapathy, Vadivel; Ignatowicz, Leszek

    2012-01-01

    We have investigated the gross, microscopic and molecular effects of carnitine deficiency in the neonatal gut using a mouse model with a loss-of-function mutation in the OCTN2 (SLC22A5) carnitine transporter. The tissue carnitine content of neonatal homozygous (OCTN2−/−) mouse small intestine was markedly reduced; the intestine displayed signs of stunted villous growth, early signs of inflammation, lymphocytic and macrophage infiltration and villous structure breakdown. Mitochondrial β-oxidation was active throughout the GI tract in wild type newborn mice as seen by expression of 6 key enzymes involved in β-oxidation of fatty acids and genes for these 6 enzymes were up-regulated in OCTN2−/− mice. There was increased apoptosis in gut samples from OCTN2−/− mice. OCTN2−/− mice developed a severe immune phenotype, where the thymus, spleen and lymph nodes became atrophied secondary to increased apoptosis. Carnitine deficiency led to increased expression of CD45-B220+ lymphocytes with increased production of basal and anti-CD3-stimulated pro-inflammatory cytokines in immune cells. Real-time PCR array analysis in OCTN2−/− mouse gut epithelium demonstrated down-regulation of TGF-β/BMP pathway genes. We conclude that carnitine plays a major role in neonatal OCTN2−/− mouse gut development and differentiation, and that severe carnitine deficiency leads to increased apoptosis of enterocytes, villous atrophy, inflammation and gut injury. PMID:23112839

  4. Carnitine deficiency in OCTN2-/- newborn mice leads to a severe gut and immune phenotype with widespread atrophy, apoptosis and a pro-inflammatory response.

    PubMed

    Sonne, Srinivas; Shekhawat, Prem S; Matern, Dietrich; Ganapathy, Vadivel; Ignatowicz, Leszek

    2012-01-01

    We have investigated the gross, microscopic and molecular effects of carnitine deficiency in the neonatal gut using a mouse model with a loss-of-function mutation in the OCTN2 (SLC22A5) carnitine transporter. The tissue carnitine content of neonatal homozygous (OCTN2(-/-)) mouse small intestine was markedly reduced; the intestine displayed signs of stunted villous growth, early signs of inflammation, lymphocytic and macrophage infiltration and villous structure breakdown. Mitochondrial β-oxidation was active throughout the GI tract in wild type newborn mice as seen by expression of 6 key enzymes involved in β-oxidation of fatty acids and genes for these 6 enzymes were up-regulated in OCTN2(-/-) mice. There was increased apoptosis in gut samples from OCTN2(-/-) mice. OCTN2(-/-) mice developed a severe immune phenotype, where the thymus, spleen and lymph nodes became atrophied secondary to increased apoptosis. Carnitine deficiency led to increased expression of CD45-B220(+) lymphocytes with increased production of basal and anti-CD3-stimulated pro-inflammatory cytokines in immune cells. Real-time PCR array analysis in OCTN2(-/-) mouse gut epithelium demonstrated down-regulation of TGF-β/BMP pathway genes. We conclude that carnitine plays a major role in neonatal OCTN2(-/-) mouse gut development and differentiation, and that severe carnitine deficiency leads to increased apoptosis of enterocytes, villous atrophy, inflammation and gut injury. PMID:23112839

  5. The low frequency of recessive disease: insights from ENU mutagenesis, severity of disease phenotype, GWAS associations, and demography: an analytical review.

    PubMed

    Erickson, Robert P; Mitchison, N Avrion

    2014-08-01

    A survey of a select panel of 14 genetic diseases with mixed inheritance confirms that, while autosomal recessive (AR) disease genes are more numerous than autosomal dominant (AD) or X-linked (XL) ones, they make a smaller average contribution to disease. Data collected from N-ethyl-N-nitrosourea (ENU) mutagenesis studies show a similar excess of AR mutations. The smaller AR contribution may partially reflect disease severity, but only in the comparison of AR with AD mutations. On the contrary, XL mutations for the 14 diseases are generally more severe. Genome-wide associations studies (GWAS) data provide fresh insight into the shortage, with a limited negative selection effect mediated by the pleiotropic expression of recessive disease genes in other deleterious phenotypes. Genomic data provide further evidence of purging selection in a past European population bottleneck followed by a dramatic population explosion, now more clearly associated with past climate change. We consider these likely to be the main factors responsible for the low AR to AD/XL inheritance ratio. PMID:24652618

  6. Genetically determined ABCB5 functionality correlates with pigmentation phenotype and melanoma risk

    PubMed Central

    Lin, Jennifer Y.; Zhang, Mingfeng; Schatton, Tobias; Wilson, Brian J.; Alloo, Allireza; Ma, Jie; Qureshi, Abrar A.; Frank, Natasha Y.; Han, Jiali; Frank, Markus H.

    2013-01-01

    ABCB5 is a multidrug resistance (MDR) member of the ATP-binding cassette (ABC) superfamily of active transporters and represents a marker for chemoresistant malignant melanoma-initiating cells. ABCB5 expression is closely linked to tumorigenicity and progression of diverse human malignancies, including melanoma, and is functionally required for tumor growth. Here, we genotyped 585 melanoma cases and 605 age-matched controls for 44 ABCB5 tagging single nucleotide polymorphisms (SNPs) to span a region covering 108.2kb of the gene on the 7p21.1 locus. We identified three SNPs that were associated with decreased melanoma risk in additive models: rs10231520 (OR: 0.83, 95% CI: 0.70–0.98), rs17817117 (OR: 0.82, 95% CI: 0.68–0.98), and rs2301641 (OR: 0.83, 95% CI: 0.69–0.98). Additionally, the rs2301641 SNP was associated with non-red compared to red hair color (OR: 0.38, 95% CI: 0.14–1.03) in controls. Twelve human melanoma cell lines were genotyped for the rs2301641 SNP, which encodes a non-synonymous ABCB5 amino acid change (K115E). Functional studies revealed that the E form associated with lower melanoma risk correlated significantly with decreased ABCB5 transport capacity (P<0.01) and increased melanin production (P<0.05). Our results identify novel associations of the ABCB5 K115E polymorphism with human pigmentation phenotype and melanoma risk and point to potential functional roles of ABCB5 in melanomagenesis. Moreover, they provide a first example that functional variation in a prospective cancer stem cell marker can be associated with disease risk for the corresponding malignancy. PMID:23770371

  7. Phenotypic Assays to Determine Virulence Factors of Uropathogenic Escherichia coli (UPEC) Isolates and their Correlation with Antibiotic Resistance Pattern

    PubMed Central

    Tabasi, Mohsen; Asadi Karam, Mohammad Reza; Habibi, Mehri; Yekaninejad, Mir Saeed; Bouzari, Saeid

    2015-01-01

    Objectives Urinary tract infection caused by uropathogenic Escherichia coli (UPEC) strains is one of the most important infections in the world. UPEC encode widespread virulence factors closely related with pathogenesis of the bacteria. The purpose of this study was to evaluate the presence of different phenotypic virulence markers in UPEC isolates and determine their correlation with antibiotic resistance pattern. Methods UPEC isolates from patients with different clinical symptoms of UTI were collected and screened for biofilm and hemolysin production, mannose resistant, and mannose sensitive hemagglutination (MRHA and MSHA, respectively). In addition, antimicrobial resistance pattern and ESBL-producing isolates were recorded. Results Of the 156 UPEC isolates, biofilm and hemolysin formation was seen in 133 (85.3%) and 53 (34%) isolates, respectively. Moreover, 98 (62.8%) and 58 (37.2%) isolates showed the presence of Types 1 fimbriae (MSHA) and P fimbriae (MRHA), respectively. Our results also showed a relationship between biofilm formation in UPEC isolated from acute cystitis patients and recurrent UTI cases. Occurrence of UTI was dramatically correlated with the patients' profiles. We observed that the difference in antimicrobial susceptibilities of the biofilm and nonbiofilm former isolates was statistically significant. The UPEC isolates showed the highest resistance to ampicillin, tetracycline, amoxicillin, and cotrimoxazole. Moreover, 26.9% of isolates were ESBL producers. Conclusion This study indicated that there is a relationship between the phenotypic virulence traits of the UPEC isolates, patients' profiles, and antibiotic resistance. Detection of the phenotypic virulence factors could help to improve understanding of pathogenesis of UPEC isolates and better medical intervention. PMID:26473094

  8. MYC/PGC-1α Balance Determines the Metabolic Phenotype and Plasticity of Pancreatic Cancer Stem Cells.

    PubMed

    Sancho, Patricia; Burgos-Ramos, Emma; Tavera, Alejandra; Bou Kheir, Tony; Jagust, Petra; Schoenhals, Matthieu; Barneda, David; Sellers, Katherine; Campos-Olivas, Ramon; Graña, Osvaldo; Viera, Catarina R; Yuneva, Mariia; Sainz, Bruno; Heeschen, Christopher

    2015-10-01

    The anti-diabetic drug metformin targets pancreatic cancer stem cells (CSCs), but not their differentiated progenies (non-CSCs), which may be related to distinct metabolic phenotypes. Here we conclusively demonstrate that while non-CSCs were highly glycolytic, CSCs were dependent on oxidative metabolism (OXPHOS) with very limited metabolic plasticity. Thus, mitochondrial inhibition, e.g., by metformin, translated into energy crisis and apoptosis. However, resistant CSC clones eventually emerged during treatment with metformin due to their intermediate glycolytic/respiratory phenotype. Mechanistically, suppression of MYC and subsequent increase of PGC-1α were identified as key determinants for the OXPHOS dependency of CSCs, which was abolished in resistant CSC clones. Intriguingly, no resistance was observed for the mitochondrial ROS inducer menadione and resistance could also be prevented/reversed for metformin by genetic/pharmacological inhibition of MYC. Thus, the specific metabolic features of pancreatic CSCs are amendable to therapeutic intervention and could provide the basis for developing more effective therapies to combat this lethal cancer. PMID:26365176

  9. MR-determined metabolic phenotype of breast cancer in prediction of lymphatic spread, grade, and hormone status.

    PubMed

    Bathen, Tone F; Jensen, Line R; Sitter, Beathe; Fjösne, Hans E; Halgunset, Jostein; Axelson, David E; Gribbestad, Ingrid S; Lundgren, Steinar

    2007-08-01

    The purpose of the study was to evaluate the use of metabolic phenotype, described by high-resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS), as a tool for prediction of histological grade, hormone status, and axillary lymphatic spread in breast cancer patients. Biopsies from breast cancer (n = 91) and adjacent non-involved tissue (n = 48) were excised from patients (n = 77) during surgery. HR MAS MR spectra of intact samples were acquired. Multivariate models relating spectral data to histological grade, lymphatic spread, and hormone status were designed. The multivariate methods applied were variable reduction by principal component analysis (PCA) or partial least-squares regression-uninformative variable elimination (PLS-UVE), and modelling by PLS, probabilistic neural network (PNN), or cascade correlation neural network. In the end, model verification by prediction of blind samples (n = 12) was performed. Validation of PNN training resulted in sensitivity and specificity ranging from 83 to 100% for all predictions. Verification of models by blind sample testing showed that hormone status was well predicted by both PNN and PLS (11 of 12 correct), lymphatic spread was best predicted by PLS (8 of 12), whereas PLS-UVE PNN was the best approach for predicting grade (9 of 12 correct). MR-determined metabolic phenotype may have a future role as a supplement for clinical decision-making-concerning adjuvant treatment and the adaptation to more individualised treatment protocols. PMID:17061040

  10. SPP1 genotype is a determinant of disease severity in Duchenne muscular dystrophy

    PubMed Central

    Pegoraro, E.; Hoffman, E.P.; Piva, L.; Gavassini, B.F.; Cagnin, S.; Ermani, M.; Bello, L.; Soraru, G.; Pacchioni, B.; Bonifati, M.D.; Lanfranchi, G.; Angelini, C.; Kesari, A.; Lee, I.; Gordish-Dressman, H.; Devaney, J.M.; McDonald, C.M.

    2011-01-01

    Objective: Duchenne muscular dystrophy (DMD) is the most common single-gene lethal disorder. Substantial patient–patient variability in disease onset and progression and response to glucocorticoids is seen, suggesting genetic or environmental modifiers. Methods: Two DMD cohorts were used as test and validation groups to define genetic modifiers: a Padova longitudinal cohort (n = 106) and the Cooperative International Neuromuscular Research Group (CINRG) cross-sectional natural history cohort (n = 156). Single nucleotide polymorphisms to be genotyped were selected from mRNA profiling in patients with severe vs mild DMD, and genome-wide association studies in metabolism and polymorphisms influencing muscle phenotypes in normal volunteers were studied. Results: Effects on both disease progression and response to glucocorticoids were observed with polymorphism rs28357094 in the gene promoter of SPP1 (osteopontin). The G allele (dominant model; 35% of subjects) was associated with more rapid progression (Padova cohort log rank p = 0.003), and 12%–19% less grip strength (CINRG cohort p = 0.0003). Conclusions: Osteopontin genotype is a genetic modifier of disease severity in Duchenne dystrophy. Inclusion of genotype data as a covariate or in inclusion criteria in DMD clinical trials would reduce intersubject variance, and increase sensitivity of the trials, particularly in older subjects. PMID:21178099

  11. How should severity be determined for the DSM-5 proposed classification of Hypersexual Disorder?

    PubMed Central

    Reid, Rory C.

    2015-01-01

    Background and Aims The concept of severity among providers working with hypersexual behavior is frequently used despite a lack of consensus about how severity should be operationalized. The paucity of dialogue about severity for hypersexual behavior is disconcerting given its relevance in determining level of care, risk, allocation of resources, and measuring treatment outcomes in clinical practice and research trials. The aim of the current article is to highlight several considerations for assessing severity based on the proposed DSM-5 criteria for hypersexual disorder. Methods A review of current conceptualizations for severity among substance-use disorders and gambling disorder in the DSM-5 were considered and challenged as lacking applicability or clinical utility for hypersexual behavior. Results and conclusions The current research in the field of hypersexual behavior is in its infancy. No concrete approach currently exists to assess severity in hypersexual populations. Several factors in operationalizing severity are discussed and alternative approaches to defining severity are offered for readers to consider. PMID:26690616

  12. Phenotype of subjects with type 2 diabetes mellitus may determine clinical response to chromium suppplementation.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The goal of this study was to assess which patient characteristics best determine response to supplemental chromium (Cr). We assessed response to Cr using hyperinsulinemic-euglycemic clamps before and after Cr supplementation in 38 subjects with Type 2 diabetes. The evaluations were double-blinded,...

  13. Fukutin mutations in non-Japanese patients with congenital muscular dystrophy: less severe mutations predominate in patients with a non-Walker-Warburg phenotype.

    PubMed

    Yis, Uluc; Uyanik, Gökhan; Heck, Pinar Bambul; Smitka, Martin; Nobel, Hannes; Ebinger, Friedrich; Dirik, Eray; Feng, Lucy; Kurul, Semra H; Brocke, Katja; Unalp, Aycan; Özer, Erdener; Cakmakci, Handan; Sewry, Caroline; Cirak, Sebahattin; Muntoni, Francesco; Hehr, Ute; Morris-Rosendahl, Deborah J

    2011-01-01

    Six genes including POMT1, POMT2, POMGNT1, FKRP, Fukutin (FKTN) and LARGE encode proteins involved in the glycosylation of α-dystroglycan (α-DG). Abnormal glycosylation of α-DG is a common finding in Walker-Warburg syndrome (WWS), muscle-eye-brain disease (MEB), Fukuyama congenital muscular dystrophy (FCMD), congenital muscular dystrophy types 1C and 1D and some forms of autosomal recessive limb-girdle muscular dystrophy (LGMD2I, LGMD2K, LGMD2M), and is associated with mutations in the above genes. FCMD, caused by mutations in Fukutin (FKTN), is most frequent in Japan, but an increasing number of FKTN mutations are being reported outside of Japan. We describe four new patients with FKTN mutations and phenotypes ranging from: severe WWS in a Greek-Croatian patient, to congenital muscular dystrophy and cobblestone lissencephaly resembling MEB-FCMD in two Turkish patients, and limb-girdle muscular dystrophy and no mental retardation in a German patient. Four of the five different FKTN mutations have not been previously described. PMID:20961758

  14. A common SCN5A polymorphism attenuates a severe cardiac phenotype caused by a nonsense SCN5A mutation in a Chinese family with an inherited cardiac conduction defect

    PubMed Central

    Niu, Dau‐Ming; Hwang, Betau; Hwang, Han‐Wei; Wang, Nana H; Wu, Jer‐Yuarn; Lee, Pi‐Chang; Chien, Jen‐Chung; Shieh, Ru‐Chi

    2006-01-01

    The SCN5A mutations have been associated with a variety of arrhythmic disorders, including type 3 long QT syndrome (LQT3), Brugada syndrome and inherited cardiac conduction defects. The relationship between genotype and phenotype in SCN5A mutations is complex. Some SCN5A mutations may cause death or severe manifestations in some people and may not cause any symptoms or arrhythmias in others. The causes of these unpredictable clinical manifestations remain incompletely understood. The molecular basis of a four‐generation family with cardiac conduction abnormalities was studied and whether variants in the SCN5A gene could account for the cardiac phenotypic variability observed in this family was determined. A novel mutation (W1421X) of SCN5A was identified in a four‐generation family with cardiac conduction abnormalities and several cases of sudden death. Most family members who carry this W1421X mutation have developed major clinical manifestations or electrocardiographic abnormalities, both of which became more prominent as the patients grew older. However, the 73‐year‐old grandfather, who carried both the W1421X and R1193Q mutations, had thus far remained healthy and presented with only subtle electrocardiographic abnormalities, whereas most of his offspring, who carried a single mutation (W1421X), had died early or had major disease manifestations. This observation suggests that the R1193Q mutation has a complementary role in alleviating the deleterious effects conferred by W1421X in the function of the SCN5A gene. This report provides a good model to explain the mechanism of penetrance of genetic disorders. PMID:16707561

  15. Paraprofessional Perspectives on Promoting Self-Determination among Elementary and Secondary Students with Severe Disabilities

    ERIC Educational Resources Information Center

    Carter, Erik W.; Sisco, Lynn G.; Lane, Kathleen Lynne

    2011-01-01

    Although paraprofessionals play a prominent role in the education of students with severe disabilities, little is known about the roles these school staff play in fostering self-determination. In this descriptive study, researchers examined the extent to which 347 paraprofessionals employed at 135 randomly selected schools (a) considered each of…

  16. In dementia with Lewy bodies, Braak stage determines phenotype, not Lewy body distribution.

    PubMed

    Weisman, D; Cho, M; Taylor, C; Adame, A; Thal, L J; Hansen, L A

    2007-07-24

    We used an autopsy series to determine whether the newest dementia with Lewy bodies (DLB) consensus pathologic classification correlates with premortem diagnosis of DLB. Neocortical sections from a total of 95 cases with Lewy bodies were stained with alpha-synuclein antibodies. We assigned cases according to the DLB consensus' categories and found a significant association with the premortem clinical diagnosis of DLB. Clinical diagnosis of DLB, however, depended on the presence of low Alzheimer disease pathology (by Braak staging) rather than on Lewy body distribution. PMID:17646627

  17. Evaluation of severe accident risks: Quantification of major input parameters. Experts` determination of structural response issues

    SciTech Connect

    Breeding, R.J.; Harper, F.T.; Brown, T.D.; Gregory, J.J.; Payne, A.C.; Gorham, E.D.; Murfin, W.; Amos, C.N.

    1992-03-01

    In support of the Nuclear Regulatory Commission`s (NRC`s) assessment of the risk from severe accidents at commercial nuclear power plants in the US reported in NUREG-1150, the Severe Accident Risk Reduction Program (SAARP) has completed a revised calculation of the risk to the general public from severe accidents at five nuclear power plants: Surry, Sequoyah, Zion, Peach Bottom, and Grand Gulf. The emphasis in this risk analysis was not on determining a ``so-called`` point estimate of risk. Rather, it was to determine the distribution of risk, and to discover the uncertainties that account for the breadth of this distribution. Off-site risk initiation by events, both internal to the power station and external to the power station were assessed. Much of the important input to the logic models was generated by expert panels. This document presents the distributions and the rationale supporting the distributions for the questions posed to the Structural Response Panel.

  18. Microbiota and host determinants of behavioural phenotype in maternally separated mice.

    PubMed

    De Palma, G; Blennerhassett, P; Lu, J; Deng, Y; Park, A J; Green, W; Denou, E; Silva, M A; Santacruz, A; Sanz, Y; Surette, M G; Verdu, E F; Collins, S M; Bercik, P

    2015-01-01

    Early-life stress is a determinant of vulnerability to a variety of disorders that include dysfunction of the brain and gut. Here we exploit a model of early-life stress, maternal separation (MS) in mice, to investigate the role of the intestinal microbiota in the development of impaired gut function and altered behaviour later in life. Using germ-free and specific pathogen-free mice, we demonstrate that MS alters the hypothalamic-pituitary-adrenal axis and colonic cholinergic neural regulation in a microbiota-independent fashion. However, microbiota is required for the induction of anxiety-like behaviour and behavioural despair. Colonization of adult germ-free MS and control mice with the same microbiota produces distinct microbial profiles, which are associated with altered behaviour in MS, but not in control mice. These results indicate that MS-induced changes in host physiology lead to intestinal dysbiosis, which is a critical determinant of the abnormal behaviour that characterizes this model of early-life stress. PMID:26218677

  19. Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster

    PubMed Central

    Newell, Peter D.; Douglas, Angela E.

    2014-01-01

    ABSTRACT Animal-associated bacteria (microbiota) affect host behaviors and physiological traits. To identify bacterial genetic determinants of microbiota-responsive host traits, we employed a metagenome-wide association (MGWA) approach in two steps. First, we measured two microbiota-responsive host traits, development time and triglyceride (TAG) content, in Drosophila melanogaster flies monoassociated with each of 41 bacterial strains. The effects of monoassociation on host traits were not confined to particular taxonomic groups. Second, we clustered protein-coding sequences of the bacteria by sequence similarity de novo and statistically associated the magnitude of the host trait with the bacterial gene contents. The animals had been monoassociated with genome-sequenced bacteria, so the metagenome content was unambiguous. This analysis showed significant effects of pyrroloquinoline quinone biosynthesis genes on development time, confirming the results of a published transposon mutagenesis screen, thereby validating the MGWA; it also identified multiple genes predicted to affect host TAG content, including extracellular glucose oxidation pathway components. To test the validity of the statistical associations, we expressed candidate genes in a strain that lacks them. Monoassociation with bacteria that ectopically expressed a predicted oxidoreductase or gluconate dehydrogenase conferred reduced Drosophila TAG contents relative to the TAG contents in empty vector controls. Consistent with the prediction that glucose oxidation pathway gene expression increased bacterial glucose utilization, the glucose content of the host diet was reduced when flies were exposed to these strains. Our findings indicate that microbiota affect host nutritional status through modulation of nutrient acquisition. Together, these findings demonstrate the utility of MGWA for identifying bacterial determinants of host traits and provide mechanistic insight into how gut microbiota modulate the

  20. Determination of Wetting Behavior, Spread Activation Energy, and Quench Severity of Bioquenchants

    NASA Astrophysics Data System (ADS)

    Prabhu, K. Narayan; Fernandes, Peter

    2007-08-01

    An investigation was conducted to study the suitability of vegetable oils such as sunflower, coconut, groundnut, castor, cashewnut shell (CNS), and palm oils as quench media (bioquenchants) for industrial heat treatment by assessing their wetting behavior and severity of quenching. The relaxation of contact angle was sharp during the initial stages, and it became gradual as the system approached equilibrium. The equilibrium contact angle decreased with increase in the temperature of the substrate and decrease in the viscosity of the quench medium. A comparison of the relaxation of the contact angle at various temperatures indicated the significant difference in spreading of oils having varying viscosity. The spread activation energy was determined using the Arrhenius type of equation. Oils with higher viscosity resulted in lower cooling rates. The quench severity of various oil media was determined by estimating heat-transfer coefficients using the lumped capacitance method. Activation energy for spreading determined using the wetting behavior of oils at various temperatures was in good agreement with the severity of quenching assessed by cooling curve analysis. A high quench severity is associated with oils having low spread activation energy.

  1. Epigenetic regulation of ID4 in the determination of the BRCAness phenotype in breast cancer.

    PubMed

    Branham, M T; Campoy, E; Laurito, S; Branham, R; Urrutia, G; Orozco, J; Gago, F; Urrutia, R; Roqué, M

    2016-01-01

    BRCAness breast tumors represent a group of sporadic tumors characterized by a reduction in BRCA1 gene expression. As BRCA1 is involved in double-strand breaks (DSBs) repair, dysfunctional BRCA pathway could make a tumor sensitive to DNA damaging drugs (e.g., platinum agents). Thus, accurately identifying BRCAness could contribute to therapeutic decision making in patients harboring these tumors. The purpose of this study was to identify if BRCAness tumors present a characteristic methylation profile and/or were related to specific clinico-pathological features. BRCAness was measured by MLPA in 63 breast tumors; methylation status of 98 CpG sites within 84 cancer-related genes was analyzed by MS-MLPA. Protein and mRNA expressions of the selected genes were measured by quantitative real-time PCR and Western Blot. BRCAness was associated with younger age, higher nuclear pleomorphism, and triple-negative (TN) status. Epigenetically, we found that the strongest predictors for BRCAness tumors were the methylations of MLH1 and PAX5 plus the unmethylations of CCND2 and ID4. We determined that ID4 unmethylation correlated with the expression levels of both its mRNA and protein. We observed an inverse relation between the expressions of ID4 and BRCA1. To the best of our knowledge, this is the first report suggesting an epigenetic regulation of ID4 in BRCAness tumors. Our findings give new information of BRCAness etiology and encourage future studies on potential drug targets for BRCAness breast tumors. PMID:26610810

  2. Presence of XIST specific sequences and apparent failure of X dosage compensation by inactivation in a patient with a severe Turner phenotype and mosaicism for X chromosome abnormalities

    SciTech Connect

    Bent-Williams, A.H.; Felton, S.M.; Driscoll, D.J.

    1994-09-01

    An XIST FISH analysis and a late replication chromosome study was performed for a 10 year old female with Turner stigmata, mental retardation, multiple congenital anomalies and a cytogenetic mosaicism of 45,X,inv(9)(p11q13)/46,X,del(X)(q22),inv(9)(p11q13)/46,X,+mar,inv(9)(p11q13). The X chromosomes from a cell line in which one was deleted for the distal long arm segment (breakpoint of Xq22), observed in 6% of metaphase cells from peripheral blood and 23.3% of metaphase cells from skin fibroblasts, did not demonstrate an asynchronous or differential staining pattern by BrDU techniques. However, both the normal X chromosome and the deleted X chromosome were demonstrated to contain XIST specific sequences by FISH analysis. A very small marker chromosome, observed in 6% of metaphase cells from peripheral blood and 3.3% of metaphase cells from skin fibroblasts, appeared to consist exclusively of X chromosome alpha satellite centromeric material (DXZ1). This finding was consistent with the morphology of the marker chromosome as observed by conventional G-banding. Due to its small size and low level frequency, analysis by late replication BrDU techniques was not possible. The predominate cell line containing a signal X chromosome was observed in 88% of metaphase cells from peripheral blood and 73.3% of metaphase cells from skin fibroblasts. This case is significant because: (1) it represents another case of an X chromosome abnormality in which XIST is apparently present but not expressed; and (2) the more severe phenotype expressed is probably attributable to the failure of X gene dosage compensation by inactivation.

  3. Molecular and phenotypic characterization of a mouse model of oculopharyngeal muscular dystrophy reveals severe muscular atrophy restricted to fast glycolytic fibres.

    PubMed

    Trollet, Capucine; Anvar, Seyed Yahya; Venema, Andrea; Hargreaves, Iain P; Foster, Keith; Vignaud, Alban; Ferry, Arnaud; Negroni, Elisa; Hourde, Christophe; Baraibar, Martin A; 't Hoen, Peter A C; Davies, Janet E; Rubinsztein, David C; Heales, Simon J; Mouly, Vincent; van der Maarel, Silvère M; Butler-Browne, Gillian; Raz, Vered; Dickson, George

    2010-06-01

    Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset disorder characterized by ptosis, dysphagia and proximal limb weakness. Autosomal-dominant OPMD is caused by a short (GCG)(8-13) expansions within the first exon of the poly(A)-binding protein nuclear 1 gene (PABPN1), leading to an expanded polyalanine tract in the mutated protein. Expanded PABPN1 forms insoluble aggregates in the nuclei of skeletal muscle fibres. In order to gain insight into the different physiological processes affected in OPMD muscles, we have used a transgenic mouse model of OPMD (A17.1) and performed transcriptomic studies combined with a detailed phenotypic characterization of this model at three time points. The transcriptomic analysis revealed a massive gene deregulation in the A17.1 mice, among which we identified a significant deregulation of pathways associated with muscle atrophy. Using a mathematical model for progression, we have identified that one-third of the progressive genes were also associated with muscle atrophy. Functional and histological analysis of the skeletal muscle of this mouse model confirmed a severe and progressive muscular atrophy associated with a reduction in muscle strength. Moreover, muscle atrophy in the A17.1 mice was restricted to fast glycolytic fibres, containing a large number of intranuclear inclusions (INIs). The soleus muscle and, in particular, oxidative fibres were spared, even though they contained INIs albeit to a lesser degree. These results demonstrate a fibre-type specificity of muscle atrophy in this OPMD model. This study improves our understanding of the biological pathways modified in OPMD to identify potential biomarkers and new therapeutic targets. PMID:20207626

  4. [Determination of several erythrocyte enzymes activity in patients with different tumors of the oral cavity].

    PubMed

    Pavel, Mariana; Foia, Liliana; Popescu, Eugenia; Iacobovici, Irina; Costuleanu, Natalia

    2002-01-01

    Considering the influence on the molecular level of the neoplasic factors, upon several proteins, nucleic acids, one can say that some of the oncogenesis determinants are represented by genetic mutations. Free radicals, including also some organic peroxides are considered as tumour promoters, although the exact mechanism of this process in still unknown. The neoplasic disease is characterized generally by disorders of the control processes, including the one displayed on the subcellular level. Considering the enzymatic changes occurred in erythrocytes and determined by the disturbances of membrane permeability, we evaluated the response of several aggressions at the erythrocyte level, in case of maxillo-facial tumours. Our results show increase of the LDH, G-6-P-DH activity and decrease of catalase activity within the erythrocyte. PMID:12638296

  5. A case of severe proximal focal femoral deficiency with overlapping phenotypes of Al-Awadi-Raas-Rothschild syndrome and Fuhrmann syndrome.

    PubMed

    Matsushita, Masaki; Kitoh, Hiroshi; Mishima, Kenichi; Nishida, Yoshihiro; Ishiguro, Naoki

    2014-12-01

    Proximal focal femoral deficiency (PFFD) is a heterogeneous disorder characterized by various degrees of femoral deficiencies and associated anomalies of the pelvis and lower limbs. The etiology of the disease has not been determined. We report on a 3-year-old boy with severe PFFD, who showed almost completely absent femora and fibulae, malformed pelvis and ectrodactyly of the left foot. These features were partially overlapped with those of Al-Awadi-Raas-Rothschild syndrome or Fuhrmann syndrome, both of which are caused by WNT7A mutations. Molecular analysis of our case, however, demonstrated no disease-causing mutations in the WNT7A gene. PMID:24839142

  6. Phenotype of NK Cells Determined on the Basis of Selected Immunological Parameters in Children Treated due to Acute Lymphoblastic Leukemia.

    PubMed

    Koltan, Sylwia; Debski, Robert; Koltan, Andrzej; Grzesk, Elzbieta; Tejza, Barbara; Eljaszewicz, Andrzej; Gackowska, Lidia; Kubicka, Malgorzata; Kolodziej, Beata; Kurylo-Rafinska, Beata; Kubiszewska, Izabela; Wiese, Malgorzata; Januszewska, Milena; Michalkiewicz, Jacek; Wysocki, Mariusz; Styczynski, Jan; Grzesk, Grzegorz

    2015-12-01

    Acute lymphoblastic leukemia (ALL) is the most frequent pediatric malignancy. The chemotherapy for ALL is associated with a profound secondary immune deficiency.We evaluated the number and phenotype of natural killer (NK) cells at diagnosis, after the intensive chemotherapy and following the completion of the entire treatment for patients with ALL. The fraction, absolute number, and percentage of NK cells expressing interferon-γ were determined in full blood samples. The fraction of NK cells expressing CD158a, CD158b, perforin, A, B, and K granzymes was examined in isolated NK cells.We have shown that patients assessed at ALL diagnosis showed significantly lower values of the fraction of NK cells and percentage of NK cells with the granzyme A expression. Additionally, the absolute number of NK cells, the expression of CD158a, CD158b, perforin, and granzyme A were significantly lower in patients who completed intensive chemotherapy. Also, there was a significantly higher fraction of NK cells expressing granzyme K in patients who completed the therapy.Abnormalities of NK cells were found at all stages of the treatment; however, the most pronounced changes were found at the end of intensive chemotherapy. PMID:26717380

  7. The Phosphorylation Flow of the Vibrio harveyi Quorum-Sensing Cascade Determines Levels of Phenotypic Heterogeneity in the Population

    PubMed Central

    Plener, Laure; Lorenz, Nicola; Reiger, Matthias; Ramalho, Tiago; Gerland, Ulrich

    2015-01-01

    ABSTRACT Quorum sensing (QS) is a communication process that enables a bacterial population to coordinate and synchronize specific behaviors. The bioluminescent marine bacterium Vibrio harveyi integrates three autoinducer (AI) signals into one quorum-sensing cascade comprising a phosphorelay involving three hybrid sensor kinases: LuxU; LuxO, an Hfq/small RNA (sRNA) switch; and the transcriptional regulator LuxR. Using a new set of V. harveyi mutants lacking genes for the AI synthases and/or sensors, we assayed the activity of the quorum-sensing cascade at the population and single-cell levels, with a specific focus on signal integration and noise levels. We found that the ratios of kinase activities to phosphatase activities of the three sensors and, hence, the extent of phosphorylation of LuxU/LuxO are important not only for the signaling output but also for the degree of noise in the system. The pools of phosphorylated LuxU/LuxO per cell directly determine the amounts of sRNAs produced and, consequently, the copy number of LuxR, generating heterogeneous quorum-sensing activation at the single-cell level. We conclude that the ability to drive the heterogeneous expression of QS-regulated genes in V. harveyi is an inherent feature of the architecture of the QS cascade. IMPORTANCE V. harveyi possesses one of the most complex quorum-sensing (QS) cascades known, using three different autoinducers (AIs) to control the induction of, e.g., bioluminescence, virulence factors, and biofilm and exoprotease production. We constructed various V. harveyi mutants to study the impact of each component and subsystem of the QS signaling cascade on QS activation at the population and single-cell levels. We found that the output was homogeneous only in the presence of all AIs. In the absence of any one AI, QS activation varied from cell to cell, resulting in phenotypic heterogeneity. This study elucidates a molecular design principle which enables a tightly integrated signaling

  8. Genetic and Pharmacological Modifications of Thrombin Formation in Apolipoprotein E-deficient Mice Determine Atherosclerosis Severity and Atherothrombosis Onset in a Neutrophil-Dependent Manner

    PubMed Central

    Borissoff, Julian I.; Otten, Jeroen J. T.; Heeneman, Sylvia; Leenders, Peter; van Oerle, René; Soehnlein, Oliver; Loubele, Sarah T. B. G.; Hamulyák, Karly; Hackeng, Tilman M.; Daemen, Mat J. A. P.; Degen, Jay L.; Weiler, Hartmut; Esmon, Charles T.; van Ryn, Joanne; Biessen, Erik A. L.; Spronk, Henri M. H.; ten Cate, Hugo

    2013-01-01

    Background Variations in the blood coagulation activity, determined genetically or by medication, may alter atherosclerotic plaque progression, by influencing pleiotropic effects of coagulation proteases. Published experimental studies have yielded contradictory findings on the role of hypercoagulability in atherogenesis. We therefore sought to address this matter by extensively investigating the in vivo significance of genetic alterations and pharmacologic inhibition of thrombin formation for the onset and progression of atherosclerosis, and plaque phenotype determination. Methodology/Principal Findings We generated transgenic atherosclerosis-prone mice with diminished coagulant or hypercoagulable phenotype and employed two distinct models of atherosclerosis. Gene-targeted 50% reduction in prothrombin (FII−/WT:ApoE−/−) was remarkably effective in limiting disease compared to control ApoE−/− mice, associated with significant qualitative benefits, including diminished leukocyte infiltration, altered collagen and vascular smooth muscle cell content. Genetically-imposed hypercoagulability in TMPro/Pro:ApoE−/− mice resulted in severe atherosclerosis, plaque vulnerability and spontaneous atherothrombosis. Hypercoagulability was associated with a pronounced neutrophilia, neutrophil hyper-reactivity, markedly increased oxidative stress, neutrophil intraplaque infiltration and apoptosis. Administration of either the synthetic specific thrombin inhibitor Dabigatran etexilate, or recombinant activated protein C (APC), counteracted the pro-inflammatory and pro-atherogenic phenotype of pro-thrombotic TMPro/Pro:ApoE−/− mice. Conclusions/Significance We provide new evidence highlighting the importance of neutrophils in the coagulation-inflammation interplay during atherogenesis. Our findings reveal that thrombin-mediated proteolysis is an unexpectedly powerful determinant of atherosclerosis in multiple distinct settings. These studies suggest that selective

  9. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps.

    PubMed

    Greenbury, S F; Ahnert, S E

    2015-12-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype-phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into 'constrained' and 'unconstrained' sequences, in the broadest possible sense. As 'constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. 'Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with 'coding' and 'non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps. PMID:26609063

  10. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

    PubMed Central

    Greenbury, S. F.; Ahnert, S. E.

    2015-01-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype–phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into ‘constrained' and ‘unconstrained' sequences, in the broadest possible sense. As ‘constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. ‘Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with ‘coding' and ‘non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps. PMID:26609063

  11. Maternal eNOS deficiency determines a fatty liver phenotype of the offspring in a sex dependent manner.

    PubMed

    Hocher, Berthold; Haumann, Hannah; Rahnenführer, Jan; Reichetzeder, Christoph; Kalk, Philipp; Pfab, Thiemo; Tsuprykov, Oleg; Winter, Stefan; Hofmann, Ute; Li, Jian; Püschel, Gerhard P; Lang, Florian; Schuppan, Detlef; Schwab, Matthias; Schaeffeler, Elke

    2016-07-01

    Maternal environmental factors can impact on the phenotype of the offspring via the induction of epigenetic adaptive mechanisms. The advanced fetal programming hypothesis proposes that maternal genetic variants may influence the offspring's phenotype indirectly via epigenetic modification, despite the absence of a primary genetic defect. To test this hypothesis, heterozygous female eNOS knockout mice and wild type mice were bred with male wild type mice. We then assessed the impact of maternal eNOS deficiency on the liver phenotype of wild type offspring. Birth weight of male wild type offspring born to female heterozygous eNOS knockout mice was reduced compared to offspring of wild type mice. Moreover, the offspring displayed a sex specific liver phenotype, with an increased liver weight, due to steatosis. This was accompanied by sex specific differences in expression and DNA methylation of distinct genes. Liver global DNA methylation was significantly enhanced in both male and female offspring. Also, hepatic parameters of carbohydrate metabolism were reduced in male and female offspring. In addition, male mice displayed reductions in various amino acids in the liver. Maternal genetic alterations, such as partial deletion of the eNOS gene, can affect liver metabolism of wild type offspring without transmission of the intrinsic defect. This occurs in a sex specific way, with more detrimental effects in females. This finding demonstrates that a maternal genetic defect can epigenetically alter the phenotype of the offspring, without inheritance of the defect itself. Importantly, these acquired epigenetic phenotypic changes can persist into adulthood. PMID:27175980

  12. Respiratory heat/water loss alone does not determine the severity of exercise-induced asthma.

    PubMed

    Noviski, N; Bar-Yishay, E; Gur, I; Godfrey, S

    1988-03-01

    Respiratory heat loss (RHL) or water loss (RWL) have been proposed as possible triggering factors in exercise and hyperventilation-induced asthma (EIA and HIA). It has recently been demonstrated that exercise intensity and climatic factors are both important in determining the severity of EIA. Eight young asthmatics performed both exercise and isocapnic hyperventilation (IHV) manoeuvres under identical climatic conditions, as part of our investigation of these interactive factors which determine the severity of the asthmatic response. It was found that, when challenged at low ventilatory levels, exercise produced a significantly attenuated asthmatic response compared to IHV. The fall in forced expired volume in 1 sec (delta FEV1) following exercise was 15 +/- 4% as compared with 27 +/- 3% after IHV (p less than 0.002). It is concluded that while the hypernoea in exercise may serve as a trigger, exercise per se introduces an additional factor which serves to limit the full response seen with IHV. This attenuated response is revealed at low ventilatory levels but is masked at high levels. PMID:3384078

  13. CD44(high)CD24(low) molecular signature determines the Cancer Stem Cell and EMT phenotype in Oral Squamous Cell Carcinoma.

    PubMed

    Ghuwalewala, Sangeeta; Ghatak, Dishari; Das, Pijush; Dey, Sanjib; Sarkar, Shreya; Alam, Neyaz; Panda, Chinmay K; Roychoudhury, Susanta

    2016-03-01

    Almost all epithelial tumours contain cancer stem-like cells, which possess a unique property of self-renewal and differentiation. In oral cancer, several biomarkers including cell surface molecules have been exploited for the identification of this highly tumorigenic population. Implicit is the role of CD44 in defining CSCs but CD24 is not well-explored. Here we show that CD44(high)CD24(low) cells isolated from the oral cancer cell lines, not only express stem cell related genes but also exhibit Epithelial-to-Mesenchymal transition (EMT) characteristics. This CD44(high)CD24(low) population gives rise to all other cell types upon differentiation. Typical Cancer Stem Cell (CSC) phenotypes like increased colony formation, sphere forming ability, migration and invasion were also confirmed in CD44(high)CD24(low) cells. Drug transporters were found to be over-expressed in CD44(high)CD24(low) sub-population thereby contributing to elevated chemo-resistance. To validate our findings in-vivo, we determined the relative expression of CD44 and CD24 in clinical samples of OSCC patients. CD44 expression was consistently high whereas CD24 showed significantly lower expression in tumour tissues. Further, the gene expression profile of the CSC and non-CSC population unravels the molecular pathways which may contribute to stemness. We conclude that CD44(high)CD24(low) represents cancer stem-like cells in Oral Squamous Cell Carcinoma. PMID:26926234

  14. Determination of awareness in patients with severe brain injury using EEG power spectral analysis

    PubMed Central

    Goldfine, Andrew M.; Victor, Jonathan D.; Conte, Mary M.; Bardin, Jonathan C.; Schiff, Nicholas D.

    2011-01-01

    Objective To determine whether EEG spectral analysis could be used to demonstrate awareness in patients with severe brain injury. Methods We recorded EEG from healthy controls and three patients with severe brain injury, ranging from minimally conscious state (MCS) to locked-in-state (LIS), while they were asked to imagine motor and spatial navigation tasks. We assessed EEG spectral differences from 4 to 24 Hz with univariate comparisons (individual frequencies) and multivariate comparisons (patterns across the frequency range). Results In controls, EEG spectral power differed at multiple frequency bands and channels during performance of both tasks compared to a resting baseline. As patterns of signal change were inconsistent between controls, we defined a positive response in patient subjects as consistent spectral changes across task performances. One patient in MCS and one in LIS showed evidence of motor imagery task performance, though with patterns of spectral change different from the controls. Conclusion EEG power spectral analysis demonstrates evidence for performance of mental imagery tasks in healthy controls and patients with severe brain injury. Significance EEG power spectral analysis can be used as a flexible bedside tool to demonstrate awareness in brain-injured patients who are otherwise unable to communicate. PMID:21514214

  15. The Triage of Injured Patients: Mechanism of Injury, Regardless of Injury Severity, Determines Hospital Destination.

    PubMed

    Staudenmayer, Kristan; Wang, N Ewen; Weiser, Thomas G; Maggio, Paul; Mackersie, Robert C; Spain, David; Hsia, Renee Y

    2016-04-01

    The target rate for trauma undertriage is <5 per cent, but rates are as high as 30 to 40 per cent in many trauma systems. We hypothesized that high undertriage rates were due to the tendency to undertriage injured elderly patients and a growing elderly population. We conducted a retrospective analysis of all hospital visits in California using the Office of Statewide Health Planning and Development Database over a 5-year period. All hospital admissions and emergency department visits associated with injury were longitudinally linked. The primary outcome was triage pattern. Triage patterns were stratified across three dimensions: age, mechanism of injury, and access to care. A total of 60,182 severely injured patients were included in the analysis. Fall-related injuries were frequently undertriaged compared with injuries from motor vehicle collisions (MVCs) and penetrating trauma (52% vs 12% and 10%, respectively). This pattern was true for all age groups. Conversely, MVCs and penetrating traumas were associated with high rates of overtriage (>70% for both). In conclusion, in contrast to our hypothesis, we found that triage is largely determined by mechanism of injury regardless of injury severity. High rates of undertriage are largely due to the undertriage of fall-related injuries, which occurs in both younger and older adults. Patients injured after MVCs and penetrating trauma victims are brought to trauma centers regardless of injury severity, resulting in high rates of overtriage. These findings suggest an opportunity to improve trauma system performance. PMID:27097630

  16. Using CO(2) to determine inhaled contaminant volumes and blower effectiveness in several types of respirators.

    PubMed

    Johnson, Arthur T; Koh, Frank C; Scott, William H; Rehak, Timothy E

    2011-01-01

    This experiment was conducted to determine how much contaminant could be expected to be inhaled when overbreathing several different types of respirators. These included several tight-fitting and loose-fitting powered air-purifying respirators (PAPRs) and one air-purifying respirator (APR). CO(2) was used as a tracer gas in the ambient air, and several loose-and tight-fitting respirators were tested on the head form of a breathing machine. CO(2) concentration in the exhaled breath was monitored as well as CO(2) concentration in the ambient air. This concentration ratio was able to give a measurement of protection factor, not for the respirator necessarily, but for the wearer. Flow rates in the filter/blower inlet and breathing machine outlet were also monitored, so blower effectiveness (defined as the blower contribution to inhaled air) could also be determined. Wearer protection factors were found to range from 1.1 for the Racal AirMate loose-fitting PAPR to infinity for the 3M Hood, 3M Breath-Easy PAPR, and SE 400 breath-responsive PAPR. Inhaled contaminant volumes depended on tidal volume but ranged from 2.02  L to 0  L for the same respirators, respectively. Blower effectiveness was about 1.0 for tight-fitting APRs, 0.18 for the Racal, and greater than 1.0 for two of the loose-fitting PAPRs. With blower effectiveness greater than 1.0, some blower flow during the exhalation phase contributes to the subsequent inhalation. Results from this experiment point to different ways to measure respirator efficacy. PMID:21792358

  17. Using CO2 to Determine Inhaled Contaminant Volumes and Blower Effectiveness in Several Types of Respirators

    PubMed Central

    Johnson, Arthur T.; Koh, Frank C.; Scott, William H.; Rehak, Timothy E.

    2011-01-01

    This experiment was conducted to determine how much contaminant could be expected to be inhaled when overbreathing several different types of respirators. These included several tight-fitting and loose-fitting powered air-purifying respirators (PAPRs) and one air-purifying respirator (APR). CO2 was used as a tracer gas in the ambient air, and several loose-and tight-fitting respirators were tested on the head form of a breathing machine. CO2 concentration in the exhaled breath was monitored as well as CO2 concentration in the ambient air. This concentration ratio was able to give a measurement of protection factor, not for the respirator necessarily, but for the wearer. Flow rates in the filter/blower inlet and breathing machine outlet were also monitored, so blower effectiveness (defined as the blower contribution to inhaled air) could also be determined. Wearer protection factors were found to range from 1.1 for the Racal AirMate loose-fitting PAPR to infinity for the 3M Hood, 3M Breath-Easy PAPR, and SE 400 breath-responsive PAPR. Inhaled contaminant volumes depended on tidal volume but ranged from 2.02 L to 0 L for the same respirators, respectively. Blower effectiveness was about 1.0 for tight-fitting APRs, 0.18 for the Racal, and greater than 1.0 for two of the loose-fitting PAPRs. With blower effectiveness greater than 1.0, some blower flow during the exhalation phase contributes to the subsequent inhalation. Results from this experiment point to different ways to measure respirator efficacy. PMID:21792358

  18. Use of Specific IgE and Skin Prick Test to Determine Clinical Reaction Severity.

    PubMed

    Ta, Von; Weldon, Brittany; Yu, Grace; Humblet, Olivier; Neale-May, Susan; Nadeau, Kari

    2011-01-01

    AIMS: To determine whether specific IgE and skin prick test correlate better in predicting reaction severity during a double-blinded placebo controlled food challenge (DBPCFC) for egg, milk, and multiple tree nut allergens. STUDY DESIGN: Prospective study. PLACE AND DURATION OF STUDY: Department of Pediatrics, Stanford University School of Medicine, August 2009 and ongoing. METHODOLOGY: We examined the reaction severity of twenty-four subjects to nine possible food allergens: milk, egg, almond, cashew, hazelnut, peanut, sesame, pecan and walnut. Specific IgE and SPT were performed before each DBPCFC. DBPCFC results were classified into mild (1), moderate (2), or severe (3) reactions using a modified Bock's criteria. RESULTS: Twenty four subjects underwent a total of 80 DBPCFC. Eighty percent of all DBPCFCs resulted in a positive reaction. A majority, 71%, were classified as mild. No reactions occurred with a SPT of zero mm while three reactions occurred with a negative specific IgE. All reactions were reversible with medication. CONCLUSION: These data suggest that SPT and specific IgE levels are not associated with reaction severity (p<0.64 and 0.27, respectively). We also found that combining specific IgE and SPT improved specificity but did not help to achieve clinically useful sensitivity. For instance, an SPT > 5mm had a sensitivity of 91% and specificity of 50%. Combining SPT > 5mm and IgE > 7 resulted in a reduced sensitivity of 64%. Unexpectedly, a history of anaphylaxis 70% (n=17) was not predictive of anaphylaxis on challenge 4% (n=2). PMID:22993721

  19. An evaluation of several methods of determining the local angle of attack on wind turbine blades

    NASA Astrophysics Data System (ADS)

    Guntur, S.; Sørensen, N. N.

    2014-12-01

    Several methods of determining the angles of attack (AOAs) on wind turbine blades are discussed in this paper. A brief survey of the methods that have been used in the past are presented, and the advantages of each method are discussed relative to their application in the BEM theory. Data from existing as well as new full rotor CFD computations of the MEXICO rotor are used in this analysis. A more accurate estimation of the AOA is possible from 3D full rotor CFD computations, but when working with experimental data, pressure measurements and sectional forces are often the only data available. The aim of this work is to analyse the reliability of some of the simpler methods of estimating the 3D effective AOA compared some of the more rigorous CFD based methods.

  20. Bone Characteristics and Their Determinants in Adolescents and Young Adults with Early-Onset Severe Obesity.

    PubMed

    Viljakainen, H T; Valta, H; Lipsanen-Nyman, M; Saukkonen, T; Kajantie, E; Andersson, S; Mäkitie, O

    2015-10-01

    Childhood obesity is associated with compromised bone health. We studied bone characteristics and their determinants in obese young adults. The study included 68 subjects with early-onset severe obesity and 73 normal-weight controls. Data on physical activity (PA), diet and smoking were collected. Bone characteristics were measured using peripheral QCT. The obese and control subjects were similar in age (mean 19.6 ± 2.6 years) and height but BMIs differed (39.7 and 22.6 kg/m(2)). A clustering of unhealthy lifestyles was marked: Obese subjects reported less supervised PA in childhood, adolescence and currently (p < 0.03) and were more likely to smoke (p = 0.005), and had a lower healthy eating index (HEI) (p = 0.007) but similar alcohol consumption compared with controls. In obese women, all crude bone characteristics were higher than in controls; in men, the differences were smaller. Associations of lifestyle factors with bone characteristics were tested using partial correlations. Independently of BMI, supervised PA in adolescence and alcohol consumption were related positively to bone characteristics in both groups. HEI associated positively with bone characteristics only in controls, while smoking was a positive determinant of bone characteristics only in obese subjects. The multivariate model showed that the contribution of lifestyle factors to bone characteristics was minimal compared with BMI. Early-onset obesity is accompanied by poor dietary quality, sedentary lifestyle, and more frequent smoking, but the overall contribution of these lifestyle factors to bone strength is limited. Bone strength is more likely to be compromised in men and in unloaded bone sites in subjects with early-onset severe obesity. The impact of obesity-related endocrine changes on bone characteristics need to be evaluated in future studies. PMID:26139232

  1. Maternal eNOS deficiency determines a fatty liver phenotype of the offspring in a sex dependent manner

    PubMed Central

    Hocher, Berthold; Haumann, Hannah; Rahnenführer, Jan; Reichetzeder, Christoph; Kalk, Philipp; Pfab, Thiemo; Tsuprykov, Oleg; Winter, Stefan; Hofmann, Ute; Li, Jian; Püschel, Gerhard P.; Lang, Florian; Schuppan, Detlef; Schwab, Matthias; Schaeffeler, Elke

    2016-01-01

    ABSTRACT Maternal environmental factors can impact on the phenotype of the offspring via the induction of epigenetic adaptive mechanisms. The advanced fetal programming hypothesis proposes that maternal genetic variants may influence the offspring's phenotype indirectly via epigenetic modification, despite the absence of a primary genetic defect. To test this hypothesis, heterozygous female eNOS knockout mice and wild type mice were bred with male wild type mice. We then assessed the impact of maternal eNOS deficiency on the liver phenotype of wild type offspring. Birth weight of male wild type offspring born to female heterozygous eNOS knockout mice was reduced compared to offspring of wild type mice. Moreover, the offspring displayed a sex specific liver phenotype, with an increased liver weight, due to steatosis. This was accompanied by sex specific differences in expression and DNA methylation of distinct genes. Liver global DNA methylation was significantly enhanced in both male and female offspring. Also, hepatic parameters of carbohydrate metabolism were reduced in male and female offspring. In addition, male mice displayed reductions in various amino acids in the liver. Maternal genetic alterations, such as partial deletion of the eNOS gene, can affect liver metabolism of wild type offspring without transmission of the intrinsic defect. This occurs in a sex specific way, with more detrimental effects in females. This finding demonstrates that a maternal genetic defect can epigenetically alter the phenotype of the offspring, without inheritance of the defect itself. Importantly, these acquired epigenetic phenotypic changes can persist into adulthood. PMID:27175980

  2. Determinants of mortality from severe dengue in Brazil: a population-based case-control study.

    PubMed

    Moraes, Giselle Hentzy; de Fátima Duarte, Eliane; Duarte, Elisabeth Carmen

    2013-04-01

    Although increases in severity of mortality from dengue infection have been observed in Brazil, their determinants are not fully known. A case-control study was conducted by using the National Notifiable Diseases Surveillance System, including patients with severe dengue during 2000-2005. Cases were defined as patients that died and controls were those who survived. Hierarchical multivariate logistic regression was performed. During the study period, there were 12,321 severe cases of dengue and 1,062 deaths. Factors independently associated with death included age ≥ 50 years (odds ratio [OR] = 2.29, 95% confidence interval [CI] = 1.59-3.29), < 4 years of schooling (OR = 1.83, 95% CI = 1.47-2.28), a rural area (OR =2.84, 95% CI = 2.19-3.69), hospitalization (OR = 1.42, 95% CI = 1.17-1.73), and a high hematocrit (OR = 2.46, 95% CI = 1.85-3.28). Factors associated with a lower chance of dying were female sex (OR = 0.76, 95% CI = 0.67-0.87), history of previous dengue (OR = 0.78, 95% CI = 0.62-0.99), positive tourniquet test result (OR = 0.47, 95% CI = 0.33-0.66), laboratory diagnosis of dengue (OR = 0.75, 95% CI = 0.61-0.92), and a platelet count of 50,000-100,000 cells/mm(3) (OR = 0.56, 95% CI = 0.36-0.87). The risk profile identified in this study should serve to direct public health interventions to minimize deaths. PMID:23400577

  3. Determination of Serum Lost Goodwill Target Proteome in Patients with Severe Traumatic Brain Injury

    PubMed Central

    Ji, Hongming; Hu, Changchen; Zhang, Gangli; Ren, Jinrui; Tan, Yihu; Sun, Wenxiao; Wang, Junwen; Li, Jun; Liu, Hongchao; Xie, Ruifan; Hao, Zhipeng; Guo, Dongsheng

    2015-01-01

    This study investigates the biokinetics of LGT proteome, a potential biomarker of severe TBI, in serum of severe TBI patients. The LGT proteome presents in the serum of severe TBI patients. The abundance diversity of LGT proteome is closely associated with pathologic condition of TBI patients. Serum LGT proteome may be used as a promising marker for evaluating severity of severe TBI. PMID:26491659

  4. Novel two wavelength spectrophotometric methods for simultaneous determination of binary mixtures with severely overlapping spectra.

    PubMed

    Lotfy, Hayam M; Saleh, Sarah S; Hassan, Nagiba Y; Salem, Hesham

    2015-02-01

    This work presents the application of different spectrophotometric techniques based on two wavelengths for the determination of severely overlapped spectral components in a binary mixture without prior separation. Four novel spectrophotometric methods were developed namely: induced dual wavelength method (IDW), dual wavelength resolution technique (DWRT), advanced amplitude modulation method (AAM) and induced amplitude modulation method (IAM). The results of the novel methods were compared to that of three well-established methods which were: dual wavelength method (DW), Vierordt's method (VD) and bivariate method (BV). The developed methods were applied for the analysis of the binary mixture of hydrocortisone acetate (HCA) and fusidic acid (FSA) formulated as topical cream accompanied by the determination of methyl paraben and propyl paraben present as preservatives. The specificity of the novel methods was investigated by analyzing laboratory prepared mixtures and the combined dosage form. The methods were validated as per ICH guidelines where accuracy, repeatability, inter-day precision and robustness were found to be within the acceptable limits. The results obtained from the proposed methods were statistically compared with official ones where no significant difference was observed. No difference was observed between the obtained results when compared to the reported HPLC method, which proved that the developed methods could be alternative to HPLC techniques in quality control laboratories. PMID:25467671

  5. Novel two wavelength spectrophotometric methods for simultaneous determination of binary mixtures with severely overlapping spectra

    NASA Astrophysics Data System (ADS)

    Lotfy, Hayam M.; Saleh, Sarah S.; Hassan, Nagiba Y.; Salem, Hesham

    2015-02-01

    This work presents the application of different spectrophotometric techniques based on two wavelengths for the determination of severely overlapped spectral components in a binary mixture without prior separation. Four novel spectrophotometric methods were developed namely: induced dual wavelength method (IDW), dual wavelength resolution technique (DWRT), advanced amplitude modulation method (AAM) and induced amplitude modulation method (IAM). The results of the novel methods were compared to that of three well-established methods which were: dual wavelength method (DW), Vierordt's method (VD) and bivariate method (BV). The developed methods were applied for the analysis of the binary mixture of hydrocortisone acetate (HCA) and fusidic acid (FSA) formulated as topical cream accompanied by the determination of methyl paraben and propyl paraben present as preservatives. The specificity of the novel methods was investigated by analyzing laboratory prepared mixtures and the combined dosage form. The methods were validated as per ICH guidelines where accuracy, repeatability, inter-day precision and robustness were found to be within the acceptable limits. The results obtained from the proposed methods were statistically compared with official ones where no significant difference was observed. No difference was observed between the obtained results when compared to the reported HPLC method, which proved that the developed methods could be alternative to HPLC techniques in quality control laboratories.

  6. [Interest of S100B protein blood level determination in severe or moderate head injury].

    PubMed

    Bouvier, Damien

    2013-01-01

    S100B, a suffering brain marker, exhibits a different interest in traumatic brain injury (TBI) as the trauma is severe (sTBI) or mild (mTBI). Our works presented for the attribution of the SFBC 2012 price talked about both aspects. Firstly, the extent of S100B elevation has been found to be useful in predicting clinical outcome after sTBI. However, few studies were realized with jugular venous blood samples. After comparing the interest between jugular venous and arterial blood concentrations evaluation of serum S100B protein in patients with sTBI, determination of S100B concentration in jugular blood samples appears to be better than in arterial ones to predict clinical outcome after brain injury. Secondly, it's difficult to determine the indication of cranial computed tomography (CCT) for patients with mTBI. Actually, 90% of patients with mTBI have unnecessary CCT or short hospitalization for observation. Serum concentrations of S100B were found to provide useful information. We have investigated in 2 studies (1 for adult, 1 for children) whether S100B concentrations in patients with mTBI could provide additional information to improve indication of the need for an initial CCT scan or for a short hospitalization. Patients with intracerebral lesions on the CCT scan (CCT+) or with bad clinical evolution were identified with a sensitivity level of 100% and a specificity level of 30%. Adding the measurement of S-100B serum concentration to the clinical decision rules for a CCT scan or hospitalization in patients with mTBI could allow a 30% reduction in scans and in hospitalization for clinical observation. PMID:23587577

  7. A Summary of Flight-Determined Transonic Lift and Drag Characteristics of Several Research Airplane Configurations

    NASA Technical Reports Server (NTRS)

    Bellman, Donald R.

    1959-01-01

    Flight-determined lift and drag data from transonic flights of seven research airplane configurations of widely varying characteristics are presented and compared with wind-tunnel and rocket-model data. The airplanes are the X-5 (590 wing sweep), XF-92A, YF-102 with cambered wing, YF-102 with symmetrical wing, D-558-ii, X-3, and X-LE. The effects of some of the basic configuration differences on the lift and drag characteristics are demonstrated. As indicated by transonic similarity laws, most of the configurations demonstrate a relationship between the transonic increase in zero-lift drag and the maximum cross-sectional area. No such relationship was found between the drag-rise Mach number and its normally related parameters. A comparison of flight and wind-tunnel data shows a generally reasonable agreement, but Reynolds number differences can cause considerable variations in the drag levels of the flight and wind-tunnel tests. Maximum lift-drag ratios vary widely in the subsonic region as would be expected from differences in aspect ratio and wing thickness ratio; however, the variations diminish as the Mach number is increased through the transonic region. The attainment of maximum lift-drag ratio in level flight by several of the airplanes was limited by engine performance, stability characteristics, and buffet boundaries.

  8. Delineating the GRIN1 phenotypic spectrum

    PubMed Central

    Geider, Kirsten; Helbig, Katherine L.; Heyne, Henrike O.; Schütz, Hannah; Hentschel, Julia; Courage, Carolina; Depienne, Christel; Nava, Caroline; Heron, Delphine; Møller, Rikke S.; Hjalgrim, Helle; Lal, Dennis; Neubauer, Bernd A.; Nürnberg, Peter; Thiele, Holger; Kurlemann, Gerhard; Arnold, Georgianne L.; Bhambhani, Vikas; Bartholdi, Deborah; Pedurupillay, Christeen Ramane J.; Misceo, Doriana; Frengen, Eirik; Strømme, Petter; Dlugos, Dennis J.; Doherty, Emily S.; Bijlsma, Emilia K.; Ruivenkamp, Claudia A.; Hoffer, Mariette J.V.; Goldstein, Amy; Rajan, Deepa S.; Narayanan, Vinodh; Ramsey, Keri; Belnap, Newell; Schrauwen, Isabelle; Richholt, Ryan; Koeleman, Bobby P.C.; Sá, Joaquim; Mendonça, Carla; de Kovel, Carolien G.F.; Weckhuysen, Sarah; Hardies, Katia; De Jonghe, Peter; De Meirleir, Linda; Milh, Mathieu; Badens, Catherine; Lebrun, Marine; Busa, Tiffany; Francannet, Christine; Piton, Amélie; Riesch, Erik; Biskup, Saskia; Vogt, Heinrich; Dorn, Thomas; Helbig, Ingo; Michaud, Jacques L.; Laube, Bodo; Syrbe, Steffen

    2016-01-01

    Objective: To determine the phenotypic spectrum caused by mutations in GRIN1 encoding the NMDA receptor subunit GluN1 and to investigate their underlying functional pathophysiology. Methods: We collected molecular and clinical data from several diagnostic and research cohorts. Functional consequences of GRIN1 mutations were investigated in Xenopus laevis oocytes. Results: We identified heterozygous de novo GRIN1 mutations in 14 individuals and reviewed the phenotypes of all 9 previously reported patients. These 23 individuals presented with a distinct phenotype of profound developmental delay, severe intellectual disability with absent speech, muscular hypotonia, hyperkinetic movement disorder, oculogyric crises, cortical blindness, generalized cerebral atrophy, and epilepsy. Mutations cluster within transmembrane segments and result in loss of channel function of varying severity with a dominant-negative effect. In addition, we describe 2 homozygous GRIN1 mutations (1 missense, 1 truncation), each segregating with severe neurodevelopmental phenotypes in consanguineous families. Conclusions: De novo GRIN1 mutations are associated with severe intellectual disability with cortical visual impairment as well as oculomotor and movement disorders being discriminating phenotypic features. Loss of NMDA receptor function appears to be the underlying disease mechanism. The identification of both heterozygous and homozygous mutations blurs the borders of dominant and recessive inheritance of GRIN1-associated disorders. PMID:27164704

  9. Molecular analysis of SUMF1 mutations: stability and residual activity of mutant formylglycine-generating enzyme determine disease severity in multiple sulfatase deficiency.

    PubMed

    Schlotawa, Lars; Steinfeld, Robert; von Figura, Kurt; Dierks, Thomas; Gärtner, Jutta

    2008-01-01

    Multiple Sulfatase Deficiency (MSD) is a rare inborn autosomal-recessive disorder, which mainly combines clinical features of metachromatic leukodystrophy, mucopolysaccharidosis and X-linked ichthyosis. The clinical course ranges from neonatal severe to mild juvenile cases. MSD is caused by mutations in the SUMF1 gene encoding the formylglycine-generating enzyme (FGE). FGE posttranslationally activates sulfatases by generating formylglycine in their catalytic sites. We analyzed the functional consequences of missense mutations p.A177P, p.W179S, p.A279V and p.R349W with regard to FGE's subcellular localization, enzymatic activity, protein stability, intracellular retention and resulting sulfatase activities. All four mutations did not affect localization of FGE in the endoplasmic reticulum of MSD fibroblasts. However, they decreased its specific enzymatic activity to less than 1% (p.A177P and p.R349W), 3% (p.W179S) or 23% (p.A279V). Protein stability was severely decreased for p.A279V and p.R349W, and almost comparable to wild type for p.A177P and p.W179S. The patient with the mildest clinical phenotype carries the mutation p.A279V leading to decreased FGE protein stability, but high residual enzymatic activity and only slightly reduced sulfatase activities. In contrast, the most severely affected patient carries the mutation p.R349W leading to drastically decreased protein stability, very low residual enzymatic activity and considerably reduced sulfatase activities. Our functional studies provide novel insight into the molecular defect underlying MSD and reveal that both residual enzyme activity and protein stability of FGE contribute to the clinical phenotype. The application of improved functional assays to determine these two molecular parameters of FGE mutants may enable the prediction of the clinical outcome in the future. PMID:18157819

  10. The Pain in Neuropathy Study (PiNS): a cross-sectional observational study determining the somatosensory phenotype of painful and painless diabetic neuropathy

    PubMed Central

    Themistocleous, Andreas C.; Ramirez, Juan D.; Shillo, Pallai R.; Lees, Jonathan G.; Selvarajah, Dinesh; Orengo, Christine; Tesfaye, Solomon; Rice, Andrew S.C.; Bennett, David L.H.

    2016-01-01

    Abstract Disabling neuropathic pain (NeuP) is a common sequel of diabetic peripheral neuropathy (DPN). We aimed to characterise the sensory phenotype of patients with and without NeuP, assess screening tools for NeuP, and relate DPN severity to NeuP. The Pain in Neuropathy Study (PiNS) is an observational cross-sectional multicentre study. A total of 191 patients with DPN underwent neurological examination, quantitative sensory testing, nerve conduction studies, and skin biopsy for intraepidermal nerve fibre density assessment. A set of questionnaires assessed the presence of pain, pain intensity, pain distribution, and the psychological and functional impact of pain. Patients were divided according to the presence of DPN, and thereafter according to the presence and severity of NeuP. The DN4 questionnaire demonstrated excellent sensitivity (88%) and specificity (93%) in screening for NeuP. There was a positive correlation between greater neuropathy severity (r = 0.39, P < 0.01), higher HbA1c (r = 0.21, P < 0.01), and the presence (and severity) of NeuP. Diabetic peripheral neuropathy sensory phenotype is characterised by hyposensitivity to applied stimuli that was more marked in the moderate/severe NeuP group than in the mild NeuP or no NeuP groups. Brush-evoked allodynia was present in only those with NeuP (15%); the paradoxical heat sensation did not discriminate between those with (40%) and without (41.3%) NeuP. The “irritable nociceptor” subgroup could only be applied to a minority of patients (6.3%) with NeuP. This study provides a firm basis to rationalise further phenotyping of painful DPN, for instance, stratification of patients with DPN for analgesic drug trials. PMID:27088890

  11. What factors determine the severity of hepatitis A-related acute liver failure?

    PubMed Central

    Ajmera, V.; Xia, G.; Vaughan, G.; Forbi, J. C.; Ganova-Raeva, L. M.; Khudyakov, Y.; Opio, C. K.; Taylor, R.; Restrepo, R.; Munoz, S.; Fontana, R. J.; Lee, W. M.

    2016-01-01

    SUMMARY The reason(s) that hepatitis A virus (HAV) infection may progress infrequently to acute liver failure are poorly understood. We examined host and viral factors in 29 consecutive adult patients with HAV-associated acute liver failure enrolled at 10 sites participating in the US ALF Study Group. Eighteen of twenty-four acute liver failure sera were PCR positive while six had no detectable virus. HAV genotype was determined using phylogenetic analysis and the full-length genome sequences of the HAV from a cute liver failure sera were compared to those from self-limited acute HAV cases selected from the CDC database. We found that rates of nucleotide substitution did not vary significantly between the liver failure and non-liver failure cases and there was no significant variation in amino acid sequences between the two groups. Four of 18 HAV isolates were subgenotype IB, acquired from the same study site over a 3.5-year period. Sub-genotype IB was found more frequently among acute liver failure cases compared to the non-liver failure cases (chi-square test, P < 0.01). At another centre, a mother and her son presented with HAV and liver failure within 1 month of each other. Predictors of spontaneous survival included detectable serum HAV RNA, while age, gender, HAV genotype and nucleotide substitutions were not associated with outcome. The more frequent appearance of rapid viral clearance and its association with poor outcomes in acute liver failure as well as the finding of familial cases imply a possible host genetic predisposition that contributes to a fulminant course. Recurrent cases of the rare subgenotype IB over several years at a single centre imply a community reservoir of infection and possible increased pathogenicity of certain infrequent viral genotypes. PMID:21143345

  12. Determinants of change in physical activity during moderate-to-severe COPD exacerbation

    PubMed Central

    Esteban, Cristóbal; Quintana, José M; Garcia-Gutierrez, Susana; Anton-Ladislao, Ane; Gonzalez, Nerea; Baré, Marisa; Fernández de Larrea, Nerea; Rivas-Ruiz, Francisco

    2016-01-01

    Background Data are scarce on patient physical activity (PA) level during exacerbations of chronic obstructive pulmonary disease (eCOPD). The objective of the study was to evaluate the level and determinants of change in PA during an eCOPD. Materials and methods We conducted a prospective cohort study with recruitment from emergency departments (EDs) of 16 participating hospitals from June 2008 to September 2010. Data were recorded on socioeconomic characteristics, dyspnea, forced expiratory volume in 1 second (FEV1%), comorbidities, health-related quality of life, factors related to exacerbation, and PA in a stable clinical condition and during the eCOPD episode. Results We evaluated 2,487 patients. Common factors related to the change in PA during hospital admission or 7 days after discharge to home from the ED were lower PA at baseline and during the first 24 hours after the index evaluation. Age, quality of life, living alone, length of hospital stay, and use of anticholinergic or systemic corticosteroids in treating the exacerbation were associated with the change in PA among hospitalized patients. Predictors of change among patients not admitted to hospital were baseline FEV1% and dyspnea at rest on ED arrival. Conclusion Among the patients evaluated in an ED for an eCOPD, the level and change in PA was markedly variable. Factors associated with exacerbation (PA 24 hours after admission, medication during admission, and length of hospital stay) and variables reflecting patients’ stable clinical condition (low level of PA, age, quality of life, FEV1%) are predictors of the change in PA during a moderate-to-severe eCOPD. PMID:26893555

  13. Meibomian Gland Dysfunction Determines the Severity of the Dry Eye Conditions in Visual Display Terminal Workers

    PubMed Central

    Dong, Nuo; Yang, Fan; Lin, Zhirong; Shang, Xumin; Li, Cheng

    2014-01-01

    Objective To explore meibomian gland dysfunction (MGD) may determine the severity of dry eye conditions in visual display terminal (VDT) workers. Methodology Prospective, case-control study carried out in China.106 eyes of 53 patients (VDT work time >4 hour per day) were recruited as the Long time VDT group; 80 eyes of 40 control subjects (VDT work time ≤4 hour per day) served as the Short time VDT group. A questionnaire of Ocular Surface Disease Index (OSDI) and multiple tests were performed. Three dry eye tests: tear film breakup time (BUT), corneal fluorescein staining, Schirmer I test; and three MGD parameters: lid margin abnormality score, meibum expression assessment (meibum score), and meibomian gland dropout degree (meiboscore) using Keratograph 5 M. Principal Findings OSDI and corneal fluorescein score were significantly higher while BUT was dramatically shorter in the long time VDT group than the short time VDT group. However, the average of Schirmer tear volumes was in normal ranges in both groups. Interestingly, the three MGD parameters were significantly higher in the long time VDT group than the short time one (P<0.0001). When 52 eyes with Schirmer <10 mm and 54 eyes with Schirmer ≥10 mm were separated from the long time VDT workers, no significant differences were found between the two subgroups in OSDI, fluorescein staining and BUT, as well as the three MGD parameters. All three MGD parameters were positively correlated with VDT working time (P<0.0001) and fluorescein scores (P<0.0001), inversely correlated with BUT (P<0.05), but not correlated with Schirmer tear volumes in the VDT workers. Conclusions Our findings suggest that a malfunction of meibomian glands is associated with dry eye patients in long term VDT workers with higher OSDI scores whereas some of those patients presenting a normal tear volume. PMID:25144638

  14. Compound heterozygosity for COL7A1 mutations in twins with dystrophic epidermolysis bullosa: A recessive paternal deletion/insertion mutation and a dominant negative maternal glycine substitution result in a severe phenotype

    SciTech Connect

    Christiano, A.M.; Uitto, J.; Anton-Lamprecht, I.; Ebschner, U.; Amano, S.; Burgeson, R.E.

    1996-04-01

    We have previously demonstrated genetic linkage between the type VII collagen gene (COL7A1) and the dominant (DDEB) and recessive (RDEB) forms of dystrophic epidermolysis bullosa (DEB) and have subsequently identified pathogenetic mutations in several families. Mutations in DDEB identified thus far are glycine substitutions in the collagenous domain of COL7A1, while the most severe forms of RDEB result from premature termination codon (PTC) mutations on both alleles. In this study, we performed mutation analysis in the COL7A1 gene in twins who displayed a severe DEB phenotype. Mutational analysis revealed a paternal 2-bp deletion/1-bp insertion in exon 56, designated 5103CC{yields}G, which results in a frameshift and downstream PTC. Analysis of the maternal COL7A1 allele revealed a glycine-to-arginine substitution in exon 91 (G2351R). Careful questioning of the mother revealed that she and her father had a history of shedding of toenails and occasional poorly heating erosions, consistent with a mild form of DDEB. Immunoprecipitation of type VII collagen from fibroblasts of the twins revealed a marked reduction in intracellular protein production, consistent with the drastic reduction in mRNA transcript from the paternal mutant allele, while the majority of polypeptides bearing the glycine substitution appeared to be degraded intracellularly. Thus, the severe RDEB phenotype in the probands results from compound heterozygosity for one glycine substitution and one PTC mutation in COL7A1. 40 refs., 7 figs.

  15. A calculator program for determining indices of neonatal respiratory distress syndrome severity.

    PubMed

    Horbar, J D

    1987-01-01

    The potential for treating and preventing neonatal respiratory distress syndrome (RDS) with exogenous surfactant has created renewed interest in quantitative measures and derived scores that can be used to assess disease severity. Many different indices of RDS severity have been suggested. They are useful as outcome measures in clinical trials and may assist in the early identification of infants at risk for severe complications. In this article, a program for the Hewlett-Packard 41CV programmable calculator is presented that calculates indices of RDS severity based on ventilator settings and arterial blood gas values. PMID:3098256

  16. Novel phenotypes of prediabetes?

    PubMed

    Häring, Hans-Ulrich

    2016-09-01

    This article describes phenotypes observed in a prediabetic population (i.e. a population with increased risk for type 2 diabetes) from data collected at the University hospital of Tübingen. We discuss the impact of genetic variation on insulin secretion, in particular the effect on compensatory hypersecretion, and the incretin-resistant phenotype of carriers of the gene variant TCF7L2 is described. Imaging studies used to characterise subphenotypes of fat distribution, metabolically healthy obesity and metabolically unhealthy obesity are described. Also discussed are ectopic fat stores in liver and pancreas that determine the phenotype of metabolically healthy and unhealthy fatty liver and the recently recognised phenotype of fatty pancreas. The metabolic impact of perivascular adipose tissue and pancreatic fat is discussed. The role of hepatokines, particularly that of fetuin-A, in the crosstalk between these organs is described. Finally, the role of brain insulin resistance in the development of the different prediabetes phenotypes is discussed. PMID:27344314

  17. Genotypic and phenotypic evaluation of Rutilus spp. from Skadar, Ohrid and Prespa Lakes supports revision of endemic as well as taxonomic status of several taxa.

    PubMed

    Milošević, D; Winkler, K A; Marić, D; Weiss, S

    2011-11-01

    One mtDNA gene (cytochrome b), one nuclear DNA fragment, five microsatellites and a suite of morphological characters were evaluated in samples of Rutilus spp. from Skadar, Ohrid and Prespa Lakes. Both genetic and phenotypic data supported two sympatric taxa in Lake Skadar, whereby Prespa and Ohrid Lakes revealed only a single taxon each. One of the taxa from Lake Skadar was similar to samples from Lake Prespa, whereas the second taxon was the most divergent in the data set. The estimated time to the most recent common ancestor of these two sympatric taxa in Lake Skadar was between 125 000 and 500 000 years. The data did not support existing taxonomic schemes for Rutilus in these lakes. This study poses the following working hypothesis: (1) Rutilus prespensis lives both in Lake Prespa and Lake Skadar and therefore is not endemic to Lake Prespa, (2) Rutilus ohridanus lives in Lake Ohrid only and therefore could be considered an endemic if its species status is retained and (3) a third recently described taxon (Rutilus albus) sympatric to R. prespensis lives in Lake Skadar. PMID:22026595

  18. Determining the association between adipokine expression in multiple tissues and phenotypic features of non-alcoholic fatty liver disease in obesity

    PubMed Central

    Wolfs, M G M; Gruben, N; Rensen, S S; Verdam, F J; Greve, J W; Driessen, A; Wijmenga, C; Buurman, W A; Franke, L; Scheja, L; Koonen, D P Y; Shiri-Sverdlov, R; van Haeften, T W; Hofker, M H; Fu, J

    2015-01-01

    Objectives: Non-alcoholic fatty liver disease (NAFLD) is an obesity-associated disease, and in obesity adipokines are believed to be involved in the development of NAFLD. However, it is still not clear whether adipokines in the liver and/or adipose tissues can be related to the development of specific characteristics of NAFLD, such as steatosis and inflammation. We aimed to address this question by simultaneously examining the adipokine expression in three tissue types in obese individuals. Methods: We enrolled 93 severely obese individuals with NAFLD, varying from simple steatosis to severe non-alcoholic steatohepatitis. Their expression of 48 adipokines in the liver, visceral and subcutaneous adipose tissue (SAT) was correlated to their phenotypic features of NAFLD. We further determined whether the correlations were tissue specific and/or independent of covariates, including age, sex, obesity, insulin resistance and type 2 diabetes (T2D). Results: The expression of adipokines showed a liver- and adipose tissue-specific pattern. We identified that the expression of leptin, angiopoietin 2 (ANGPT2) and chemerin in visceral adipose tissue (VAT) was associated with different NAFLD features, including steatosis, ballooning, portal and lobular inflammation. In addition, the expression of tumor necrosis factor (TNF), plasminogen activator inhibitor type 1 (PAI-1), insulin-like growth factor 1 (somatomedin C) (IGF1) and chemokine (C-X-C motif) ligand 10 (CXCL10) in the liver tissue and the expression of interleukin 1 receptor antagonist (IL1RN) in both the liver and SAT were associated with NAFLD features. The correlations between ANGPT2 and CXCL10, and NAFLD features were dependent on insulin resistance and T2D, but for the other genes the correlation with at least one NAFLD feature remained significant after correcting for the covariates. Conclusions: Our results suggest that in obese individuals, VAT-derived leptin and chemerin, and hepatic expression of TNF, IGF1, IL

  19. Determining Relative Contributions of Vegetation and Topography to Burn Severity from LANDSAT Imagery

    NASA Astrophysics Data System (ADS)

    Wu, Zhiwei; He, Hong S.; Liang, Yu; Cai, Longyan; Lewis, Bernard J.

    2013-10-01

    Fire is a dominant process in boreal forest landscapes and creates a spatial patch mosaic with different burn severities and age classes. Quantifying effects of vegetation and topography on burn severity provides a scientific basis on which forest fire management plans are developed to reduce catastrophic fires. However, the relative contribution of vegetation and topography to burn severity is highly debated especially under extreme weather conditions. In this study, we hypothesized that relationships of vegetation and topography to burn severity vary with fire size. We examined this hypothesis in a boreal forest landscape of northeastern China by computing the burn severity of 24 fire patches as the difference between the pre- and post-fire Normalized Difference Vegetation Index obtained from two Landsat TM images. The vegetation and topography to burn severity relationships were evaluated at three fire-size levels of small (<100 ha, n = 12), moderate (100-1,000 ha, n = 9), and large (>1,000 ha, n = 3). Our results showed that vegetation and topography to burn severity relationships were fire-size-dependent. The burn severity of small fires was primary controlled by vegetation conditions (e.g., understory cover), and the burn severity of large fires was strongly influenced by topographic conditions (e.g., elevation). For moderate fires, the relationships were complex and indistinguishable. Our results also indicated that the pattern trends of relative importance for both vegetation and topography factors were not dependent on fire size. Our study can help managers to design fire management plans according to vegetation characteristics that are found important in controlling burn severity and prioritize management locations based on the relative importance of vegetation and topography.

  20. Phenotypic switching in bacteria

    NASA Astrophysics Data System (ADS)

    Merrin, Jack

    Living matter is a non-equilibrium system in which many components work in parallel to perpetuate themselves through a fluctuating environment. Physiological states or functionalities revealed by a particular environment are called phenotypes. Transitions between phenotypes may occur either spontaneously or via interaction with the environment. Even in the same environment, genetically identical bacteria can exhibit different phenotypes of a continuous or discrete nature. In this thesis, we pursued three lines of investigation into discrete phenotypic heterogeneity in bacterial populations: the quantitative characterization of the so-called bacterial persistence, a theoretical model of phenotypic switching based on those measurements, and the design of artificial genetic networks which implement this model. Persistence is the phenotype of a subpopulation of bacteria with a reduced sensitivity to antibiotics. We developed a microfluidic apparatus, which allowed us to monitor the growth rates of individual cells while applying repeated cycles of antibiotic treatments. We were able to identify distinct phenotypes (normal and persistent) and characterize the stochastic transitions between them. We also found that phenotypic heterogeneity was present prior to any environmental cue such as antibiotic exposure. Motivated by the experiments with persisters, we formulated a theoretical model describing the dynamic behavior of several discrete phenotypes in a periodically varying environment. This theoretical framework allowed us to quantitatively predict the fitness of dynamic populations and to compare survival strategies according to environmental time-symmetries. These calculations suggested that persistence is a strategy used by bacterial populations to adapt to fluctuating environments. Knowledge of the phenotypic transition rates for persistence may provide statistical information about the typical environments of bacteria. We also describe a design of artificial

  1. Winter severity determines functional trait composition of phytoplankton in seasonally ice-covered lakes.

    PubMed

    Özkundakci, Deniz; Gsell, Alena S; Hintze, Thomas; Täuscher, Helgard; Adrian, Rita

    2016-01-01

    How climate change will affect the community dynamics and functionality of lake ecosystems during winter is still little understood. This is also true for phytoplankton in seasonally ice-covered temperate lakes which are particularly vulnerable to the presence or absence of ice. We examined changes in pelagic phytoplankton winter community structure in a north temperate lake (Müggelsee, Germany), covering 18 winters between 1995 and 2013. We tested how phytoplankton taxa composition varied along a winter-severity gradient and to what extent winter severity shaped the functional trait composition of overwintering phytoplankton communities using multivariate statistical analyses and a functional trait-based approach. We hypothesized that overwintering phytoplankton communities are dominated by taxa with trait combinations corresponding to the prevailing winter water column conditions, using ice thickness measurements as a winter-severity indicator. Winter severity had little effect on univariate diversity indicators (taxon richness and evenness), but a strong relationship was found between the phytoplankton community structure and winter severity when taxon trait identity was taken into account. Species responses to winter severity were mediated by the key functional traits: motility, nutritional mode, and the ability to form resting stages. Accordingly, one or the other of two functional groups dominated the phytoplankton biomass during mild winters (i.e., thin or no ice cover; phototrophic taxa) or severe winters (i.e., thick ice cover; exclusively motile taxa). Based on predicted milder winters for temperate regions and a reduction in ice-cover durations, phytoplankton communities during winter can be expected to comprise taxa that have a relative advantage when the water column is well mixed (i.e., need not be motile) and light is less limiting (i.e., need not be mixotrophic). A potential implication of this result is that winter severity promotes different

  2. A Challenge to Self-Determination: Disagreement between the Vocational Choices Made by Individuals with Severe Disabilities and Their Caregivers

    ERIC Educational Resources Information Center

    Martin, James E.; Woods, Lee L.; Sylvester, Lorraine; Gardner, J. Emmett

    2005-01-01

    Individuals become self-determined when they are empowered to make choices that match their interests. But caregivers' perceptions of what they think individuals with severe disabilities like often direct vocational decision making. This choice by proxy denies individuals with disabilities an opportunity to become self-determined. We examined…

  3. Exploring the Phenotype of Phonological Reading Disability as a Function of the Phonological Deficit Severity: Evidence from the Error Analysis Paradigm in Arabic

    ERIC Educational Resources Information Center

    Taha, Haitham; Ibrahim, Raphiq; Khateb, Asaid

    2014-01-01

    The dominant error types were investigated as a function of phonological processing (PP) deficit severity in four groups of impaired readers. For this aim, an error analysis paradigm distinguishing between four error types was used. The findings revealed that the different types of impaired readers were characterized by differing predominant error…

  4. The role of Th2 immune pathway modulation in the treatment of severe asthma and its phenotypes: Are we getting closer?

    PubMed Central

    Levine, Stewart J.; Wenzel, Sally E.

    2010-01-01

    New therapeutic approaches are needed for severe asthmatics who are refractory to standard therapy with high doses of inhaled corticosteroids plus long-acting β2-agonists. Current treatment guidelines for severe asthmatics from the National Asthma Education and Prevention Program recommend the addition of oral corticosteroids, which are associated with significant morbidity, and for those with allergic asthma, anti-IgE. Genetic and translational studies, as well as clinical trials, suggest that in a sub-group of patients the pathobiology of severe asthma is mediated by immune pathways driven by Th2-type CD4+ T cells which produce a characteristic repertoire of interleukins, including IL-4, IL-5 and IL-13. Therefore, biological modifiers of Th2-type interleukins, such as monoclonal antibodies, soluble receptors and receptor antagonists, represent a rational strategy for developing new treatment approaches, but will need to be targeted to selected individuals in whom the appropriate Th2 immune pathway is “active.” The benefits of immune modifier therapies targeting Th2-type cytokines, however, will need to be weighed against the toxicities associated with inhibition of key biological pathways, as well as the expense of future medications. Therefore, future clinical trials will need to clearly establish the efficacy and safety of biological modifiers of Th2 immune pathways before these approaches can enter routine clinical practice for the treatment of severe asthma. PMID:20157138

  5. Phenotypic variations of cartilage hair hypoplasia: granulomatous skin inflammation and severe T cell immunodeficiency as initial clinical presentation in otherwise well child with short stature.

    PubMed

    McCann, Liza J; McPartland, Jo; Barge, Dawn; Strain, Lisa; Bourn, David; Calonje, Eduardo; Verbov, Julian; Riordan, Andrew; Kokai, George; Bacon, Chris M; Wright, Michael; Abinun, Mario

    2014-01-01

    We report a child with short stature since birth who was otherwise well, presenting at 2.8 years with progressive granulomatous skin lesions when diagnosed with severe T cell immunodeficiency. When previously investigated for short stature, and at the time of current investigations, she had no radiological skeletal features characteristics for cartilage hair hypoplasia, but we found a disease causing RMRP (RNase mitochondrial RNA processing endoribonuclease) gene mutation. Whilst search for HLA matched unrelated donor for haematopoietic stem cell transplantation (HSCT) was underway, she developed rapidly progressive EBV-related lymphoproliferative disorder requiring laparotomy and small bowel resection, and was treated with anti-B cell monoclonal antibody and eventually curative allogeneic HSCT. Screening for RMRP gene mutations should be part of immunological evaluation of patients with 'severe and/or combined' T cell immunodeficiency of unknown origin, especially when associated with short stature and regardless of presence or absence of radiological skeletal features. PMID:24217815

  6. Multiple correlation computer program determines relationships between several independent and dependent variables

    NASA Technical Reports Server (NTRS)

    Kaspar, H.; Newsbaum, J. B.

    1967-01-01

    Relationships between independent and dependent variables are determined by multiple correlation computer program. This is applied to research and experimental design and development of complex hardware and components that require test programs.

  7. The R215W mutation in NBS1 impairs {gamma}-H2AX binding and affects DNA repair: molecular bases for the severe phenotype of 657del5/R215W Nijmegen breakage syndrome patients

    SciTech Connect

    Masi, Alessandra di Viganotti, Mara; Polticelli, Fabio; Ascenzi, Paolo; Tanzarella, Caterina; Antoccia, Antonio

    2008-05-09

    Nijmegen breakage syndrome (NBS) is a genetic disorder characterized by chromosomal instability and hypersensitivity to ionising radiation. Compound heterozygous 657del5/R215W NBS patients display a clinical phenotype more severe than the majority of NBS patients homozygous for the 657del5 mutation. The NBS1 protein, mutated in NBS patients, contains a FHA/BRCT domain necessary for the DNA-double strand break (DSB) damage response. Recently, a second BRCT domain has been identified, however, its role is still unknown. Here, we demonstrate that the R215W mutation in NBS1 impairs histone {gamma}-H2AX binding after induction of DNA damage, leading to a delay in DNA-DSB rejoining. Molecular modelling reveals that the 215 residue of NBS1 is located between the two BRCT domains, affecting their relative orientation that appears critical for {gamma}-H2AX binding. Present data represent the first evidence for the role of NBS1 tandem BRCT domains in {gamma}-H2AX recognition, and could explain the severe phenotype observed in 657del5/R215W NBS patients.

  8. Development of a Fuzzy Decision Support System to Determine the Severity of Obstructive Pulmonary in Chemical Injured Victims

    PubMed Central

    Samad-Soltani, Taha; Ghanei, Mostafa; Langarizadeh, Mostafa

    2015-01-01

    Background: Chronic Obstructive Pulmonary Disease (COPD) is the most common known complication of exposure to mustard gas. Thus, all clinical guidelines have provided some recommendation for diagnosis, clinical management and treatment of this disease. Decision support systems are used to increase the acceptance of clinical guidelines. The purpose of this research is to develop a CDSS to determine the severity of COPD in chemical injured victims. Objectives: Development of a decision support system to determine the severity of COPD. Patients and Methods: First, the variables influencing to determining the severity of the disease was classified through studying the clinical guidelines. Then, the fuzzy model was implemented. To testing the system, the data from 50 patients were used. Results: the overall accuracy in determining the severity of the injury is equal to 92%, these indicators reflect the proper functioning of the system to assist the physician regarding the diagnosis of chronic obstructive pulmonary disease and determining its severity. Conclusions: The CDSS has efficient results and satisfactory performance. Although, the medical expert systems cannot be expected to provide 100 percent correct responses, however, they can be useful in the areas of patient management, diagnosis and treatment planning. PMID:26236078

  9. Comparison of Several Methods for Determining the Internal Resistance of Lithium Ion Cells

    PubMed Central

    Schweiger, Hans-Georg; Obeidi, Ossama; Komesker, Oliver; Raschke, André; Schiemann, Michael; Zehner, Christian; Gehnen, Markus; Keller, Michael; Birke, Peter

    2010-01-01

    The internal resistance is the key parameter for determining power, energy efficiency and lost heat of a lithium ion cell. Precise knowledge of this value is vital for designing battery systems for automotive applications. Internal resistance of a cell was determined by current step methods, AC (alternating current) methods, electrochemical impedance spectroscopy and thermal loss methods. The outcomes of these measurements have been compared with each other. If charge or discharge of the cell is limited, current step methods provide the same results as energy loss methods. PMID:22219678

  10. Will Temperature Effects or Phenotypic Plasticity Determine the Thermal Response of a Heterothermic Tropical Bat to Climate Change?

    PubMed Central

    Stawski, Clare; Geiser, Fritz

    2012-01-01

    The proportion of organisms exposed to warm conditions is predicted to increase during global warming. To better understand how bats might respond to climate change, we aimed to obtain the first data on how use of torpor, a crucial survival strategy of small bats, is affected by temperature in the tropics. Over two mild winters, tropical free-ranging bats (Nyctophilus bifax, 10 g, n = 13) used torpor on 95% of study days and were torpid for 33.5±18.8% of 113 days measured. Torpor duration was temperature-dependent and an increase in ambient temperature by the predicted 2°C for the 21st century would decrease the time in torpor to 21.8%. However, comparisons among Nyctophilus populations show that regional phenotypic plasticity attenuates temperature effects on torpor patterns. Our data suggest that heterothermy is important for energy budgeting of bats even under warm conditions and that flexible torpor use will enhance bats’ chance of survival during climate change. PMID:22802959

  11. Modulation of the inflammatory response by increasing fetal wound size or interleukin-10 overexpression determines wound phenotype and scar formation.

    PubMed

    Morris, Michael W; Allukian, Myron; Herdrich, Benjamin J; Caskey, Robert C; Zgheib, Carlos; Xu, Junwang; Dorsett-Martin, Wanda; Mitchell, Marc E; Liechty, Kenneth W

    2014-01-01

    Wound size impacts the threshold between scarless regeneration and reparative healing in the fetus with increased inflammation showed in fetal scar formation. We hypothesized that increased fetal wound size increases pro-inflammatory and fibrotic genes with resultant inflammation and fibroplasia and that transition to scar formation could be reversed by overexpression of interleukin-10 (IL-10). To test this hypothesis, 2-mm and 8-mm dermal wounds were created in mid-gestation fetal sheep. A subset of 8-mm wounds were injected with a lentiviral vector containing the IL-10 transgene (n = 4) or vehicle (n = 4). Wounds were harvested at 3 or 30 days for histology, immunohistochemistry, analysis of gene expression by microarray, and validation with real-time polymerase chain reaction. In contrast to the scarless 2-mm wounds, 8-mm wounds showed scar formation with a differential gene expression profile, increased inflammatory cytokines, decreased CD45+ cells, and subsequent inflammation. Lentiviral-mediated overexpression of the IL-10 gene resulted in conversion to a regenerative phenotype with decreased inflammatory cytokines and regeneration of dermal architecture. In conclusion, increased fetal wounds size leads to a unique gene expression profile that promotes inflammation and leads to scar formation and furthermore, these results show the significance of attenuated inflammation and IL-10 in the transition from fibroplasia to fetal regenerative healing. PMID:24844340

  12. Accurate age determinations of several nearby open clusters containing magnetic Ap stars

    NASA Astrophysics Data System (ADS)

    Silaj, J.; Landstreet, J. D.

    2014-06-01

    Context. To study the time evolution of magnetic fields, chemical abundance peculiarities, and other characteristics of magnetic Ap and Bp stars during their main sequence lives, a sample of these stars in open clusters has been obtained, as such stars can be assumed to have the same ages as the clusters to which they belong. However, in exploring age determinations in the literature, we find a large dispersion among different age determinations, even for bright, nearby clusters. Aims: Our aim is to obtain ages that are as accurate as possible for the seven nearby open clusters α Per, Coma Ber, IC 2602, NGC 2232, NGC 2451A, NGC 2516, and NGC 6475, each of which contains at least one magnetic Ap or Bp star. Simultaneously, we test the current calibrations of Te and luminosity for the Ap/Bp star members, and identify clearly blue stragglers in the clusters studied. Methods: We explore the possibility that isochrone fitting in the theoretical Hertzsprung-Russell diagram (i.e. log (L/L⊙) vs. log Te), rather than in the conventional colour-magnitude diagram, can provide more precise and accurate cluster ages, with well-defined uncertainties. Results: Well-defined ages are found for all the clusters studied. For the nearby clusters studied, the derived ages are not very sensitive to the small uncertainties in distance, reddening, membership, metallicity, or choice of isochrones. Our age determinations are all within the range of previously determined values, but the associated uncertainties are considerably smaller than the spread in recent age determinations from the literature. Furthermore, examination of proper motions and HR diagrams confirms that the Ap stars identified in these clusters are members, and that the presently accepted temperature scale and bolometric corrections for Ap stars are approximately correct. We show that in these theoretical HR diagrams blue stragglers are particularly easy to identify. Conclusions: Constructing the theoretical HR diagram

  13. Gender disparities in HIV health care utilization among the severely disadvantaged: can we determine the reasons?

    PubMed

    Sohler, Nancy L; Li, Xuan; Cunningham, Chinazo O

    2009-09-01

    Data repeatedly demonstrate that HIV-infected people who regularly utilize primary health care services are more likely to have access to lifesaving treatments (including antiretroviral medications); have better indicators of health status; survive longer; and use acute care services far less. Women tend to have poorer HIV outcomes than men, which is likely due to gender disparities in optimal utilization of HIV primary care services. To understand the relationship between gender and the HIV health care system, we collected interview and medical record data between August 12, 2004 and June 7, 2005 from 414 severely marginalized, HIV-infected people in New York City and examined whether gender-related disparities in HIV health care utilization existed, and, if so, whether these patterns were explained by patient sociodemographic/behavioral characteristics and/or attitudes toward the health care system and providers. Women were significantly less likely to have optimal HIV health care services utilization, including lower use of HIV primary care services (odds ratio [OR] = 0.56, 95% confidence interval [CI] = 0.35, 0.90) and greater use of the emergency department (OR = 2.13, 95% CI = 1.31, 3.46). Although we identified several factors associated with suboptimal HIV health care services utilization patterns in addition to female gender (low education, insurance status, mistrust of the health care system, and poor trust in health care providers), we were unable to identify factors that explained the observed gender disparities. We conclude that gender disparities in HIV health care utilization are due to a complex array of factors, which require more qualitative and quantitative research attention. Development of intervention strategies that specifically target severely disadvantaged women's HIV health care utilization is in great need. PMID:19663745

  14. Short-interval SMS wind vector determinations for a severe local storms area

    NASA Technical Reports Server (NTRS)

    Peslen, C. A.

    1980-01-01

    Short-interval SMS-2 visible digital image data are used to derive wind vectors from cloud tracking on time-lapsed sequences of geosynchronous satellite images. The cloud tracking areas are located in the Central Plains, where on May 6, 1975 hail-producing thunderstorms occurred ahead of a well defined dry line. Cloud tracking is performed on the Goddard Space Flight Center Atmospheric and Oceanographic Information Processing System. Lower tropospheric cumulus tracers are selected with the assistance of a cloud-top height algorithm. Divergence is derived from the cloud motions using a modified Cressman (1959) objective analysis technique which is designed to organize irregularly spaced wind vectors into uniformly gridded wind fields. The results demonstrate the feasibility of using satellite-derived wind vectors and their associated divergence fields in describing the conditions preceding severe local storm development. For this case, an area of convergence appeared ahead of the dry line and coincided with the developing area of severe weather. The magnitude of the maximum convergence varied between -10 to the -5th and -10 to the -14th per sec. The number of satellite-derived wind vectors which were required to describe conditions of the low-level atmosphere was adequate before numerous cumulonimbus cells formed. This technique is limited in areas of advanced convection.

  15. Prevalence and determinants of fatigue in patients with moderate to severe chronic GvHD.

    PubMed

    Im, A; Mitchell, S A; Steinberg, S M; Curtis, L; Berger, A; Baird, K; Kuzmina, Z; Joe, G; Comis, L E; Juckett, M; Avila, D; Baruffaldi, J; Masuch, L; Pirsl, F; Pavletic, S Z

    2016-05-01

    Although fatigue is common after allogeneic hematopoietic cell transplantation, little is known about fatigue in patients with chronic GvHD (cGvHD). The aim of this study was to explore factors associated with fatigue in cGvHD. Data were drawn from a sequentially recruited, cross-sectional study of adults with moderate or severe cGvHD (n=263). Respondents were classified as fatigued or not fatigued based on their response to a single item regarding loss of energy from the Lee cGvHD Symptom Scale. In univariate analysis, factors significantly associated with fatigue included performance status, number of prior cGvHD therapies, cGvHD symptom bother, self-assessed physical and mental health, nutritional status, walk velocity and self-reported physical activity. There were no significant associations between fatigue and disease-related cGvHD variables. Multivariable logistic regression demonstrated that being less active and having pulmonary and/or muscle/joint symptoms were independently associated with fatigue. In conclusion, clinically significant fatigue was prevalent in more than one-third of subjects with cGvHD, and was disabling. Absence of association with measures of cGvHD severity underscores the need to elucidate the pathogenesis of fatigue and its relationship with inflammatory activity. Pulmonary and muscle/joint symptoms and physical inactivity represent potential targets for intervention in clinical studies. PMID:26828906

  16. Severity of infantile nystagmus syndrome-like ocular motor phenotype is linked to the extent of the underlying optic nerve projection defect in zebrafish belladonna mutant.

    PubMed

    Huber-Reggi, Sabina P; Chen, Chien-Cheng; Grimm, Lea; Straumann, Dominik; Neuhauss, Stephan C F; Huang, Melody Ying-Yu

    2012-12-12

    Infantile nystagmus syndrome (INS), formerly known as congenital nystagmus, is an ocular motor disorder in humans characterized by spontaneous eye oscillations (SOs) and, in several cases, reversed optokinetic response (OKR). Its etiology and pathomechanism is largely unknown, but misrouting of the optic nerve has been observed in some patients. Likewise, optic nerve misrouting, a reversed OKR and SOs with INS-like waveforms are observed in zebrafish belladonna (bel) mutants. We aimed to investigate whether and how misrouting of the optic nerve correlates with the ocular motor behaviors in bel larvae. OKR and SOs were quantified and subsequently the optic nerve fibers were stained with fluorescent lipophilic dyes. Eye velocity during OKR was reduced in larvae with few misprojecting optic nerve fibers and reversed in larvae with a substantial fraction of misprojecting fibers. All larvae with reversed OKR also displayed SOs. A stronger reversed OKR correlated with more frequent SOs. Since we did not find a correlation between additional retinal defects and ocular motor behavior, we suggest that axon misrouting is in fact origin of INS in the zebrafish animal model. Depending on the ratio between misprojecting ipsilateral and correctly projecting contralateral fibers, the negative feedback loop normally regulating OKR can turn into a positive loop, resulting in an increase in retinal slip. Our data not only give new insights into the etiology of INS but may also be of interest for studies on how the brain deals with and adapts to conflicting inputs. PMID:23238723

  17. Use of Platelet Indices for Determining Illness Severity and Predicting Prognosis in Critically Ill Patients

    PubMed Central

    Zhang, Sheng; Cui, Yun-Liang; Diao, Meng-Yuan; Chen, Deng-Chang; Lin, Zhao-Fen

    2015-01-01

    Background: Decreased platelet (PLT) count is one of the independent risk factors for mortality in intensive care unit (ICU) patients. This study was to investigate the relationship between PLT indices and illness severity and their performances in predicting hospital mortality. Methods: Adult patients who admitted to ICU of Changzheng Hospital from January 2011 to September 2012 and met inclusion criteria were included in this study. Univariate analysis was used to identify potential independent risk factors for mortality. Multiple logistic regression analysis was used to calculate adjusted odds ratio for mortality in patients with normal or abnormal PLT indices. The relationship between PLT indices and illness severity were assessed by the Acute Physiology and Chronic Health Evaluation II (APACHE II) scores or sequential organ failure assessment (SOFA) scores in patients with normal and abnormal PLT indices. The performances of PLT indices in predicting mortality were assessed by receiver operating curves and diagnostic parameters. The survival curves between patients with normal and abnormal PLT indices were compared using Kaplan–Meier method. Results: From January 2011 to September 2012, 261 of 361 patients (204 survivors and 57 nonsurvivors) met the inclusion criteria. After adjustment for clinical variables, PLT count <100 × 1012/L (P = 0.011), plateletcrit (PCT) <0.108 (P = 0.002), mean platelet volume (MPV) >11.3 fL (P = 0.023) and platelet distribution width (PDW) percentage >17% (P = 0.009) were identified as independent risk factors for mortality. The APACHE II and SOFA scores were 14.0 (9.0–20.0) and 7.0 (5.0–10.5) in the “low PLT” tertile, 13.0 (8.0–16.0) and 7.0 (4.0–11.0) in the “low PCT” tertile, 14.0 (9.3–19.0) and 7.0 (4.0–9.8) in the “high MPV” tertile, 14.0 (10.5–20.0) and 7.0 (5.0–11.0) in the “high PDW” tertile, all of which were higher than those in patients with normal indices. Patients with decreased PLT

  18. Protease activated receptor-1 inhibits the Maspin tumor-suppressor gene to determine the melanoma metastatic phenotype

    PubMed Central

    Villares, Gabriel J.; Zigler, Maya; Dobroff, Andrey S.; Wang, Hua; Song, Renduo; Melnikova, Vladislava O.; Huang, Li; Braeuer, Russell R.; Bar-Eli, Menashe

    2011-01-01

    The thrombin receptor protease activated receptor-1 (PAR-1) is overexpressed in metastatic melanoma cell lines and tumor specimens. Previously, we demonstrated a significant reduction in tumor growth and experimental lung metastasis after PAR-1 silencing via systemic delivery of siRNA encapsulated into nanoliposomes. Gene expression profiling identified a 40-fold increase in expression of Maspin in PAR-1–silenced metastatic melanoma cell lines. Maspin promoter activity was significantly increased after PAR-1 silencing, suggesting that PAR1 negatively regulates Maspin at the transcriptional level. ChIP analyses revealed that PAR-1 decreases binding of Ets-1 and c-Jun transcription factors to the Maspin promoter, both known to activate Maspin transcription. PAR-1 silencing did not affect Ets-1 or c-Jun expression; rather it resulted in increased expression of the chromatin remodeling complex CBP/p300, as well as decreased activity of the CBP/p300 inhibitor p38, resulting in increased binding of Ets-1 and c-Jun to the Maspin promoter and higher Maspin expression. Functionally, Maspin expression reduced the invasive capability of melanoma cells after PAR-1 silencing, which was abrogated after rescuing with PAR-1. Furthermore, tumor growth and experimental lung metastasis was significantly decreased after expressing Maspin in a metastatic melanoma cell line. Moreover, silencing Maspin in PAR-1–silenced cells reverted the inhibition of tumor growth and experimental lung metastasis. Herein, we demonstrate a mechanism by which PAR-1 negatively regulates the expression of the Maspin tumor-suppressor gene in the acquisition of the metastatic melanoma phenotype, thus attributing an alternative function to PAR-1 other than coagulation. PMID:21187389

  19. Protease activated receptor-1 inhibits the Maspin tumor-suppressor gene to determine the melanoma metastatic phenotype.

    PubMed

    Villares, Gabriel J; Zigler, Maya; Dobroff, Andrey S; Wang, Hua; Song, Renduo; Melnikova, Vladislava O; Huang, Li; Braeuer, Russell R; Bar-Eli, Menashe

    2011-01-11

    The thrombin receptor protease activated receptor-1 (PAR-1) is overexpressed in metastatic melanoma cell lines and tumor specimens. Previously, we demonstrated a significant reduction in tumor growth and experimental lung metastasis after PAR-1 silencing via systemic delivery of siRNA encapsulated into nanoliposomes. Gene expression profiling identified a 40-fold increase in expression of Maspin in PAR-1-silenced metastatic melanoma cell lines. Maspin promoter activity was significantly increased after PAR-1 silencing, suggesting that PAR1 negatively regulates Maspin at the transcriptional level. ChIP analyses revealed that PAR-1 decreases binding of Ets-1 and c-Jun transcription factors to the Maspin promoter, both known to activate Maspin transcription. PAR-1 silencing did not affect Ets-1 or c-Jun expression; rather it resulted in increased expression of the chromatin remodeling complex CBP/p300, as well as decreased activity of the CBP/p300 inhibitor p38, resulting in increased binding of Ets-1 and c-Jun to the Maspin promoter and higher Maspin expression. Functionally, Maspin expression reduced the invasive capability of melanoma cells after PAR-1 silencing, which was abrogated after rescuing with PAR-1. Furthermore, tumor growth and experimental lung metastasis was significantly decreased after expressing Maspin in a metastatic melanoma cell line. Moreover, silencing Maspin in PAR-1-silenced cells reverted the inhibition of tumor growth and experimental lung metastasis. Herein, we demonstrate a mechanism by which PAR-1 negatively regulates the expression of the Maspin tumor-suppressor gene in the acquisition of the metastatic melanoma phenotype, thus attributing an alternative function to PAR-1 other than coagulation. PMID:21187389

  20. Distinct phenotype of a Wilson disease mutation reveals a novel trafficking determinant in the copper transporter ATP7B

    PubMed Central

    Braiterman, Lelita T.; Murthy, Amrutha; Jayakanthan, Samuel; Nyasae, Lydia; Tzeng, Eric; Gromadzka, Grazyna; Woolf, Thomas B.; Lutsenko, Svetlana; Hubbard, Ann L.

    2014-01-01

    Wilson disease (WD) is a monogenic autosomal-recessive disorder of copper accumulation that leads to liver failure and/or neurological deficits. WD is caused by mutations in ATP7B, a transporter that loads Cu(I) onto newly synthesized cupro-enzymes in the trans-Golgi network (TGN) and exports excess copper out of cells by trafficking from the TGN to the plasma membrane. To date, most WD mutations have been shown to disrupt ATP7B activity and/or stability. Using a multidisciplinary approach, including clinical analysis of patients, cell-based assays, and computational studies, we characterized a patient mutation, ATP7BS653Y, which is stable, does not disrupt Cu(I) transport, yet renders the protein unable to exit the TGN. Bulky or charged substitutions at position 653 mimic the phenotype of the patient mutation. Molecular modeling and dynamic simulation suggest that the S653Y mutation induces local distortions within the transmembrane (TM) domain 1 and alter TM1 interaction with TM2. S653Y abolishes the trafficking-stimulating effects of a secondary mutation in the N-terminal apical targeting domain. This result indicates a role for TM1/TM2 in regulating conformations of cytosolic domains involved in ATP7B trafficking. Taken together, our experiments revealed an unexpected role for TM1/TM2 in copper-regulated trafficking of ATP7B and defined a unique class of WD mutants that are transport-competent but trafficking-defective. Understanding the precise consequences of WD-causing mutations will facilitate the development of advanced mutation-specific therapies. PMID:24706876

  1. New insights into the metabolic and nutritional determinants of severe combined immunodeficiency

    PubMed Central

    Field, Martha S; Kamynina, Elena; Watkins, David; Rosenblatt, David S; Stover, Patrick J

    2015-01-01

    Human mutations in MTHFD1 have recently been identified in patients with severe combined immunodeficiency (SCID). SCID results from inborn errors of metabolism that cause impaired T- and B-cell proliferation and function. One of the most common causes of SCID is adenosine deaminase (ADA) deficiency, which ultimately inhibits DNA synthesis and cell division. MTHFD1 has been shown to translocate to the nucleus during S-phase of the cell cycle; this localization is critical for synthesis of thymidyate (dTMP or the “T” base in DNA) and subsequent progression through the cell cycle and cell proliferation. Identification of MTHFD1 mutations that are associated with SCID highlights the potential importance of adequate dTMP synthesis in the etiology of SCID. PMID:27123375

  2. Determining the ice seasons severity during 1982-2015 using the ice extents sum as a new characteristic

    NASA Astrophysics Data System (ADS)

    Rjazin, Jevgeni; Pärn, Ove

    2016-04-01

    Sea ice is a key climate factor and it restricts considerably the winter navigation in sever seasons on the Baltic Sea. So determining ice conditions severity and describing ice cover behaviour at severe seasons interests scientists, engineers and navigation managers. The present study is carried out to determine the ice seasons severity degree basing on the ice seasons 1982 to 2015. A new integrative characteristic is introduced to describe the ice season severity. It is the sum of ice extents of the ice season id est the daily ice extents of the season are summed. The commonly used procedure to determine the ice season severity degree by the maximal ice extent is in this research compared to the new characteristic values. The remote sensing data on the ice concentrations on the Baltic Sea published in the European Copernicus Programme are used to obtain the severity characteristic values. The ice extents are calculated on these ice concentration data. Both the maximal ice extent of the season and a newly introduced characteristic - the ice extents sum are used to classify the winters with respect of severity. The most severe winter of the reviewed period is 1986/87. Also the ice seasons 1981/82, 1984/85, 1985/86, 1995/96 and 2002/03 are classified as severe. Only three seasons of this list are severe by both the criteria. They are 1984/85, 1985/86 and 1986/87. We interpret this coincidence as the evidence of enough-during extensive ice cover in these three seasons. In several winters, for example 2010/11 ice cover extended enough for some time, but did not endure. At few other ice seasons as 2002/03 the Baltic Sea was ice-covered in moderate extent, but the ice cover stayed long time. At 11 winters the ice extents sum differed considerably (> 10%) from the maximal ice extent. These winters yield one third of the studied ice seasons. The maximal ice extent of the season is simple to use and enables to reconstruct the ice cover history and to predict maximal ice

  3. Factors determining gastrointestinal transit time of several markers in the domestic fowl.

    PubMed

    Vergara, P; Ferrando, C; Jiménez, M; Fernández, E; Goñalons, E

    1989-11-01

    The aim of this study was to find out how marker characteristics could affect digestive transit time in Gallus gallus. One soluble marker, Cr-EDTA, and two insoluble markers, Cr2O3 and chromium-mordanted plant cells of two sizes, were used. Three- to six-week-old chickens were killed in series after the oral administration of the markers at intervals of 0, 0.5, 1, 2, 3, 5, 7, and 9 h. The amount of chromium in each digestive segment was determined by atomic absorption. There were some differences in the initial distribution of markers; whereas almost the total amount of the chromium-mordanted rice husk of the largest size was found in the crop at time 0, less than half of the Cr-EDTA was found. Marker emptying out of the crop was fast and not related to either the type or size. In contrast, the emptying rate of the gizzard depended on marker particle size. As far as the caeca were concerned, the ileocaecal junction allowed the passage of soluble Cr-EDTA whereas solid markers were impeded (Cr2O3) or not allowed to pass through at all (vegetable fibre of any size). It can be concluded that marker selection is of major importance to transit time studies in chickens, since its characteristics can determine transit time in an absolute way. PMID:2512590

  4. The level of an intracellular antioxidant during development determines the adult phenotype in a bird species: a potential organizer role for glutathione.

    PubMed

    Romero-Haro, Ana Angela; Alonso-Alvarez, Carlos

    2015-03-01

    Life-history traits are often involved in trade-offs whose outcome would depend on the availability of resources but also on the state of specific molecular signals. Early conditions can influence trade-offs and program the phenotype throughout the lifetime, with oxidative stress likely involved in many taxa. Here we address the potential regulatory role of a single intracellular antioxidant in life-history trade-offs. Blood glutathione levels were reduced in a large sample of birds (zebra finch Taeniopygia guttata) during development using the synthesis inhibitor buthionine sulfoximine (BSO). Results revealed several modifications in the adult phenotype. BSO-treated nestlings showed lower glutathione and plasma antioxidant levels. In adulthood, BSO birds endured greater oxidative damage in erythrocytes but stronger expression of a sexual signal. Moreover, adult BSO females also showed weaker resistance to oxidative stress but were heavier and showed better body condition. Results suggest that low glutathione values during growth favor the investment in traits that should improve fitness returns, probably in the form of early reproduction. Higher oxidative stress in adulthood may be endured if this cost is paid later in life. Either the presence of specific signaling mechanisms or the indirect effect of increased oxidative stress can explain our findings. PMID:25674693

  5. Environmental determinants of coral reef fish diversity across several French Polynesian atolls.

    PubMed

    Planes, Serge; Lecchini, David; Mellin, Camille; Charton, José Garcia; Harmelin-Vivien, Mireille; Kulbicki, Michel; Mou-Tham, Gérard; Galzin, René

    2012-06-01

    The present study aimed at exploring the diversity of coral reef fishes in 10 French Polynesian atolls and sought to determine which environmental variables best explain diversity. A total of 136,614 fish belonging to 302 species were recorded in 1995 and 1996. The stepwise multiple regression analysis showed that the best model of variation in species richness (55% of total variation) incorporated three geomorphologic descriptors (atoll perimeter, submerged rim and abundance of pinnacles) and two habitat descriptors (percentage cover of dead coral and sand). The best model of variation in Shannon-Wiener's species diversity index (43% of total variation) included two geomorphologic descriptors (mean depth and level of water exchange) and three habitat descriptors (percentage cover of mud, dead coral and gravel). Overall, our survey recognises the importance of both geomorphologic and habitat descriptors as leading contenders in explaining biodiversity in relation to energy input and habitat area hypothesis. PMID:22721563

  6. Application of several methods for determining transfer functions and frequency response of aircraft from flight data

    NASA Technical Reports Server (NTRS)

    Eggleston, John M; Mathews, Charles W

    1954-01-01

    In the process of analyzing the longitudinal frequency-response characteristics of aircraft, information on some of the methods of analysis has been obtained by the Langley Aeronautical Laboratory of the National Advisory Committee for Aeronautics. In the investigation of these methods, the practical applications and limitations were stressed. In general, the methods considered may be classed as: (1) analysis of sinusoidal response, (2) analysis of transient response as to harmonic content through determination of the Fourier integral by manual or machine methods, and (3) analysis of the transient through the use of least-squares solutions of the coefficients of an assumed equation for either the transient time response or frequency response (sometimes referred to as curve-fitting methods). (author)

  7. Early Marriage, Rape, Child Prostitution, and Related Factors Determining the Psychosocial Effects Severity of Child Sexual Abuse in Ethiopia

    ERIC Educational Resources Information Center

    Wondie, Yemataw; Zemene, Workie; Reschke, Konrad; Schroder, Harry

    2011-01-01

    This study was aimed at identifying factors that determine the psychosocial effects severity of child sexual abuse. Data were collected from 318 female children in Ethiopia using the Children's Impact of Traumatic Events Scale-Revised and the Rosenberg Self-Esteem Scale. The results revealed that respondents who survived rape and child…

  8. The role of isohydric and anisohydric species in determining ecosystem-scale response to severe drought.

    PubMed

    Roman, D T; Novick, K A; Brzostek, E R; Dragoni, D; Rahman, F; Phillips, R P

    2015-11-01

    Ongoing shifts in the species composition of Eastern US forests necessitate the development of frameworks to explore how species-specific water-use strategies influence ecosystem-scale carbon (C) cycling during drought. Here, we develop a diagnostic framework to classify plant drought-response strategies along a continuum of isohydric to anisohydric regulation of leaf water potential (Ψ(L)). The framework is applied to a 3-year record of weekly leaf-level gas exchange and Ψ measurements collected in the Morgan-Monroe State Forest (Indiana, USA), where continuous observations of the net ecosystem exchange of CO2 (NEE) have been ongoing since 1999. A severe drought that occurred in the middle of the study period reduced the absolute magnitude of NEE by 55%, though species-specific responses to drought conditions varied. Oak species were characterized by anisohydric regulation of Ψ(L) that promoted static gas exchange throughout the study period. In contrast, Ψ(L) of the other canopy dominant species was more isohydric, which limited gas exchange during the drought. Ecosystem-scale estimates of NEE and gross ecosystem productivity derived by upscaling the leaf-level data agreed well with tower-based observations, and highlight how the fraction of isohydric and anisohydric species in forests can mediate net ecosystem C balance. PMID:26130023

  9. A CapG gain-of-function mutant reveals critical structural and functional determinants for actin filament severing

    PubMed Central

    Zhang, Y; Vorobiev, Sergey M; Gibson, Bruce G; Hao, Binghua; Sidhu, Gurjit S; Mishra, Vishnu S; Yarmola, Elena G; Bubb, Michael R; Almo, Steven C; Southwick, Frederick S

    2006-01-01

    CapG is the only member of the gelsolin family unable to sever actin filaments. Changing amino acids 84–91 (severing domain) and 124–137 (WH2-containing segment) simultaneously to the sequences of gelsolin results in a mutant, CapG-sev, capable of severing actin filaments. The gain of severing function does not alter actin filament capping, but is accompanied by a higher affinity for monomeric actin, and the capacity to bind and sequester two actin monomers. Analysis of CapG-sev crystal structure suggests a more loosely folded inactive conformation than gelsolin, with a shorter S1–S2 latch. Calcium binding to S1 opens this latch and S1 becomes separated from a closely interfaced S2–S3 complex by an extended arm consisting of amino acids 118–137. Modeling with F-actin predicts that the length of this WH2-containing arm is critical for severing function, and the addition of a single amino acid (alanine or histidine) eliminates CapG-sev severing activity, confirming this prediction. We conclude that efficient severing utilizes two actin monomer-binding sites, and that the length of the WH2-containing segment is a critical functional determinant for severing. PMID:16977317

  10. The role of aortic compliance in determination of coarctation severity: lumped parameter modeling, in vitro study and clinical evaluation

    PubMed Central

    Keshavarz-Motamed, Zahra; Edelman, Elazer R.; Motamed, Payam K.; Garcia, Julio; Dahdah, Nagib; Kadem, Lyes

    2015-01-01

    Early detection and accurate estimation of the extent of coarctation of the aorta (COA) is critical to long-term outcome. Peak-to-peak trans-coarctation pressure gradient (PKdP) higher than 20 mmHg is an indication for interventional/surgical repair. Patients with COA have reduced proximal and distal aortic compliances. A comprehensive study investigating the effects of variations of proximal COA and systemic compliances on PKdP, and consequently on the COA severity evaluation has never been done. This study evaluates the effect of aortic compliance on diagnostic accuracy of PKdP. Lumped parameter modeling and in vitro experiments were performed for COA severities of 50%, 75% and 90% by area. Modeling and in vitro results were validated against retrospective clinical data of PKdP, measured in fifty-four patients with COA. Modeling and in vitro. PKdP increases with reduced proximal COA compliance (+36%, +38% and +53% for COA severities of 50%, 75% and 90%, respectively; p<0.05), but decreases with reduced systemic compliance (−62%, −41% and −36% for COA severities of 50%, 75% and 90%, respectively; p<0.01). Clinical study. PKdP has a modest correlation with COA severity (R=0.29). The main determinants of PKdP are COA severity, stroke volume index and systemic compliance. Systemic compliance was found to be as influential as COA severity in PKdP determination (R=0.30 vs. R=0.34). In conclusion, PKdP is highly influenced by both stroke volume index and arterial compliance. Low values of PKdP cannot be used to exclude the severe COA presence since COA severity may be masked by reduced systemic compliance and/or low flow conditions. PMID:26596718

  11. Use of gene expression data to determine effects on gonad phenotype in Japanese medaka after exposure to trenbolone or estradiol

    EPA Science Inventory

    Various aquatic bioassays using one of several fish species have been developed or are in the process of being developed by organizations like the US Environmental Protection Agency and the Office of Economic Cooperation and Development for testing potential endocrine disrupting ...

  12. Anemia and iron deficiency among school adolescents: burden, severity, and determinant factors in southwest Ethiopia

    PubMed Central

    Tesfaye, Melkam; Yemane, Tilahun; Adisu, Wondimagegn; Asres, Yaregal; Gedefaw, Lealem

    2015-01-01

    Background Adolescence is the period of most rapid growth second to childhood. The physical and physiological changes that occur in adolescents place a great demand on their nutritional requirements and make them more vulnerable to anemia. Anemia in the adolescence causes reduced physical and mental capacity and diminished concentration in work and educational performance, and also poses a major threat to future safe motherhood in girls. The purpose of this study was to determine the prevalence of anemia and its associated factors among school adolescents in Bonga Town, southwest Ethiopia. Methods A cross-sectional study was conducted among 408 school adolescents in Bonga Town, southwest Ethiopia, from March 15, 2014 to May 25, 2014. An interviewer-administered questionnaire was used to collect sociodemographic and other data. A total of 7 mL of venous blood and 4 g of stool samples were collected from each study participant. Blood and stool samples were analyzed for hematological and parasitological analyses, respectively. Data were analyzed using SPSS Version 20 software for Windows. Results The overall prevalence of anemia was 15.2% (62/408), of which 83.9% comprised mild anemia. The proportion of microcytic, hypochromic anemia was 53% (33/62). Being female (adjusted odds ratio [AOR] =3.04, 95% confidence interval (CI) =1.41–6.57), household size ≥5 (AOR =2.58, 95% CI =1.11–5.96), father’s illiteracy (AOR =9.03, 95% CI =4.29–18.87), intestinal parasitic infection (AOR =5.37, 95% CI =2.65–10.87), and low body mass index (AOR =2.54, 95% CI =1.17–5.51) were identified as determinants of anemia among school adolescents. Conclusion This study showed that anemia was a mild public health problem in this population. School-based interventions on identified associated factors are important to reduce the burden of anemia among school adolescents. PMID:26719736

  13. Multiple Interactions across the Surface of the gp120 Core Structure Determine the Global Neutralization Resistance Phenotype of Human Immunodeficiency Virus Type 1

    PubMed Central

    Bouma, Peter; Leavitt, Maria; Zhang, Peng Fei; Sidorov, Igor A.; Dimitrov, Dimiter S.; Quinnan, Gerald V.

    2003-01-01

    Resistance to neutralization is an important characteristic of primary isolates of human immunodeficiency virus type 1 (HIV-1) that relates to the potential for successful vaccination to prevent infection and use of immunotherapeutics for treatment of established infection. In order to further elucidate mechanisms responsible for neutralization resistance, we studied the molecular mechanisms that determine the resistance of the primary virus isolate of the strain HIV-1 MN to neutralization by soluble CD4 (sCD4). As is the case for the global neutralization resistance phenotype, sCD4 resistance depended upon sequences in the amino-terminal heptad repeat region of gp41 (HR1), as well as on multiple functional interactions within the envelope complex. The functional interactions that determined the resistance included interactions between the variable loop 1 and 2 (V1/V2) region and sequences in or near the CD4 binding site (CD4bs) and with the V3 loop. Additionally, the V3 loop region was found to interact functionally with sequences in the outer domain of gp120, distant from the CD4bs and coreceptor-binding site, as well as with a residue thought to be located centrally in the coreceptor-binding site. These and previous results provide the basis for a model by which functional signals that determine the neutralization resistance, high-infectivity phenotype depend upon interactions occurring across the surface of the gp120 core structure and involving variable loop structures and gp41. This model should be useful in efforts to define epitopes that may be important for primary virus neutralization. PMID:12829845

  14. Macrophage phenotypes in atherosclerosis.

    PubMed

    Colin, Sophie; Chinetti-Gbaguidi, Giulia; Staels, Bart

    2014-11-01

    Initiation and progression of atherosclerosis depend on local inflammation and accumulation of lipids in the vascular wall. Although many cells are involved in the development and progression of atherosclerosis, macrophages are fundamental contributors. For nearly a decade, the phenotypic heterogeneity and plasticity of macrophages has been studied. In atherosclerotic lesions, macrophages are submitted to a large variety of micro-environmental signals, such as oxidized lipids and cytokines, which influence the phenotypic polarization and activation of macrophages resulting in a dynamic plasticity. The macrophage phenotype spectrum is characterized, at the extremes, by the classical M1 macrophages induced by T-helper 1 (Th-1) cytokines and by the alternative M2 macrophages induced by Th-2 cytokines. M2 macrophages can be further classified into M2a, M2b, M2c, and M2d subtypes. More recently, additional plaque-specific macrophage phenotypes have been identified, termed as Mox, Mhem, and M4. Understanding the mechanisms and functional consequences of the phenotypic heterogeneity of macrophages will contribute to determine their potential role in lesion development and plaque stability. Furthermore, research on macrophage plasticity could lead to novel therapeutic approaches to counteract cardiovascular diseases such as atherosclerosis. The present review summarizes our current knowledge on macrophage subsets in atherosclerotic plaques and mechanism behind the modulation of the macrophage phenotype. PMID:25319333

  15. Complex de novo chromosomal rearrangement at 15q11-q13 involving an intrachromosomal triplication in a patient with a severe neuropsychological phenotype: clinical report and review of the literature.

    PubMed

    Castronovo, Chiara; Crippa, Milena; Bestetti, Ilaria; Rusconi, Daniela; Russo, Silvia; Larizza, Lidia; Sangermani, Roberto; Bonati, Maria Teresa; Finelli, Palma

    2015-01-01

    Interstitial triplications of 15q11-q13, leading to tetrasomy of the involved region, are very rare, with only 11 cases reported to date. Their pathogenicity is independent of the parental origin of the rearranged chromosome. The associated phenotype resembles, but is less severe, than that of patients bearing inv dup(15) marker chromosomes. Here, we describe a boy of 3 years and 9 months of age who exhibited very mild craniofacial dysmorphism (arched eyebrows, hypertelorism, and a wide mouth), developmental delay, generalized hypotonia, ataxic gait, severe intellectual disability, and autism. Array comparative genomic hybridization (CGH) analysis identified a heterozygous duplication of 1.1 Mb at 15q11.2 (between low-copy repeats BP1 and BP2), and a heterozygous triplication of 6.8 Mb at 15q11.2-q13.1 (BP2-BP4). Both acquisitions were de novo and contiguous. Microsatellite polymorphism analysis revealed the maternal origin of the triplication and the involvement of both maternal chromosomes 15. Furthermore, fluorescence in situ hybridization (FISH) analysis using BAC clones revealed that the rearrangement was complex, containing three differently sized tandem repeats of which the middle one was inverted. Our study confirms and extends the model proposed to explain the formation of intrachromosomal triplications through recombination events between non-allelic duplicons. The comparison of the proband's clinical presentation with those of previously described cases attests the existence of endophenotypes due to the parental origin of the 15q11-q13 triplicated segment and suggests a timetable for achievement of developmental milestones, thereby contributing to improved genotype-phenotype correlations. PMID:25339188

  16. Down Syndrome: Cognitive Phenotype

    ERIC Educational Resources Information Center

    Silverman, Wayne

    2007-01-01

    Down syndrome is the most prevalent cause of intellectual impairment associated with a genetic anomaly, in this case, trisomy of chromosome 21. It affects both physical and cognitive development and produces a characteristic phenotype, although affected individuals vary considerably with respect to severity of specific impairments. Studies…

  17. Determination the total neutron yields of several semiconductor compounds using various alpha emitters

    NASA Astrophysics Data System (ADS)

    Abdullah, Ramadhan Hayder; Sabr, Barzan Nehmat

    2016-03-01

    In the present work, the cross-sections of (α,n) reactions available in the literature as a function of α-particle energies for light and medium elements have been rearranged for α-particle energies from near threshold up to 10 MeV in steps of (0.050MeV) using the (Excel and Matlab) computer programs. The obtained data were used to calculate the neutron yields (n/106α) using the quick basic-computer program (Simpson Rules). The stopping powers of alpha particle energies from near threshold to 10 MeV for light and medium elements such as (nat.Be,10B,11B,13C,14N,nat.O,nat.F,nat.Mg,nat.Al,29Si,30Si, nat.P and 46.48Ti) have been calculated using the Zeigler formula. The kinetic energies (Tα) and the branching ratios of each α-emitters such as (211Bi, 210Po, 211Po, 215Po, 217At, 218Rn, 219Rn, 222Rn, 224Ra, 226Ra, 215Th, 228Th, 232U, 234U, 236U, 238U, 238Pu, 239Pu, 241Am, 245Es, 252Fm, 254Fm, 256Fm, 257Fm and 257Md) are taken into consideration to calculate the mean kinetic energy . The polynomial expressions were used to fitting the calculated weighted average of neutron yields (n/106α) for natural light and medium elements such as (Be, B, C, N, O, F, Mg, Al, Si, P and Ti) to determine the adopted neutron yields from the best fitting equation with minimum (CHISQ) at mean kinetic energies of various α-emitters. The total neutron yields (n/s/gx/ppmi) of the mentioned natural light and medium elements have been calculated using the adopted neutron yields (n/106α) from the fitting equations at mean kinetic energies of various α-emitters. The total neutron yields (n/s/gα-emitters/gcompounds) of semiconductor compounds such as (AlN, AlP, BN, BP, SiC, TiO2, BeSiN2, MgCN2, MgSiN2 and MgSiP2) have been calculated by mixing (1gram) of compounds with (1gram) of pure α-emitters using the quick basic computer program. The aim of the present work is to constructed and fabricate the neutron sources theoretically

  18. A determinant of disease symptom severity is located in RNA2 of broad bean wilt virus 2.

    PubMed

    Kwak, Hae-Ryun; Lee, Ye-Ji; Kim, Jaedeok; Kim, Mi-Kyeong; Kim, Jeong-Soo; Choi, Hong-Soo; Seo, Jang-Kyun

    2016-01-01

    Broad bean wilt virus 2 (BBWV2), which belongs to the genus Fabavirus, is a destructive pathogen of many economically important horticultural and ornamental crops. In this study, we constructed infectious full-length cDNA clones of two distinct isolates of BBWV2 under control of the cauliflower mosaic virus 35S promoter. BBWV2-PAP1 isolated from paprika (Capsicum annuum var. gulosum) induces severe disease symptoms in various pepper varieties, whereas BBWV2-RP1 isolated from red pepper (Capsicum annuum L.) causes mild symptoms. Agrobacterium-mediated inoculation of the infectious cDNA clones of BBWV2-PAP1 and RP1 resulted in the same symptoms as the original virus isolates. The infectious cDNA clones of BBWV2-PAP1 and RP1 were used to examine the symptoms induced by pseudorecombinants between the two isolates to localize in which of the two genomic RNAs are the symptom severity determinants in BBWV2. The pseudorecombinant of RP1-RNA1 and PAP1-RNA2 induced severe symptoms, similar to those caused by the parental isolate PAP1, whereas the pseudorecombinant of PAP1-RNA1 and RP1-RNA2 induced mild symptoms, similar to those caused by the parental isolate RP1. Our results suggest that BBWV2 RNA2 contains a symptom determinant(s) capable of enhancing symptom severity. PMID:26428303

  19. Alternative Sampling Strategies for Cytochrome P450 Phenotyping.

    PubMed

    De Kesel, Pieter M M; Lambert, Willy E; Stove, Christophe P

    2016-02-01

    Interindividual variability in the expression and function of drug metabolizing cytochrome P (CYP) 450 enzymes, determined by a combination of genetic, non-genetic and environmental parameters, is a major source of variable drug response. Phenotyping by administration of a selective enzyme substrate, followed by the determination of a specific phenotyping metric, is an appropriate approach to assess the in vivo activity of CYP450 enzymes as it takes into account all influencing factors. A phenotyping protocol should be as simple and convenient as possible. Typically, phenotyping metrics are determined in traditional matrices, such as blood, plasma or urine. Several sampling strategies have been proposed as an alternative for these traditional sampling techniques. In this review, we provide a comprehensive overview of available methods using dried blood spots (DBS), hair, oral fluid, exhaled breath and sweat for in vivo CYP450 phenotyping. We discuss the relation between phenotyping metrics measured in these samples and those in conventional matrices, along with the advantages and limitations of the alternative sampling techniques. Reliable phenotyping procedures for several clinically relevant CYP450 enzymes, including CYP1A2, CYP2C19 and CYP2D6, are currently available for oral fluid, breath or DBS, while additional studies are needed for other CYP450 isoforms, such as CYP3A4. The role of hair analysis for this purpose remains to be established. Being non- or minimally invasive, these sampling strategies provide convenient and patient-friendly alternatives for classical phenotyping procedures, which may contribute to the implementation of CYP450 phenotyping in clinical practice. PMID:26239501

  20. Determinants of Disease Phenotype Differences Caused by Closely-Related Isolates of Begomovirus Betasatellites Inoculated with the Same Species of Helper Virus

    PubMed Central

    Zhang, Jie; Dang, Mingqing; Huang, Qingqing; Qian, Yajuan

    2015-01-01

    Tomato yellow leaf curl China virus (TYLCCNV) is a monopartite begomovirus associated with different betasatellites. In this study, we investigate two different isolates of Tomato yellow leaf curl China betasatellite (TYLCCNB) to determine what features of the viral genome are required for induction of characteristic phenotypic differences between closely-related betasatellite. When co-agroinoculated with TYLCCNV into Nicotiana spp. and tomato plants, TYLCCNB-Y25 induced only leaf curling on all hosts, while TYLCCNB-Y10 also induced enations, vein yellowing, and shoot distortions. Further assays showed that βC1 of TYLCCNB-Y25 differs from that of TYLCCNB-Y10 in symptom induction and transcriptional modulating. Hybrid satellites were constructed in which the βC1 gene or 200 nt partial promoter-like fragment upstream of the βC1 were exchanged. Infectivity assays showed that a TYLCCNB-Y25 hybrid with the intact TYLCCNB-Y10 βC1 gene was able to induce vein yellowing, shoot distortions, and a reduced size and number of enations. A TYLCCNB-Y10 hybrid with the intact TYLCCNB-Y25 βC1 gene produced only leaf curling. In contrast, the TYLCCNB-Y25 and TYLCCNB-Y10 hybrids with swapped partial promoter-like regions had little effect on the phenotypes induced by wild-type betasatellites. Further experiments showed that the TYLCCNB-Y25 hybrid carrying the C-terminal region of TYLCCNB-Y10 βC1 induced TYLCCNB-Y10-like symptoms. These findings indicate that the βC1 protein is the major symptom determinant and that the C-terminal region of βC1 plays an important role in symptom induction. PMID:26389936

  1. [Investigation of pathogenic phenotypes and virulence determinants of food-borne Salmonella enterica strains in Caenorhabditis elegans animal model].

    PubMed

    Aksoy, Deniz; Şen, Ece

    2015-10-01

    Salmonellosis, caused by non-typhoidal Salmonella enterica serovars with the consumption of contaminated food, is one of the leading food-borne disease that makes microbial food safety an important public health issue. This study was performed in order to determine the antibiotic resistance, serotyping, plasmid profiles and pathogenicity potentials of food-borne Salmonella isolates in Caenorhabditis elegans animal model system in Edirne province, located at Thrace region of Turkey. In this study, 32 Salmonella isolates, of which 26 belonged to Infantis, four to Enteritidis, one to Telaviv and one to Kentucky serovars, isolated from chicken carcasses were used. Antibiotic resistance profiles were determined by disc diffusion and broth microdilution methods. A new C.elegans nematode animal model system was used to determine the pathogenicity potential of the isolates. The antibiotic resistance profiles revealed that one (3.1%) isolate was resistant to gentamicin, two (6.2%) to ciprofloxacin, three (9.4%) to ampicillin, 18 (56.3%) to kanamycin, 19 (60.8%) to neomycin, 25 (78.1%) to tetracycline, 25 (78.1%) to trimethoprim, 26 (81.25%) to nalidixic acid, 27 (84.4%) to streptomycin and 32 (100%) to sulfonamide. All of the 32 strains were susceptible to chloramphenicol and ampicillin/sulbactam. High levels of resistance to streptomycin, nalidixic acid, tetracycline, trimethoprim, sulfonamide, kanamycin and neomycin was determined. According to the plasmid analysis, six isolates (18.75%) harboured 1-3 plasmids with sizes between 1.2 and 42.4 kb. In C.elegans nematode animal model system, the time (in days) required to kill 50% (TD50) of nematodes was calculated for each experimental group. TD50 values of the nematode group fed with S.Typhimurium ATCC 14028 that was used as the positive control and another group fed with E.coli OP50 as the negative control were 4.2 ± 0.5 days and 8.0 ± 0.02 days, respectively. TD50 of the groups fed with Salmonella isolates ranged

  2. Determinants of symptom profile and severity of conduct disorder in a tertiary level pediatric care set up: A pilot study

    PubMed Central

    Jayaprakash, R.; Rajamohanan, K.; Anil, P.

    2014-01-01

    Background: Conduct disorders (CDs) are one of the most common causes for referral to child and adolescent mental health centers. CD varies in its environmental factors, symptom profile, severity, co-morbidity, and functional impairment. Aims: The aim was to analyze the determinants of symptom profile and severity among childhood and adolescent onset CD. Settings and Design: Clinic based study with 60 consecutive children between 6 and 18 years of age satisfying International Classification of Disease-10 Development Control Rules guidelines for CD, attending behavioral pediatrics unit outpatient. Materials and Methods: The family psychopathology, symptom severity, and functional level were assessed using parent interview schedule, revised behavioral problem checklist and Children's Global Assessment Scale. Statistical Analysis: The correlation and predictive power of the variables were analyzed using SPSS 16.0 version. Results: There was significant male dominance (88.3%) with boy girl ratio 7.5:1. Most common comorbidity noticed was hyperkinetic disorders (45%). Childhood onset group was more predominant (70%). Prevalence of comorbidity was more among early onset group (66.7%) than the late-onset group (33.3%). The family psychopathology, symptom severity, and the functional impairment were significantly higher in the childhood onset group. Conclusion: The determinants of symptom profile and severity are early onset (childhood onset CD), nature, and quantity of family psychopathology, prevalence, and type of comorbidity and nature of symptom profile itself. The family psychopathology is positively correlated with the symptom severity and negatively correlated with the functional level of the children with CD. The symptom severity was negatively correlated with the functional level of the child with CD. PMID:25568472

  3. Dynamics of Dengue Disease Severity Determined by the Interplay Between Viral Genetics and Serotype-Specific Immunity

    PubMed Central

    OhAinle, Molly; Balmaseda, Angel; Macalalad, Alexander R.; Tellez, Yolanda; Zody, Michael C.; Saborío, Saira; Nuñez, Andrea; Lennon, Niall J.; Birren, Bruce W.; Gordon, Aubree; Henn, Matthew R.; Harris, Eva

    2015-01-01

    The rapid spread of dengue is a worldwide public health problem. In two clinical studies of dengue in Managua, Nicaragua, we observed an abrupt increase in disease severity across several epidemic seasons of dengue virus serotype 2 (DENV-2) transmission. Waning DENV-1 immunity appeared to increase the risk of severe disease in subsequent DENV-2 infections after a period of cross-protection. The increase in severity coincided with replacement of the Asian/American DENV-2 NI-1 clade with a new virus clade, NI-2B. In vitro analyses of viral isolates from the two clades and analysis of viremia in patient blood samples support the emergence of a fitter virus in later, relative to earlier, epidemic seasons. In addition, the NI-1 clade of viruses was more virulent specifically in children who were immune to DENV-1, while DENV-3 immunity was associated with more severe disease among NI-2B infections. Our data demonstrate that the complex interaction between viral genetics and population dynamics of serotype-specific immunity contribute to the risk of severe dengue disease. Furthermore, this work provides insights into viral evolution and the interaction between viral and immunological determinants of viral fitness and virulence. PMID:22190239

  4. Determinants of symptom pattern in idiopathic severely delayed gastric emptying: gastric emptying rate or proximal stomach dysfunction?

    PubMed Central

    Karamanolis, G; Caenepeel, P; Arts, J; Tack, J

    2007-01-01

    Background Idiopathic gastroparesis is a syndrome characterised by severely delayed gastric emptying of solids without an obvious underlying organic cause. Although delayed gastric emptying is traditionally considered the mechanism underlying the symptoms in these patients, poor correlations with symptom severity have been reported. Aims To investigate proximal stomach function and to study the correlation of delayed gastric emptying and proximal stomach dysfunction with symptom pattern and severity in idiopathic gastroparesis. Methods 58 consecutive patients (19 men, mean (standard deviation) age 41 (2) years) with severely delayed solid gastric emptying (gastric half‐emptying time (t1/2)>109 min) without an organic cause were recruited. They filled out a symptom‐severity questionnaire and underwent a gastric barostat study for assessment of gastric sensitivity and accommodation. Correlation of these mechanisms with symptom pattern and overall symptom severity (sum of individual symptoms) was analysed. Results At two different cut‐off levels for gastric emptying (upper limit of normal t1/2 up to 1.5 and 2 times), no significant change in symptom pattern occurred. 25 (43%) patients had impaired accommodation, and this was associated with higher prevalence of early satiety (p<0.005) and weight loss (p = 0.009). 17 (29%) patients had hypersensitivity to gastric distension, and this was associated with higher prevalences of epigastric pain (p = 0.005), early satiety (p = 0.04) and weight loss (p<0.005). Overall symptom severity was not correlated with gastric emptying or accommodation, but only with sensitivity to gastric distension (R = −0.3898, p = 0.003) and body weight (R = −0.4233, p = 0.001). Conclusions In patients with idiopathic gastroparesis, the symptom pattern is determined by proximal stomach dysfunction rather than by the severity of delayed emptying. PMID:16840507

  5. IgG (Gm) allotypes and multiple sclerosis in a French population: phenotype distribution and quantitative abnormalities in CSF with respect to sex, disease severity, and presence of intrathecal antibodies.

    PubMed

    Sesboüé, R; Daveau, M; Degos, J D; Martin-Mondiere, C; Goust, J M; Schuller, E; Rivat-Peran, L; Coquerel, A; Dujardin, M; Salier, J P

    1985-11-01

    The association of a given Gm allotype or phenotype with MS susceptibility, as previously described in some Caucasian populations, was not observed in a large French MS group, whether or not considering the possible influence of sex or disease severity. This result could be related to variations in geographical distribution of Gm alleles and MS susceptibility gene(s) or suggests the simultaneous involvement of Gm and other genetic system(s). In contrast, the corresponding CSFs exhibited already known MS-associated abnormalities of IgG1 (G1m) allotype contents, which therefore did not merely result from a Gm-associated MS susceptibility. These quantitative abnormalities were not sex dependent, but may fluctuate with MS severity. The G1m allotype levels in each CSF were not correlated with titers of various intrathecal antibodies but with the number of antibody specificities detected, a picture arguing for a polyclonal, non-antigen-specific activation of G1m allotype-producing B cells present in MS brain. PMID:4042430

  6. Families with familial combined hyperlipidemia and families enriched for coronary artery disease share genetic determinants for the atherogenic lipoprotein phenotype

    SciTech Connect

    Allayee, H.; Aouizerat, B.E.; Lusis, A.J.; Cantor, R.M.; Lanning, C.D.; Rotter, J.I.; Dallinga-Thie, G.M.; Krauss, R.M.; Bruin, T.W.A. de

    1998-08-01

    Small, dense LDL particles consistently have been associated with hypertriglyceridemia, premature coronary artery disease (CAD), and familial combined hyperlipidemia (FCH). Previously, the authors have observed linkage of LDL particle size with four separate candidate-gene loci in a study of families enriched for CAD. These loci contain the genes for manganese superoxide dismutase (MnSOD), on chromosome 6q; for apolipoprotein AI-CIII-AIV, on chromosome 11q; for cholesteryl ester transfer protein (CETP) and lecithin:cholesterol acyl-transferase (LCAT), on chromosome 16q; and for the LDL receptor (LDLR), on chromosome 19p. The authors have now tested whether these loci also contribute to LDL particle size in families ascertained for FCH. The members of 18 families (481 individuals) were typed for genetic markers at the four loci, and linkage to LDL particle size was assessed by nonparametric sib-pair linkage analysis. The presence of small, dense LDL (pattern B) was much more frequent in the FCH probands than in the spouse controls. Evidence for linkage was observed at the MnSOD (P = .02), CETP/LCAT (P = .03), and apolipoprotein AI0CIII0AIV loci (P = .005) but not at the LDLR locus. The authors conclude that there is a genetically based association between FCH and small, dense LDL and that the genetic determinants for LDL particle size are shared, at least in part, among FCH families and the more general population at risk for CAD.

  7. Cerebral blood flow and metabolism in children with severe head injuries. Part 2: Cerebrovascular resistance and its determinants.

    PubMed Central

    Sharples, P M; Matthews, D S; Eyre, J A

    1995-01-01

    It has been proposed that in children with severe head injuries the cerebral circulation does not respond appropriately to normal physiological control mechanisms, making children more susceptible than adults to low cerebrovascular resistance, increased cerebral blood flow (cerebral hyperaemia), and raised intracranial pressure. To investigate this issue, 122 serial measurements of cerebrovascular resistance in 17 children with severe head injuries have been performed and related to cerebral perfusion pressure, arterial CO2 (PaCO2), arterial oxygen content (AO2), and the cerebral metabolic rate of oxygen (CMRO2). Cerebrovascular resistance values (mean (SD) 1.54 (0.61) mm Hg.ml-1.100 g.min) were normal or raised in most cases; 71 values (58%) were within the normal range, 39 (32%) above the upper limit, and only 12 (10%) below the lower limit. There was a significant correlation between cerebral perfusion pressure and cerebrovascular resistance (r = 0.32, p = 0.0003), suggesting preservation of pressure autoregulation. This correlation was absent in four of the five children who died or survived with severe handicap. Analysis by multilevel modelling indicated that, as in normal subjects, CMRO2, CPP, AO2, PaCO2, and cerebrovenous pH were important independent determinants of cerebrovascular resistance. The results indicate that normal cerebrovascular reactivity is often preserved in children with severe head injuries but may be impaired in the most severely injured patients. PMID:7876844

  8. Interactions between ultraviolet light and MC1R and OCA2 variants are determinants of childhood nevus and freckle phenotypes

    PubMed Central

    Barón, Anna E.; Asdigian, Nancy L.; Gonzalez, Victoria; Aalborg, Jenny; Terzian, Tamara; Stiegmann, Regan A.; C.Torchia, Enrique; Berwick, Marianne; Dellavalle, Robert P.; G.Morelli, Joseph; Mokrohisky, Stefan T.; Crane, Lori A.; Box, Neil F.

    2014-01-01

    Background Melanocytic nevi (moles) and freckles are well known biomarkers of melanoma risk, and they are influenced by similar ultraviolet (UV) light exposures and genetic susceptibilities to those that increase melanoma risk. Nevertheless, the selective interactions between UV exposures and nevus and freckling genes remain largely undescribed. Methods We conducted a longitudinal study from ages 6 through 10 in 477 Colorado children who had annual information collected for sun exposure, sun protection behaviors, and full body skin exams. MC1R and HERC2/OCA2 rs12913832 were genotyped and linear mixed models were used to identify main and interaction effects. Results All measures of sun exposure (chronic, sunburns and waterside vacations) contributed to total nevus counts, and cumulative chronic exposure acted as the major driver of nevus development. Waterside vacations strongly increased total nevus counts in children with rs12913832 blue eye color alleles and facial freckling scores in those with MC1R red hair color variants. Sunburns increased numbers of larger nevi (≥2 mm) in subjects with certain MC1R and rs12913832 genotypes. Conclusions Complex interactions between different UV exposure profiles and genotype combinations determine nevus numbers and size, and the degree of facial freckling. Impact Our findings emphasize the importance of implementing sun-protective behavior in childhood regardless of genetic make-up; although children with particular genetic variants may benefit from specifically targeted preventive measures to counteract their inherent risk of melanoma. Moreover, we demonstrate, for the first time, that longitudinal studies are a highly powered tool to uncover new gene-environment interactions that increase cancer risk. PMID:25410285

  9. Hormonal determinants of the severity of andropausal and depressive symptoms in middle-aged and elderly men with prediabetes

    PubMed Central

    Rabijewski, Michał; Papierska, Lucyna; Kuczerowski, Roman; Piątkiewicz, Paweł

    2015-01-01

    Andropausal and depressive symptoms are common in aging males and may be associated with hormone deficiency. We investigated the severity of andropausal and depressive symptoms, as well as their hormonal determinants, in 196 middle-aged and elderly men (age range: 40–80 years) with prediabetes (PD) and in 184 healthy peers. PD was diagnosed according to the definition of the American Diabetes Association. The severity of andropausal and depressive symptoms was assessed using the Aging Males’ Symptoms Rating Scale and the Self-Rating Depression Scale. Total testosterone (TT), calculated free testosterone (cFT), dehydroepiandrosterone sulfate (DHEAS), and insulin-like growth factor 1 (IGF-1) were measured. The prevalence of andropausal syndrome in men with PD was significantly higher than that in healthy men (35% vs 11%, respectively). In men with PD aged 40–59 years, the severity of sexual, psychological, and all andropausal symptoms was greater than in healthy peers, while in elderly men (60–80 years), only the severity of psychological symptoms was greater than in healthy peers. The severity of depressive symptoms in the middle-aged men with PD was greater than in healthy peers, while the severity of depressive symptoms in elderly men with PD and healthy peers was similar. The higher prevalence of andropausal symptoms was independently associated with cFT and IGF-1 in middle-aged men and with TT and DHEAS in elderly men with PD. The more severe depression symptoms were associated with low TT and DHEAS in middle-aged men and with low cFT and DHEAS in elderly men with PD. In conclusion, the prevalence of andropausal symptoms, especially psychological, was higher in prediabetic patients as compared to healthy men, while the severity of depressive symptoms was higher only in middle-aged men with PD. Hormonal determinants of andropausal and depressive symptoms are different in middle-aged and elderly patients, but endocrine tests are necessary in all men with

  10. A general framework for the analysis of phenotypic trajectories in evolutionary studies.

    PubMed

    Adams, Dean C; Collyer, Michael L

    2009-05-01

    Many evolutionary studies require an understanding of phenotypic change. However, while analyses of phenotypic variation across pairs of evolutionary levels (populations or time steps) are well established, methods for testing hypotheses that compare evolutionary sequences across multiple levels are less developed. Here we describe a general analytical procedure for quantifying and comparing patterns of phenotypic evolution. The phenotypic evolution of a lineage is defined as a trajectory across a set of evolutionary levels in a multivariate phenotype space. Attributes of these trajectories (their size, direction, and shape), are quantified, and statistically compared across pairs of taxa, and a summary statistic is used to determine the extent to which patterns of phenotypic evolution are concordant across multiple taxa. This approach provides a direct quantitative description of how patterns of phenotypic evolution differ, as well as a statistical assessment of the degree of repeatability in the evolutionary responses to selection among taxa. We describe how this approach can quantify phenotypic trajectories from many ecological and evolutionary processes, whose data encode multivariate characterizations of the phenotype, including: phenotypic plasticity, ecological selection, ontogeny and growth, local adaptation, and biomechanics. We illustrate the approach by examining the phenotypic evolution of several fossil lineages of Globorotalia. PMID:19210539

  11. The Broad Autism Phenotype. Findings from an Epidemiological Survey

    ERIC Educational Resources Information Center

    Micali, N.; Chakrabarti, S.; Fombonne, E.

    2004-01-01

    This study aimed to determine if relatives of children with autism and less severe pervasive developmental disorders (PDDs) have higher rates of various components of the broad autistic phenotype. Psychiatric and medical disorders were investigated. Parents of children with PDDs were selected from an epidemiological survey and compared with…

  12. A novel donor splice site in intron 11 of the CFTR gene, created by mutation 1811+1.6kbA-->G, produces a new exon: high frequency in Spanish cystic fibrosis chromosomes and association with severe phenotype.

    PubMed Central

    Chillón, M; Dörk, T; Casals, T; Giménez, J; Fonknechten, N; Will, K; Ramos, D; Nunes, V; Estivill, X

    1995-01-01

    mRNA analysis of the cystic fibrosis transmembrane regulator (CFTR) gene in tissues of cystic fibrosis (CF) patients has allowed us to detect a cryptic exon. The new exon involves 49 base pairs between exons 11 and 12 and is due to a point mutation (1811+1.6kbA-->G) that creates a new donor splice site in intron 11. Semiquantitative mRNA analysis showed that 1811+1.6kbA-->G-mRNA was 5-10-fold less abundant than delta F508 mRNA. Mutation 1811+1.6kbA-->G was found in 21 Spanish and 1 German CF chromosomes, making it the fourth-most-frequent mutation (2%) in the Spanish population. Individuals with genotype delta F508/1811+1.6kbA-->G have only 1%-3% of normal CFTR mRNA. This loss of 97% of normal CFTR mRNA must be responsible for the pancreatic insufficiency and for the severe CF phenotype in these patients. Images Figure 3 PMID:7534040

  13. A novel donor splice site in intron 11 of the CFTR gene, created by mutation 1811 + 1.6kbA {yields} G, produces a new exon: High frequency in spanish cystic fibrosis chromosomes and association with severe phenotype

    SciTech Connect

    Chillon, M.; Casals, T.; Gimenez, J.; Ramos, D.; Nunes, V.; Estivill, X.; Doerk, T.; Will, K.; Fonknechten, N.

    1995-03-01

    mRNA analysis of the cystic fibrosis transmembrane regulator (CFTR) gene in tissues of cystic fibrosis (CF) patients has allowed us to detect a cryptic exon. The new exon involves 49 base pairs between exons 11 and 12 and is due to a point mutation (1811+1.6bA{yields}G) that creates a new donor splice site in intron 11. Semiquantitative mRNA analysis showed that 1811+1.6kbA{r_arrow}G-mRNA was 5-10-fold less abundant than {triangle}F508 mRNA. Mutations 1811+1.6kbA{yields}G was found in 21 Spanish and 1 German CF chromosome(s), making it the fourth-most-frequent mutation (2%) in the Spanish population. Individuals with genotype {triangle}F508/1811+1.6kbA{yields}G have only 1%-3% of normal CFTR mRNA. This loss of 97% of normal CFTR mRNA must be responsible for the pancreatic insufficiency and for the severe CF phenotype in these patients. 30 refs., 3 figs., 2 tabs.

  14. Non-invasive In-cell Determination of Free Cytosolic [NAD+]/[NADH] Ratios Using Hyperpolarized Glucose Show Large Variations in Metabolic Phenotypes*

    PubMed Central

    Christensen, Caspar Elo; Karlsson, Magnus; Winther, Jakob R.; Jensen, Pernille Rose; Lerche, Mathilde H.

    2014-01-01

    Accumulating evidence suggest that the pyridine nucleotide NAD has far wider biological functions than its classical role in energy metabolism. NAD is used by hundreds of enzymes that catalyze substrate oxidation and, as such, it plays a key role in various biological processes such as aging, cell death, and oxidative stress. It has been suggested that changes in the ratio of free cytosolic [NAD+]/[NADH] reflects metabolic alterations leading to, or correlating with, pathological states. We have designed an isotopically labeled metabolic bioprobe of free cytosolic [NAD+]/[NADH] by combining a magnetic enhancement technique (hyperpolarization) with cellular glycolytic activity. The bioprobe reports free cytosolic [NAD+]/[NADH] ratios based on dynamically measured in-cell [pyruvate]/[lactate] ratios. We demonstrate its utility in breast and prostate cancer cells. The free cytosolic [NAD+]/[NADH] ratio determined in prostate cancer cells was 4 times higher than in breast cancer cells. This higher ratio reflects a distinct metabolic phenotype of prostate cancer cells consistent with previously reported alterations in the energy metabolism of these cells. As a reporter on free cytosolic [NAD+]/[NADH] ratio, the bioprobe will enable better understanding of the origin of diverse pathological states of the cell as well as monitor cellular consequences of diseases and/or treatments. PMID:24302737

  15. The Relative Importance of Genetic Diversity and Phenotypic Plasticity in Determining Invasion Success of a Clonal Weed in the USA and China

    PubMed Central

    Geng, Yupeng; van Klinken, Rieks D.; Sosa, Alejandro; Li, Bo; Chen, Jiakuan; Xu, Cheng-Yuan

    2016-01-01

    Phenotypic plasticity has been proposed as an important adaptive strategy for clonal plants in heterogeneous habitats. Increased phenotypic plasticity can be especially beneficial for invasive clonal plants, allowing them to colonize new environments even when genetic diversity is low. However, the relative importance of genetic diversity and phenotypic plasticity for invasion success remains largely unknown. Here, we performed molecular marker analyses and a common garden experiment to investigate the genetic diversity and phenotypic plasticity of the globally important weed Alternanthera philoxeroides in response to different water availability (terrestrial vs. aquatic habitats). This species relies predominantly on clonal propagation in introduced ranges. We therefore expected genetic diversity to be restricted in the two sampled introduced ranges (the USA and China) when compared to the native range (Argentina), but that phenotypic plasticity may allow the species' full niche range to nonetheless be exploited. We found clones from China had very low genetic diversity in terms of both marker diversity and quantitative variation when compared with those from the USA and Argentina, probably reflecting different introduction histories. In contrast, similar patterns of phenotypic plasticity were found for clones from all three regions. Furthermore, despite the different levels of genetic diversity, bioclimatic modeling suggested that the full potential bioclimatic distribution had been invaded in both China and USA. Phenotypic plasticity, not genetic diversity, was therefore critical in allowing A. philoxeroides to invade diverse habitats across broad geographic areas. PMID:26941769

  16. The Relative Importance of Genetic Diversity and Phenotypic Plasticity in Determining Invasion Success of a Clonal Weed in the USA and China.

    PubMed

    Geng, Yupeng; van Klinken, Rieks D; Sosa, Alejandro; Li, Bo; Chen, Jiakuan; Xu, Cheng-Yuan

    2016-01-01

    Phenotypic plasticity has been proposed as an important adaptive strategy for clonal plants in heterogeneous habitats. Increased phenotypic plasticity can be especially beneficial for invasive clonal plants, allowing them to colonize new environments even when genetic diversity is low. However, the relative importance of genetic diversity and phenotypic plasticity for invasion success remains largely unknown. Here, we performed molecular marker analyses and a common garden experiment to investigate the genetic diversity and phenotypic plasticity of the globally important weed Alternanthera philoxeroides in response to different water availability (terrestrial vs. aquatic habitats). This species relies predominantly on clonal propagation in introduced ranges. We therefore expected genetic diversity to be restricted in the two sampled introduced ranges (the USA and China) when compared to the native range (Argentina), but that phenotypic plasticity may allow the species' full niche range to nonetheless be exploited. We found clones from China had very low genetic diversity in terms of both marker diversity and quantitative variation when compared with those from the USA and Argentina, probably reflecting different introduction histories. In contrast, similar patterns of phenotypic plasticity were found for clones from all three regions. Furthermore, despite the different levels of genetic diversity, bioclimatic modeling suggested that the full potential bioclimatic distribution had been invaded in both China and USA. Phenotypic plasticity, not genetic diversity, was therefore critical in allowing A. philoxeroides to invade diverse habitats across broad geographic areas. PMID:26941769

  17. Pseudomonas Aeruginosa Resistance Phenotypes and Phenotypic Highlighting Methods

    PubMed Central

    BĂLĂŞOIU, MARIA; BĂLĂŞOIU, A.T.; MĂNESCU, RODICA; AVRAMESCU, CARMEN; IONETE, OANA

    2014-01-01

    Pseudomonas aeruginosa genus bacteria are well known for their increased drug resistance (phenotypic ang genotypic resistance). The most important resistance mechanisms are: enzyme production, reduction of pore expression, reduction of the external membrane proteins expression, efflux systems, topoisomerase mutations. These mechanisms often accumulate and lead to multidrug ressitance strains emergence. The most frequent acquired resistance mechanisms are betalactamase-type enzyme production (ESBLs, AmpC, carbapenemases), which determine variable phenotypes of betalactamines resistance, phenotypes which are associated with aminoglycosides and quinolones resistance. The nonenzymatic drug resistance mechanisms are caused by efflux systems, pore reduction and penicillin-binding proteins (PBP) modification, which are often associated to other resistance mechanisms. Phenotypic methods used for testing these mechanisms are based on highlighting these phenotypes using Kirby Bauer antibiogram, clinical breakpoints, and “cut off” values recommended by EUCAST 2013 standard, version 3.1. PMID:25729587

  18. Virulence plasmid (pYV)-associated expression of phenotypic virulent determinants in pathogenic Yersinia species: a convenient method for monitoring the presence of pYV under culture conditions and its application for...food

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In Yersinia pestis, Y. pseudotuberculosis, and Y, enterocolitica, phenotypic expression of virulence plasmid (pYV: 70-kb)-associated genetic determinants may include low calcium response (Lcr, pin point colony, size = 0.36 mm), colony morphology (size = 1.13 mm), crystal violet (CV) binding (dark-v...

  19. Emerging molecular phenotypes of asthma.

    PubMed

    Ray, Anuradha; Oriss, Timothy B; Wenzel, Sally E

    2015-01-15

    Although asthma has long been considered a heterogeneous disease, attempts to define subgroups of asthma have been limited. In recent years, both clinical and statistical approaches have been utilized to better merge clinical characteristics, biology, and genetics. These combined characteristics have been used to define phenotypes of asthma, the observable characteristics of a patient determined by the interaction of genes and environment. Identification of consistent clinical phenotypes has now been reported across studies. Now the addition of various 'omics and identification of specific molecular pathways have moved the concept of clinical phenotypes toward the concept of molecular phenotypes. The importance of these molecular phenotypes is being confirmed through the integration of molecularly targeted biological therapies. Thus the global term asthma is poised to become obsolete, being replaced by terms that more specifically identify the pathology associated with the disease. PMID:25326577

  20. Rescue of Very Virulent and Mosaic Infectious Bursal Disease Virus from Cloned cDNA: VP2 Is Not the Sole Determinant of the Very Virulent Phenotype

    PubMed Central

    Boot, Hein J.; ter Huurne, A. Agnes H. M.; Hoekman, Arjan J. W.; Peeters, Ben P. H.; Gielkens, Arno L. J.

    2000-01-01

    Many recent outbreaks of infectious bursal disease in commercial chicken flocks worldwide are due to the spread of very virulent strains of infectious bursal disease virus (vvIBDV). The molecular determinants for the enhanced virulence of vvIBDV compared to classical IBDV are unknown. The lack of a reverse genetics system to rescue vvIBDV from its cloned cDNA hampers the identification and study of these determinants. In this report we describe, for the first time, the rescue of vvIBDV from its cloned cDNA. Two plasmids containing a T7 promoter and either the full-length A- or B-segment cDNA of vvIBDV (D6948) were cotransfected into QM5 cells expressing T7 polymerase. The presence of vvIBDV could be detected after passage of the transfection supernatant in either primary bursa cells (in vitro) or embryonated eggs (in vivo), but not QM5 cells. Rescued vvIBDV (rD6948) appeared to have the same virulence as the parental isolate, D6948. Segment-reassorted IBDV, in which one of the two genomic segments originated from cDNA of classical attenuated IBDV CEF94 and the other from D6948, could also be rescued by using this system. Segment-reassorted virus containing the A segment of the classical attenuated isolate (CEF94) and the B segment of the very virulent isolate (D6948) is not released until 15 h after an in vitro infection. This indicates a slightly retarded replication, as the first release of CEF94 is already found at 10 h after infection. Next to segment reassortants, we generated and analyzed mosaic IBDVs (mIBDVs). In these mIBDVs we replaced the region of CEF94 encoding one of the viral proteins (pVP2, VP3, or VP4) by the corresponding region of D6948. Analysis of these mIBDV isolates showed that tropism for non-B-lymphoid cells was exclusively determined by the viral capsid protein VP2. However, the very virulent phenotype was not solely determined by this protein, since mosaic virus containing VP2 of vvIBDV induced neither morbidity nor mortality in young

  1. Early marriage, rape, child prostitution, and related factors determining the psychosocial effects severity of child sexual abuse in Ethiopia.

    PubMed

    Wondie, Yemataw; Zemene, Workie; Reschke, Konrad; Schröder, Harry

    2011-05-01

    This study was aimed at identifying factors that determine the psychosocial effects severity of child sexual abuse. Data were collected from 318 female children in Ethiopia using the Children's Impact of Traumatic Events Scale-Revised and the Rosenberg Self-Esteem Scale. The results revealed that respondents who survived rape and child prostitution were more symptomatic than those who were married early. Respondents for whom less time had elapsed since their first experience of abuse demonstrated a significantly higher level of post-traumatic stress disorder symptoms, negative reactions by others, self-blame, and guilt than those for whom more time had elapsed since such an experience. The respondents in an intact marital relationship were found to be less symptomatic than their never married and divorced counterparts. Implications for intervention and further investigations are discussed. PMID:21660816

  2. Vitamin D receptor expression levels determine the severity and complexity of disease progression among leprosy reaction patients

    PubMed Central

    Mandal, D.; Reja, A.H.H.; Biswas, N.; Bhattacharyya, P.; Patra, P.K.; Bhattacharya, B.

    2015-01-01

    We studied the roles of vitamin D and its receptor, VDR, in the progression of leprosy. The majority of individuals with leprosy from Kolkata, India, with a type 1 or type 2 reaction have low levels of vitamin D3 in serum samples. Interestingly, individuals with a type 2 reaction associated with neuritis/erythema nodosum leprosum had very low VDR mRNA expression levels, ranging from 5% to 10%, compared to that of healthy control subjects; these patients also had a high bacilli index, ranging from 3+ to 5+. This is the first report to indicate that VDR expression levels may determine the complexity and severity of the progression of leprosy. PMID:26106480

  3. Vitamin D receptor expression levels determine the severity and complexity of disease progression among leprosy reaction patients.

    PubMed

    Mandal, D; Reja, A H H; Biswas, N; Bhattacharyya, P; Patra, P K; Bhattacharya, B

    2015-07-01

    We studied the roles of vitamin D and its receptor, VDR, in the progression of leprosy. The majority of individuals with leprosy from Kolkata, India, with a type 1 or type 2 reaction have low levels of vitamin D3 in serum samples. Interestingly, individuals with a type 2 reaction associated with neuritis/erythema nodosum leprosum had very low VDR mRNA expression levels, ranging from 5% to 10%, compared to that of healthy control subjects; these patients also had a high bacilli index, ranging from 3+ to 5+. This is the first report to indicate that VDR expression levels may determine the complexity and severity of the progression of leprosy. PMID:26106480

  4. Severe dental caries, impacts and determinants among children 2-6 years of age in Inuvik Region, Northwest Territories, Canada.

    PubMed

    Leake, James; Jozzy, Simon; Uswak, Gerald

    2008-01-01

    In 2004-2005, 349 of 541 eligible, mostly preschool, children in the Inuvik Region in the Northwest Territories of Canada were examined clinically, and the parents or caregivers of 315 of these children were interviewed to measure their oral health status, and its impacts and determinants. Dental caries is a highly prevalent health problem among these preschool children in Inuvik Region: we found that 66% (230/349 children) had the disease and had, on average, 4.8 affected teeth, of which 2.4 had untreated decay. Twelve percent (42/349) of the children needed urgent dental care. Among the 315 children whose parents or caregivers were interviewed, 46% (144/315) had severe early childhood tooth decay. Significantly more of the parents of children with severe decay reported that their children had pain and a decreased ability to chew than the parents of children with no or moderate disease. Using logistic regression, we found that protective factors for severe early childhood tooth decay were higher family income (OR = 0.68; 90% CI = 0.54-0.85), community water fluoridation (OR = 0.49; 90% CI = 0.26-0.91), and drinking milk (OR = 0.44; 90% CI = 0.24-0.81) and fruit juices (OR = 0.46; 90% CI = 0.24-0.90) after the child began to walk, whereas significant risks were consuming drinks made from flavour crystals before (OR = 2.4; 90% CI = 1.3-4.6) and after (OR = 2.0; 90% CI = 1.2-3.2) that age. This information should enable the Health and Social Services Authority to plan health promotion and service delivery programs for the children in Inuvik Region. PMID:18644236

  5. Mayombian ethnic, vegetables low intake, insulin treatment, diabetic nephropathy and severe diabetic retinopathy are determinants of blindness in diabetic Africans

    PubMed Central

    Moise, Mvitu Muaka; Benjamin, Longo-Mbenza; Enoch, Cibanda Yokobo; Igor, Longo Phemba

    2013-01-01

    AIM To determine the frequency and causes of blindness in diabetic Africans. METHODS The study was a cross-sectional survey carried out among known black diabetics consecutively admitted at the Teaching Hospital, University of Kinshasa, between 2005 and 2007. Examination methods included interviewer-administered structured questionnaire, eye examinations (visual acuity, tonometry, funduscopy), and fasting plasma glycaemia test. RESULTS Of the 227 patients examined, 15.9% had blindness. Univariate analyses showed significant association between female, severity of diabetic retinopathy, Mayombian ethnic group, use of insulin treatment, low intake of vegetables, diabetic nephropathy, open angle glaucoma and blindness in all diabetics. After logistic regression, only diabetic nephropathy, use of insulin treatment, macular oedema, Mayombian ethnic group and vegetables low intake were the independent risk factors of blindness in all diabetics. However, after logistic regression in the sub-group with diabetic retinopathy, only open angle glaucoma and proliferative diabetic retinopathy were the independent determinants of blindness. CONCLUSION The majority of the causes of blindness in these diabetic Africans are avoidable. It is recommended that appropriate diabetes care, nutrition education, periodic eye examination and laser photocoagulation facilities should be provided for treating diabetics in sub-Saharan Africa. PMID:24195057

  6. Phenotypic debrisoquine 4-hydroxylase activity among extensive metabolizers is unrelated to genotype as determined by the Xba-I restriction fragment length polymorphism.

    PubMed Central

    Turgeon, J; Evans, W E; Relling, M V; Wilkinson, G R; Roden, D M

    1991-01-01

    1. The major pathway for 4-hydroxylation of debrisoquine in man is polymorphic and under genetic control. More than 90% of subjects (extensive metabolizers, EMs) have active debrisoquine 4-hydroxylase (cytochrome P450IID6) while in the remainder (poor metabolizers, PMs), cytochrome P450IID6 activity is greatly impaired. 2. Within the EM group, cytochrome P450IID6-mediated metabolism of a range of substrates varies widely. Some of this intra-phenotype non-uniformity may be explained by the presence of two subsets of subjects with different genotypes (heterozygotes and homozygotes). 3. Cytochrome P450IID6 substrates have not differentiated between these two genotypes. However, a restriction fragment length polymorphism (RFLP) which identifies mutant alleles of cytochrome P450IID6 locus has been described and can definitively assign genotype in some heterozygous EM subjects. 4. In this study, we used RFLP analysis and encainide as a model substrate to determine if non-uniformity in cytochrome P450IID6 activity among EMs is related to genotype. We tested the hypothesis that heterozygotes exhibit intermediate metabolic activity and that homozygous dominants exhibit the highest activity. We proposed encainide as a useful substrate for this purpose since cytochrome P450IID6 catalyzes not only its biotransformation to O-desmethyl encainide (ODE) but also the subsequent metabolism of ODE to 3-methoxy-O-desmethyl encainide (MODE). 5. A single 50 mg oral dose of encainide was administered to 139 normal volunteers and 14 PMs were identified. Urinary ratios among encainide, ODE and MODE in the remaining 125 EM subjects revealed a wide range of cytochrome P450IID6 activity. However, Southern blotting of genomic DNA digested with XbaI identified obligate heterozygotes in both extremes of all ratio distributions.(ABSTRACT TRUNCATED AT 250 WORDS) Images Figure 2 PMID:1685663

  7. Phenotypic mapping and clinical ideology

    SciTech Connect

    Lurie, I.W.; Opitz, J.M.

    1995-07-17

    Scientists have been trying to determine whether the main clinical findings in the 4p deletion syndrome are due to a deletion of one small critical segment, or whether deletions of some particular segments of 4p are responsible for different phenotypic manifestations. This is the basic issue for the whole group of autosomal deletion syndromes, as well as for our understanding of mechanisms of the origin of the abnormal phenotype. All circumstances need to be taken into consideration when trying to apply molecular methods for the mapping of phenotypic findings in the 4p deletion or in any other autosomal deletion syndrome. 8 refs.

  8. Legacy of Pre-Disturbance Spatial Pattern Determines Early Structural Diversity following Severe Disturbance in Montane Spruce Forests

    PubMed Central

    Bače, Radek; Svoboda, Miroslav; Janda, Pavel; Morrissey, Robert C.; Wild, Jan; Clear, Jennifer L.; Čada, Vojtěch; Donato, Daniel C.

    2015-01-01

    Background Severe canopy-removing disturbances are native to many temperate forests and radically alter stand structure, but biotic legacies (surviving elements or patterns) can lend continuity to ecosystem function after such events. Poorly understood is the degree to which the structural complexity of an old-growth forest carries over to the next stand. We asked how pre-disturbance spatial pattern acts as a legacy to influence post-disturbance stand structure, and how this legacy influences the structural diversity within the early-seral stand. Methods Two stem-mapped one-hectare forest plots in the Czech Republic experienced a severe bark beetle outbreak, thus providing before-and-after data on spatial patterns in live and dead trees, crown projections, down logs, and herb cover. Results Post-disturbance stands were dominated by an advanced regeneration layer present before the disturbance. Both major species, Norway spruce (Picea abies) and rowan (Sorbus aucuparia), were strongly self-aggregated and also clustered to former canopy trees, pre-disturbance snags, stumps and logs, suggesting positive overstory to understory neighbourhood effects. Thus, although the disturbance dramatically reduced the stand’s height profile with ~100% mortality of the canopy layer, the spatial structure of post-disturbance stands still closely reflected the pre-disturbance structure. The former upper tree layer influenced advanced regeneration through microsite and light limitation. Under formerly dense canopies, regeneration density was high but relatively homogeneous in height; while in former small gaps with greater herb cover, regeneration density was lower but with greater heterogeneity in heights. Conclusion These findings suggest that pre-disturbance spatial patterns of forests can persist through severe canopy-removing disturbance, and determine the spatial structure of the succeeding stand. Such patterns constitute a subtle but key legacy effect, promoting structural

  9. Characterization of the oral absorption of several aminopenicillins: determination of intrinsic membrane absorption parameters in the rat intestine in situ

    NASA Technical Reports Server (NTRS)

    Sinko, P. J.; Amidon, G. L.

    1992-01-01

    The absorption mechanism of several penicillins was characterized using in situ single-pass intestinal perfusion in the rat. The intrinsic membrane parameters were determined using a modified boundary layer model (fitted value +/- S.E.): Jmax* = 11.78 +/- 1.88 mM, Km = 15.80 +/- 2.92 mM, Pm* = 0, Pc* = 0.75 +/- 0.04 for ampicillin; Jmax* = 0.044 +/- 0.018 mM, Km = 0.058 +/- 0.026 mM, Pm* = 0.558 +/- 0.051, Pc* = 0.757 +/- 0.088 for amoxicillin; and Jmax* = 16.30 +/- 3.40 mM, Km = 14.00 +/- 3.30 mM, Pm* = 0, Pc* = 1.14 +/- 0.05 for cyclacillin. All of the aminopenicillins studied demonstrated saturable absorption kinetics as indicated by their concentration-dependent wall permeabilities. Inhibition studies were performed to confirm the existence of a nonpassive absorption mechanism. The intrinsic wall permeability (Pw*) of 0.01 mM ampicillin was significantly lowered by 1 mM amoxicillin and the Pw* of 0.01 mM amoxicillin was reduced by 2 mM cephradine consistent with competitive inhibition.

  10. A MULTIDIMENSIONAL ASSESSMENT OF THE VALIDITY AND UTILITY OF ALCOHOL USE DISORDER SEVERITY AS DETERMINED BY ITEM RESPONSE THEORY MODELS

    PubMed Central

    Dawson, Deborah A.; Saha, Tulshi D.; Grant, Bridget F.

    2010-01-01

    Background The relative severity of the 11 DSM-IV alcohol use disorder (AUD) criteria are represented by their severity threshold scores, an item response theory (IRT) model parameter inversely proportional to their prevalence. These scores can be used to create a continuous severity measure comprising the total number of criteria endorsed, each weighted by its relative severity. Methods This paper assesses the validity of the severity ranking of the 11 criteria and the overall severity score with respect to known AUD correlates, including alcohol consumption, psychological functioning, family history, antisociality, and early initiation of drinking, in a representative population sample of U.S. past-year drinkers (n=26,946). Results The unadjusted mean values for all validating measures increased steadily with the severity threshold score, except that legal problems, the criterion with the highest score, was associated with lower values than expected. After adjusting for the total number of criteria endorsed, this direct relationship was no longer evident. The overall severity score was no more highly correlated with the validating measures than a simple count of criteria endorsed, nor did the two measures yield different risk curves. This reflects both within-criterion variation in severity and the fact that the number of criteria endorsed and their severity are so highly correlated that severity is essentially redundant. Conclusions Attempts to formulate a scalar measure of AUD will do as well by relying on simple counts of criteria or symptom items as by using scales weighted by IRT measures of severity. PMID:19782481

  11. Determining the potential link between irrigation water quality and the microbiological quality of onions by phenotypic and genotypic characterization of Escherichia coli isolates.

    PubMed

    du Plessis, Erika M; Duvenage, Francois; Korsten, Lise

    2015-04-01

    The potential transfer of human pathogenic bacteria present in irrigation water onto fresh produce was investigated, because surface water sources used for irrigation purposes in South Africa have increasingly been reported to be contaminated with enteric bacterial pathogens. A microbiological analysis was performed of a selected river in Limpopo Province, South Africa, that is often contaminated with raw sewage from municipal sewage works and overhead irrigated onions produced on a commercial farm. Counts of Escherichia coli, coliforms, aerobic bacteria, fungi, and yeasts and the prevalence of E. coli O157:H7, Salmonella, and Listeria monocytogenes were determined. Identities of bacterial isolates from irrigation water and onions were confirmed using matrix-assisted laser desorption ionization-time of flight mass spectrometry, PCR, and biochemical tests. To establish a potential link between the microbiological quality of the irrigation source and the onions, the E. coli isolates from both were subjected to antibiotic resistance, virulence gene, and enterobacterial repetitive intergenic consensus PCR analyses. River water E. coli counts exceeded South African Department of Water Affairs and World Health Organization irrigation water guidelines. Counts of aerobic bacteria, coliforms, fungi, and yeasts of onions from the market were acceptable according to Department of Health Directorate, Food Control, South Africa, microbiological guidelines for ready-to-eat fresh fruits and vegetables. E. coli O157:H7, Salmonella, and L. monocytogenes were not detected in onions, whereas only Salmonella was detected in 22% of water samples. Matrix-assisted laser desorption ionization-time of flight mass spectrometry and PCR identification of E. coli isolates from water and onions correlated. Of the 45 E. coli isolates from water and onions, 42.2% were resistant to multiple antibiotics. Virulence genes eae, stx1, and stx2 were detected in 2.2, 6.6, and 2.2% of the E. coli isolates

  12. Timing of the loss of Pten protein determines disease severity in a mouse model of myeloid malignancy

    PubMed Central

    Yan, Yan; Webster, Cody; Shao, Lijian; Lensing, Shelly Y.; Ni, Hongyu; Feng, Wei; Colorado, Natalia; Pathak, Rupak; Xiang, Zhifu; Hauer-Jensen, Martin; Li, Shaoguang; Zhou, Daohong; Emanuel, Peter D.

    2016-01-01

    Juvenile myelomonocytic leukemia (JMML) is an aggressive pediatric mixed myelodysplastic/myeloproliferative neoplasm (MDS/MPN). JMML leukemogenesis is linked to a hyperactivated RAS pathway, with driver mutations in the KRAS, NRAS, NF1, PTPN11, or CBL genes. Previous murine models demonstrated how those genes contributed to the selective hypersensitivity of JMML cells to granulocyte macrophage–colony-stimulating factor (GM-CSF), a unifying characteristic in the disease. However, it is unclear what causes the early death in children with JMML, because transformation to acute leukemia is rare. Here, we demonstrate that loss of Pten (phosphatase and tensin homolog) protein at postnatal day 8 in mice harboring Nf1 haploinsufficiency results in an aggressive MPN with death at a murine prepubertal age of 20 to 35 days (equivalent to an early juvenile age in JMML patients). The death in the mice was due to organ infiltration with monocytes/macrophages. There were elevated activities of protein kinase B (Akt) and mitogen-activated protein kinase (MAPK) in cells at physiological concentrations of GM-CSF. These were more pronounced in mice with Nf1 haploinsufficiency than in littermates with wild-type Nf1, but this model is insufficient to cause cells to be GM-CSF hypersensitive. This new model represents a murine MPN model with features of a pediatric unclassifiable mixed MDS/MPN and mimics many clinical manifestations of JMML in terms of age of onset, aggressiveness, and organ infiltration with monocytes/macrophages. Our data suggest that the timing of the loss of PTEN protein plays a critical role in determining the disease severity in myeloid malignancies. This model may be useful for studying the pathogenesis of pediatric diseases with alterations in the Ras pathway. PMID:26764354

  13. The PDZ-Binding Motif of Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Is a Determinant of Viral Pathogenesis

    PubMed Central

    Jimenez-Guardeño, Jose M.; Nieto-Torres, Jose L.; DeDiego, Marta L.; Regla-Nava, Jose A.; Fernandez-Delgado, Raul; Castaño-Rodriguez, Carlos; Enjuanes, Luis

    2014-01-01

    A recombinant severe acute respiratory syndrome coronavirus (SARS-CoV) lacking the envelope (E) protein is attenuated in vivo. Here we report that E protein PDZ-binding motif (PBM), a domain involved in protein-protein interactions, is a major determinant of virulence. Elimination of SARS-CoV E protein PBM by using reverse genetics caused a reduction in the deleterious exacerbation of the immune response triggered during infection with the parental virus and virus attenuation. Cellular protein syntenin was identified to bind the E protein PBM during SARS-CoV infection by using three complementary strategies, yeast two-hybrid, reciprocal coimmunoprecipitation and confocal microscopy assays. Syntenin redistributed from the nucleus to the cell cytoplasm during infection with viruses containing the E protein PBM, activating p38 MAPK and leading to the overexpression of inflammatory cytokines. Silencing of syntenin using siRNAs led to a decrease in p38 MAPK activation in SARS-CoV infected cells, further reinforcing their functional relationship. Active p38 MAPK was reduced in lungs of mice infected with SARS-CoVs lacking E protein PBM as compared with the parental virus, leading to a decreased expression of inflammatory cytokines and to virus attenuation. Interestingly, administration of a p38 MAPK inhibitor led to an increase in mice survival after infection with SARS-CoV, confirming the relevance of this pathway in SARS-CoV virulence. Therefore, the E protein PBM is a virulence domain that activates immunopathology most likely by using syntenin as a mediator of p38 MAPK induced inflammation. PMID:25122212

  14. Timing of the loss of Pten protein determines disease severity in a mouse model of myeloid malignancy.

    PubMed

    Liu, Y Lucy; Yan, Yan; Webster, Cody; Shao, Lijian; Lensing, Shelly Y; Ni, Hongyu; Feng, Wei; Colorado, Natalia; Pathak, Rupak; Xiang, Zhifu; Hauer-Jensen, Martin; Li, Shaoguang; Zhou, Daohong; Emanuel, Peter D

    2016-04-14

    Juvenile myelomonocytic leukemia (JMML) is an aggressive pediatric mixed myelodysplastic/myeloproliferative neoplasm (MDS/MPN). JMML leukemogenesis is linked to a hyperactivated RAS pathway, with driver mutations in theKRAS,NRAS,NF1,PTPN11, orCBLgenes. Previous murine models demonstrated how those genes contributed to the selective hypersensitivity of JMML cells to granulocyte macrophage-colony-stimulating factor (GM-CSF), a unifying characteristic in the disease. However, it is unclear what causes the early death in children with JMML, because transformation to acute leukemia is rare. Here, we demonstrate that loss of Pten (phosphatase and tensin homolog) protein at postnatal day 8 in mice harboringNf1haploinsufficiency results in an aggressive MPN with death at a murine prepubertal age of 20 to 35 days (equivalent to an early juvenile age in JMML patients). The death in the mice was due to organ infiltration with monocytes/macrophages. There were elevated activities of protein kinase B (Akt) and mitogen-activated protein kinase (MAPK) in cells at physiological concentrations of GM-CSF. These were more pronounced in mice withNf1haploinsufficiency than in littermates with wild-typeNf1,but this model is insufficient to cause cells to be GM-CSF hypersensitive. This new model represents a murine MPN model with features of a pediatric unclassifiable mixed MDS/MPN and mimics many clinical manifestations of JMML in terms of age of onset, aggressiveness, and organ infiltration with monocytes/macrophages. Our data suggest that the timing of the loss of PTEN protein plays a critical role in determining the disease severity in myeloid malignancies. This model may be useful for studying the pathogenesis of pediatric diseases with alterations in the Ras pathway. PMID:26764354

  15. Multivariate Analysis of Genotype-Phenotype Association.

    PubMed

    Mitteroecker, Philipp; Cheverud, James M; Pavlicev, Mihaela

    2016-04-01

    With the advent of modern imaging and measurement technology, complex phenotypes are increasingly represented by large numbers of measurements, which may not bear biological meaning one by one. For such multivariate phenotypes, studying the pairwise associations between all measurements and all alleles is highly inefficient and prevents insight into the genetic pattern underlying the observed phenotypes. We present a new method for identifying patterns of allelic variation (genetic latent variables) that are maximally associated-in terms of effect size-with patterns of phenotypic variation (phenotypic latent variables). This multivariate genotype-phenotype mapping (MGP) separates phenotypic features under strong genetic control from less genetically determined features and thus permits an analysis of the multivariate structure of genotype-phenotype association, including its dimensionality and the clustering of genetic and phenotypic variables within this association. Different variants of MGP maximize different measures of genotype-phenotype association: genetic effect, genetic variance, or heritability. In an application to a mouse sample, scored for 353 SNPs and 11 phenotypic traits, the first dimension of genetic and phenotypic latent variables accounted for >70% of genetic variation present in all 11 measurements; 43% of variation in this phenotypic pattern was explained by the corresponding genetic latent variable. The first three dimensions together sufficed to account for almost 90% of genetic variation in the measurements and for all the interpretable genotype-phenotype association. Each dimension can be tested as a whole against the hypothesis of no association, thereby reducing the number of statistical tests from 7766 to 3-the maximal number of meaningful independent tests. Important alleles can be selected based on their effect size (additive or nonadditive effect on the phenotypic latent variable). This low dimensionality of the genotype-phenotype map

  16. p21-activated kinase 1 determines stem-like phenotype and sunitinib resistance via NF-κB/IL-6 activation in renal cell carcinoma

    PubMed Central

    Zhu, Y; Liu, H; Xu, L; An, H; Liu, W; Liu, Y; Lin, Z; Xu, J

    2015-01-01

    The p21-activated kinase 1 (PAK1), a serine/threonine kinase that orchestrates cytoskeletal remodeling and cell motility, has been shown to function as downstream node for various oncogenic signaling pathways to promote cell proliferation, regulate apoptosis and accelerate mitotic abnormalities, resulting in tumor formation and invasiveness. Although alterations in PAK1 expression and activity have been detected in various human malignancies, its potential biological and clinical significance in renal cell carcinoma (RCC) remains obscure. In this study, we found increased PAK1 and phosphorylated PAK1 levels in tumor tissues according to TNM stage progression. Elevated phosphorylated PAK1 levels associated with progressive features and indicated unfavorable overall survival (OS) as an independent adverse prognosticator for patients with RCC. Moreover, PAK1 kinase activation with constitutive active PAK1 mutant T423E promoted growth, colony formation, migration, invasion and stem-like phenotype of RCC cells, and vice versa, in PAK1 inhibition by PAK1 kinase inactivation with specific PAK1 shRNA, dead kinase PAK1 mutant K299R or allosteric inhibitor IPA3. Stem-like phenotype due to sunitinib administration via increased PAK1 kinase activation could be ameliorated by PAK1 shRNA, PAK1 mutant K299R and IPA3. Furthermore, nuclear factor-κB (NF-κB)/interleukin-6 (IL-6) activation was found to be responsible for PAK1-mediated stem-like phenotype following sunitinib treatment. Both IL-6 neutralizing antibody and IPA3 administration enhanced tumor growth inhibition effect of sunitinib treatment on RCC cells in vitro and in vivo. Our results unraveled that oncogenic activation of PAK1 defines an important mechanism for maintaining stem-like phenotype and sunitinib resistance through NF-κB/IL-6 activation in RCC, lending PAK1-mediated NF-κB/IL-6 activation considerable appeal as novel pharmacological therapeutic targets against sunitinib resistance. PMID:25675297

  17. Cross-Age Peer Tutoring: A Strategy for Promoting Self-Determination in Students with Severe Emotional Disabilities/Behavior Disorders.

    ERIC Educational Resources Information Center

    Miller, Sidney R.; And Others

    1995-01-01

    This article describes a federally funded model self-determination project for students with severe emotional disabilities/behavioral disorders (SED/BD). The project promotes self-determination through instruction in problem solving, self-assertiveness, and self-management skills, and utilizes cross-age peer tutoring involving college students…

  18. Using Norm-Referenced Tests to Determine Severity of Language Impairment in Children: Disconnect between U.S. Policy Makers and Test Developers

    ERIC Educational Resources Information Center

    Spaulding, Tammie J.; Szulga, Margaret Swartwout; Figueroa, Cecilia

    2012-01-01

    Purpose: The purpose of this study was to identify various U.S. state education departments' criteria for determining the severity of language impairment in children, with particular focus on the use of norm-referenced tests. A secondary objective was to determine if norm-referenced tests of child language were developed for the purpose of…

  19. Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

    PubMed Central

    D’Ursi, Pasqualina; Milanesi, Luciano; Di Canito, Alessandra; Zampolli, Jessica; Collina, Elena; Decorosi, Francesca; Viti, Carlo; Fedi, Stefano; Presentato, Alessandro; Zannoni, Davide; Di Gennaro, Patrizia

    2015-01-01

    In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination

  20. Impact of Short Interval SMS Digital Data on Wind Vector Determination for a Severe Local Storms Area

    NASA Technical Reports Server (NTRS)

    Peslen, C. A.

    1979-01-01

    The impact of 5 minute interval SMS-2 visible digital image data in analyzing severe local storms is examined using wind vectors derived from cloud tracking on time lapsed sequence of geosynchronous satellite images. The cloud tracking areas are located in the Central Plains, where on 6 May 1975, hail-producing thunderstorms occurred ahead of a well defined dry line. The results demonstrate that satellite-derived wind vectors and their associated divergence fields complement conventional meteorological analyses in describing the conditions preceding severe local storm development.

  1. Development of a HPLC method for the simultaneous determination of several B-vitamins and ascorbic acid.

    PubMed

    Khor, S; Tee, E S

    1996-03-01

    In cognizance of the difficulties involved in the colorimetric and titrimetric methods for the determination of individual vitamins, this laboratory has been carrying out a series of studies into the use of HPLC for improved analysis of these nutrients. Preliminary studies have been carried out for the determination of four B-vitamins. The present paper reports on further improvements made to enable the simultaneous determination of eight vitamins i.e. B1, B2, B6, B12, C, niacin, niacinamide and folic acid. Trials were carried out to determine the most suitable chromatographic system include changing the proportion of methanol in the mobile phase, the use of different ion-pairing reagents and other additives such as triethylamine and ammonia. Three sets of HPLC mobile phase systems are proposed to enable successful separation of all eight vitamins in less than 20 minutes, varying slightly with the type of ion-pairing reagent and mobile phase additive. This laboratory is currently carrying out trials to determine if the developed methods could be used for the determination of pharmaceutical products and food samples. PMID:22692099

  2. Use of microdose phenotyping to individualise dosing of patients.

    PubMed

    Hohmann, Nicolas; Haefeli, Walter E; Mikus, Gerd

    2015-09-01

    Administering the right amount of the right drug at the right time is a key mission of clinical medicine. This comprises dose adaptation according to a patient's intrinsic and extrinsic factors influencing drug disposition. Several biomarkers are available for dose adaptation; still, prediction of individual drug disposition may be improved. Phenotyping is the quantification of drug metabolism with probe substrates specific to drug-metabolising enzymes. This allows measurement of baseline metabolism and changes after modulation of drug metabolism. This article explores the concept of phenotyping using pharmacologically ineffective microdoses of probe substrates to obtain information on drug metabolism. Several probe drugs such as midazolam for cytochrome P450 3A have already been used, but validation of other microdosed probe drugs, analytical procedures and drug formulations still face some challenges that have to be overcome. Since microdosed probe drugs have no risk of adverse drug reactions or interference with therapy, more widespread use is possible. This allows drug-drug interaction data to be safely obtained during first-in-man studies, enhancing the clinical safety of human healthy volunteers and patients in clinical trials, and, most importantly, allows determination of the drug-metabolising phenotype in severely ill patients. With harmless probe drugs at hand quantifying drug metabolism and adapting the dose accordingly, a phenotyping-based dosing strategy could become reality, offering the possibility of individualised drug therapy with reduced adverse effects and fewer therapeutic failures. PMID:25925712

  3. Effect of chromosome constitution variations on the expression of Turner phenotype.

    PubMed

    Bispo, A V S; Dos Santos, L O; Burégio-Frota, P; Galdino, M B; Duarte, A R; Leal, G F; Araújo, J; Gomes, B; Soares-Ventura, E M; Muniz, M T C; Santos, N

    2013-01-01

    Turner syndrome (TS) is a chronic disease related to haploinsufficiency of genes that are normally expressed in both X chromosomes in patients with female phenotype that is associated with a wide range of somatic malformations. We made detailed cytogenetic and clinical analysis of 65 patients with TS from the region of Recife, Brazil, to determine the effects of different chromosome constitutions on expression of the TS phenotype. Overall, patients with X-monosomy exhibited a tendency to have more severe phenotypes with higher morbidity, showing its importance in TS prognosis. Additionally, we found rare genetic and phenotypic abnormalities associated with this syndrome. To the best of our knowledge, this is the first case of 45,X,t(11;12)(q22;q22) described as a TS karyotype. Turner patients usually have normal intelligence; however, moderate to severe levels of mental retardation were found in 5 TS cases, which is considerate a very uncommon feature in this syndrome. PMID:23546984

  4. Optofluidic Detection for Cellular Phenotyping

    PubMed Central

    Tung, Yi-Chung; Huang, Nien-Tsu; Oh, Bo-Ram; Patra, Bishnubrata; Pan, Chi-Chun; Qiu, Teng; Paul, K. Chu; Zhang, Wenjun; Kurabayashi, Katsuo

    2012-01-01

    Quantitative analysis of the output of processes and molecular interactions within a single cell is highly critical to the advancement of accurate disease screening and personalized medicine. Optical detection is one of the most broadly adapted measurement methods in biological and clinical assays and serves cellular phenotyping. Recently, microfluidics has obtained increasing attention due to several advantages, such as small sample and reagent volumes, very high throughput, and accurate flow control in the spatial and temporal domains. Optofluidics, which is the attempt to integrate optics with microfluidic, shows great promise to enable on-chip phenotypic measurements with high precision, sensitivity, specificity, and simplicity. This paper reviews the most recent developments of optofluidic technologies for cellular phenotyping optical detection. PMID:22854915

  5. The Neuroanatomy of the Autistic Phenotype

    ERIC Educational Resources Information Center

    Fahim, Cherine; Meguid, Nagwa A.; Nashaat, Neveen H.; Yoon, Uicheul; Mancini-Marie, Adham; Evans, Alan C.

    2012-01-01

    The autism phenotype is associated with an excess of brain volume due in part to decreased pruning during development. Here we aimed at assessing brain volume early in development to further elucidate previous findings in autism and determine whether this pattern is restricted to idiopathic autism or shared within the autistic phenotype (fragile X…

  6. Biosensor analysis of blood esterases for organophosphorus compounds exposure assessment: approaches to simultaneous determination of several esterases.

    PubMed

    Sigolaeva, Larisa; Makhaeva, Galina; Rudakova, Elena; Boltneva, Natalia; Porus, Marya; Dubacheva, Galina; Eremenko, Arkadi; Kurochkin, Ilya; Richardson, Rudy J

    2010-09-01

    This paper reviews our previously published data and presents new results on biosensor assay of blood esterases. Tyrosinase and choline oxidase biosensors based on nanostructured polyelectrolyte films were developed for these purposes. Experiments were performed on the quantitative determination of acetylcholinesterase (AChE), butyrylcholinesterase (BChE), carboxylesterase (CaE), and neuropathy target esterase (NTE) in samples of whole blood of rats, mice, and humans. Good agreement was found between biosensor and spectrophotometric assays for AChE, BChE, and CaE. No direct comparison could be made for NTE because its activity cannot be measured spectrophotometrically in whole blood. A new method of simultaneous quantitative determination of AChE and BChE in test mixtures is also described. This method represents a bifunctional biosensor for the simultaneous analysis of choline and phenol based on integration of individual sensors. Algorithms for calculation of separate concentrations of AChE and BChE in the mixture were developed. The mean error of calculated component concentrations was approximately 6% for binary test mixtures. The present work provides a foundation for building multiplexed systems for the simultaneous determination of multiple esterases with applications to biomonitoring for exposures to organophosphorus compounds. PMID:20097186

  7. Comparison of apically extruded debris associated with several nickel-titanium systems after determining working length by apex locator

    PubMed Central

    Çiçek, Ersan; Akkocan, Oguzhan; Furuncuoglu, Fatma

    2016-01-01

    Background/Aim: To compare apically extruded debris using ProTaper Universal (PTU), ProTaper Next (PTN), WaveOne (WO), Twisted File (TF), M-Two (MT), and Revo-S (RS) after determining the working length (WL) with root ZX. Materials and Methods: Seventy-two teeth were selected. The WL determination was performed with root ZX. The teeth were divided into six experimental groups, randomly. In groups, root canals were prepared with PTU to size F4/0.06, with PTN to size X4/0.06, with WO to size 40/0.08, with TF to size 40/0.04, with MT to size 40/0.06, and with RS to size AS40/0.06. After preparations were completed, final irrigation was performed with 2 mL distilled water, and a total of 10 mL of distilled water was used in each tooth. Tubes were stored in an incubator at 68°C for 5 days to evaporate the distilled water before weighing the dry debris. Data were analyzed by the Mann–Whitney U-test. Results: The RS group led to the highest amount of extruded debris, however, WO led to the least amount of extruded debris. There was no statistically difference among the groups (P > 0.05). Conclusions: The authors conclude that the results obtained might depend on the apex locator used to determine the WL. PMID:26957797

  8. The Role of Spleen Stiffness in Determining the Severity and Bleeding Risk of Esophageal Varices in Cirrhotic Patients

    PubMed Central

    Kim, Hwi Young; Jin, Eun Hyo; Kim, Won; Lee, Jae Young; Woo, Hyunsik; Oh, Sohee; Seo, Ji-Yeon; Oh, Hong Sang; Chung, Kwang Hyun; Jung, Yong Jin; Kim, Donghee; Kim, Byeong Gwan; Lee, Kook Lae

    2015-01-01

    Abstract Esophageal varix and its hemorrhage are serious complications of liver cirrhosis. Recent studies have focused on noninvasive prediction of esophageal varices. We attempted to evaluate the association of liver and spleen stiffness (LS and SS) as measured by acoustic radiation force impulse imaging, with the presence and severity of esophageal varices and variceal hemorrhage in cirrhotic patients. We measured LS and SS, along with endoscopic examination of esophageal varices for a total of 125 cirrhotic patients at a single referral hospital in this prospective observational study. The diagnostic utility of noninvasive methods for identifying varices and their bleeding risk was compared, including LS, SS, spleen length, Child-Pugh score, and various serum fibrosis indices. Esophageal varices were present in 77 patients (61.6%). SS was significantly higher in patients with varices than in those without varices (3.58 ± 0.47 vs 3.02 ± 0.49; P < 0.001). A tendency toward increasing SS levels was observed with increasing severity of varices (no varix, 3.02 ± 0.49; F1, 3.39 ± 0.51; F2, 3.60 ± 0.42; F3, 3.85 ± 0.37; P < 0.001). SS was significantly higher in patients who experienced variceal hemorrhage than in those who did not (3.80 ± 0.36 vs 3.20 ± 0.51; P = 0.002). An optimal cut-off value of SS for high-risk varices (≥F2) or variceal hemorrhage was 3.40 m/s. SS was significantly correlated with the presence, severity, and bleeding risk of esophageal varices. Prompt endoscopic evaluation of variceal status and prophylactic measures based on the SS may be warranted for cirrhotic patients. PMID:26091449

  9. Determination of mercury by cold-vapor technique in several tissues of treated American red crayfish (Procambarus clarkii)

    SciTech Connect

    Del Ramo, J.; Pastor, A.; Diaz-Mayans, J.; Medina, J.; Torreblanca, A.

    1988-01-01

    Adult intermolt specimens of American red crayfish (Procambarus clarkii) collected from Lake Albufera (Valencia, Spain), were exposed to mercury during 96 h. The Hg-concentrations used were 50, 100, and 250 ..mu..g Hg/l as Cl/sub 2/Hg. The content of mercury in muscle, midgut gland, antennal glands and gills was investigated. Determinations of mercury were made by cold-vapor technique and AAS. The mercury levels in all examined tissues increased significantly with increasing Hg-concentration in the water.

  10. Liquid chromatographic-mass spectrometric method for simultaneous determination of small organic acids potentially contributing to acidosis in severe malaria.

    PubMed

    Sriboonvorakul, Natthida; Leepipatpiboon, Natchanun; Dondorp, Arjen M; Pouplin, Thomas; White, Nicholas J; Tarning, Joel; Lindegardh, Niklas

    2013-12-15

    Acidosis is an important cause of mortality in severe falciparum malaria. Lactic acid is a major contributor to metabolic acidosis, but accounts for only one-quarter of the strong anion gap. Other unidentified organic acids have an independent strong prognostic significance for a fatal outcome. In this study, a simultaneous bio-analytical method for qualitative and quantitative assessment in plasma and urine of eight small organic acids potentially contributing to acidosis in severe malaria was developed and validated. High-throughput strong anion exchange solid-phase extraction in a 96-well plate format was used for sample preparation. Hydrophilic interaction liquid chromatography (HILIC) coupled to negative mass spectroscopy was utilized for separation and detection. Eight possible small organic acids; l-lactic acid (LA), α-hydroxybutyric acid (aHBA), β-hydroxybutyric acid (bHBA), p-hydroxyphenyllactic acid (pHPLA), malonic acid (MA), methylmalonic acid (MMA), ethylmalonic acid (EMA) and α-ketoglutaric acid (aKGA) were analyzed simultaneously using a ZIC-HILIC column with an isocratic elution containing acetonitrile and ammonium acetate buffer. This method was validated according to U.S. Food and Drug Administration guidelines with additional validation procedures for endogenous substances. Accuracy for all eight acids ranged from 93.1% to 104.0%, and the within-day and between-day precisions (i.e. relative standard deviations) were lower than 5.5% at all tested concentrations. The calibration ranges were: 2.5-2500μg/mL for LA, 0.125-125μg/mL for aHBA, 7.5-375μg/mL for bHBA, 0.1-100μg/mL for pHPLA, 1-1000μg/mL for MA, 0.25-250μg/mL for MMA, 0.25-100μg/mL for EMA, and 30-1500μg/mL for aKGA. Clinical applicability was demonstrated by analyzing plasma and urine samples from five patients with severe falciparum malaria; five acids had increased concentrations in plasma (range LA=177-1169μg/mL, aHBA=4.70-38.4μg/mL, bHBA=7.70-38.0μg/mL, pHPLA=0.900-4.30

  11. Liquid chromatographic–mass spectrometric method for simultaneous determination of small organic acids potentially contributing to acidosis in severe malaria☆

    PubMed Central

    Sriboonvorakul, Natthida; Leepipatpiboon, Natchanun; Dondorp, Arjen M.; Pouplin, Thomas; White, Nicholas J.; Tarning, Joel; Lindegardh, Niklas

    2013-01-01

    Acidosis is an important cause of mortality in severe falciparum malaria. Lactic acid is a major contributor to metabolic acidosis, but accounts for only one-quarter of the strong anion gap. Other unidentified organic acids have an independent strong prognostic significance for a fatal outcome. In this study, a simultaneous bio-analytical method for qualitative and quantitative assessment in plasma and urine of eight small organic acids potentially contributing to acidosis in severe malaria was developed and validated. High-throughput strong anion exchange solid-phase extraction in a 96-well plate format was used for sample preparation. Hydrophilic interaction liquid chromatography (HILIC) coupled to negative mass spectroscopy was utilized for separation and detection. Eight possible small organic acids; l-lactic acid (LA), α-hydroxybutyric acid (aHBA), β-hydroxybutyric acid (bHBA), p-hydroxyphenyllactic acid (pHPLA), malonic acid (MA), methylmalonic acid (MMA), ethylmalonic acid (EMA) and α-ketoglutaric acid (aKGA) were analyzed simultaneously using a ZIC-HILIC column with an isocratic elution containing acetonitrile and ammonium acetate buffer. This method was validated according to U.S. Food and Drug Administration guidelines with additional validation procedures for endogenous substances. Accuracy for all eight acids ranged from 93.1% to 104.0%, and the within-day and between-day precisions (i.e. relative standard deviations) were lower than 5.5% at all tested concentrations. The calibration ranges were: 2.5–2500 μg/mL for LA, 0.125–125 μg/mL for aHBA, 7.5–375 μg/mL for bHBA, 0.1–100 μg/mL for pHPLA, 1–1000 μg/mL for MA, 0.25–250 μg/mL for MMA, 0.25–100 μg/mL for EMA, and 30–1500 μg/mL for aKGA. Clinical applicability was demonstrated by analyzing plasma and urine samples from five patients with severe falciparum malaria; five acids had increased concentrations in plasma (range LA = 177–1169 μg/mL, aHBA = 4.70–38.4

  12. Molecular determinants of severe acute respiratory syndrome coronavirus pathogenesis and virulence in young and aged mouse models of human disease.

    PubMed

    Frieman, Matthew; Yount, Boyd; Agnihothram, Sudhakar; Page, Carly; Donaldson, Eric; Roberts, Anjeanette; Vogel, Leatrice; Woodruff, Becky; Scorpio, Diana; Subbarao, Kanta; Baric, Ralph S

    2012-01-01

    SARS coronavirus (SARS-CoV) causes severe acute respiratory tract disease characterized by diffuse alveolar damage and hyaline membrane formation. This pathology often progresses to acute respiratory distress (such as acute respiratory distress syndrome [ARDS]) and atypical pneumonia in humans, with characteristic age-related mortality rates approaching 50% or more in immunosenescent populations. The molecular basis for the extreme virulence of SARS-CoV remains elusive. Since young and aged (1-year-old) mice do not develop severe clinical disease following infection with wild-type SARS-CoV, a mouse-adapted strain of SARS-CoV (called MA15) was developed and was shown to cause lethal infection in these animals. To understand the genetic contributions to the increased pathogenesis of MA15 in rodents, we used reverse genetics and evaluated the virulence of panels of derivative viruses encoding various combinations of mouse-adapted mutations. We found that mutations in the viral spike (S) glycoprotein and, to a much less rigorous extent, in the nsp9 nonstructural protein, were primarily associated with the acquisition of virulence in young animals. The mutations in S likely increase recognition of the mouse angiotensin-converting enzyme 2 (ACE2) receptor not only in MA15 but also in two additional, independently isolated mouse-adapted SARS-CoVs. In contrast to the findings for young animals, mutations to revert to the wild-type sequence in nsp9 and the S glycoprotein were not sufficient to significantly attenuate the virus compared to other combinations of mouse-adapted mutations in 12-month-old mice. This panel of SARS-CoVs provides novel reagents that we have used to further our understanding of differential, age-related pathogenic mechanisms in mouse models of human disease. PMID:22072787

  13. Molecular Determinants of Severe Acute Respiratory Syndrome Coronavirus Pathogenesis and Virulence in Young and Aged Mouse Models of Human Disease

    PubMed Central

    Yount, Boyd; Agnihothram, Sudhakar; Page, Carly; Donaldson, Eric; Roberts, Anjeanette; Vogel, Leatrice; Woodruff, Becky; Scorpio, Diana; Subbarao, Kanta; Baric, Ralph S.

    2012-01-01

    SARS coronavirus (SARS-CoV) causes severe acute respiratory tract disease characterized by diffuse alveolar damage and hyaline membrane formation. This pathology often progresses to acute respiratory distress (such as acute respiratory distress syndrome [ARDS]) and atypical pneumonia in humans, with characteristic age-related mortality rates approaching 50% or more in immunosenescent populations. The molecular basis for the extreme virulence of SARS-CoV remains elusive. Since young and aged (1-year-old) mice do not develop severe clinical disease following infection with wild-type SARS-CoV, a mouse-adapted strain of SARS-CoV (called MA15) was developed and was shown to cause lethal infection in these animals. To understand the genetic contributions to the increased pathogenesis of MA15 in rodents, we used reverse genetics and evaluated the virulence of panels of derivative viruses encoding various combinations of mouse-adapted mutations. We found that mutations in the viral spike (S) glycoprotein and, to a much less rigorous extent, in the nsp9 nonstructural protein, were primarily associated with the acquisition of virulence in young animals. The mutations in S likely increase recognition of the mouse angiotensin-converting enzyme 2 (ACE2) receptor not only in MA15 but also in two additional, independently isolated mouse-adapted SARS-CoVs. In contrast to the findings for young animals, mutations to revert to the wild-type sequence in nsp9 and the S glycoprotein were not sufficient to significantly attenuate the virus compared to other combinations of mouse-adapted mutations in 12-month-old mice. This panel of SARS-CoVs provides novel reagents that we have used to further our understanding of differential, age-related pathogenic mechanisms in mouse models of human disease. PMID:22072787

  14. Determination of mineralogy and grain size of the magnetic fraction from outdoor and indoor urban dust from several Bulgarian cities

    NASA Astrophysics Data System (ADS)

    Petrov, Petar; Jordanova, Neli; Jordanova, Diana

    2014-05-01

    Dust is the most important factor determining urban air quality. The identification of magnetic minerals, carriers of magnetic signal of dust samples, is important for a correct interpretation of concentration, domain state and grain-size indicative parameters. The aim of the present study is to characterize magnetically indoor and outdoor dusts from six big cities in Bulgaria and to link them to degree of pollution of the environment. The aim is also to propose the most effective methods for characterization: thermomagnetic analysis of magnetic susceptibility, anhysteretic remanent magnetization (ARM), isothermal remanent magnetization (IRM), hysteresis loops. Dust material was collected monthly during the period May 2009- November 2010. The main magnetic mineral in outdoor and indoor dust, identified by thermomagnetic analysis of magnetic susceptibility, is magnetite (Fe3O4). The dominant role of magnetite in determination of magnetic signal of the studied dusts allows the use of hysteresis parameters as proxies for the effective magnetic grain size of ferrimagnetic grains. The calculated ratios Mrs/Ms and Bcr/Bc vary in the intervals (0.055 - 0.1) and (3.08 - 5.14), respectively. The coercivity of magnetic fraction in indoor dust is lower compared to that of outdoor dust. This dependence probably shows that the main source of dust is the outside pollution with PM10. Higher values typical for outdoor dust in comparison with respective sample from indoor dust show that quantity of the paramagnetic minerals is higher in outdoor dust. Probable source of such particles is dust from erosion of soils in the area.

  15. THE COMPARISON OF SEVERAL STANDARD MATERIALS AND TECHNIQUES FOR THE WARREN-AVERBACH DETERMINATION OF MICRO-STRUCTURE CHARACTERISTICS OF CALCIUM HYDROXIDE SORBENT MATERIALS

    EPA Science Inventory

    The paper gives results of a comparison of several standard materials and techniques for the Warren-Averbach determination of microstructure characteristics of calcium hydroxide--Ca(OH)2--sorbent materials. The comparison is part of an investigation of the injection of dry Ca(OH)...

  16. End-of-Life Discussion, Patient Understanding and Determinants of Preferences in Very Severe COPD Patients: A Multicentric Study.

    PubMed

    Carlucci, Annalisa; Vitacca, Michele; Malovini, Alberto; Pierucci, Paola; Guerrieri, Aldo; Barbano, Luca; Ceriana, Piero; Balestrino, Antonella; Santoro, Carmen; Pisani, Lara; Corcione, Nadia; Nava, Stefano

    2016-10-01

    Discussion about patients' end-of-life (E-o-L) preferences should be part of the routine practice. Using a semi-structured interview with a scenario-based decision, we performed a prospective multicentre study to elicit the patients' E-o-L preferences in very severe chronic obstructive pulmonary disease (COPD). We also checked their ability to retain this information and the respect of their decisions when they die. Forty-three out of ninety-one of the eligible patients completed the study. The choice of E-o-L practice was equally distributed among the three proposed options: endotracheal intubation (ETI), 'ceiling' non-invasive ventilation (NIV), and palliation of symptoms with oxygen and morphine. NIV and ETI were more frequently chosen by patients who already experienced them. ETI preference was also associated with the use of anti-depressant drugs and a low educational level, while a higher educational level and a previous discussion with a pneumologist significantly correlated with the preference for oxygen and morphine. Less than 50% of the patients retained a full comprehension of the options at 24 hours. About half of the patients who died in the follow-up period were not treated according to their wishes. In conclusion, in end-stage COPD more efforts are needed to improve communication, patients' knowledge of the disease and E-o-L practice. PMID:27027671

  17. Genetic Factors in Systemic Lupus Erythematosus: Contribution to Disease Phenotype

    PubMed Central

    Ceccarelli, Fulvia; Perricone, Carlo; Borgiani, Paola; Ciccacci, Cinzia; Rufini, Sara; Cipriano, Enrica; Alessandri, Cristiano; Spinelli, Francesca Romana; Sili Scavalli, Antonio; Novelli, Giuseppe; Valesini, Guido; Conti, Fabrizio

    2015-01-01

    Genetic factors exert an important role in determining Systemic Lupus Erythematosus (SLE) susceptibility, interplaying with environmental factors. Several genetic studies in various SLE populations have identified numerous susceptibility loci. From a clinical point of view, SLE is characterized by a great heterogeneity in terms of clinical and laboratory manifestations. As widely demonstrated, specific laboratory features are associated with clinical disease subset, with different severity degree. Similarly, in the last years, an association between specific phenotypes and genetic variants has been identified, allowing the possibility to elucidate different mechanisms and pathways accountable for disease manifestations. However, except for Lupus Nephritis (LN), no studies have been designed to identify the genetic variants associated with the development of different phenotypes. In this review, we will report data currently known about this specific association. PMID:26798662

  18. Evaluation of severe accident risks: Quantification of major input parameters. Experts` determination of source term issues: Volume 2, Revision 1, Part 4

    SciTech Connect

    Harper, F.T.; Breeding, R.J.; Brown, T.D.; Gregory, J.J.; Jow, H.N.; Payne, A.C.; Gorham, E.D.; Amos, C.N.; Helton, J.; Boyd, G.

    1992-06-01

    In support of the Nuclear Regulatory Commission`s (NRC`s) assessment of the risk from severe accidents at commercial nuclear power plants in the US reported in NUREG-1150, the Severe Accident Risk Reduction Program (SAARP) has completed a revised calculation of the risk to the general public from severe accidents at five nuclear power plants: Surry, Sequoyah, Zion, Peach Bottom and Grand Gulf. The emphasis in this risk analysis was not on determining a point estimate of risk, but to determine the distribution of risk, and to assess the uncertainties that account for the breadth of this distribution. Off-site risk initiation by events, both internal to the power station and external to the power station. Much of this important input to the logic models was generated by expert panels. This document presents the distributions and the rationale supporting the distributions for the questions posed to the Source Term Panel.

  19. Understanding COPD: A vision on phenotypes, comorbidities and treatment approach.

    PubMed

    Fragoso, E; André, S; Boleo-Tomé, J P; Areias, V; Munhá, J; Cardoso, J

    2016-01-01

    Chronic Obstructive Pulmonary Disease (COPD) phenotypes have become increasingly recognized as important for grouping patients with similar presentation and/or behavior, within the heterogeneity of the disease. The primary aim of identifying phenotypes is to provide patients with the best health care possible, tailoring the therapeutic approach to each patient. However, the identification of specific phenotypes has been hindered by several factors such as which specific attributes are relevant, which discriminant features should be used for assigning patients to specific phenotypes, and how relevant are they to the therapeutic approach, prognostic and clinical outcome. Moreover, the definition of phenotype is still not consensual. Comorbidities, risk factors, modifiable risk factors and disease severity, although not phenotypes, have impact across all COPD phenotypes. Although there are some identified phenotypes that are fairly consensual, many others have been proposed, but currently lack validation. The on-going debate about which instruments and tests should be used in the identification and definition of phenotypes has contributed to this uncertainty. In this paper, the authors review present knowledge regarding COPD phenotyping, discuss the role of phenotypes and comorbidities on the severity of COPD, propose new phenotypes and suggest a phenotype-based pharmacological therapeutic approach. The authors conclude that a patient-tailored treatment approach, which takes into account each patient's specific attributes and specificities, should be pursued. PMID:26827246

  20. Renal 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase Is an Important Determinant of AKI Severity after Ischemia-Reperfusion.

    PubMed

    Jackson, Edwin K; Menshikova, Elizabeth V; Mi, Zaichuan; Verrier, Jonathan D; Bansal, Rashmi; Janesko-Feldman, Keri; Jackson, Travis C; Kochanek, Patrick M

    2016-07-01

    A positional isomer of 3',5'-cAMP, 2',3'-cAMP, is produced by kidneys in response to energy depletion, and renal 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) metabolizes 2',3'-cAMP to 2'-AMP; 2',3'-cAMP is a potent opener of mitochondrial permeability transition pores (mPTPs), which can stimulate autophagy. Because autophagy protects against AKI, it is conceivable that inhibition of CNPase protects against ischemia-reperfusion (IR) -induced AKI. Therefore, we investigated renal outcomes, mitochondrial function, number, area, and autophagy in CNPase-knockout (CNPase(-/-)) versus wild-type (WT) mice using a unique two-kidney, hanging-weight model of renal bilateral IR (20 minutes of ischemia followed by 48 hours of reperfusion). Analysis of urinary purines showed attenuated metabolism of 2',3'-cAMP to 2'-AMP in CNPase(-/-) mice. Neither genotype nor IR affected BP, heart rate, urine volume, or albumin excretion. In WT mice, renal IR reduced (14)C-inulin clearance (index of GFR) and increased renal vascular resistance (measured by transit time nanoprobes) and urinary excretion of kidney injury molecule-1 and neutrophil gelatinase-associated lipocalin. IR did not affect these parameters in CNPase(-/-) mice. Histologic analysis revealed that IR induced severe damage in kidneys from WT mice, whereas histologic changes were minimal after IR in CNPase(-/-) mice. Measurements of renal cardiolipin levels, citrate synthase activity, rotenone-sensitive NADH oxidase activity, and proximal tubular mitochondrial and autophagosome area and number (by transmission electron microscopy) indicted accelerated autophagy/mitophagy in injured CNPase(-/-) mice. We conclude that CNPase deletion attenuates IR-induced AKI, in part by accelerating autophagy with targeted removal of damaged mitochondria. PMID:26574047

  1. MRI Based Preterm White Matter Injury Classification: The Importance of Sequential Imaging in Determining Severity of Injury

    PubMed Central

    Martinez-Biarge, Miriam; Groenendaal, Floris; Kersbergen, Karina J.; Benders, Manon J. N. L.; Foti, Francesca; Cowan, Frances M.; de Vries, Linda S.

    2016-01-01

    Background The evolution of non-hemorrhagic white matter injury (WMI) based on sequential magnetic resonance imaging (MRI) has not been well studied. Our aim was to describe sequential MRI findings in preterm infants with non-hemorrhagic WMI and to develop an MRI classification system for preterm WMI based on these findings. Methods Eighty-two preterm infants (gestation ≤35 weeks) were retrospectively included. WMI was diagnosed and classified based on sequential cranial ultrasound (cUS) and confirmed on MRI. Results 138 MRIs were obtained at three time-points: early (<2 weeks; n = 32), mid (2–6 weeks; n = 30) and term equivalent age (TEA; n = 76). 63 infants (77%) had 2 MRIs during the neonatal period. WMI was non-cystic in 35 and cystic in 47 infants. In infants with cystic-WMI early MRI showed extensive restricted diffusion abnormalities, cysts were already present in 3 infants; mid MRI showed focal or extensive cysts, without acute diffusion changes. A significant reduction in the size and/or extent of the cysts was observed in 32% of the infants between early/mid and TEA MRI. In 4/9 infants previously seen focal cysts were no longer identified at TEA. All infants with cystic WMI showed ≥2 additional findings at TEA: significant reduction in WM volume, mild-moderate irregular ventriculomegaly, several areas of increased signal intensity on T1-weighted-images, abnormal myelination of the PLIC, small thalami. Conclusion In infants with extensive WM cysts at 2–6 weeks, cysts may be reduced in number or may even no longer be seen at TEA. A single MRI at TEA, without taking sequential cUS data and pre-TEA MRI findings into account, may underestimate the extent of WMI; based on these results we propose a new MRI classification for preterm non-hemorrhagic WMI. PMID:27257863

  2. Comparison of several analytical methods for the determination of tin in geochemical samples as a function of tin speciation

    USGS Publications Warehouse

    Kane, J.S.; Evans, J.R.; Jackson, J.C.

    1989-01-01

    Accurate and precise determinations of tin in geological materials are needed for fundamental studies of tin geochemistry, and for tin prospecting purposes. Achieving the required accuracy is difficult because of the different matrices in which Sn can occur (i.e. sulfides, silicates and cassiterite), and because of the variability of literature values for Sn concentrations in geochemical reference materials. We have evaluated three methods for the analysis of samples for Sn concentration: graphite furnace atomic absorption spectrometry (HGA-AAS) following iodide extraction, inductively coupled plasma atomic emission spectrometry (ICP-OES), and energy-dispersive X-ray fluorescence (EDXRF) spectrometry. Two of these methods (HGA-AAS and ICP-OES) required sample decomposition either by acid digestion or fusion, while the third (EDXRF) was performed directly on the powdered sample. Analytical details of all three methods, their potential errors, and the steps necessary to correct these errors were investigated. Results showed that similar accuracy was achieved from all methods for unmineralized samples, which contain no known Sn-bearing phase. For mineralized samples, which contain Sn-bearing minerals, either cassiterite or stannous sulfides, only EDXRF and fusion ICP-OES methods provided acceptable accuracy. This summary of our study provides information which helps to assure correct interpretation of data bases for underlying geochemical processes, regardless of method of data collection and its inherent limitations. ?? 1989.

  3. Spectrophotometric methods manipulating ratio spectra for simultaneous determination of binary mixtures with sever overlapping spectra: A comparative study

    NASA Astrophysics Data System (ADS)

    Moustafa, H.; Fayez, Y.

    2014-12-01

    Three simple, specific and accurate spectrophotometric methods manipulating ratio spectra were developed and validated for simultaneous determination of Rabeprazole sodium (RB) and Domperidone (DP) in their binary mixture without prior separation. Method A, is constant center spectrophotometric method (CC). Method B is a ratio difference spectrophotometric one (RD), while method C is a combined ratio isoabsorptive point-ratio difference method (RIRD). Linear correlations were obtained in range of 4-44 μg/mL for both Rabeprazole sodium and Domperidone. The mean percentage recoveries of RB were 99.69 ± 0.504 for method A, 99.83 ± 0.483 for (B) and 100.31 ± 0.499 for (C), respectively, and that of DP were 99.52 ± 0.474 for method A, 100.12 ± 0.505 for (B) and 100.16 ± 0.498 for (C), respectively. Specificity was investigated by analysis of laboratory prepared mixtures containing the cited drugs and their combined tablet dosage form. The obtained results were statistically compared with those obtained by the reported methods, showing no significant difference with respect to accuracy and precision. The three methods were validated as per ICH guidelines and can be applied for routine analysis in quality control laboratories.

  4. Dynamic regulation of cardiolipin by the lipid pump Atp8b1 determines the severity of lung injury in experimental pneumonia.

    PubMed

    Ray, Nancy B; Durairaj, Lakshmi; Chen, Bill B; McVerry, Bryan J; Ryan, Alan J; Donahoe, Michael; Waltenbaugh, Alisa K; O'Donnell, Christopher P; Henderson, Florita C; Etscheidt, Christopher A; McCoy, Diann M; Agassandian, Marianna; Hayes-Rowan, Emily C; Coon, Tiffany A; Butler, Phillip L; Gakhar, Lokesh; Mathur, Satya N; Sieren, Jessica C; Tyurina, Yulia Y; Kagan, Valerian E; McLennan, Geoffrey; Mallampalli, Rama K

    2010-10-01

    Pneumonia remains the leading cause of death from infection in the US, yet fundamentally new conceptual models underlying its pathogenesis have not emerged. We show that humans and mice with bacterial pneumonia have markedly elevated amounts of cardiolipin, a rare, mitochondrial-specific phospholipid, in lung fluid and find that it potently disrupts surfactant function. Intratracheal cardiolipin administration in mice recapitulates the clinical phenotype of pneumonia, including impaired lung mechanics, modulation of cell survival and cytokine networks and lung consolidation. We have identified and characterized the activity of a unique cardiolipin transporter, the P-type ATPase transmembrane lipid pump Atp8b1, a mutant version of which is associated with severe pneumonia in humans and mice. Atp8b1 bound and internalized cardiolipin from extracellular fluid via a basic residue-enriched motif. Administration of a peptide encompassing the cardiolipin binding motif or Atp8b1 gene transfer in mice lessened bacteria-induced lung injury and improved survival. The results unveil a new paradigm whereby Atp8b1 is a cardiolipin importer whose capacity to remove cardiolipin from lung fluid is exceeded during inflammation or when Atp8b1 is defective. This discovery opens the door for new therapeutic strategies directed at modulating the abundance or molecular interactions of cardiolipin in pneumonia. PMID:20852622

  5. Using Phenotype MicroArrays to Determine Culture Conditions That Induce or Repress Toxin Production by Clostridium difficile and Other Microorganisms

    PubMed Central

    Lei, Xiang-He; Bochner, Barry R.

    2013-01-01

    Toxin production is a central issue in the pathogenesis of Clostridium difficile and many other pathogenic microorganisms. Toxin synthesis is influenced by a variety of known and unknown factors of genetics, physiology, and environment. To facilitate the study of toxin production by C. difficile, we have developed a new, reliable, quantitative, and robust cell-based cytotoxicity assay. Then we combined this new assay with Phenotype MicroArrays (PM) technology which provides high throughput testing of culture conditions. This allowed us to quantitatively measure toxin production by C. difficile type strain ATCC 9689 under 768 culture conditions. The culture conditions include different carbon, nitrogen, phosphorus, and sulfur sources. Among these, 89 conditions produced strong toxin induction and 31 produced strong toxin repression. Strong toxin inducers included adenine, guanosine, arginine dipeptides, γ-D-Glu-Gly, methylamine, and others. Some leucine dipeptides and the triple-leucine tripeptide were among the strongest toxin repressors. While some results are consistent with previous observations, others are new observations that provide insights into toxin regulation and pathogenesis of C. difficile. Additionally, we have demonstrated that this combined assay technology can be applied broadly to a wide range of toxin producing microorganisms. This study is the first demonstration of simultaneous assessment of a large number of culture conditions influencing bacterial toxin production. The new functional cytotoxin quantitation method developed provides a valuable tool for studying toxigenic microorganisms and may also find applications in clinical and epidemiological research. PMID:23437164

  6. Comparison of virulence plasmid (pYV/pCD)-associated phenotypes in Yersinia species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotypic expression of several virulence plasmid (pYV/pCD; 70-kb)-associated genetic determinants were compared among Yesinia species; Yesinia pestis, (an attenuated strain which does not cause plague designated to be used in BSL2 facility), Y. pseudotuberculosis and Y. enterocolitica including lo...

  7. Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ontology engineering and knowledge modeling for the plant sciences is expected to contribute to the understanding of the basis of plant traits that determine phenotypic expression in a given environment. Several crop- or clade-specific plant trait ontologies have been developed to describe plant tr...

  8. Binding of radioiodinated human. beta. -endorphin to serum proteins from rats and humans, determined by several methods

    SciTech Connect

    Sato, H.; Sugiyama, Y.; Sawada, Y.; Iga, T.; Hanano, M.

    1985-10-07

    Binding of immunoreactive radioiodinated human ..beta..-endorphin (/sup 125/I-..beta..-EP) to rat serum was demonstrated by gel filtration of /sup 125/I-..beta..-EP in pooled rat serum on Sephadex G-200. Two radioactive peaks associated with proteins eluted from the column. The first peak eluted at the void volume containing lipoproteins, ..cap alpha../sub 2/- and ..beta../sub 2/-macroglobulins, and the second peak at the fraction of albumin. Binding of /sup 125/I-..beta..-EP to albumin was directly proved by gel filtration of /sup 125/I-..beta..-EP in buffer containing 4% human serum albumin on Sephadex G-200. Equilibrium dialysis was not applicable to investigating the interaction of /sup 125/I-..beta..-EP with serum proteins, because of the intense nonspecific adsorption to the semi-permeable membrane and the degradation of the peptide during dialysis. Therefore, in order to quantitatively evaluate the binding of /sup 125/I-..beta..-EP in sera from rats and humans, the authors utilized four other methods (ultrafiltration, charcoal adsorption, polyethylene glycol precipitation and equilibrium gel filtration). These methods corresponded well with each other and indicated 35-44% binding of /sup 125/I-..beta..-EP in rat serum. Binding of /sup 125/I-..beta..-EP in normal human serum was 36%, determined by ultrafiltration. Serum protein binding of /sup 125/I-..beta..-EP was concentration independent over the concentration range studied (1-1000 nM). 23 references, 4 figures, 1 table.

  9. Phenotypic heterogeneity of Streptococcus mutans in dentin.

    PubMed

    Rupf, S; Hannig, M; Breitung, K; Schellenberger, W; Eschrich, K; Remmerbach, T; Kneist, S

    2008-12-01

    Information concerning phenotypic heterogeneity of Streptococcus mutans in carious dentin is sparse. Matrix-assisted laser-desorption/ionization-time-of-flight mass-spectrometry (MALDI-TOF-MS) facilitates the phenotypic differentiation of bacteria to the subspecies level. To verify a supposed influence of restorative treatment on the phenotypic heterogeneity of S. mutans, we isolated and compared a total of 222 S. mutans strains from dentin samples of 21 human deciduous molars during caries excavation (T(1)) and 8 wks (T(2)) after removal of the temporary restoration. Phenotypic heterogeneity was determined by MALDI-TOF-MS and hierarchical clustering. Thirty-six distinct S. mutans phenotypes could be identified. Although indistinguishable phenotypes were found in the same teeth at T(1) and T(2), as well as in different teeth of individual participants, the phenotypic heterogeneity increased significantly, from 1.4 phenotypes per S. mutans-positive dentin sample at T(1) to 2.2 phenotypes at T(2). We attribute this to an adaptation of S. mutans to the modified environment under the restoration following caries excavation. PMID:19029088

  10. Acetylator phenotypes in Papua New Guinea

    PubMed Central

    Penketh, R J A; Gibney, S F A; Nurse, G T; Hopkinson, D A

    1983-01-01

    Acetylator phenotypes have been determined in 139 unrelated subjects from the hitherto untested populations of Papua New Guinea, and their relevance to current antituberculous isoniazid chemotherapy is discussed. PMID:6842533

  11. Primary oocyte transcriptional activation of aqp1ab by the nuclear progestin receptor determines the pelagic egg phenotype of marine teleosts.

    PubMed

    Zapater, Cinta; Chauvigné, François; Tingaud-Sequeira, Angèle; Finn, Roderick Nigel; Cerdà, Joan

    2013-05-15

    In marine teleosts, the aqp1ab water channel plays a vital role in the development of the pelagic egg phenotype. However, the developmental control of aqp1ab activation during oogenesis remains to be established. Here, we report the isolation of the 5'-flanking region of the teleost gilthead seabream aqp1ab gene, in which we identify conserved cis-regulatory elements for the binding of the nuclear progestin receptor (Pgr) and members of the Sox family of transcription factors. Subcellular localization studies indicated that the Pgr, as well as sox3 and -8b transcripts, are co-expressed in seabream oogonia, whereas in meiosis-arrested primary growth (pre-vitellogenic) oocytes, when aqp1ab mRNA and protein are first synthesized, the Pgr appears to be completely translocated from the ooplasm into the nucleus. By contrast, sox9b is highly expressed in more advanced oocytes, coinciding with a strong depletion of aqp1ab transcripts in the oocyte. Functional characterization of wild-type and mutated aqp1ab promoter constructs, using mammalian cells and Xenopus laevis oocytes, demonstrated that aqp1ab transcription is initiated by the Pgr, which is activated by the progestin 17α,20β-dihydroxy-4-pregnen-3-one (17,20β-P), the natural ligand of the seabream Pgr. In vitro incubation of seabream primary ovarian explants with the follicle-stimulating hormone or 17,20β-P confirmed that progestin-activated Pgr enhanced Aqp1ab synthesis via the aqp1ab promoter. However, transactivation assays in heterologous systems showed that Sox transcription factors can potentially modulate this mechanism. These data uncover the existence of an endocrine pathway involved in the early activation of a water channel necessary for egg formation in marine teleosts. PMID:23499660

  12. Influence of different susceptibility testing methods and media on determination of the relevant fluconazole minimum inhibitory concentrations for heavy trailing Candida isolates with low-high phenotype.

    PubMed

    Alp, Sehnaz; Sancak, Banu; Hascelik, Gulsen; Arikan, Sevtap

    2010-11-01

    We investigated the incidence of trailing growth with fluconazole in 101 clinical Candida isolates (49 C. albicans and 52 C. tropicalis) and tried to establish the convenient susceptibility testing method and medium for fluconazole minimum inhibitory concentration (MIC) determination. MICs were determined by CLSI M27-A2 broth microdilution (BMD) and Etest methods on RPMI-1640 agar supplemented with 2% glucose (RPG) and on Mueller-Hinton agar supplemented with 2% glucose and 0.5 μg ml(-1) methylene blue (GMB). BMD and Etest MICs were read at 24 and 48 h, and susceptibility categories were compared. All isolates were determined as susceptible with BMD, Etest-RPG and Etest-GMB at 24 h. While all isolates were interpreted as susceptible at 48 h on Etest-RPG and Etest-GMB, one C. albicans isolate was interpreted as susceptible-dose dependent (S-DD) and two C. tropicalis isolates were interpreted as resistant with BMD. On Etest-RPG, trailing growth caused widespread microcolonies within the inhibition zone and resulted in confusion in MIC determination. On Etest-GMB, because of the nearly absence of microcolonies within the zone of inhibition, MICs were evaluated more easily. We conclude that, for the determination of fluconazole MICs of trailing Candida isolates, the Etest method has an advantage over BMD and can be used along with this reference method. Moreover, GMB appears more beneficial than RPG for the fluconazole Etest. PMID:19563491

  13. Emerging semantics to link phenotype and environment

    PubMed Central

    Bunker, Daniel E.; Buttigieg, Pier Luigi; Cooper, Laurel D.; Dahdul, Wasila M.; Domisch, Sami; Franz, Nico M.; Jaiswal, Pankaj; Lawrence-Dill, Carolyn J.; Midford, Peter E.; Mungall, Christopher J.; Ramírez, Martín J.; Specht, Chelsea D.; Vogt, Lars; Vos, Rutger Aldo; Walls, Ramona L.; White, Jeffrey W.; Zhang, Guanyang; Deans, Andrew R.; Huala, Eva; Lewis, Suzanna E.; Mabee, Paula M.

    2015-01-01

    Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments. PMID:26713234

  14. Emerging semantics to link phenotype and environment

    SciTech Connect

    Thessen, Anne E.; Bunker, Daniel E.; Buttigieg, Pier Luigi; Cooper, Laurel D.; Dahdul, Wasila M.; Domisch, Sami; Franz, Nico M.; Jaiswal, Pankaj; Lawrence-Dill, Carolyn J.; Midford, Peter E.; Mungall, Christopher J.; Ramirez, Martin J.; Specht, Chelsea D.; Vogt, Lars; Vos, Rutger Aldo; Walls, Ramona L.; White, Jeffrey W.; Zhang, Guanyang; Deans, Andrew R.; Huala, Eva; Lewis, Suzanna E.; Mabee, Paula M.

    2015-12-14

    Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. Lastly, in this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.

  15. Emerging semantics to link phenotype and environment

    DOE PAGESBeta

    Thessen, Anne E.; Bunker, Daniel E.; Buttigieg, Pier Luigi; Cooper, Laurel D.; Dahdul, Wasila M.; Domisch, Sami; Franz, Nico M.; Jaiswal, Pankaj; Lawrence-Dill, Carolyn J.; Midford, Peter E.; et al

    2015-12-14

    Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies aremore » well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. Lastly, in this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.« less

  16. Emerging semantics to link phenotype and environment.

    PubMed

    Thessen, Anne E; Bunker, Daniel E; Buttigieg, Pier Luigi; Cooper, Laurel D; Dahdul, Wasila M; Domisch, Sami; Franz, Nico M; Jaiswal, Pankaj; Lawrence-Dill, Carolyn J; Midford, Peter E; Mungall, Christopher J; Ramírez, Martín J; Specht, Chelsea D; Vogt, Lars; Vos, Rutger Aldo; Walls, Ramona L; White, Jeffrey W; Zhang, Guanyang; Deans, Andrew R; Huala, Eva; Lewis, Suzanna E; Mabee, Paula M

    2015-01-01

    Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments. PMID:26713234

  17. Phenotype Standardization for Statin-Induced Myotoxicity

    PubMed Central

    Alfirevic, A; Neely, D; Armitage, J; Chinoy, H; Cooper, R G; Laaksonen, R; Carr, D F; Bloch, K M; Fahy, J; Hanson, A; Yue, Q-Y; Wadelius, M; Maitland-van Der Zee, A H; Voora, D; Psaty, B M; Palmer, C N A; Pirmohamed, M

    2014-01-01

    Statins are widely used lipid-lowering drugs that are effective in reducing cardiovascular disease risk. Although they are generally well tolerated, they can cause muscle toxicity, which can lead to severe rhabdomyolysis. Research in this area has been hampered to some extent by the lack of standardized nomenclature and phenotypic definitions. We have used numerical and descriptive classifications and developed an algorithm to define statin-related myotoxicity phenotypes, including myalgia, myopathy, rhabdomyolysis, and necrotizing autoimmune myopathy. PMID:24897241

  18. Phenotypic Screens in Antimalarial Drug Discovery.

    PubMed

    Hovlid, Marisa L; Winzeler, Elizabeth A

    2016-09-01

    Phenotypic high-throughput screens are a valuable tool for identifying new chemical compounds with antimalarial activity. Traditionally, these screens have focused solely on the symptomatic asexual blood stage of the parasite life cycle; however, to discover new medicines for malaria treatment and prevention, robust screening technologies against other parasite life-cycle stages are required. This review highlights recent advances and progress toward phenotypic screening methodologies over the past several years, with a focus on exoerythrocytic stage screens. PMID:27247245

  19. In search of the perfect phenotype: an analysis of linkage and association studies of reading and reading-related processes.

    PubMed

    Skiba, Thomas; Landi, Nicole; Wagner, Richard; Grigorenko, Elena L

    2011-01-01

    Reading ability and specific reading disability (SRD) are complex traits involving several cognitive processes and are shaped by a complex interplay of genetic and environmental forces. Linkage studies of these traits have identified several susceptibility loci. Association studies have gone further in detecting candidate genes that might underlie these signals. These results have been obtained in samples of mainly European ancestry, which vary in their languages, inclusion criteria, and phenotype assessments. Such phenotypic heterogeneity across samples makes understanding the relationship between reading (dis)ability and reading-related processes and the genetic factors difficult; in addition, it may negatively influence attempts at replication. In moving forward, the identification of preferable phenotypes for future sample collection may improve the replicability of findings. This review of all published linkage and association results from the past 15 years was conducted to determine if certain phenotypes produce more replicable and consistent results than others. PMID:21243420

  20. Adaptive evolution of molecular phenotypes

    NASA Astrophysics Data System (ADS)

    Held, Torsten; Nourmohammad, Armita; Lässig, Michael

    2014-09-01

    Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.

  1. Discordant clinical phenotype in monozygotic twins with Alagille syndrome: Possible influence of non-genetic factors.

    PubMed

    Izumi, Kosuke; Hayashi, Daisuke; Grochowski, Christopher M; Kubota, Noriko; Nishi, Eriko; Arakawa, Michiko; Hiroma, Takehiko; Hatata, Tomoko; Ogiso, Yoshifumi; Nakamura, Tomohiko; Falsey, Alexandra M; Hidaka, Eiko; Spinner, Nancy B

    2016-02-01

    Alagille syndrome is a multisystem developmental disorder characterized by bile duct paucity, congenital heart disease, vertebral anomalies, posterior embryotoxon, and characteristic facial features. Alagille syndrome is typically the result of germline mutations in JAG1 or NOTCH2 and is one of several human diseases caused by Notch signaling abnormalities. A wide phenotypic spectrum has been well documented in Alagille syndrome. Therefore, monozygotic twins with Alagille syndrome provide a unique opportunity to evaluate potential phenotypic modifiers such as environmental factors or stochastic effects of gene expression. In this report, we describe an Alagille syndrome monozygotic twin pair with discordant placental and clinical findings. We propose that environmental factors such as prenatal hypoxia may have played a role in determining the phenotypic severity. PMID:26463753

  2. A method for analysis of phenotypic change for phenotypes described by high-dimensional data.

    PubMed

    Collyer, M L; Sekora, D J; Adams, D C

    2015-10-01

    The analysis of phenotypic change is important for several evolutionary biology disciplines, including phenotypic plasticity, evolutionary developmental biology, morphological evolution, physiological evolution, evolutionary ecology and behavioral evolution. It is common for researchers in these disciplines to work with multivariate phenotypic data. When phenotypic variables exceed the number of research subjects--data called 'high-dimensional data'--researchers are confronted with analytical challenges. Parametric tests that require high observation to variable ratios present a paradox for researchers, as eliminating variables potentially reduces effect sizes for comparative analyses, yet test statistics require more observations than variables. This problem is exacerbated with data that describe 'multidimensional' phenotypes, whereby a description of phenotype requires high-dimensional data. For example, landmark-based geometric morphometric data use the Cartesian coordinates of (potentially) many anatomical landmarks to describe organismal shape. Collectively such shape variables describe organism shape, although the analysis of each variable, independently, offers little benefit for addressing biological questions. Here we present a nonparametric method of evaluating effect size that is not constrained by the number of phenotypic variables, and motivate its use with example analyses of phenotypic change using geometric morphometric data. Our examples contrast different characterizations of body shape for a desert fish species, associated with measuring and comparing sexual dimorphism between two populations. We demonstrate that using more phenotypic variables can increase effect sizes, and allow for stronger inferences. PMID:25204302

  3. Identification and Severity Determination of Wheat Stripe Rust and Wheat Leaf Rust Based on Hyperspectral Data Acquired Using a Black-Paper-Based Measuring Method.

    PubMed

    Wang, Hui; Qin, Feng; Ruan, Liu; Wang, Rui; Liu, Qi; Ma, Zhanhong; Li, Xiaolong; Cheng, Pei; Wang, Haiguang

    2016-01-01

    It is important to implement detection and assessment of plant diseases based on remotely sensed data for disease monitoring and control. Hyperspectral data of healthy leaves, leaves in incubation period and leaves in diseased period of wheat stripe rust and wheat leaf rust were collected under in-field conditions using a black-paper-based measuring method developed in this study. After data preprocessing, the models to identify the diseases were built using distinguished partial least squares (DPLS) and support vector machine (SVM), and the disease severity inversion models of stripe rust and the disease severity inversion models of leaf rust were built using quantitative partial least squares (QPLS) and support vector regression (SVR). All the models were validated by using leave-one-out cross validation and external validation. The diseases could be discriminated using both distinguished partial least squares and support vector machine with the accuracies of more than 99%. For each wheat rust, disease severity levels were accurately retrieved using both the optimal QPLS models and the optimal SVR models with the coefficients of determination (R2) of more than 0.90 and the root mean square errors (RMSE) of less than 0.15. The results demonstrated that identification and severity evaluation of stripe rust and leaf rust at the leaf level could be implemented based on the hyperspectral data acquired using the developed method. A scientific basis was provided for implementing disease monitoring by using aerial and space remote sensing technologies. PMID:27128464

  4. Identification and Severity Determination of Wheat Stripe Rust and Wheat Leaf Rust Based on Hyperspectral Data Acquired Using a Black-Paper-Based Measuring Method

    PubMed Central

    Ruan, Liu; Wang, Rui; Liu, Qi; Ma, Zhanhong; Li, Xiaolong; Cheng, Pei; Wang, Haiguang

    2016-01-01

    It is important to implement detection and assessment of plant diseases based on remotely sensed data for disease monitoring and control. Hyperspectral data of healthy leaves, leaves in incubation period and leaves in diseased period of wheat stripe rust and wheat leaf rust were collected under in-field conditions using a black-paper-based measuring method developed in this study. After data preprocessing, the models to identify the diseases were built using distinguished partial least squares (DPLS) and support vector machine (SVM), and the disease severity inversion models of stripe rust and the disease severity inversion models of leaf rust were built using quantitative partial least squares (QPLS) and support vector regression (SVR). All the models were validated by using leave-one-out cross validation and external validation. The diseases could be discriminated using both distinguished partial least squares and support vector machine with the accuracies of more than 99%. For each wheat rust, disease severity levels were accurately retrieved using both the optimal QPLS models and the optimal SVR models with the coefficients of determination (R2) of more than 0.90 and the root mean square errors (RMSE) of less than 0.15. The results demonstrated that identification and severity evaluation of stripe rust and leaf rust at the leaf level could be implemented based on the hyperspectral data acquired using the developed method. A scientific basis was provided for implementing disease monitoring by using aerial and space remote sensing technologies. PMID:27128464

  5. Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination1[W][OPEN

    PubMed Central

    Sekhon, Rajandeep S.; Hirsch, Candice N.; Childs, Kevin L.; Breitzman, Matthew W.; Kell, Paul; Duvick, Susan; Spalding, Edgar P.; Buell, C. Robin; de Leon, Natalia; Kaeppler, Shawn M.

    2014-01-01

    Seed size is a component of grain yield and an important trait in crop domestication. To understand the mechanisms governing seed size in maize (Zea mays), we examined transcriptional and developmental changes during seed development in populations divergently selected for large and small seed size from Krug, a yellow dent maize cultivar. After 30 cycles of selection, seeds of the large seed population (KLS30) have a 4.7-fold greater weight and a 2.6-fold larger size compared with the small seed population (KSS30). Patterns of seed weight accumulation from the time of pollination through 30 d of grain filling showed an earlier onset, slower rate, and earlier termination of grain filling in KSS30 relative to KLS30. This was further supported by transcriptome patterns in seeds from the populations and derived inbreds. Although the onset of key genes was earlier in small seeds, similar maximum transcription levels were observed in large seeds at later stages, suggesting that functionally weaker alleles, rather than transcript abundance, may be the basis of the slow rate of seed filling in KSS30. Gene coexpression networks identified several known genes controlling cellularization and proliferation as well as novel genes that will be useful candidates for biotechnological approaches aimed at altering seed size in maize and other cereals. PMID:24710068

  6. TLR2, TLR4 and Dectin-1 signalling in hematopoietic stem and progenitor cells determines the antifungal phenotype of the macrophages they produce.

    PubMed

    Megías, Javier; Martínez, Alba; Yáñez, Alberto; Goodridge, Helen S; Gozalbo, Daniel; Gil, M Luisa

    2016-05-01

    TLRs represent an attractive target for the stimulation of myeloid cell production by HSPCs. We have previously demonstrated that HSPCs use TLR2 to sense Candida albicans in vivo and induce the production of macrophages. In this work, we used an in vitro model of HSPCs differentiation to investigate the functional consequences for macrophages of exposure of HSPCs to various PAMPs and C. albicans cells. Mouse HSPCs (Lin(-) cells) were cultured with M-CSF to induce macrophage differentiation, in the presence or absence of the following PRR agonists: Pam3CSK4 (TLR2 ligand), LPS (TLR4 ligand), depleted zymosan (which only activates Dectin-1), or C. albicans yeasts (which activate several PRRs, but principally TLR2 and Dectin-1). Our data show that these PAMPs differentially impact the anti-microbial function of the macrophages produced by the exposed HSPCs. Pure TLR2 and TLR4 ligands generate macrophages with a diminished ability to produce inflammatory cytokines. In contrast, HSPCs activation in response to C. albicans leads to the generation of macrophages that are better prepared to deal with the infection, as they produce higher amounts of inflammatory cytokines and have higher fungicidal capacity than control macrophages. Therefore, the tailored manipulation of the differentiation process may help to boost the innate immune response to infection. PMID:26828664

  7. [MORPHOLOGICAL CRITERIA OF THE ENTERAL INSUFFICIENCE SEVERITY IN A DIFFUSE PERITONITIS FOR DETERMINATION OF A SUBSEQUENT TACTICS OF THE PATIENTS TREATMENT].

    PubMed

    Ioffe, I V; Lesnoy, V V

    2016-03-01

    The results of treatment of 87 patients for diffuse peritonitis (DP) were analyzed, in whom the enteral insufficiency (El) was estimated. The small intestine biopsies for morphological investigations were taken during its resection performance on the border between the pathologically changed and intact wall. Comparative morphometric analysis of destructive and inflammatory processes in a small intestine was conducted for establishment of morphological criteria for the EI prognosis in a DP. Morphological criteria of the EI severity were established for determination of a subsequent tactics for the patients' treatment and prognosis. PMID:27514089

  8. Heterogeneity of Severe Asthma in Childhood: Confirmation by Cluster Analysis of Children in the NIH/NHLBI Severe Asthma Research Program (SARP)

    PubMed Central

    Fitzpatrick, Anne M.; Teague, W. Gerald; Meyers, Deborah A.; Peters, Stephen P.; Li, Xingnan; Li, Huashi; Wenzel, Sally E.; Aujla, Shean; Castro, Mario; Bacharier, Leonard B.; Gaston, Benjamin M.; Bleecker, Eugene R.; Moore, Wendy C.

    2011-01-01

    Background Asthma in children is a heterogeneous disorder with many phenotypes. Although unsupervised cluster analysis is a useful tool for identifying phenotypes, it has not been applied to school-age children with persistent asthma across a wide range of severities. Objectives This study determined how children with severe asthma are distributed across a cluster analysis and how well these clusters conform to current definitions of asthma severity. Methods Cluster analysis was applied to 12 continuous and composite variables from 161 children at 5 centers enrolled in the Severe Asthma Research Program (SARP). Results Four clusters of asthma were identified. Children in Cluster 1 (n = 48) had relatively normal lung function and less atopy, while children in Cluster 2 (n = 52) had slightly lower lung function, more atopy, and increased symptoms and medication usage. Cluster 3 (n = 32) had greater co-morbidity, increased bronchial responsiveness and lower lung function. Cluster 4 (n = 29) had the lowest lung function and the greatest symptoms and medication usage. Predictors of cluster assignment were asthma duration, the number of asthma controller medications, and baseline lung function. Children with severe asthma were present in all clusters, and no cluster corresponded to definitions of asthma severity provided in asthma treatment guidelines. Conclusions Severe asthma in children is highly heterogeneous. Unique phenotypic clusters previously identified in adults can also be identified in children, but with important differences. Larger validation and longitudinal studies are needed to determine the baseline and predictive validity of these phenotypic clusters in the larger clinical setting. PMID:21195471

  9. Influence of severe combined immunodeficiency phenotype on the outcome of HLA non-identical, T-cell-depleted bone marrow transplantation: a retrospective European survey from the European group for bone marrow transplantation and the european society for immunodeficiency.

    PubMed

    Bertrand, Y; Landais, P; Friedrich, W; Gerritsen, B; Morgan, G; Fasth, A; Cavazzana-Calvo, M; Porta, F; Cant, A; Espanol, T; Müller, S; Veys, P; Vossen, J; Haddad, E; Fischer, A

    1999-06-01

    We analyzed the outcomes of 214 HLA non-identical T-cell-depleted bone marrow transplantations (BMTs), performed in 178 consecutive patients for treatment of severe combined immunodeficiencies (SCID). Patients were treated in 18 European centers between 1981 and March 1995. SCID variants, that is, absence of T and B lymphocytes (B-) or absence of T cells with presence of B lymphocytes (B+) were found to have a major influence on outcome. The disease-free survival was significantly better for patients with B+ SCID (60%) as compared with patients with B- SCID (35%) (P =.002), with a median follow-up of 57 months and 52 months, respectively. Other factors associated with a poor prognosis were the presence of a lung infection before BMT (odds ratio = 2.47 [1.99-2.94]) and the use of monoclonal antibodies for T-cell depletion of the graft (odds ratio = 1.67 [1. 18-2.15]). Additional factors influencing outcome were age at BMT (<6 months) and period during which BMT was performed. Better results were achieved after 1991. Reduced survival of patients with B- SCID was associated with a higher incidence of early deaths from infection, a diminished rate of marrow engraftment, a trend to a higher incidence of chronic graft-versus-host disease, and slower kinetics of T/B immune function development. In both groups of patients, the use of busulfan (8 mg/kg total dose) and cyclophosphamide (200 mg/kg total dose) as a conditioning regimen provided the best cure rate (74% for patients with B+ SCID and 43% for patients with B- SCID, respectively), although results were not statistically significantly different from other regimens. This retrospective analysis should lead to the design of adapted measures to the performance of HLA non-identical BMT in patients with distinct SCID conditions. PMID:10356144

  10. Determination of midazolam and its metabolite as a probe for cytochrome P450 3A4 phenotype by liquid chromatography-mass spectrometry.

    PubMed

    Kanazawa, Hideko; Okada, Akiko; Igarashi, Eri; Higaki, Megumu; Miyabe, Takako; Sano, Tadashi; Nishimura, Ryouhei

    2004-03-26

    This study demonstrated the analysis of midazolam and its metabolites by liquid chromatography-mass spectrometry (LC-MS) with a sonic spray ionization (SSI) interface. The analytical column was a YMC-Pak Pro C18 (50 mm x 2.0 mm i.d.) using 10 mM ammonium acetate (pH 4.8)-methanol (1:1) at a flow rate of 0.2 ml min(-1). The drift voltage was 100 V. The sampling aperture was heated at 110 degrees C and the shield temperature was 230 degrees C. The lower limits for the detection of midazolam and 1'-hydroxymidazolam were 26.3 and 112.76 pg injected, respectively. The calibration curves for midazolam and 1'-hydroxymidazolam were linear in the range of 0.1-5 microg ml(-1). Within-day relative standard deviations was less than 7%. The method was applied to the determination of midazolam in monkey plasma, and the analysis of midazolam and its metabolites in an in vitro study with recombinant cytochrome P450 (CYP) 3A4. This method is sufficiently sensitive and useful to elucidate the kinetics of midazolam metabolite formation. We also investigated the effect of propofol on the metabolism of midazolam using recombinant CYP3A4. Propofol competitively inhibited the metabolism of midazolam to 1'-hydroxymidazolam by CYP3A4. PMID:15058585

  11. Normal phenotype with paternal uniparental isodisomy for chromosome 21

    SciTech Connect

    Blouin, J.L.; Avramopoulos, D. ); Pangalos, C.; Antonarakis, S.E.

    1993-11-01

    Uniparental disomy (UPD) involving several different chromosomes has been described in several cases of human pathologies. In order to investigate whether UPD for chromosome 21 is associated with abnormal phenotypes, the authors analyzed DNA polymorphisms in DNA from a family with de novo Robertsonian translocation t(21q;21q). The proband was a healthy male with 45 dup(21q) who was ascertained through his trisomy 21 offspring. No phenotypic abnormalities were noted in the physical exam, and his past medical history was unremarkable. The authors obtained genotypes for the proband and his parents' leukocyte DNAs from 17 highly informative short sequence repeat polymorphisms that map in the pericentromeric region and along the entire length of 21q. The order of the markers has been previously determined through the linkage and physical maps of this chromosome. For the nine informative markers there was no maternal allele contribution to the genotype of the proband; in addition, there was always reduction to homozygosity of a paternal allele. These data indicated that there was paternal uniparental isodisomy for chromosome 21 (pUPiD21). The authors conclude that pUPiD21 is not associated with abnormal phenotypes and that there are probably no imprinted genes on chromosome 21. 36 refs., 3 figs.

  12. Phenotype profile of a genetic mouse model for Muenke syndrome

    PubMed Central

    Koyama, Eiki; Agochukwu, Nneamaka B.; Bartlett, Scott P.; Muenke, Maximilian

    2014-01-01

    Purpose The Muenke syndrome mutation (FGFR3P250R), which was discovered 15 years ago, represents the single most common craniosynostosis mutation. Muenke syndrome is characterized by coronal suture synostosis, mid-face hypoplasia, subtle limb anomalies, and hearing loss. However, the spectrum of clinical presentation continues to expand. To better understand the pathophysiology of the Muenke syndrome, we present collective findings from several recent studies that have characterized a genetically equivalent mouse model for Muenke syndrome (FgfR3P244R) and compare them with human phenotypes. Conclusions FgfR3P244R mutant mice show premature fusion of facial sutures, premaxillary and/or zygomatic sutures, but rarely the coronal suture. The mice also lack the typical limb phenotype. On the other hand, the mutant mice display maxillary retrusion in association with a shortening of the anterior cranial base and a premature closure of intersphenoidal and spheno-occipital synchondroses, resembling human midface hypoplasia. In addition, sensorineural hearing loss is detected in all FgfR3P244R mutant mice as in the majority of Muenke syndrome patients. It is caused by a defect in the mechanism of cell fate determination in the organ of Corti. The mice also express phenotypes that have not been previously described in humans, such as reduced cortical bone thickness, hypoplastic trabecular bone, and defective temporomandibular joint structure. Therefore, the FgfR3P244R mouse provides an excellent opportunity to study disease mechanisms of some classical phenotypes of Muenke syndrome and to test novel therapeutic strategies. The mouse model can also be further explored to discover previously unreported yet potentially significant phenotypes of Muenke syndrome. PMID:22872265

  13. Phenotypes of childhood asthma: are they real?

    PubMed

    Spycher, B D; Silverman, M; Kuehni, C E

    2010-08-01

    It has been suggested that there are several distinct phenotypes of childhood asthma or childhood wheezing. Here, we review the research relating to these phenotypes, with a focus on the methods used to define and validate them. Childhood wheezing disorders manifest themselves in a range of observable (phenotypic) features such as lung function, bronchial responsiveness, atopy and a highly variable time course (prognosis). The underlying causes are not sufficiently understood to define disease entities based on aetiology. Nevertheless, there is a need for a classification that would (i) facilitate research into aetiology and pathophysiology, (ii) allow targeted treatment and preventive measures and (iii) improve the prediction of long-term outcome. Classical attempts to define phenotypes have been one-dimensional, relying on few or single features such as triggers (exclusive viral wheeze vs. multiple trigger wheeze) or time course (early transient wheeze, persistent and late onset wheeze). These definitions are simple but essentially subjective. Recently, a multi-dimensional approach has been adopted. This approach is based on a wide range of features and relies on multivariate methods such as cluster or latent class analysis. Phenotypes identified in this manner are more complex but arguably more objective. Although phenotypes have an undisputed standing in current research on childhood asthma and wheezing, there is confusion about the meaning of the term 'phenotype' causing much circular debate. If phenotypes are meant to represent 'real' underlying disease entities rather than superficial features, there is a need for validation and harmonization of definitions. The multi-dimensional approach allows validation by replication across different populations and may contribute to a more reliable classification of childhood wheezing disorders and to improved precision of research relying on phenotype recognition, particularly in genetics. Ultimately, the underlying

  14. How Variability in Clinical Phenotypes Should Guide Research into Disease Mechanisms in Asthma

    PubMed Central

    Adcock, Ian M.

    2013-01-01

    Asthma is increasingly being considered as a collection of different phenotypes that present with intermittent wheezing. Unbiased approaches to classifying asthma have led to the identification of distinct phenotypes based on age of onset of disease, atopic state, disease severity or activity, degree of chronic airflow obstruction, and sputum eosinophilia. Linking phenotypes to known disease mechanism is likely to be more fruitful in determining the potential targets necessary for successful therapies of specific endotypes. A “Th2-high expression” signature from the epithelium of patients with asthma identifies a subset of patients with high eosinophilia and good therapeutic responsiveness to corticosteroids. Other characteristic traits of asthma include noneosinophilic asthma, corticosteroid insensitivity, obesity-associated, and exacerbation-prone. Further progress into asthma mechanisms will be driven by unbiased data integration of multiscale data sets from omics technologies with those phenotypic characteristics and by using mathematical modeling. This will lead to the discovery of new pathways and their integration into endotypes and also set up further hypothesis-driven research. Continued iteration through experimentation or modeling will be needed to refine the phenotypes that relate to outcomes and also delineate specific treatments for specific phenotypes. PMID:24313760

  15. Statistical models for trisomic phenotypes

    SciTech Connect

    Lamb, N.E.; Sherman, S.L.; Feingold, E.

    1996-01-01

    Certain genetic disorders are rare in the general population but more common in individuals with specific trisomies, which suggests that the genes involved in the etiology of these disorders may be located on the trisomic chromosome. As with all aneuploid syndromes, however, a considerable degree of variation exists within each phenotype so that any given trait is present only among a subset of the trisomic population. We have previously presented a simple gene-dosage model to explain this phenotypic variation and developed a strategy to map genes for such traits. The mapping strategy does not depend on the simple model but works in theory under any model that predicts that affected individuals have an increased likelihood of disomic homozygosity at the trait locus. This paper explores the robustness of our mapping method by investigating what kinds of models give an expected increase in disomic homozygosity. We describe a number of basic statistical models for trisomic phenotypes. Some of these are logical extensions of standard models for disomic phenotypes, and some are more specific to trisomy. Where possible, we discuss genetic mechanisms applicable to each model. We investigate which models and which parameter values give an expected increase in disomic homozygosity in individuals with the trait. Finally, we determine the sample sizes required to identify the increased disomic homozygosity under each model. Most of the models we explore yield detectable increases in disomic homozygosity for some reasonable range of parameter values, usually corresponding to smaller trait frequencies. It therefore appears that our mapping method should be effective for a wide variety of moderately infrequent traits, even though the exact mode of inheritance is unlikely to be known. 21 refs., 8 figs., 1 tab.

  16. DETECTION OF YERSINIA PESTIS BY COMPARISON OF VIRULENCE PLASMID (PYV/PCD)-ASSOCIATED PHENOTYPES IN YERSINIA SPECIES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotypic expression of several virulence plasmid (pYV/pCD; 70-kb)-associated genetic determinants including low calcium response (Lcr; pin point colony, size= 0.36 mm), colony morphology (size= 1.13 mm), crystal violet (CV) binding (dark-violet colony), Congo Red (CR) uptake (red pin point colony;...

  17. Mutations in CEP120 cause Joubert syndrome as well as complex ciliopathy phenotypes

    PubMed Central

    Romani, Marta; Isrie, Mala; Rosti, Rasim Ozgur; Micalizzi, Alessia; Musaev, Damir; Mazza, Tommaso; Al-gazali, Lihadh; Altunoglu, Umut; Boltshauser, Eugen; D'Arrigo, Stefano; De Keersmaecker, Bart; Kayserili, Hülya; Brandenberger, Sarah; Kraoua, Ichraf; Mark, Paul R; McKanna, Trudy; Van Keirsbilck, Joachim; Moerman, Philippe; Poretti, Andrea; Puri, Ratna; Van Esch, Hilde; Gleeson, Joseph G; Valente, Enza Maria

    2016-01-01

    Background Ciliopathies are an extensive group of autosomal recessive or X-linked disorders with considerable genetic and clinical overlap, which collectively share multiple organ involvement and may result in lethal or viable phenotypes. In large numbers of cases the genetic defect remains yet to be determined. The aim of this study is to describe the mutational frequency and phenotypic spectrum of the CEP120 gene. Methods Exome sequencing was performed in 145 patients with Joubert syndrome (JS), including 15 children with oral-facial-digital syndrome type VI (OFDVI) and 21 Meckel syndrome (MKS) fetuses. Moreover, exome sequencing was performed in one fetus with tectocerebellar dysraphia with occipital encephalocele (TCDOE), molar tooth sign and additional skeletal abnormalities. As a parallel study, 346 probands with a phenotype consistent with JS or related ciliopathies underwent next-generation sequencing-based targeted sequencing of 120 previously described and candidate ciliopathy genes. Results We present six probands carrying nine distinct mutations (of which eight are novel) in the CEP120 gene, previously found mutated only in Jeune asphyxiating thoracic dystrophy (JATD). The CEP120-associated phenotype ranges from mild classical JS in four patients to more severe conditions in two fetuses, with overlapping features of distinct ciliopathies that include TCDOE, MKS, JATD and OFD syndromes. No obvious correlation is evident between the type or location of identified mutations and the ciliopathy phenotype. Conclusion Our findings broaden the spectrum of phenotypes caused by CEP120 mutations that account for nearly 1% of patients with JS as well as for more complex ciliopathy phenotypes. The lack of clear genotype–phenotype correlation highlights the relevance of comprehensive genetic analyses in the diagnostics of ciliopathies. PMID:27208211

  18. Significance of Lewis phenotyping using saliva and gastric tissue: comparison with the Lewis phenotype inferred from Lewis and secretor genotypes.

    PubMed

    Hong, Yun Ji; Hwang, Sang Mee; Kim, Taek Soo; Song, Eun Young; Park, Kyoung Un; Song, Junghan; Han, Kyou-Sup

    2014-01-01

    Lewis phenotypes using various types of specimen were compared with the Lewis phenotype predicted from Lewis and Secretor genotypes. This is the first logical step in explaining the association between the Lewis expression and Helicobacter pylori. We performed a study of the followings on 209 patients who underwent routine gastroscopy: erythrocyte and saliva Lewis phenotyping, gastric Lewis phenotyping by the tissue array, and the Lewis and Secretor genes genotyping. The results of phenotyping were as follows [Le(a-b-), Le(a+b-), Le(a-b+), and Le(a+b+), respectively, in order]: erythrocyte (12.4%, 25.8%, 61.2%, and 0.5%); saliva (2.4%, 27.3%, 70.3%, and 0.0%); gastric mucosa (8.1%, 6.7%, 45.5%, and 39.7%). The frequency of Le, le (59/508) , le (59/1067) , and le (59) alleles was 74.6%, 21.3%, 3.1%, and 1.0%, respectively, among 418 alleles. The saliva Lewis phenotype was completely consistent with the Lewis phenotype inferred from Lewis and Secretor genotypes, but that of gastric mucosa could not be predicted from genotypes. Lewis phenotyping using erythrocytes is only adequate for transfusion needs. Saliva testing for the Lewis phenotype is a more reliable method for determining the peripheral Lewis phenotype of an individual and the gastric Lewis phenotype must be used for the study on the association between Helicobacter pylori and the Lewis phenotype. PMID:24783214

  19. First insights into the genotype–phenotype map of phenotypic stability in rye

    PubMed Central

    Wang, Yu; Mette, Michael Florian; Miedaner, Thomas; Wilde, Peer; Reif, Jochen C.; Zhao, Yusheng

    2015-01-01

    Improving phenotypic stability of crops is pivotal for coping with the detrimental impacts of climate change. The goal of this study was to gain first insights into the genetic architecture of phenotypic stability in cereals. To this end, we determined grain yield, thousand kernel weight, test weight, falling number, and both protein and soluble pentosan content for two large bi-parental rye populations connected through one common parent and grown in multi-environmental field trials involving more than 15 000 yield plots. Based on these extensive phenotypic data, we calculated parameters for static and dynamic phenotypic stability of the different traits and applied linkage mapping using whole-genome molecular marker profiles. While we observed an absence of large-effect quantitative trait loci (QTLs) underlying yield stability, large and stable QTLs were found for phenotypic stability of test weight, soluble pentosan content, and falling number. Applying genome-wide selection, which in contrast to marker-assisted selection also takes into account loci with small-effect sizes, considerably increased the accuracy of prediction of phenotypic stability for all traits by exploiting both genetic relatedness and linkage between single-nucleotide polymorphisms and QTLs. We conclude that breeding for crop phenotypic stability can be improved in related populations using genomic selection approaches established upon extensive phenotypic data. PMID:25873667

  20. Molecular definition of deletions of different segments of distal 5p that result in distinct phenotypic features

    SciTech Connect

    Church, D.M.; Bengtsson, U.; Wasmuth, J.J.; Niebuhr, E.

    1995-05-01

    Cri du chat syndrome (CDC) is a segmental aneusomy associated with deletions of chromosome 5p15. In an effort to define regions that produce the phenotypes associated with CDC, we have analyzed deletions from 17 patients. The majority of these patients had atypical CDC features or were asymptomatic. Using these patients, we have mapped several phenotypes associated with deletions of 5p, including speech delay, catlike cry, newborn facial dysmorphism, and adult facial dysmorphism. This phenotypic map should provide a framework with which to begin identification of genes associated with various phenotypic features associated with deletions of distal 5p. We have also analyzed the parental origin of the de novo deletions, to determine if genomic imprinting could be occurring in this region. In addition, we have isolated cosmids that could be useful for both prenatal and postnatal assessments of del5(p) individuals. 25 refs., 4 figs., 3 tabs.

  1. Geographically multifarious phenotypic divergence during speciation

    PubMed Central

    Gompert, Zachariah; Lucas, Lauren K; Nice, Chris C; Fordyce, James A; Alex Buerkle, C; Forister, Matthew L

    2013-01-01

    Speciation is an important evolutionary process that occurs when barriers to gene flow evolve between previously panmictic populations. Although individual barriers to gene flow have been studied extensively, we know relatively little regarding the number of barriers that isolate species or whether these barriers are polymorphic within species. Herein, we use a series of field and lab experiments to quantify phenotypic divergence and identify possible barriers to gene flow between the butterfly species Lycaeides idas and Lycaeides melissa. We found evidence that L. idas and L. melissa have diverged along multiple phenotypic axes. Specifically, we identified major phenotypic differences in female oviposition preference and diapause initiation, and more moderate divergence in mate preference. Multiple phenotypic differences might operate as barriers to gene flow, as shown by correlations between genetic distance and phenotypic divergence and patterns of phenotypic variation in admixed Lycaeides populations. Although some of these traits differed primarily between species (e.g., diapause initiation), several traits also varied among conspecific populations (e.g., male mate preference and oviposition preference). PMID:23532669

  2. FYPO: the fission yeast phenotype ontology

    PubMed Central

    Harris, Midori A.; Lock, Antonia; Bähler, Jürg; Oliver, Stephen G.; Wood, Valerie

    2013-01-01

    Motivation: To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast. Results: The fission yeast phenotype ontology (FYPO) is a modular ontology that uses several existing ontologies from the open biological and biomedical ontologies (OBO) collection as building blocks, including the phenotypic quality ontology PATO, the Gene Ontology and Chemical Entities of Biological Interest. Modular ontology development facilitates partially automated effective organization of detailed phenotype descriptions with complex relationships to each other and to underlying biological phenomena. As a result, FYPO supports sophisticated querying, computational analysis and comparison between different experiments and even between species. Availability: FYPO releases are available from the Subversion repository at the PomBase SourceForge project page (https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/). The current version of FYPO is also available on the OBO Foundry Web site (http://obofoundry.org/). Contact: mah79@cam.ac.uk or vw253@cam.ac.uk PMID:23658422

  3. Metabolic phenotype of bladder cancer.

    PubMed

    Massari, Francesco; Ciccarese, Chiara; Santoni, Matteo; Iacovelli, Roberto; Mazzucchelli, Roberta; Piva, Francesco; Scarpelli, Marina; Berardi, Rossana; Tortora, Giampaolo; Lopez-Beltran, Antonio; Cheng, Liang; Montironi, Rodolfo

    2016-04-01

    Metabolism of bladder cancer represents a key issue for cancer research. Several metabolic altered pathways are involved in bladder tumorigenesis, representing therefore interesting targets for therapy. Tumor cells, including urothelial cancer cells, rely on a peculiar shift to aerobic glycolysis-dependent metabolism (the Warburg-effect) as the main energy source to sustain their uncontrolled growth and proliferation. Therefore, the high glycolytic flux depends on the overexpression of glycolysis-related genes (SRC-3, glucose transporter type 1 [GLUT1], GLUT3, lactic dehydrogenase A [LDHA], LDHB, hexokinase 1 [HK1], HK2, pyruvate kinase type M [PKM], and hypoxia-inducible factor 1-alpha [HIF-1α]), resulting in an overproduction of pyruvate, alanine and lactate. Concurrently, bladder cancer metabolism displays an increased expression of genes favoring the pentose phosphate pathway (glucose-6-phosphate dehydrogenase [G6PD]) and the fatty-acid synthesis (fatty acid synthase [FASN]), along with a decrease of AMP-activated protein kinase (AMPK) and Krebs cycle activities. Moreover, the PTEN/PI3K/AKT/mTOR pathway, hyper-activated in bladder cancer, acts as central regulator of aerobic glycolysis, hence contributing to cancer metabolic switch and tumor cell proliferation. Besides glycolysis, glycogen metabolism pathway plays a robust role in bladder cancer development. In particular, the overexpression of GLUT-1, the loss of the tumor suppressor glycogen debranching enzyme amylo-α-1,6-glucosidase, 4-α-glucanotransferase (AGL), and the increased activity of the tumor promoter enzyme glycogen phosphorylase impair glycogen metabolism. An increase in glucose uptake, decrease in normal cellular glycogen storage, and overproduction of lactate are consequences of decreased oxidative phosphorylation and inability to reuse glucose into the pentose phosphate and de novo fatty acid synthesis pathways. Moreover, AGL loss determines augmented levels of the serine-to-glycine enzyme

  4. Comparison of several solid-phase extraction sorbents for continuous determination of amines in water by gas chromatography-mass spectrometry.

    PubMed

    Jurado-Sánchez, Beatriz; Ballesteros, Evaristo; Gallego, Mercedes

    2009-08-15

    A semiautomatic method has been proposed for the determination of different types of amines in water samples including anilines, chloroanilines, N-nitrosamines and aliphatic amines. The analytes were retained on a solid-phase extraction sorbent column and after elution, 1 microL of the extract was analysed by gas chromatography coupled with electron impact ionization mass spectrometry. A systematic overview is given of the advantages and disadvantages of several sorbents (LiChrolut EN, Oasis HLB, RP-C(18), graphitized carbon black, fullerenes and nanotubes) in the retention of amine compounds and based on sensitivity, selectivity and reliability. The retention efficiency for the studied amines was higher (ca. 100%) with LiChrolut EN and Oasis HLB than it was with RP-C(18) and fullerenes (53 and 62%, respectively, on average). Detection limits of 0.5-16 ng L(-1) for the 27 amines studied were obtained when using a sorbent column containing 75 mg of LiChrolut EN for 100mL of sample, the RSD being lower than 6.5%. The method was applied with good accuracy and precision in the determination of amines in various types of water including river, pond, tap, well, drinking, swimming pool and waste. PMID:19576420

  5. Electrochemical preparation of polyaniline-polypyrrole solid-phase microextraction coating and its application in the GC determination of several esters.

    PubMed

    Zhao, Shasha; Wu, Mian; Zhao, Faqiong; Zeng, Baizhao

    2013-12-15

    A novel polyaniline-polypyrrole (PANI-PPY) composite film coated stainless steel wire was prepared by cyclic voltammetry. Firstly, PANI was electrodeposited on a stainless steel wire from a solution containing 0.1 M aniline and 1M HNO3, after the PANI coating was dried in air PPY was electrodeposited on it from a solution containing 0.1 M pyrrole and 0.1 M p-methylbenzene sulfonic acid. The resulting PANI-PPY fiber showed reticulate structure and had large specific surface area. When it was used for the headspace solid-phase microextraction of several esters (i.e. methyl anthranilate, ethyl-o-aminobenzoate, dimethyl phthalate, methyl laurate, and diethyl phthalate), followed by gas chromatographic determination, it presented higher extraction capability in comparison with PPY and PANI coatings. Under the optimized conditions, the linear ranges were 0.07-300 μg L(-1) and the detection limits were 0.05-0.38 μg L(-1) for different esters. The PANI-PPY fiber also showed high durability, after being used for about 160 times its extraction capacity only changed a little. The proposed method was successfully applied to the determination of these esters in real samples and the recoveries were 90-102%. PMID:24209323

  6. Current concepts of severe asthma.

    PubMed

    Ray, Anuradha; Raundhal, Mahesh; Oriss, Timothy B; Ray, Prabir; Wenzel, Sally E

    2016-07-01

    The term asthma encompasses a disease spectrum with mild to very severe disease phenotypes whose traditional common characteristic is reversible airflow limitation. Unlike milder disease, severe asthma is poorly controlled by the current standard of care. Ongoing studies using advanced molecular and immunological tools along with improved clinical classification show that severe asthma does not identify a specific patient phenotype, but rather includes patients with constant medical needs, whose pathobiologic and clinical characteristics vary widely. Accordingly, in recent clinical trials, therapies guided by specific patient characteristics have had better outcomes than previous therapies directed to any subject with a diagnosis of severe asthma. However, there are still significant gaps in our understanding of the full scope of this disease that hinder the development of effective treatments for all severe asthmatics. In this Review, we discuss our current state of knowledge regarding severe asthma, highlighting different molecular and immunological pathways that can be targeted for future therapeutic development. PMID:27367183

  7. Extremely varied phenotypes in granular corneal dystrophy type 2 heterozygotes

    PubMed Central

    Han, Kyung Eun; Choi, Seung-il; Chung, Woo Suk; Jung, Se Hwan; Katsanis, Nicholas; Kim, Tae-im

    2012-01-01

    Purpose To investigate the phenotypic variability of patients bearing the heterozygous R124H mutation in the TGFBI (transforming growth factor-beta-induced) gene that causes granular corneal dystrophy type 2 (GCD2). Methods We describe the phenotypic range of GCD2 heterozygotes for the common R124H mutation in TGFBI; seven with an extremely mild phenotype and six with an extremely severe phenotype. Detailed slit-lamp photographs of these patients were generated. All patients had no history of ocular surgery and were diagnosed as being heterozygous for GCD2 by DNA analysis from peripheral blood. Expression levels of transforming growth factor-beta-induced protein (TGFBIp) were compared among cultured corneal fibroblasts from ten normal donors. Results We report profound differences in the severity of the phenotype across our case series. Two patients with a mild phenotype were diagnosed as unaffected at presentation; however follow-up examinations revealed granular deposits. Importantly, we also observed familial clustering of phenotypic variance; five patients from two families with a mild phenotype showed a similarly mild phenotype within family members. Similarly, six patients from two families with severe phenotypes showed corneal deposits with similar patterns and severity within each distinct family, but distinct patterns between families. TGFBIp expressions from different donor derived cultured corneal fibroblasts were different between one another. Conclusions GCD2 heterozygotes have extremely varied phenotypes between individual patients. However phenotypes were broadly consistent within families, suggesting that the observed variable expressivity might be regulated by other genetic factors that could influence the abundance of TGFBIp or the function of the pathway. From a clinical perspective, our data also highlighted that genetic analysis and meticulous slit-lamp examination in both eyes at multiple time intervals is necessary. PMID:22815629

  8. High antigen levels induce an exhausted phenotype in a chronic infection without impairing T cell expansion and survival.

    PubMed

    Utzschneider, Daniel T; Alfei, Francesca; Roelli, Patrick; Barras, David; Chennupati, Vijaykumar; Darbre, Stephanie; Delorenzi, Mauro; Pinschewer, Daniel D; Zehn, Dietmar

    2016-08-22

    Chronic infections induce T cells showing impaired cytokine secretion and up-regulated expression of inhibitory receptors such as PD-1. What determines the acquisition of this chronic phenotype and how it impacts T cell function remain vaguely understood. Using newly generated recombinant antigen variant-expressing chronic lymphocytic choriomeningitis virus (LCMV) strains, we uncovered that T cell differentiation and acquisition of a chronic or exhausted phenotype depend critically on the frequency of T cell receptor (TCR) engagement and less significantly on the strength of TCR stimulation. In fact, we noted that low-level antigen exposure promotes the formation of T cells with an acute phenotype in chronic infections. Unexpectedly, we found that T cell populations with an acute or chronic phenotype are maintained equally well in chronic infections and undergo comparable primary and secondary expansion. Thus, our observations contrast with the view that T cells with a typical chronic infection phenotype are severely functionally impaired and rapidly transition into a terminal stage of differentiation. Instead, our data unravel that T cells primarily undergo a form of phenotypic and functional differentiation in the early phase of a chronic LCMV infection without inheriting a net survival or expansion deficit, and we demonstrate that the acquired chronic phenotype transitions into the memory T cell compartment. PMID:27455951

  9. Association between severity and the determinant-based classification, Atlanta 2012 and Atlanta 1992, in acute pancreatitis: a clinical retrospective study.

    PubMed

    Chen, Yuhui; Ke, Lu; Tong, Zhihui; Li, Weiqin; Li, Jieshou

    2015-04-01

    Recently, the determinant-based classification (DBC) and the Atlanta 2012 have been proposed to provide a basis for study and treatment of acute pancreatitis (AP). The present study aimed to evaluate the association between severity and the DBC, the Atlanta 2012 and the Atlanta 1992, in AP. Patients admitted to our center with AP from January 2007 to July 2013 were reviewed retrospectively. Patients were assigned to severity categories for all the 3 classification systems. The primary outcomes include long-term clinical prognosis (mortality and length-of-hospital stay), major complications (intraabdominal hemorrhage, multiple-organ dysfunction, single organ failure [OF], and sepsis) and clinical interventions (surgical drainage, continuous renal replace therapy [CRRT] lasting time, and mechanical ventilation [MV] lasting time). The classification systems were validated and compared in terms of these abovementioned primary outcomes. A total of 395 patients were enrolled in this retrospective study with an overall 8.86% in-hospital mortality. Intraabdominal hemorrhage was present in 27 (6.84%) of the patients, multiple-organ dysfunction in 73(18.48%), single OF in 67 (16.96%), and sepsis in 73(18.48%). For each classification system, different categories regarding severity were associated with statistically different clinical mortality, major complications, and clinical interventions (P < 0.05). However, the Atlanta 2012 and the DBC performed better than the Atlanta 1992, and they were comparable in predicting mortality (area under curve [AUC] 0.899 and 0.955 vs 0.585, P < 0.05); intraabdominal hemorrhage (AUC 0.930 and 0.961 vs 0.583, P < 0.05), multiple-organ dysfunction (AUC 0.858 and 0.881 vs 0.595, P < 0.05), sepsis (AUC 0.826 and 0.879 vs 0.590, P < 0.05), and surgical drainage (AUC 0.900 and 0.847 vs 0.606, P < 0.05). For continuous variables, the Atlanta 2012 and the DBC were also better than the Atlanta 1992, and they were similar in

  10. Genetic resources for phenotyping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotyping of structured populations, along with molecular genotyping, will be essential for marker development in peanut. This research is essential for making the peanut genome sequence and genomic tools useful to breeders because it makes the connection between genes, gene markers, genetic maps...

  11. Severe Weather

    ERIC Educational Resources Information Center

    Forde, Evan B.

    2004-01-01

    Educating the public about safety issues related to severe weather is part of the National Oceanic and Atmospheric Administration's (NOAA) mission. This article deals with a poster entitled, "Severe Weather," that has been created by NOAA to help educate the public about hazardous weather conditions. The four types of severe weather highlighted in…

  12. Severe Weather

    ERIC Educational Resources Information Center

    Forde, Evan B.

    2004-01-01

    Educating the public about safety issues related to severe weather is part of the National Oceanic and Atmospheric Administration's (NOAA) mission. This month's insert, Severe Weather, has been created by NOAA to help educate the public about hazardous weather conditions. The four types of severe weather highlighted in this poster are hurricanes,…

  13. Discovery of the gray phenotype and white-gray-opaque tristable phenotypic transitions in Candida dubliniensis.

    PubMed

    Yue, Huizhen; Hu, Jian; Guan, Guobo; Tao, Li; Du, Han; Li, Houmin; Huang, Guanghua

    2016-04-01

    Candida dubliniensis is closely related to Candida albicans, a major causative agent of candidiasis, and is primarily associated with oral colonization and infection in human immunodeficiency virus (HIV)-positive patients. Despite the high similarity of genomic and phenotypic features between the 2 species, C. dubliniensis is much less virulent and less prevalent than C. albicans. The ability to change morphological phenotypes is a striking feature of Candida species and is linked to virulence. In this study, we report a novel phenotype, the gray phenotype, in C. dubliniensis. Together with the previously reported white and opaque cell types, the gray phenotype forms a tristable phenotypic switching system in C. dubliniensis that is similar to the white-gray-opaque tristable switching system in C. albicans. Gray cells of C. dubliniensis are similar to their counterparts in C. albicans in terms of several biological aspects including cellular morphology, mating competence, and genetic regulatory mechanisms. However, the gray phenotypes of the 2 species have some distinguishing features. For example, the secreted aspartyl protease (Sap) activity is induced by bovine serum albumin (BSA) in gray cells of C. albicans, but not in gray cells of C. dubliniensis. Taken together, our results demonstrate that the biological features and regulatory mechanisms of white-gray-opaque tristable transitions are largely conserved in the 2 pathogenic Candida species. PMID:26714067

  14. [Effects of Gut Microbiota on Stress Response and Behavioral Phenotype of the Host].

    PubMed

    Sudo, Nobuyuki

    2016-06-01

    Gut microbiota are involved in host patho-physiological functions; however, little is known about whether or not they can affect brain function. Several recent works including ours have shown that gut microbiota play a critical role in the determination of stress response and behavioral phenotype of the host. We here review recent advances in this area, i.e. the interaction between gut microbiota and the brain-gut axis, based on our series of experimental data. PMID:27279157

  15. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

    PubMed

    Köhler, Sebastian; Doelken, Sandra C; Mungall, Christopher J; Bauer, Sebastian; Firth, Helen V; Bailleul-Forestier, Isabelle; Black, Graeme C M; Brown, Danielle L; Brudno, Michael; Campbell, Jennifer; FitzPatrick, David R; Eppig, Janan T; Jackson, Andrew P; Freson, Kathleen; Girdea, Marta; Helbig, Ingo; Hurst, Jane A; Jähn, Johanna; Jackson, Laird G; Kelly, Anne M; Ledbetter, David H; Mansour, Sahar; Martin, Christa L; Moss, Celia; Mumford, Andrew; Ouwehand, Willem H; Park, Soo-Mi; Riggs, Erin Rooney; Scott, Richard H; Sisodiya, Sanjay; Van Vooren, Steven; Wapner, Ronald J; Wilkie, Andrew O M; Wright, Caroline F; Vulto-van Silfhout, Anneke T; de Leeuw, Nicole; de Vries, Bert B A; Washingthon, Nicole L; Smith, Cynthia L; Westerfield, Monte; Schofield, Paul; Ruef, Barbara J; Gkoutos, Georgios V; Haendel, Melissa; Smedley, Damian; Lewis, Suzanna E; Robinson, Peter N

    2014-01-01

    The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online. PMID:24217912

  16. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

    PubMed Central

    Köhler, Sebastian; Doelken, Sandra C.; Mungall, Christopher J.; Bauer, Sebastian; Firth, Helen V.; Bailleul-Forestier, Isabelle; Black, Graeme C. M.; Brown, Danielle L.; Brudno, Michael; Campbell, Jennifer; FitzPatrick, David R.; Eppig, Janan T.; Jackson, Andrew P.; Freson, Kathleen; Girdea, Marta; Helbig, Ingo; Hurst, Jane A.; Jähn, Johanna; Jackson, Laird G.; Kelly, Anne M.; Ledbetter, David H.; Mansour, Sahar; Martin, Christa L.; Moss, Celia; Mumford, Andrew; Ouwehand, Willem H.; Park, Soo-Mi; Riggs, Erin Rooney; Scott, Richard H.; Sisodiya, Sanjay; Vooren, Steven Van; Wapner, Ronald J.; Wilkie, Andrew O. M.; Wright, Caroline F.; Vulto-van Silfhout, Anneke T.; de Leeuw, Nicole; de Vries, Bert B. A.; Washingthon, Nicole L.; Smith, Cynthia L.; Westerfield, Monte; Schofield, Paul; Ruef, Barbara J.; Gkoutos, Georgios V.; Haendel, Melissa; Smedley, Damian; Lewis, Suzanna E.; Robinson, Peter N.

    2014-01-01

    The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online. PMID:24217912

  17. Determination of PCT on admission is a useful tool for the assessment of disease severity in travelers with imported Plasmodium falciparum malaria.

    PubMed

    Righi, Elda; Merelli, Maria; Arzese, Alessandra; Siega, Paola Della; Scarparo, Claudio; Bassetti, Matteo

    2016-06-01

    Procalcitonin (PCT) and C-reactive protein (CRP) may be useful to predict complicated forms of malaria. A total of 30 consecutive travelers diagnosed with Plasmodium falciparum malaria over a two-year period were included in the study. Patients with complicated Plasmodium falciparum malaria showed higher levels of parasitemia (P = 0.0001), PCT (P = 0.0018), CRP (P = 0.0005), bilirubinemia (P = 0.004), and a lower platelet count (P<0.0001) compared with patients with uncomplicated forms. PCT levels above 5 ng/mL showed the highest value of specificity (0.86) and positive predictive factor (0.67) among other parameters, and equal sensitivity (0.67) was displayed by CRP levels above 150 mg/dl. None of the patients with complicated malaria showed PCT levels within normal limits (<0.5 ng/ml). Both PCT and CRP correlated with parasitemia (P<0.001) and showed areas under ROC curve of 0.83. At multivariate analysis, only PCT was associated with an increased risk of complicated malaria (OR 8.2, IC 95% 1.2-57.2, P = 0.03). The determination of PCT on admission showed better results compared to CRP, platelet count, and bilirubinemia and can be useful in non-endemic areas for the initial clinical assessment of disease severity in travelers with Plasmodium falciparum malaria. PMID:27078668

  18. Appropriate Implementation of Severity Ratings, Regulations, and State Guidance: A Response to "Using Norm-Referenced Tests to Determine Severity of Language Impairment in Children: Disconnect between U.S. Policy Makers and Test Developers" by Spaulding, Szulga, & Figueria (2012)

    ERIC Educational Resources Information Center

    Ireland, Marie; Hall-Mills, Shannon; Millikin, Cindy

    2013-01-01

    In this response to Spaulding et al.'s examination of state education agency (SEA) guidance on severity ratings, these authors contend that Spaulding et al. provided an incomplete view of current practices in public schools. These authors state that, ultimately, school speech-language pathologists (SLPs) must follow all state regulations and…

  19. Genotype/Phenotype Correlations in Tuberous Sclerosis Complex.

    PubMed

    Curatolo, Paolo; Moavero, Romina; Roberto, Denis; Graziola, Federica

    2015-12-01

    Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by the development of widespread hamartomatous lesions in various organs, including brain, skin, kidneys, heart, and eyes. Central nervous system is almost invariably involved, with up to 85% of patients presenting with epilepsy, and at least half of patients having intellectual disability or other neuropsychiatric disorders including autism spectrum disorder. TSC is caused by the mutation in one of the 2 genes TSC1, at 9q34, and TSC2, at 16p13.3. They respectively encode for hamartin and tuberin, which form an intracellular complex inhibiting the mammalian target of rapamycin. Mammalian target of rapamycin overactivation following the genetic defect determines the cell growth and proliferation responsible for TSC-related lesions, as well as the alterations in neuronal excitability and synaptogenesis leading to epilepsy and neuropsychiatric disorders. A causative mutation for the disorder is identified in about 85% of patients with a clinical diagnosis of TSC. Mosaicism and technology limits likely explain most of the no mutation identified cases. This review confirms that patients with TSC2 mutations considered as a group usually present a more severe phenotype, characterized by higher number of tubers, earlier age at seizure onset and higher prevalence of intellectual disability. However, the clinical phenotype of the disease presents a high variability, thus making the prediction of the phenotype on an individual basis still challenging. The increasing application of new molecular techniques to subjects with TSC has the potential to significantly reduce the rate of patients with no mutation demonstrated and to identify an increasing higher number of mutations. This would hopefully allow a better characterization of higher risk mutations, which might help clinicians to plan individualized surveillance plans. Furthermore, the increasing availability of disease registries to collect

  20. Sever's Disease

    MedlinePlus

    ... Tests How do I know if my child's heel pain is caused by Sever's disease? In Sever's disease, heel pain can be in one or both heels. It ... cut down or stop any activity that causes heel pain. Apply ice to the injured heel for 20 ...

  1. Semi-supervised Learning for Phenotyping Tasks

    PubMed Central

    Dligach, Dmitriy; Miller, Timothy; Savova, Guergana K.

    2015-01-01

    Supervised learning is the dominant approach to automatic electronic health records-based phenotyping, but it is expensive due to the cost of manual chart review. Semi-supervised learning takes advantage of both scarce labeled and plentiful unlabeled data. In this work, we study a family of semi-supervised learning algorithms based on Expectation Maximization (EM) in the context of several phenotyping tasks. We first experiment with the basic EM algorithm. When the modeling assumptions are violated, basic EM leads to inaccurate parameter estimation. Augmented EM attenuates this shortcoming by introducing a weighting factor that downweights the unlabeled data. Cross-validation does not always lead to the best setting of the weighting factor and other heuristic methods may be preferred. We show that accurate phenotyping models can be trained with only a few hundred labeled (and a large number of unlabeled) examples, potentially providing substantial savings in the amount of the required manual chart review. PMID:26958183

  2. Impact of Feed Supplementation with Antimicrobial Agents on Growth Performance of Broiler Chickens, Clostridium perfringens and Enterococcus Counts, and Antibiotic Resistance Phenotypes and Distribution of Antimicrobial Resistance Determinants in Escherichia coli Isolates▿

    PubMed Central

    Diarra, Moussa S.; Silversides, Fred G.; Diarrassouba, Fatoumata; Pritchard, Jane; Masson, Luke; Brousseau, Roland; Bonnet, Claudie; Delaquis, Pascal; Bach, Susan; Skura, Brent J.; Topp, Edward

    2007-01-01

    The effects of feed supplementation with the approved antimicrobial agents bambermycin, penicillin, salinomycin, and bacitracin or a combination of salinomycin plus bacitracin were evaluated for the incidence and distribution of antibiotic resistance in 197 commensal Escherichia coli isolates from broiler chickens over 35 days. All isolates showed some degree of multiple antibiotic resistance. Resistance to tetracycline (68.5%), amoxicillin (61.4%), ceftiofur (51.3%), spectinomycin (47.2%), and sulfonamides (42%) was most frequent. The levels of resistance to streptomycin, chloramphenicol, and gentamicin were 33.5, 35.5, and 25.3%, respectively. The overall resistance levels decreased from day 7 to day 35 (P < 0.001). Comparing treatments, the levels of resistance to ceftiofur, spectinomycin, and gentamicin (except for resistance to bacitracin treatment) were significantly higher in isolates from chickens receiving feed supplemented with salinomycin than from the other feeds (P < 0.001). Using a DNA microarray analysis capable of detecting commonly found antimicrobial resistance genes, we characterized 104 tetracycline-resistant E. coli isolates from 7- to 28-day-old chickens fed different growth promoters. Results showed a decrease in the incidence of isolates harboring tet(B), blaTEM, sulI, and aadA and class 1 integron from days 7 to 35 (P < 0.01). Of the 84 tetracycline-ceftiofur-resistant E. coli isolates, 76 (90.5%) were positive for blaCMY-2. The proportions of isolates positive for sulI, aadA, and integron class 1 were significantly higher in salinomycin-treated chickens than in the control or other treatment groups (P < 0.05). These data demonstrate that multiantibiotic-resistant E. coli isolates can be found in broiler chickens regardless of the antimicrobial growth promoters used. However, the phenotype and the distribution of resistance determinants in E. coli can be modulated by feed supplementation with some of the antimicrobial agents used in broiler

  3. Phenotypic plasticity in bacterial plasmids.

    PubMed Central

    Turner, Paul E

    2004-01-01

    Plasmid pB15 was previously shown to evolve increased horizontal (infectious) transfer at the expense of reduced vertical (intergenerational) transfer and vice versa, a key trade-off assumed in theories of parasite virulence. Whereas the models predict that susceptible host abundance should determine which mode of transfer is selectively favored, host density failed to mediate the trade-off in pB15. One possibility is that the plasmid's transfer deviates from the assumption that horizontal spread (conjugation) occurs in direct proportion to cell density. I tested this hypothesis using Escherichia coli/pB15 associations in laboratory serial culture. Contrary to most models of plasmid transfer kinetics, my data show that pB15 invades static (nonshaking) bacterial cultures only at intermediate densities. The results can be explained by phenotypic plasticity in traits governing plasmid transfer. As cells become more numerous, the plasmid's conjugative transfer unexpectedly declines, while the trade-off between transmission routes causes vertical transfer to increase. Thus, at intermediate densities the plasmid's horizontal transfer can offset selection against plasmid-bearing cells, but at high densities pB15 conjugates so poorly that it cannot invade. I discuss adaptive vs. nonadaptive causes for the phenotypic plasticity, as well as potential mechanisms that may lead to complex transfer dynamics of plasmids in liquid environments. PMID:15166133

  4. Severe Sarcoidosis.

    PubMed

    Kouranos, Vasileios; Jacob, Joe; Wells, Athol U

    2015-12-01

    In sarcoidosis, reduction in mortality and the prevention of disability due to major organ involvement are treatment goals. Thus, it is important to recognize severe disease and identify patients at higher risk of progression to severe disease. In this article, fibrotic lung disease and cardiac sarcoidosis are reviewed as the major contributors to sarcoidosis mortality and morbidity. In the absence of a standardized definition of severe pulmonary disease, a multidisciplinary approach to clinical staging is suggested, based on symptoms, pulmonary function tests, and imaging findings at presentation, integrated with the duration of disease and longitudinal disease behavior during early follow-up. PMID:26593144

  5. Sever's Disease

    MedlinePlus

    ... Are Reading Upsetting News Reports? What to Say Vaccines: Which Ones & When? Smart School Lunches Emmy-Nominated Video "Cerebral Palsy: Shannon's Story" 5 Things to Know About Zika & Pregnancy Sever's Disease KidsHealth > ...

  6. Model-Based Determination of Effective Blood Concentrations of Cyclosporine for Neutrophil Response in the Treatment of Severe Aplastic Anemia in Children.

    PubMed

    Philippe, Michaël; Hénin, Emilie; Bertrand, Yves; Plantaz, Dominique; Goutelle, Sylvain; Bleyzac, Nathalie

    2015-09-01

    Optimal immunosuppressive therapy in acquired severe aplastic anemia (SAA) remains to be refined, especially cyclosporine (CsA) use. Current recommendations state that CsA trough blood concentrations (TBC) should be maintained between 200 and 400 ng/mL despite the lack of supporting data. This study aimed at quantifying relationships between CsA exposure and neutrophil response and determining an effective range for CsA TBC. Twenty-three SAA patients treated with CsA were retrospectively analyzed. Nonlinear mixed effect modeling approaches were used to develop a pharmacokinetic-pharmacodynamic model. The pharmacokinetic model described the relationships between CsA doses and TBC. The pharmacodynamic model allowed to estimate boundaries for optimal CsA effects, neutrophils being used as biomarker of response. A time-to-event model linked effective concentration to time-to-therapeutic success. CsA TBC were adequately described by a two-compartment model with first-order absorption, a lag time, and a linear elimination. The efficient range of CsA TBC was estimated between 87 and 120 ng/mL. Model-based simulations and external validation in three additional patients confirmed these results. This original modeling approach was successful in describing the relationship between CsA TBC and neutrophil response in SAA patients. Although further evaluation of the model is necessary, this work suggests that an optimal CsA TBC target of 100 ng/mL would be associated with a better neutrophil response in children with SAA. PMID:25975616

  7. Root phenotyping: from component trait in the lab to breeding.

    PubMed

    Kuijken, René C P; van Eeuwijk, Fred A; Marcelis, Leo F M; Bouwmeester, Harro J

    2015-09-01

    In the last decade cheaper and faster sequencing methods have resulted in an enormous increase in genomic data. High throughput genotyping, genotyping by sequencing and genomic breeding are becoming a standard in plant breeding. As a result, the collection of phenotypic data is increasingly becoming a limiting factor in plant breeding. Genetic studies on root traits are being hampered by the complexity of these traits and the inaccessibility of the rhizosphere. With an increasing interest in phenotyping, breeders and scientists try to overcome these limitations, resulting in impressive developments in automated phenotyping platforms. Recently, many such platforms have been thoroughly described, yet their efficiency to increase genetic gain often remains undiscussed. This efficiency depends on the heritability of the phenotyped traits as well as the correlation of these traits with agronomically relevant breeding targets. This review provides an overview of the latest developments in root phenotyping and describes the environmental and genetic factors influencing root phenotype and heritability. It also intends to give direction to future phenotyping and breeding strategies for optimizing root system functioning. A quantitative framework to determine the efficiency of phenotyping platforms for genetic gain is described. By increasing heritability, managing effects caused by interactions between genotype and environment and by quantifying the genetic relation between traits phenotyped in platforms and ultimate breeding targets, phenotyping platforms can be utilized to their maximum potential. PMID:26071534

  8. Comparative Analyses of QTLs Influencing Obesity and Metabolic Phenotypes in Pigs and Humans

    PubMed Central

    Jacobsen, Mette J.; Cirera, Susanna; Kogelman, Lisette J. A.; Bruun, Camilla S.; Mark, Thomas; Jørgensen, Claus B.; Grarup, Niels; Appel, Emil V. R.; Galjatovic, Ehm A. A.; Hansen, Torben; Pedersen, Oluf; Guerin, Maryse; Huby, Thierry; Lesnik, Philipppe; Meuwissen, Theo H. E.; Kadarmideen, Haja N.; Fredholm, Merete

    2015-01-01

    The pig is a well-known animal model used to investigate genetic and mechanistic aspects of human disease biology. They are particularly useful in the context of obesity and metabolic diseases because other widely used models (e.g. mice) do not completely recapitulate key pathophysiological features associated with these diseases in humans. Therefore, we established a F2 pig resource population (n = 564) designed to elucidate the genetics underlying obesity and metabolic phenotypes. Segregation of obesity traits was ensured by using breeds highly divergent with respect to obesity traits in the parental generation. Several obesity and metabolic phenotypes were recorded (n = 35) from birth to slaughter (242 ± 48 days), including body composition determined at about two months of age (63 ± 10 days) via dual-energy x-ray absorptiometry (DXA) scanning. All pigs were genotyped using Illumina Porcine 60k SNP Beadchip and a combined linkage disequilibrium-linkage analysis was used to identify genome-wide significant associations for collected phenotypes. We identified 229 QTLs which associated with adiposity- and metabolic phenotypes at genome-wide significant levels. Subsequently comparative analyses were performed to identify the extent of overlap between previously identified QTLs in both humans and pigs. The combined analysis of a large number of obesity phenotypes has provided insight in the genetic architecture of the molecular mechanisms underlying these traits indicating that QTLs underlying similar phenotypes are clustered in the genome. Our analyses have further confirmed that genetic heterogeneity is an inherent characteristic of obesity traits most likely caused by segregation or fixation of different variants of the individual components belonging to cellular pathways in different populations. Several important genes previously associated to obesity in human studies, along with novel genes were identified. Altogether, this study provides novel insight that

  9. Bioimaging for quantitative phenotype analysis.

    PubMed

    Chen, Weiyang; Xia, Xian; Huang, Yi; Chen, Xingwei; Han, Jing-Dong J

    2016-06-01

    With the development of bio-imaging techniques, an increasing number of studies apply these techniques to generate a myriad of image data. Its applications range from quantification of cellular, tissue, organismal and behavioral phenotypes of model organisms, to human facial phenotypes. The bio-imaging approaches to automatically detect, quantify, and profile phenotypic changes related to specific biological questions open new doors to studying phenotype-genotype associations and to precisely evaluating molecular changes associated with quantitative phenotypes. Here, we review major applications of bioimage-based quantitative phenotype analysis. Specifically, we describe the biological questions and experimental needs addressable by these analyses, computational techniques and tools that are available in these contexts, and the new perspectives on phenotype-genotype association uncovered by such analyses. PMID:26850283

  10. Minireview: Clinical severity in sickle cell disease: the challenges of definition and prognostication.

    PubMed

    Quinn, Charles T

    2016-04-01

    Sickle cell disease (SCD) is a monogenic, yet highly phenotypically variable disease with multisystem pathology. This manuscript provides an overview of many of the known determinants, modifiers, and correlates of disease severity in SCD. Despite this wealth of data, modeling the variable and multisystem pathology of SCD continues to be difficult. The current status of prediction of specific adverse outcomes and global disease severity in SCD is also reviewed, highlighting recent successes and ongoing challenges. PMID:27013545

  11. Genotype-phenotype correlations in Rubinstein-Taybi syndrome.

    PubMed

    Schorry, E K; Keddache, M; Lanphear, N; Rubinstein, J H; Srodulski, S; Fletcher, D; Blough-Pfau, R I; Grabowski, G A

    2008-10-01

    Rubinstein-Taybi syndrome (RTS) is a rare multiple congenital anomaly/intellectual impairment syndrome. Loss of function in CREBBP or EP300 genes has been found in about 50% of patients with RTS. Genotype-phenotype correlations were investigated in 93 patients meeting diagnostic criteria for RTS during 2 international RTS family conferences. Mutation analysis of CREBBP was performed on all 31 coding exons and exon-intron junctions; a subset of patients had FISH analysis for large deletions. A total of 64 different variations were observed in the DNA sequence, and determined to be definitive mutations in 52 patients (56%). Mutations detected included: 10 missense mutations; 36 truncating or splice-site mutations; and 6 large deletions detectable by FISH. Fourteen patients had synonymous changes of unknown significance. The majority of mutations affected the HAT domain of CREBBP or predicted termination of the protein before the HAT region. Extensive phenotypic data were collected on each patient and analyzed to determine correlations with mutation types, that is, truncating, large deletions, single amino acid substitutions, or no CREBBP mutation. All four groups displayed the characteristic facial and thumb dysmorphology. Growth retardation in height and weight was seen more frequently in patients with no CREBBP mutation; seizure disorder was more frequent in those with CREBBP mutations. Degree of mental retardation was similar in all groups, although there was a trend toward lower IQ and autistic features in patients with large deletions. Similarity in phenotype between the groups implies that the several genes involved in causing RTS likely have effects through the same pathway. PMID:18792986

  12. Intramolecular phenotypic capacitance in a modular RNA molecule

    PubMed Central

    Hayden, Eric J.; Bendixsen, Devin P.; Wagner, Andreas

    2015-01-01

    Phenotypic capacitance refers to the ability of a genome to accumulate mutations that are conditionally hidden and only reveal phenotype-altering effects after certain environmental or genetic changes. Capacitance has important implications for the evolution of novel forms and functions, but experimentally studied mechanisms behind capacitance are mostly limited to complex, multicomponent systems often involving several interacting protein molecules. Here we demonstrate phenotypic capacitance within a much simpler system, an individual RNA molecule with catalytic activity (ribozyme). This naturally occurring RNA molecule has a modular structure, where a scaffold module acts as an intramolecular chaperone that facilitates folding of a second catalytic module. Previous studies have shown that the scaffold module is not absolutely required for activity, but dramatically decreases the concentration of magnesium ions required for the formation of an active site. Here, we use an experimental perturbation of magnesium ion concentration that disrupts the folding of certain genetic variants of this ribozyme and use in vitro selection followed by deep sequencing to identify genotypes with altered phenotypes (catalytic activity). We identify multiple conditional mutations that alter the wild-type ribozyme phenotype under a stressful environmental condition of low magnesium ion concentration, but preserve the phenotype under more relaxed conditions. This conditional buffering is confined to the scaffold module, but controls the catalytic phenotype, demonstrating how modularity can enable phenotypic capacitance within a single macromolecule. RNA’s ancient role in life suggests that phenotypic capacitance may have influenced evolution since life’s origins. PMID:26401020

  13. The evolution of phenotypic correlations and ‘developmental memory’

    PubMed Central

    Watson, Richard A.; Wagner, Günter P.; Pavlicev, Mihaela; Weinreich, Daniel M.; Mills, Rob

    2014-01-01

    Development introduces structured correlations among traits that may constrain or bias the distribution of phenotypes produced. Moreover, when suitable heritable variation exists, natural selection may alter such constraints and correlations, affecting the phenotypic variation available to subsequent selection. However, exactly how the distribution of phenotypes produced by complex developmental systems can be shaped by past selective environments is poorly understood. Here we investigate the evolution of a network of recurrent non-linear ontogenetic interactions, such as a gene regulation network, in various selective scenarios. We find that evolved networks of this type can exhibit several phenomena that are familiar in cognitive learning systems. These include formation of a distributed associative memory that can ‘store’ and ‘recall’ multiple phenotypes that have been selected in the past, recreate complete adult phenotypic patterns accurately from partial or corrupted embryonic phenotypes, and ‘generalise’ (by exploiting evolved developmental modules) to produce new combinations of phenotypic features. We show that these surprising behaviours follow from an equivalence between the action of natural selection on phenotypic correlations and associative learning, well-understood in the context of neural networks. This helps to explain how development facilitates the evolution of high-fitness phenotypes and how this ability changes over evolutionary time. PMID:24351058

  14. Intramolecular phenotypic capacitance in a modular RNA molecule.

    PubMed

    Hayden, Eric J; Bendixsen, Devin P; Wagner, Andreas

    2015-10-01

    Phenotypic capacitance refers to the ability of a genome to accumulate mutations that are conditionally hidden and only reveal phenotype-altering effects after certain environmental or genetic changes. Capacitance has important implications for the evolution of novel forms and functions, but experimentally studied mechanisms behind capacitance are mostly limited to complex, multicomponent systems often involving several interacting protein molecules. Here we demonstrate phenotypic capacitance within a much simpler system, an individual RNA molecule with catalytic activity (ribozyme). This naturally occurring RNA molecule has a modular structure, where a scaffold module acts as an intramolecular chaperone that facilitates folding of a second catalytic module. Previous studies have shown that the scaffold module is not absolutely required for activity, but dramatically decreases the concentration of magnesium ions required for the formation of an active site. Here, we use an experimental perturbation of magnesium ion concentration that disrupts the folding of certain genetic variants of this ribozyme and use in vitro selection followed by deep sequencing to identify genotypes with altered phenotypes (catalytic activity). We identify multiple conditional mutations that alter the wild-type ribozyme phenotype under a stressful environmental condition of low magnesium ion concentration, but preserve the phenotype under more relaxed conditions. This conditional buffering is confined to the scaffold module, but controls the catalytic phenotype, demonstrating how modularity can enable phenotypic capacitance within a single macromolecule. RNA's ancient role in life suggests that phenotypic capacitance may have influenced evolution since life's origins. PMID:26401020

  15. Phenotype as Agent for Epigenetic Inheritance.

    PubMed

    Torday, John S; Miller, William B

    2016-01-01

    The conventional understanding of phenotype is as a derivative of descent with modification through Darwinian random mutation and natural selection. Recent research has revealed Lamarckian inheritance as a major transgenerational mechanism for environmental action on genomes whose extent is determined, in significant part, by germ line cells during meiosis and subsequent stages of embryological development. In consequence, the role of phenotype can productively be reconsidered. The possibility that phenotype is directed towards the effective acquisition of epigenetic marks in consistent reciprocation with the environment during the life cycle of an organism is explored. It is proposed that phenotype is an active agent in niche construction for the active acquisition of epigenetic marks as a dominant evolutionary mechanism rather than a consequence of Darwinian selection towards reproductive success. The reproductive phase of the life cycle can then be appraised as a robust framework in which epigenetic inheritance is entrained to affect growth and development in continued reciprocal responsiveness to environmental stresses. Furthermore, as first principles of physiology determine the limits of epigenetic inheritance, a coherent justification can thereby be provided for the obligate return of all multicellular eukaryotes to the unicellular state. PMID:27399791

  16. Effects of IL1B single nucleotide polymorphisms on depressive and anxiety symptoms are determined by severity and type of life stress.

    PubMed

    Kovacs, David; Eszlari, Nora; Petschner, Peter; Pap, Dorottya; Vas, Szilvia; Kovacs, Peter; Gonda, Xenia; Juhasz, Gabriella; Bagdy, Gyorgy

    2016-08-01

    Interleukin-1β is one of the main mediators in the cross-talk between the immune system and the central nervous system. Higher interleukin-1β levels are found in mood spectrum disorders, and the stress-induced expression rate of the interleukin-1β gene (IL1B) is altered by polymorphisms in the region. Therefore we examined the effects of rs16944 and rs1143643 single nucleotide polymorphisms (SNPs) within the IL1B gene on depressive and anxiety symptoms, as measured by the Brief Symptom Inventory, in a Hungarian population sample of 1053 persons. Distal and proximal environmental stress factors were also included in our analysis, namely childhood adversity and recent negative life-events. We found that rs16944 minor (A) allele specifically interacted with childhood adversity increasing depressive and anxiety symptoms, while rs1143643's minor (A) allele showed protective effect against depressive symptoms after recent life stress. The genetic main effects of the two SNPs were not significant in the main analysis, but the interaction effects remained significant after correction for multiple testing. In addition, the effect of rs16944 A allele was reversed in a subsample with low-exposure to life stress, suggesting a protective effect against depressive symptoms, in the post hoc analysis. In summary, both of the two IL1B SNPs showed specific environmental stressor-dependent effects on mood disorder symptoms. We also demonstrated that the presence of exposure to childhood adversity changed the direction of the rs16944 effect on depression phenotype. Therefore our results suggest that it is advisable to include environmental factors in genetic association studies when examining the effect of the IL1B gene. PMID:26891860

  17. EHR Big Data Deep Phenotyping

    PubMed Central

    Lenert, L.; Lopez-Campos, G.

    2014-01-01

    Summary Objectives Given the quickening speed of discovery of variant disease drivers from combined patient genotype and phenotype data, the objective is to provide methodology using big data technology to support the definition of deep phenotypes in medical records. Methods As the vast stores of genomic information increase with next generation sequencing, the importance of deep phenotyping increases. The growth of genomic data and adoption of Electronic Health Records (EHR) in medicine provides a unique opportunity to integrate phenotype and genotype data into medical records. The method by which collections of clinical findings and other health related data are leveraged to form meaningful phenotypes is an active area of research. Longitudinal data stored in EHRs provide a wealth of information that can be used to construct phenotypes of patients. We focus on a practical problem around data integration for deep phenotype identification within EHR data. The use of big data approaches are described that enable scalable markup of EHR events that can be used for semantic and temporal similarity analysis to support the identification of phenotype and genotype relationships. Conclusions Stead and colleagues’ 2005 concept of using light standards to increase the productivity of software systems by riding on the wave of hardware/processing power is described as a harbinger for designing future healthcare systems. The big data solution, using flexible markup, provides a route to improved utilization of processing power for organizing patient records in genotype and phenotype research. PMID:25123744

  18. Parasitism and phenotypic change in colonial hosts.

    PubMed

    Hartikainen, Hanna; Fontes, Inês; Okamura, Beth

    2013-09-01

    Changes in host phenotype are often attributed to manipulation that enables parasites to complete trophic transmission cycles. We characterized changes in host phenotype in a colonial host–endoparasite system that lacks trophic transmission (the freshwater bryozoan Fredericella sultana and myxozoan parasite Tetracapsuloides bryosalmonae). We show that parasitism exerts opposing phenotypic effects at the colony and module levels. Thus, overt infection (the development of infectious spores in the host body cavity) was linked to a reduction in colony size and growth rate, while colony modules exhibited a form of gigantism. Larger modules may support larger parasite sacs and increase metabolite availability to the parasite. Host metabolic rates were lower in overtly infected relative to uninfected hosts that were not investing in propagule production. This suggests a role for direct resource competition and active parasite manipulation (castration) in driving the expression of the infected phenotype. The malformed offspring (statoblasts) of infected colonies had greatly reduced hatching success. Coupled with the severe reduction in statoblast production this suggests that vertical transmission is rare in overtly infected modules. We show that although the parasite can occasionally infect statoblasts during overt infections, no infections were detected in the surviving mature offspring, suggesting that during overt infections, horizontal transmission incurs a trade-off with vertical transmission. PMID:23965820

  19. Traditional Therapies for Severe Asthma.

    PubMed

    Wang, Eileen; Hoyte, Flavia C L

    2016-08-01

    Severe asthma is a complex and heterogeneous disease. The European Respiratory Society and American Thoracic Society guidelines define severe asthma for patients 6 years or older as "asthma which requires treatment with high-dose inhaled corticosteroids…plus a second controller or systemic corticosteroids to prevent it from becoming 'uncontrolled' or which remains 'uncontrolled' despite this therapy." This article reviews available traditional therapies, data behind their uses in severe asthma, and varying recommendations. As various asthma endotypes and phenotypes are better understood and characterized, targeted therapies should help improve disease outcomes, efficacy, and cost-effectiveness. PMID:27401628

  20. [Severe asthma].

    PubMed

    González, Claudio D

    2016-01-01

    The objectives of this work were to investigate the frequency of severe asthma (SA) according to WHO definition and to compare SA patients' characteristics with those of non-severe asthma (NSA); secondly, to investigate the level of control reached throughout a period of regular treatment. Between 1-1-2005 and 12-31-2014, 471 medical records from patients with bronchial asthma assisted in Buenos Aires City were analyzed. SA frequency was 40.1% (189/471), being significantly higher among patients from the public health system (47.7%, 108/226 vs. 33%, 81/245, p = 0.001). SA patients were older than NSA ones (51.3 ± 17.4 vs. 42.6 ± 17.1 years, p = 0.000), presented longer time since onset of the disease (median 30 vs. 20 years, p = 0.000), lower educational levels (secondary level or higher 41.7% vs. 58.1%, p = 0.000), lower frequency of rhinitis (47% vs. 60.6%, p = 0.004), more severe levels of airway obstruction (FEV% 50.2 ± 13.7 vs. 77.7 ± 12.4, p = 0.000), more frequent antecedents of Near Fatal Asthma (11.1% vs. 2.8%, p = 0.000), higher levels of serum IgE (median of 410 vs. 279 UI/l, p = 0.01) and higher demand of systemic steroids requirements and hospitalizations (68.7% vs. 50.7%, p = 0.000 and 37.5% vs. 15.9%, p = 0.000, respectively). A 30.6% of SA patients (58/189) reached a follow-up period of 12 months, 13 (22.5%) of whom reached the controlled asthma level. The frequency of SA found seems to be considerable. Multicenter studies to investigate the levels of control reached by SA patients with access to proper treatment are recommended. PMID:26826988

  1. Phenotypic robustness and the assortativity signature of human transcription factor networks.

    PubMed

    Pechenick, Dov A; Payne, Joshua L; Moore, Jason H

    2014-08-01

    Many developmental, physiological, and behavioral processes depend on the precise expression of genes in space and time. Such spatiotemporal gene expression phenotypes arise from the binding of sequence-specific transcription factors (TFs) to DNA, and from the regulation of nearby genes that such binding causes. These nearby genes may themselves encode TFs, giving rise to a transcription factor network (TFN), wherein nodes represent TFs and directed edges denote regulatory interactions between TFs. Computational studies have linked several topological properties of TFNs - such as their degree distribution - with the robustness of a TFN's gene expression phenotype to genetic and environmental perturbation. Another important topological property is assortativity, which measures the tendency of nodes with similar numbers of edges to connect. In directed networks, assortativity comprises four distinct components that collectively form an assortativity signature. We know very little about how a TFN's assortativity signature affects the robustness of its gene expression phenotype to perturbation. While recent theoretical results suggest that increasing one specific component of a TFN's assortativity signature leads to increased phenotypic robustness, the biological context of this finding is currently limited because the assortativity signatures of real-world TFNs have not been characterized. It is therefore unclear whether these earlier theoretical findings are biologically relevant. Moreover, it is not known how the other three components of the assortativity signature contribute to the phenotypic robustness of TFNs. Here, we use publicly available DNaseI-seq data to measure the assortativity signatures of genome-wide TFNs in 41 distinct human cell and tissue types. We find that all TFNs share a common assortativity signature and that this signature confers phenotypic robustness to model TFNs. Lastly, we determine the extent to which each of the four components of the

  2. The Determinants of Staff and Resident Activity in Residential Services for People with Severe Intellectual Disability: Moving beyond Size, Building Design, Location and Number of Staff.

    ERIC Educational Resources Information Center

    Felce, David

    1998-01-01

    Draws together the results of seven studies that investigated factors influencing the effects of service quality in community-based residential services for people with severe mental retardation. Results found that quality of staff and resident activity is dependent on an interaction between the structure, orientation, and procedures followed…

  3. Biodiversity of spoilage lactobacilli: phenotypic characterisation.

    PubMed

    Sanders, J W; Oomes, S J C M; Membré, J-M; Wegkamp, A; Wels, M

    2015-02-01

    Preventing food spoilage is a challenge for the food industry, especially when applying mild preservation methods and when avoiding the use of preservatives. Therefore, it is essential to explore the boundaries of preservation by better understanding the causative microbes, their phenotypic behaviour and their genetic makeup. Traditionally in food microbiology, single strains or small sets of selected strains are studied. Here a collection of 120 strains of 6 different spoilage related Lactobacillus species and a multitude of sources was prepared and their growth characteristics determined in 384-well plates by optical density measurements (OD) over 20 days, for 20 carbon source-related phenotypic parameters and 25 preservation-related phenotypic parameters. Growth under all conditions was highly strain specific and there was no correlation of phenotypes at the species level. On average Lactobacillus brevis strains were amongst the most robust whereas Lactobacillus fructivorans strains had a much narrower growth range. The biodiversity data allowed the definition of preservation boundaries on the basis of the number of Lactobacillus strains that reached a threshold OD, which is different from current methods that are based on growth ability or growth rate of a few selected strains. Genetic information on these microbes and a correlation study will improve the mechanistic understanding of preservation resistance and this will support the future development of superior screening and preservation methods. PMID:25481060

  4. Phenotypic plasticity with instantaneous but delayed switches.

    PubMed

    Utz, Margarete; Jeschke, Jonathan M; Loeschcke, Volker; Gabriel, Wilfried

    2014-01-01

    Phenotypic plasticity is a widespread phenomenon, allowing organisms to better adapt to changing environments. Most empirical and theoretical studies are restricted to irreversible plasticity where the expression of a specific phenotype is mostly determined during development. However, reversible plasticity is not uncommon; here, organisms are able to switch back and forth between phenotypes. We present two optimization models for the fitness of (i) non-plastic, (ii) irreversibly plastic, and (iii) reversibly plastic genotypes in a fluctuating environment. In one model, the fitness values of an organism during different life phases act together multiplicatively (so as to consider traits that are related to survival). The other model additionally considers additive effects (corresponding to traits related to fecundity). Both models yield qualitatively similar results. If the only costs of reversible plasticity are due to temporal maladaptation while switching between phenotypes, reversibility is virtually always advantageous over irreversibility, especially for slow environmental fluctuations. If reversibility implies an overall decreased fitness, then irreversibility is advantageous if the environment fluctuates quickly or if stress events last relatively short. Our results are supported by observations from different types of organisms and have implications for many basic and applied research questions, e.g., on invasive alien species. PMID:24041594

  5. Determination of potassium in several plants and study of potassium transfer to different beverages, including tequila, by measurement of 40K

    NASA Astrophysics Data System (ADS)

    Navarrete, J. M.; Muller, G.; Cabrera, L.; Martinez, T.

    2006-01-01

    Measurement of 40K was used for determination of potassium concentrations in leaves of agave and maguey cactus leaves, and coffee beans of various origins. The procedure was also used to study potassium transfer to tequila (alcoholic drink made of agave cactus), and the cactus and coffee infusions using 40K as a natural radioactive tracer. Counting of 40K in Marinelli containers with the aid of a low background NaI(Ti) scintillation detection system for 12 24 hours was employed. The method appeared to be simple and suitable for determination of potassium concentrations in large samples, which eliminates homogeneity problems.

  6. Refined Phenotyping of Modic Changes

    PubMed Central

    Määttä, Juhani H.; Karppinen, Jaro; Paananen, Markus; Bow, Cora; Luk, Keith D.K.; Cheung, Kenneth M.C.; Samartzis, Dino

    2016-01-01

    Abstract Low back pain (LBP) is the world's most disabling condition. Modic changes (MC) are vertebral bone marrow changes adjacent to the endplates as noted on magnetic resonance imaging. The associations of specific MC types and patterns with prolonged, severe LBP and disability remain speculative. This study assessed the relationship of prolonged, severe LBP and back-related disability, with the presence and morphology of lumbar MC in a large cross-sectional population-based study of Southern Chinese. We addressed the topographical and morphological dimensions of MC along with other magnetic resonance imaging phenotypes (eg, disc degeneration and displacement) on the basis of axial T1 and sagittal T2-weighted imaging of L1-S1. Prolonged severe LBP was defined as LBP lasting ≥30 days during the past year, and a visual analog scale severest pain intensity of at least 6/10. An Oswestry Disability Index score of 15% was regarded as significant disability. We also assessed subject demographics, occupation, and lifestyle factors. In total, 1142 subjects (63% females, mean age 53 years) were assessed. Of these, 282 (24.7%) had MC (7.1% type I, 17.6% type II). MC subjects were older (P = 0.003), had more frequent disc displacements (P < 0.001) and greater degree of disc degeneration (P < 0.001) than non-MC subjects. In adjusted models, any MC (odds ratio [OR] 1.48, 95% confidence interval [CI] 1.01–2.18), MC affecting whole anterior-posterior length (OR 1.62, 95% CI 1.04–2.51), and MC affecting 2/3 posterior length (OR 2.79, 95% CI 1.17–6.65) were associated with prolonged severe LBP. Type I MC tended to associate with pain more strongly than type II MC (OR 1.80, 95% CI 0.94–3.44 vs OR 1.36, 95% CI 0.88–2.09, respectively). Any MC (OR 1.47, 95% CI 1.04–2.10), type II MC (OR 1.56, 95% CI 1.06–2.31), MC affecting 2/3 posterior length (OR 2.96, 95% CI 1.27–6.89), and extensive MC (OR 1.95, 95% CI 1.21–3.15) were associated with disability

  7. A Comprehensive Evaluation of Disease Phenotype Networks for Gene Prioritization

    PubMed Central

    Li, Jianhua; Lin, Xiaoyan; Teng, Yueyang; Qi, Shouliang; Xiao, Dayu; Zhang, Jianying; Kang, Yan

    2016-01-01

    Identification of disease-causing genes is a fundamental challenge for human health studies. The phenotypic similarity among diseases may reflect the interactions at the molecular level, and phenotype comparison can be used to predict disease candidate genes. Online Mendelian Inheritance in Man (OMIM) is a database of human genetic diseases and related genes that has become an authoritative source of disease phenotypes. However, disease phenotypes have been described by free text; thus, standardization of phenotypic descriptions is needed before diseases can be compared. Several disease phenotype networks have been established in OMIM using different standardization methods. Two of these networks are important for phenotypic similarity analysis: the first and most commonly used network (mimMiner) is standardized by medical subject heading, and the other network (resnikHPO) is the first to be standardized by human phenotype ontology. This paper comprehensively evaluates for the first time the accuracy of these two networks in gene prioritization based on protein–protein interactions using large-scale, leave-one-out cross-validation experiments. The results show that both networks can effectively prioritize disease-causing genes, and the approach that relates two diseases using a logistic function improves prioritization performance. Tanimoto, one of four methods for normalizing resnikHPO, generates a symmetric network and it performs similarly to mimMiner. Furthermore, an integration of these two networks outperforms either network alone in gene prioritization, indicating that these two disease networks are complementary. PMID:27415759

  8. Genomic characterization of phenotypic variants of beet curly top virus.

    PubMed

    Stenger, D C; Carbonaro, D; Duffus, J E

    1990-10-01

    Full-length infectious DNA clones were constructed for four distinct phenotypic variants of beet curly top virus (BCTV). Southern hybridization assays indicated that each cloned BCTV genome shared sequence homology with pBCT-028, a full-length infectious DNA clone of a California isolate of BCTV previously characterized by others. Restriction endonuclease maps of the cloned BCTV genomes were distinct from one another. Infectivity assays determined that plasmids containing tandem repeats of BCTV genomes were generally more infectious than excised linear DNA inserts. Progeny virus, derived from plants inoculated with cloned DNAs, differed in their ability to infect sugarbeet, Beta vulgaris L., and the severity of symptoms produced in B. vulgaris and other experimental hosts. PMID:2230726

  9. Rosetting in Plasmodium vivax: A Cytoadhesion Phenotype Associated with Anaemia

    PubMed Central

    Marín-Menéndez, Alejandro; Bardají, Azucena; Martínez-Espinosa, Flor E.; Bôtto-Menezes, Camila; Lacerda, Marcus V.; Ortiz, Jon; Cisteró, Pau; Piqueras, Mireia; Felger, Ingrid; Müeller, Ivo; Ordi, Jaume; del Portillo, Hernando; Menéndez, Clara; Wahlgren, Mats; Mayor, Alfredo

    2013-01-01

    Background Plasmodium vivax can potentially lead to life-threatening episodes but the mechanisms underlying severe disease remain poorly defined. Cytoadhesion of infected erythrocytes may contribute to P. vivax sequestration and organ injury although its physiological impact is still unknown. Here, we aimed to describe clinically-relevant cytoadhesive phenotypes of P. vivax isolates. Methodology/Principal findings Rosetting and adhesion to CSA, CD36, ICAM1, placental and brain cryosections were determined in P. vivax peripheral isolates from 12 pregnant women, 24 non-pregnant women and 23 men from Manaus (Brazil). P. falciparum co-infection was excluded by PCR and P. vivax isolates were genotyped by assessing the size polymorphism of microsatellites ms2, ms20 and msp1F3 through capillary electrophoresis of PCR products. P. vivax monoinfection was confirmed by PCR in 59 isolates, with 50 (85%) of them being single-clone infections. One P. vivax haplotype was more frequently found among pregnant women (33%) than in non-pregnant women (0%) and men (4%; p = 0.010). Rosetting was observed in 64% of the isolates, adhesion to CSA in 15%, to ICAM1 in 12% and to placental cryosections in 9%, being similar among pregnant and non-pregnant groups. Intensity of rosetting was higher among anaemic individuals compared to non-anaemic (p = 0.010) and decreased with increasing haematocrit (p = 0.033) and haemoglobin levels (p = 0.015). Conclusions/Significance P. vivax peripheral isolates from pregnant women do not exhibit a prominent adhesion to CSA, although other parasite phenotypes still unknown may increase the propagation of certain P. vivax clones observed among pregnant hosts. Rosetting is a frequent cytoadhesive phenotype in P. vivax infections that may contribute to the development of anaemia. PMID:23593522

  10. Association between airflow limitation severity and arterial stiffness as determined by the brachial-ankle pulse wave velocity: a cross-sectional study.

    PubMed

    Oda, Masako; Omori, Hisamitsu; Onoue, Ayumi; Cui, Xiaoyi; Lu, Xi; Yada, Hironori; Hisada, Aya; Miyazaki, Wataru; Higashi, Noritaka; Ogata, Yasuhiro; Katoh, Takahiko

    2015-01-01

    Objective Chronic obstructive pulmonary disease (COPD) is often associated with concomitant systemic manifestations and comorbidities, such as cardiovascular disease. There are limited data regarding airflow limitation (AL) and atherosclerosis in Japanese patients, and the potential association between AL and arterial stiffness has not yet been investigated in Japanese patients. Therefore, the purpose of this study was to investigate the association between AL severity and arterial stiffness using the brachial-ankle pulse wave velocity (baPWV). Methods This cross-sectional study included 1,356 subjects aged 40-79 years without clinical cardiovascular diseases who underwent a comprehensive health screening that included spirometry, the baPWV measurement, and blood sampling during medical check-ups in 2009 at the Japanese Red Cross Kumamoto Health Care Center. AL was defined in accordance with the Global Initiative for COPD criteria (forced expiratory volume in one second / forced vital capacity of < 0.7). A cut-off baPWV value of >1,400 cm/s was used for risk prediction and screening. Results The average baPWV (SD) results were 1,578.0 (317.9), 1,647.3 (374.4), and 1,747.3 (320.1) cm/s in the patients with a normal pulmonary function, mild AL, and moderate-to-severe AL, respectively (p< 0.001). Using logistic regression models adjusted for the age, body mass index, smoking status, hypersensitive C-reactive protein levels, hypertension, hyperglycemia, and dyslipidemia, an increased baPWV (>1,400 cm/s) was significantly associated with moderate-to-severe AL compared with a normal pulmonary function (odds ratio=2.76; 95% confidence intervals, 1.37-5.55; p=0.004). Conclusion Our results indicated an association between AL and increased arterial stiffness. Arterial stiffness may therefore worsen with an increase in the severity of AL. PMID:26466690

  11. Factors that determine the severity of Betula spp. pollen seasons in Poland (Poznań and Krakow) and the United Kingdom (Worcester and London)

    NASA Astrophysics Data System (ADS)

    Stach, A.; Emberlin, J.; Smith, M.; Adams-Groom, B.; Myszkowska, D.

    2008-03-01

    The aim of this paper is to analyse variations in the severity of Betula pollen seasons, particularly in relation to meteorological parameters at four sites, Poznań and Krakow in Poland, and Worcester and London in the United Kingdom. Results show that there is a significant relationship between Betula pollen season severity and weather conditions both in the year before pollination and in the same year that pollen is released from the plant. Furthermore, it is likely that the magnitude of birch pollen seasons in Poznań, Worcester and London is linked in some way to different phases of the North Atlantic Oscillation (NAO). Significant positive relationships exist between birch pollen counts at Poznań and temperatures, rainfall and averages of the NAO in the year before pollination. An opposite relationship is evident at the two sites studied in the United Kingdom. There were significant positive correlations between the severity of birch pollen seasons recorded at Worcester and temperatures and averages of the NAO during the winter and spring in the year of pollination, and negative correlations at both Worcester and London with similar variables from the previous year. In addition, Betula pollen seasons in Krakow do not appear to be influenced by the NAO, which is probably the result of Krakow having a more continental climate.

  12. Plant Phenotype Characterization System

    SciTech Connect

    Daniel W McDonald; Ronald B Michaels

    2005-09-09

    This report is the final scientific report for the DOE Inventions and Innovations Project: Plant Phenotype Characterization System, DE-FG36-04GO14334. The period of performance was September 30, 2004 through July 15, 2005. The project objective is to demonstrate the viability of a new scientific instrument concept for the study of plant root systems. The root systems of plants are thought to be important in plant yield and thus important to DOE goals in renewable energy sources. The scientific study and understanding of plant root systems is hampered by the difficulty in observing root activity and the inadequacy of existing root study instrumentation options. We have demonstrated a high throughput, non-invasive, high resolution technique for visualizing plant root systems in-situ. Our approach is based upon low-energy x-ray radiography and the use of containers and substrates (artificial soil) which are virtually transparent to x-rays. The system allows us to germinate and grow plant specimens in our containers and substrates and to generate x-ray images of the developing root system over time. The same plant can be imaged at different times in its development. The system can be used for root studies in plant physiology, plant morphology, plant breeding, plant functional genomics and plant genotype screening.

  13. Citrullinemia: phenotypic variations.

    PubMed

    Whelan, D T; Brusso, T; Spate, M

    1976-06-01

    An 18-month-old female infant was found to have citrullinemia on routine plasma screening by the Scriver Method at 5 days of age. At 10 days of age, plasma citrulline concentration was 0.704mumol/ml (normal, 0.010 to 0.030mumol/ml) and has remained 60 to 80 times higher than normal. Urine citrulline concentration was markedly elevated. Hyperammonemia occurred at 1 month of age. The serum ammonia concentration was 473mug/100 ml (normal, 50 to 250 mug/100 ml) and rose to 770mug/100 ml at 4 months of age. Dietary protein was restricted to 1.6 gm/kg/day. Without further change in protein intake, the serum ammonia concentration decreased to 280mug/100 ml and, since then, it has returned to normal. The addition of three synthetic L-amino acids was required for a short time during dietary therapy. At 10 months of age, the infant was given a normal diet. At 18 months of age, her physical and mental development is normal. Activity of argininosuccinic acid synthetase measured in skin fibroblasts was 0.0037mumol of radioactive carbon dioxide per milligram of protein per hour. To demonstrate heterozygosity, fasting plasma citrulline concentrations were measured in five members of the family. Comparison of findings in this patient with those reported in the literature suggests phenotypical variation of the disease, probably due to genetic heterogeneity. PMID:934749

  14. Obstructive Sleep Apnea Syndrome: From Phenotype to Genetic Basis

    PubMed Central

    Casale, M; Pappacena, M; Rinaldi, V; Bressi, F; Baptista, P; Salvinelli, F

    2009-01-01

    Obstructive sleep apnea syndrome (OSAS) is a complex chronic clinical syndrome, characterized by snoring, periodic apnea, hypoxemia during sleep, and daytime hypersomnolence. It affects 4-5% of the general population. Racial studies and chromosomal mapping, familial studies and twin studies have provided evidence for the possible link between the OSAS and genetic factors and also most of the risk factors involved in the pathogenesis of OSAS are largely genetically determined. A percentage of 35-40% of its variance can be attributed to genetic factors. It is likely that genetic factors associated with craniofacial structure, body fat distribution and neural control of the upper airway muscles interact to produce the OSAS phenotype. Although the role of specific genes that influence the development of OSAS has not yet been identified, current researches, especially in animal model, suggest that several genetic systems may be important. In this chapter, we will first define the OSAS phenotype, the pathogenesis and the risk factors involved in the OSAS that may be inherited, then, we will review the current progress in the genetics of OSAS and suggest a few future perspectives in the development of therapeutic agents for this complex disease entity. PMID:19794884

  15. Y genetic variation and phenotypic diversity in health and disease.

    PubMed

    Case, Laure K; Teuscher, Cory

    2015-01-01

    Sexually dimorphic traits arise through the combined effects of sex hormones and sex chromosomes on sex-biased gene expression, and experimental mouse models have been instrumental in determining their relative contribution in modulating sex differences. A role for the Y chromosome (ChrY) in mediating sex differences outside of development and reproduction has historically been overlooked due to its unusual genetic composition and the predominant testes-specific expression of ChrY-encoded genes. However, ample evidence now exists supporting ChrY as a mediator of other physiological traits in males, and genetic variation in ChrY has been linked to several diseases, including heart disease, cancer, and autoimmune diseases in experimental animal models, as well as humans. The genetic and molecular mechanisms by which ChrY modulates phenotypic variation in males remain unknown but may be a function of copy number variation between homologous X-Y multicopy genes driving differential gene expression. Here, we review the literature identifying an association between ChrY polymorphism and phenotypic variation and present the current evidence depicting the mammalian ChrY as a member of the regulatory genome in males and as a factor influencing paternal parent-of-origin effects in female offspring. PMID:25866616

  16. Epigenetic heredity: RNA-mediated modes of phenotypic variation.

    PubMed

    Rassoulzadegan, Minoo; Cuzin, François

    2015-04-01

    In addition to the Mendelian mutations, several instances of heritable phenotypic variation have been reported. We have observed, in mice, a role for sperm RNAs in the induction of such stable phenotypic variation. When experimentally transferred by RNA microinjection into fertilized mouse eggs, the noncoding RNAs homologous in sequence to the target locus are efficient inducers of variation at the transcriptional level. Transmission of the phenotypic variation to progeny is highly efficient and independent of gender. Here, we have summarized these finding and how they relate to other reports of epigenetic variation. PMID:25726734

  17. Modeling the autism spectrum disorder phenotype.

    PubMed

    McCray, Alexa T; Trevvett, Philip; Frost, H Robert

    2014-04-01

    Autism Spectrum Disorder (ASD) is highly heritable, and although there has been active research in an attempt to discover the genetic factors underlying ASD, diagnosis still depends heavily on behavioral assessments. Recently, several large-scale initiatives, including those of the Autism Consortium, have contributed to the collection of extensive information from families affected by ASD. Our goal was to develop an ontology that can be used 1) to provide improved access to the data collected by those who study ASD and other neurodevelopmental disorders, and 2) to assess and compare the characteristics of the instruments that are used in the assessment of ASD. We analyzed two dozen instruments used to assess ASD, studying the nature of the questions asked and items assessed, the method of delivery, and the overall scope of the content. These data together with the extensive literature on ASD contributed to our iterative development of an ASD phenotype ontology. The final ontology comprises 283 concepts distributed across three high-level classes, 'Personal Traits', 'Social Competence', and 'Medical History'. The ontology is fully integrated with the Autism Consortium database, allowing researchers to pose ontology-based questions. The ontology also allows researchers to assess the degree of overlap among a set of candidate instruments according to several objective criteria. The ASD phenotype ontology has promise for use in research settings where extensive phenotypic data have been collected, allowing a concept-based approach to identifying behavioral features of importance and for correlating these with genotypic data. PMID:24163114

  18. Unbiased analysis of senescence associated secretory phenotype (SASP) to identify common components following different genotoxic stresses.

    PubMed

    Özcan, Servet; Alessio, Nicola; Acar, Mustafa B; Mert, Eda; Omerli, Fatih; Peluso, Gianfranco; Galderisi, Umberto

    2016-07-01

    Senescent cells secrete senescence-associated secretory phenotype (SASP) proteins to carry out several functions, such as sensitizing surrounding cells to senesce; immunomodulation; impairing or fostering cancer growth; and promoting tissue development. Identifying secreted factors that achieve such tasks is a challenging issue since the profile of secreted proteins depends on genotoxic stress and cell type. Currently, researchers are trying to identify common markers for SASP. The present investigation compared the secretome composition of five different senescent phenotypes in two different cell types: bone marrow and adipose mesenchymal stromal cells (MSC). We induced MSC senescence by oxidative stress, doxorubicin treatment, X-ray irradiation, and replicative exhaustion. We took advantage of LC-MS/MS proteome identification and subsequent gene ontology (GO) evaluation to perform an unbiased analysis (hypothesis free manner) of senescent secretomes. GO analysis allowed us to distribute SASP components into four classes: extracellular matrix/cytoskeleton/cell junctions; metabolic processes; ox-redox factors; and regulators of gene expression. We used Ingenuity Pathway Analysis (IPA) to determine common pathways among the different senescent phenotypes. This investigation, along with identification of eleven proteins that were exclusively expressed in all the analyzed senescent phenotypes, permitted the identification of three key signaling paths: MMP2 - TIMP2; IGFBP3 - PAI-1; and Peroxiredoxin 6 - ERP46 - PARK7 - Cathepsin D - Major vault protein. We suggest that these paths could be involved in the paracrine circuit that induces senescence in neighboring cells and may confer apoptosis resistance to senescent cells. PMID:27288264

  19. Unbiased analysis of senescence associated secretory phenotype (SASP) to identify common components following different genotoxic stresses

    PubMed Central

    Özcan, Servet; Alessio, Nicola; Acar, Mustafa B.; Mert, Eda; Omerli, Fatih; Peluso, Gianfranco; Galderisi, Umberto

    2016-01-01

    Senescent cells secrete senescence-associated secretory phenotype (SASP) proteins to carry out several functions, such as sensitizing surrounding cells to senesce; immunomodulation; impairing or fostering cancer growth; and promoting tissue development. Identifying secreted factors that achieve such tasks is a challenging issue since the profile of secreted proteins depends on genotoxic stress and cell type. Currently, researchers are trying to identify common markers for SASP. The present investigation compared the secretome composition of five different senescent phenotypes in two different cell types: bone marrow and adipose mesenchymal stromal cells (MSC). We induced MSC senescence by oxidative stress, doxorubicin treatment, X-ray irradiation, and replicative exhaustion. We took advantage of LC-MS/MS proteome identification and subsequent gene ontology (GO) evaluation to perform an unbiased analysis (hypothesis free manner) of senescent secretomes. GO analysis allowed us to distribute SASP components into four classes: extracellular matrix/cytoskeleton/cell junctions; metabolic processes; ox-redox factors; and regulators of gene expression. We used Ingenuity Pathway Analysis (IPA) to determine common pathways among the different senescent phenotypes. This investigation, along with identification of eleven proteins that were exclusively expressed in all the analyzed senescent phenotypes, permitted the identification of three key signaling paths: MMP2 - TIMP2; IGFBP3 - PAI-1; and Peroxiredoxin 6 - ERP46 - PARK7 - Cathepsin D - Major vault protein. We suggest that these paths could be involved in the paracrine circuit that induces senescence in neighboring cells and may confer apoptosis resistance to senescent cells. PMID:27288264

  20. Exopolysaccharide (EPS) synthesis by Oenococcus oeni: from genes to phenotypes.

    PubMed

    Dimopoulou, Maria; Vuillemin, Marlène; Campbell-Sills, Hugo; Lucas, Patrick M; Ballestra, Patricia; Miot-Sertier, Cécile; Favier, Marion; Coulon, Joana; Moine, Virginie; Doco, Thierry; Roques, Maryline; Williams, Pascale; Petrel, Melina; Gontier, Etienne; Moulis, Claire; Remaud-Simeon, Magali; Dols-Lafargue, Marguerite

    2014-01-01

    Oenococcus oeni is the bacterial species which drives malolactic fermentation in wine. The analysis of 50 genomic sequences of O. oeni (14 already available and 36 newly sequenced ones) provided an inventory of the genes potentially involved in exopolysaccharide (EPS) biosynthesis. The loci identified are: two gene clusters named eps1 and eps2, three isolated glycoside-hydrolase genes named dsrO, dsrV and levO, and three isolated glycosyltransferase genes named gtf, it3, it4. The isolated genes were present or absent depending on the strain and the eps gene clusters composition diverged from one strain to another. The soluble and capsular EPS production capacity of several strains was examined after growth in different culture media and the EPS structure was determined. Genotype to phenotype correlations showed that several EPS biosynthetic pathways were active and complementary in O. oeni. Can be distinguished: (i) a Wzy-dependent synthetic pathway, allowing the production of heteropolysaccharides made of glucose, galactose and rhamnose, mainly in a capsular form, (ii) a glucan synthase pathway (Gtf), involved in β-glucan synthesis in a free and a cell-associated form, giving a ropy phenotype to growth media and (iii) homopolysaccharide synthesis from sucrose (α-glucan or β-fructan) by glycoside-hydrolases of the GH70 and GH68 families. The eps gene distribution on the phylogenetic tree was examined. Fifty out of 50 studied genomes possessed several genes dedicated to EPS metabolism. This suggests that these polymers are important for the adaptation of O. oeni to its specific ecological niche, wine and possibly contribute to the technological performance of malolactic starters. PMID:24901216

  1. Exopolysaccharide (EPS) Synthesis by Oenococcus oeni: From Genes to Phenotypes

    PubMed Central

    Dimopoulou, Maria; Vuillemin, Marlène; Campbell-Sills, Hugo; Lucas, Patrick M.; Ballestra, Patricia; Miot-Sertier, Cécile; Favier, Marion; Coulon, Joana; Moine, Virginie; Doco, Thierry; Roques, Maryline; Williams, Pascale; Petrel, Melina; Gontier, Etienne; Moulis, Claire; Remaud-Simeon, Magali; Dols-Lafargue, Marguerite

    2014-01-01

    Oenococcus oeni is the bacterial species which drives malolactic fermentation in wine. The analysis of 50 genomic sequences of O. oeni (14 already available and 36 newly sequenced ones) provided an inventory of the genes potentially involved in exopolysaccharide (EPS) biosynthesis. The loci identified are: two gene clusters named eps1 and eps2, three isolated glycoside-hydrolase genes named dsrO, dsrV and levO, and three isolated glycosyltransferase genes named gtf, it3, it4. The isolated genes were present or absent depending on the strain and the eps gene clusters composition diverged from one strain to another. The soluble and capsular EPS production capacity of several strains was examined after growth in different culture media and the EPS structure was determined. Genotype to phenotype correlations showed that several EPS biosynthetic pathways were active and complementary in O. oeni. Can be distinguished: (i) a Wzy -dependent synthetic pathway, allowing the production of heteropolysaccharides made of glucose, galactose and rhamnose, mainly in a capsular form, (ii) a glucan synthase pathway (Gtf), involved in β-glucan synthesis in a free and a cell-associated form, giving a ropy phenotype to growth media and (iii) homopolysaccharide synthesis from sucrose (α-glucan or β-fructan) by glycoside-hydrolases of the GH70 and GH68 families. The eps gene distribution on the phylogenetic tree was examined. Fifty out of 50 studied genomes possessed several genes dedicated to EPS metabolism. This suggests that these polymers are important for the adaptation of O. oeni to its specific ecological niche, wine and possibly contribute to the technological performance of malolactic starters. PMID:24901216

  2. Characterization of X-linked hypohidrotic ectodermal dysplasia (XL-HED) hair and sweat gland phenotypes using phototrichogram analysis and live confocal imaging.

    PubMed

    Jones, Kyle B; Goodwin, Alice F; Landan, Maya; Seidel, Kerstin; Tran, Dong-Kha; Hogue, Jacob; Chavez, Miquella; Fete, Mary; Yu, Wenli; Hussein, Tarek; Johnson, Ramsey; Huttner, Kenneth; Jheon, Andrew H; Klein, Ophir D

    2013-07-01

    Hypohidrotic ectodermal dysplasia (HED) is the most common type of ectodermal dysplasia (ED), which encompasses a large group of syndromes that share several phenotypic features such as missing or malformed ectodermal structures, including skin, hair, sweat glands, and teeth. X-linked hypohidrotic ectodermal dysplasia (XL-HED) is associated with mutations in ectodysplasin (EDA1). Hypohidrosis due to hypoplastic sweat glands and thin, sparse hair are phenotypic features that significantly affect the daily lives of XL-HED individuals and therefore require systematic analysis. We sought to determine the quality of life of individuals with XL-HED and to quantify sweat duct and hair phenotypes using confocal imaging, pilocarpine iontophoresis, and phototrichogram analysis. Using these highly sensitive and non-invasive techniques, we demonstrated that 11/12 XL-HED individuals presented with a complete absence of sweat ducts and that none produced sweat. We determined that the thin hair phenotype observed in XL-HED was due to multiple factors, such as fewer terminal hairs with decreased thickness and slower growth rate, as well as fewer follicular units and fewer hairs per unit. The precise characterization of XL-HED phenotypes using sensitive and non-invasive techniques presented in our study will improve upon larger genotype-phenotype studies and the assessment of future therapies in XL-HED. PMID:23687000

  3. Expanding the phenotype of GMPPB mutations.

    PubMed

    Cabrera-Serrano, Macarena; Ghaoui, Roula; Ravenscroft, Gianina; Johnsen, Russell D; Davis, Mark R; Corbett, Alastair; Reddel, Stephen; Sue, Carolyn M; Liang, Christina; Waddell, Leigh B; Kaur, Simranpreet; Lek, Monkol; North, Kathryn N; MacArthur, Daniel G; Lamont, Phillipa J; Clarke, Nigel F; Laing, Nigel G

    2015-04-01

    Dystroglycanopathies are a heterogeneous group of diseases with a broad phenotypic spectrum ranging from severe disorders with congenital muscle weakness, eye and brain structural abnormalities and intellectual delay to adult-onset limb-girdle muscular dystrophies without mental retardation. Most frequently the disease onset is congenital or during childhood. The exception is FKRP mutations, in which adult onset is a common presentation. Here we report eight patients from five non-consanguineous families where next generation sequencing identified mutations in the GMPPB gene. Six patients presented as an adult or adolescent-onset limb-girdle muscular dystrophy, one presented with isolated episodes of rhabdomyolysis, and one as a congenital muscular dystrophy. This report expands the phenotypic spectrum of GMPPB mutations to include limb-girdle muscular dystrophies with adult onset with or without intellectual disability, or isolated rhabdomyolysis. PMID:25681410

  4. Evolution of environmental cues for phenotypic plasticity.

    PubMed

    Chevin, Luis-Miguel; Lande, Russell

    2015-10-01

    Phenotypically plastic characters may respond to multiple variables in their environment, but the evolutionary consequences of this phenomenon have rarely been addressed theoretically. We model the evolution of linear reaction norms in response to several correlated environmental variables, in a population undergoing stationary environmental fluctuations. At evolutionary equilibrium, the linear combination of environmental variables that acts as a developmental cue for the plastic trait is the multivariate best linear predictor of changes in the optimum. However, the reaction norm with respect to any single environmental variable may exhibit nonintuitive patterns. Apparently maladaptive, or hyperadaptive plasticity can evolve with respect to single environmental variables, and costs of plasticity may increase, rather than reduce, plasticity in response to some variables. We also find conditions for the evolution of an indirect environmental indicator that affects expression of a plastic phenotype, despite not influencing natural selection on it. PMID:26292649

  5. The behavioral phenotype of FMR1 mutations.

    PubMed

    Boyle, Lia; Kaufmann, Walter E

    2010-11-15

    The purpose of this article is to provide an overview of the behavioral phenotype of FMR1 mutations, including fragile X syndrome (FXS) in order to better understand the clinical involvement of individuals affected by mutations in this gene. FXS is associated with a wide range of intellectual and behavioral problems, some relatively mild and others quite severe. FXS is the most common cause of inherited intellectual disability and one of the most prevalent genetic causes of autism spectrum disorder. Learning difficulties, attentional problems, anxiety, aggressive behavior, stereotypies, and mood disorders are also frequent in FXS. Recent studies of children and adults have identified associations between FMR1 premutation and many of the same disorders. We examine the neurobehavioral phenotypes of FXS and FMR1 premutation as they manifest across the lifespan of the individual. PMID:20981777

  6. Haptoglobin phenotype, preeclampsia risk and the efficacy of vitamin C and E supplementation to prevent preeclampsia in a racially diverse population.

    PubMed

    Weissgerber, Tracey L; Gandley, Robin E; McGee, Paula L; Spong, Catherine Y; Myatt, Leslie; Leveno, Kenneth J; Thorp, John M; Mercer, Brian M; Peaceman, Alan M; Ramin, Susan M; Carpenter, Marshall W; Samuels, Philip; Sciscione, Anthony; Harper, Margaret; Tolosa, Jorge E; Saade, George; Sorokin, Yoram

    2013-01-01

    Haptoglobin's (Hp) antioxidant and pro-angiogenic properties differ between the 1-1, 2-1, and 2-2 phenotypes. Hp phenotype affects cardiovascular disease risk and treatment response to antioxidant vitamins in some non-pregnant populations. We previously demonstrated that preeclampsia risk was doubled in white Hp 2-1 women, compared to Hp 1-1 women. Our objectives were to determine whether we could reproduce this finding in a larger cohort, and to determine whether Hp phenotype influences lack of efficacy of antioxidant vitamins in preventing preeclampsia and serious complications of pregnancy-associated hypertension (PAH). This is a secondary analysis of a randomized controlled trial in which 10,154 low-risk women received daily vitamin C and E, or placebo, from 9-16 weeks gestation until delivery. Hp phenotype was determined in the study prediction cohort (n = 2,393) and a case-control cohort (703 cases, 1,406 controls). The primary outcome was severe PAH, or mild or severe PAH with elevated liver enzymes, elevated serum creatinine, thrombocytopenia, eclampsia, fetal growth restriction, medically indicated preterm birth or perinatal death. Preeclampsia was a secondary outcome. Odds ratios were estimated by logistic regression. Sampling weights were used to reduce bias from an overrepresentation of women with preeclampsia or the primary outcome. There was no relationship between Hp phenotype and the primary outcome or preeclampsia in Hispanic, white/other or black women. Vitamin supplementation did not reduce the risk of the primary outcome or preeclampsia in women of any phenotype. Supplementation increased preeclampsia risk (odds ratio 3.30; 95% confidence interval 1.61-6.82, p<0.01) in Hispanic Hp 2-2 women. Hp phenotype does not influence preeclampsia risk, or identify a subset of women who may benefit from vitamin C and E supplementation to prevent preeclampsia. PMID:23573260

  7. Cardiac hypertrophy, arrhythmogenicity and the new myocardial phenotype. II. The cellular adaptational process.

    PubMed

    Swynghedauw, B; Chevalier, B; Charlemagne, D; Mansier, P; Carré, F

    1997-07-01

    Ventricular fibrosis is not the only structural determinant of arrhythmias in left ventricular hypertrophy. In an experimental model of compensatory cardiac hypertrophy (CCH) the degree of cardiac hypertrophy is also independently linked to ventricular arrhythmias. Cardiac hypertrophy reflects the level of adaptation, and matches the adaptational modifications of the myocardial phenotype. We suggest that these modifications have detrimental aspects. The increased action potential (AP) and QT duration and the prolonged calcium transient both favour spontaneous calcium oscillations, and both are potentially arrhythmogenic and linked to phenotypic changes in membrane proteins. To date, only two ionic currents have been studied in detail: Ito is depressed (likely the main determinant in AP durations), and If, the pacemaker current, is induced in the overloaded ventricular myocytes. In rat CCH, the two components of the sarcoplasmic reticulum, namely Ca(2+)-ATPase and ryanodine receptors, are down-regulated in parallel. Nevertheless, while the inward calcium current is unchanged, the functionally linked duo composed of the Na+/Ca2+ exchanged and (Na+, K+)-ATPase, is less active. Such an imbalance may explain the prolonged calcium transient. The changes in heart rate variability provide information about the state of the autonomic nervous system and has prognostic value even in CCH. Transgenic studies have demonstrated that the myocardial adrenergic and muscarinic receptor content is also a determining factor. During CCH, several phenotypic membrane changes participate in the slowing of contraction velocity and are thus adaptational. They also have a detrimental counterpart and, together with fibrosis, favour arrhythmias. PMID:9302342

  8. A novel begomovirus isolated from sida contains putative cis- and trans-acting replication specificity determinants that have evolved independently in several geographical lineages.

    PubMed

    Mauricio-Castillo, J A; Torres-Herrera, S I; Cárdenas-Conejo, Y; Pastor-Palacios, G; Méndez-Lozano, J; Argüello-Astorga, G R

    2014-09-01

    A novel begomovirus isolated from a Sida rhombifolia plant collected in Sinaloa, Mexico, was characterized. The genomic components of sida mosaic Sinaloa virus (SiMSinV) shared highest sequence identity with DNA-A and DNA-B components of chino del tomate virus (CdTV), suggesting a vertical evolutionary relationship between these viruses. However, recombination analysis indicated that a short segment of SiMSinV DNA-A encompassing the plus-strand replication origin and the 5´-proximal 43 codons of the Rep gene was derived from tomato mottle Taino virus (ToMoTV). Accordingly, the putative cis- and trans-acting replication specificity determinants of SiMSinV were identical to those of ToMoTV but differed from those of CdTV. Modeling of the SiMSinV and CdTV Rep proteins revealed significant differences in the region comprising the small β1/β5 sheet element, where five putative DNA-binding specificity determinants (SPDs) of Rep (i.e., amino acid residues 5, 8, 10, 69 and 71) were previously identified. Computer-assisted searches of public databases led to identification of 33 begomoviruses from three continents encoding proteins with SPDs identical to those of the Rep encoded by SiMSinV. Sequence analysis of the replication origins demonstrated that all 33 begomoviruses harbor potential Rep-binding sites identical to those of SiMSinV. These data support the hypothesis that the Rep β1/β5 sheet region determines specificity of this protein for DNA replication origin sequences. PMID:24737005

  9. Diagnosis, assessment, and phenotyping of COPD: beyond FEV1

    PubMed Central

    Lange, Peter; Halpin, David M; O’Donnell, Denis E; MacNee, William

    2016-01-01

    COPD is now widely recognized as a complex heterogeneous syndrome, having both pulmonary and extrapulmonary features. In clinical practice, the diagnosis of COPD is based on the presence of chronic airflow limitation, as assessed by post-bronchodilator spirometry. The severity of the airflow limitation, as measured by percent predicted FEV1, provides important information to the physician to enable optimization of management. However, in order to accurately assess the complexity of COPD, there need to be other measures made beyond FEV1. At present, there is a lack of reliable and simple blood biomarkers to confirm and further assess the diagnosis of COPD. However, it is possible to identify patients who display different phenotypic characteristics of COPD that relate to clinically relevant outcomes. Currently, validated phenotypes of COPD include alpha-1 antitrypsin deficiency, and “frequent exacerbators”. Recently, a definition and assessment of a new phenotype comprising patients with overlapping features of asthma and COPD has been suggested and is known as “asthma COPD overlap syndrome”. Several other phenotypes have been proposed, but require validation against clinical outcomes. Defining phenotypes requires the assessment of multiple factors indicating disease severity, its impact, and its activity. Recognition and validation of COPD phenotypes has an important role to play in the selection of evidence-based targeted therapy in the future management of COPD, but regardless of the diagnostic terms, patients with COPD should be assessed and treated according to their individual treatable characteristics. PMID:26937185

  10. Choline acetyltransferase mutations causing congenital myasthenic syndrome: molecular findings and genotype-phenotype correlations

    PubMed Central

    Arredondo, Juan; Lara, Marian; Gospe, Sídney M.; Mazia, Claudio G.; Vaccarezza, Maria; Garcia-Erro, Marcela; Bowe, Constance; Chang, Celia; Mezei, Michelle; Maselli, Ricardo A.

    2015-01-01

    Choline acetyltransferase catalyzes the synthesis of acetylcholine at cholinergic nerves. Mutations in human CHAT cause a congenital myasthenic syndrome (CMS) due to impaired synthesis of ACh; this severe variant of the disease is frequently associated with unexpected episodes of potentially fatal apnea. The severity of this condition varies remarkably, and the molecular factors determining this variability are poorly understood. Furthermore, genotype–phenotype correlations have been difficult to establish in patients with biallelic mutations. We analyzed the protein expression of seven ChAT mutations, p.Val136Met, p.Arg207His, p.Arg186Trp, p.Val194Leu, p.Pro211Ala, p.Arg566Cys and p.Ser694Cys, in HEK-293 cells to phosphorylated ChAT, determined their enzyme kinetics and thermal instability, and examined their structural changes. Three mutations, p.Arg207His, p.Arg186Trp and p.Arg566Cys, are novel, and p.Val136Met and p.Arg207His are homozygous in three families and associated with severe disease. The characterization of mutants showed a decrease in the overall catalytic efficiency of ChAT; in particular, those located near the active-site tunnel produced the most seriously disruptive phenotypic effects. On the other hand, p.Val136Met is located far from both active and substrate-binding sites produced the most drastic reduction of ChAT expression. Overall, CHAT mutations producing low enzyme expression and severe kinetic effects are associated with the most severe phenotypes. PMID:26080897

  11. Biophysical Mechanistic Modelling Quantifies the Effects of Plant Traits on Fire Severity: Species, Not Surface Fuel Loads, Determine Flame Dimensions in Eucalypt Forests.

    PubMed

    Zylstra, Philip; Bradstock, Ross A; Bedward, Michael; Penman, Trent D; Doherty, Michael D; Weber, Rodney O; Gill, A Malcolm; Cary, Geoffrey J

    2016-01-01

    The influence of plant traits on forest fire behaviour has evolutionary, ecological and management implications, but is poorly understood and frequently discounted. We use a process model to quantify that influence and provide validation in a diverse range of eucalypt forests burnt under varying conditions. Measured height of consumption was compared to heights predicted using a surface fuel fire behaviour model, then key aspects of our model were sequentially added to this with and without species-specific information. Our fully specified model had a mean absolute error 3.8 times smaller than the otherwise identical surface fuel model (p < 0.01), and correctly predicted the height of larger (≥1 m) flames 12 times more often (p < 0.001). We conclude that the primary endogenous drivers of fire severity are the species of plants present rather than the surface fuel load, and demonstrate the accuracy and versatility of the model for quantifying this. PMID:27529789

  12. Biophysical Mechanistic Modelling Quantifies the Effects of Plant Traits on Fire Severity: Species, Not Surface Fuel Loads, Determine Flame Dimensions in Eucalypt Forests

    PubMed Central

    Bedward, Michael; Penman, Trent D.; Doherty, Michael D.; Weber, Rodney O.; Gill, A. Malcolm; Cary, Geoffrey J.

    2016-01-01

    The influence of plant traits on forest fire behaviour has evolutionary, ecological and management implications, but is poorly understood and frequently discounted. We use a process model to quantify that influence and provide validation in a diverse range of eucalypt forests burnt under varying conditions. Measured height of consumption was compared to heights predicted using a surface fuel fire behaviour model, then key aspects of our model were sequentially added to this with and without species-specific information. Our fully specified model had a mean absolute error 3.8 times smaller than the otherwise identical surface fuel model (p < 0.01), and correctly predicted the height of larger (≥1 m) flames 12 times more often (p < 0.001). We conclude that the primary endogenous drivers of fire severity are the species of plants present rather than the surface fuel load, and demonstrate the accuracy and versatility of the model for quantifying this. PMID:27529789

  13. [Acceleration injuries of the cervical spine in seat-belted automobile drivers. Determination of the trauma mechanism and severity of injury].

    PubMed

    Richter, M; Otte, D; Blauth, M

    1999-05-01

    The analysis of 1,176 whiplash-type neck distortions was sought from a total of 3,838 restrained car driver incident reports. The percentage of these injuries increased from less than 10% in 1985 to over 30% in 1997. These occurred mostly with head-on or with multiple collisions, and only in 15% with pure rear-end collisions. In 23.2%, delta v amounted 10 km/h or less, which corresponds to a very minor crash. The average delta v was the highest in the cases of head-on collisions. Letters were sent to the injured to find out about the duration and type of complaints caused by a cervical spine injury. Of the 138 patients who returned the questionnaires, 121 (88%) indicated that they had or were still suffering from their symptoms. Percentage of various complaints were as follows: pain (74%), tension (6%) and stiffness (5%) in the head (27%), neck (55%) and shoulder (8%). The duration of the complaints was longest after multiple collisions and when the onset of complaints was later than 24 hours after trauma. Women and elderly persons predominated slightly in the group with longer duration of complaints. A correlation between the severity of the accompanying injuries and duration of complaints occurred. Also, with this retrospective study there was considerable difficulties in the lack of adequate follow-up for these patients with less severe injuries. In order to better evaluate this problem, prospective studies are necessary which include documentation of diagnosis, treatment protocols, duration and type of complaints. PMID:10394600

  14. The levels of urinary glycosaminoglycans of patients with attenuated and severe type of mucopolysaccharidosis II determined by liquid chromatography-tandem mass spectrometry.

    PubMed

    Mashima, Ryuichi; Sakai, Eri; Tanaka, Misa; Kosuga, Motomichi; Okuyama, Torayuki

    2016-06-01

    Glycosaminoglycans (GAGs) play important roles on the regulation of extracellular signaling, neuronal development, and cartilage maintenance. The extracellular concentration of total GAGs has been used as an established measure for the diagnosis of mucopolysaccharidoses (MPSs). Heparan sulfate (HS), Dermatan sulfate (DS) and chondroitin sulfate are known to be elevated in the GAGs under pathological conditions associated with MPS. Furthermore, the selective accumulation of disease-specific one of, or a combination of, them has also been used for the estimation of subtypes of MPS. A previously developed method [Auray-Blais C et al. Molecular Genetics and Metabolism 102 (2011) 49-56.] measures the concentration of GAGs using liquid chromatography with tandem mass spectrometry (LC-MS/MS) with higher precision. To ask whether the selective accumulation of HS and DS in the urine of MPS II patients discriminate the attenuated and severe type of MPS II, we examined the concentrations of HS and DS by this methodology. Compared to the healthy controls, we found a marked elevation of HS and DS in all of the MPS II-affected patients. Among patients who received ERT with confirmed elevation of antibody titer, the concentrations of HS in the urine of patients with attenuated type were lower than those with severe type of MPS II. In these patients, the concentrations of DS by LC-MS/MS and of total GAG by DMB failed to depend on the accumulation of antibody. These results suggest that the LC-MS/MS method employed in this study might discriminate the subtypes of MPS II in different clinical background. PMID:27331006

  15. Differences in the timing and magnitude of Pkd1 gene deletion determine the severity of polycystic kidney disease in an orthologous mouse model of ADPKD.

    PubMed

    Rogers, Kelly A; Moreno, Sarah E; Smith, Laurie A; Husson, Hervé; Bukanov, Nikolay O; Ledbetter, Steven R; Budman, Yeva; Lu, Yuefeng; Wang, Bing; Ibraghimov-Beskrovnaya, Oxana; Natoli, Thomas A

    2016-06-01

    Development of a disease-modifying therapy to treat autosomal dominant polycystic kidney disease (ADPKD) requires well-characterized preclinical models that accurately reflect the pathology and biochemical changes associated with the disease. Using a Pkd1 conditional knockout mouse, we demonstrate that subtly altering the timing and extent of Pkd1 deletion can have a significant impact on the origin and severity of kidney cyst formation. Pkd1 deletion on postnatal day 1 or 2 results in cysts arising from both the cortical and medullary regions, whereas deletion on postnatal days 3-8 results in primarily medullary cyst formation. Altering the extent of Pkd1 deletion by modulating the tamoxifen dose produces dose-dependent changes in the severity, but not origin, of cystogenesis. Limited Pkd1 deletion produces progressive kidney cystogenesis, accompanied by interstitial fibrosis and loss of kidney function. Cyst growth occurs in two phases: an early, rapid growth phase, followed by a later, slow growth period. Analysis of biochemical pathway changes in cystic kidneys reveals dysregulation of the cell cycle, increased proliferation and apoptosis, activation of Mek-Erk, Akt-mTOR, and Wnt-β-catenin signaling pathways, and altered glycosphingolipid metabolism that resemble the biochemical changes occurring in human ADPKD kidneys. These pathways are normally active in neonatal mouse kidneys until repressed around 3 weeks of age; however, they remain active following Pkd1 deletion. Together, this work describes the key parameters to accurately model the pathological and biochemical changes associated with ADPKD in a conditional mouse model. PMID:27356569

  16. Epidemiology and Pulmonary Physiology of Severe Asthma.

    PubMed

    O'Toole, Jacqueline; Mikulic, Lucas; Kaminsky, David A

    2016-08-01

    The epidemiology and physiology of severe asthma are inherently linked because of varying phenotypes and expressions of asthma throughout the population. To understand how to better treat severe asthma, we must use both population data and physiologic principles to individualize therapies among groups with similar expressions of this disease. PMID:27401616

  17. On-time clinical phenotype prediction based on narrative reports

    PubMed Central

    Bejan, Cosmin A.; Vanderwende, Lucy; Evans, Heather L.; Wurfel, Mark M.; Yetisgen-Yildiz, Meliha

    2013-01-01

    In this paper we describe a natural language processing system which is able to predict whether or not a patient exhibits a specific phenotype using the information extracted from the narrative reports associated with the patient. Furthermore, the phenotypic annotations from our report dataset were performed at the report level which allows us to perform the prediction of the clinical phenotype at any point in time during the patient hospitalization period. Our experiments indicate that an important factor in achieving better results for this problem is to determine how much information to extract from the patient reports in the time interval between the patient admission time and the current prediction time. PMID:24551325

  18. Precision Medicine for Continuing Phenotype Expansion of Human Genetic Diseases

    PubMed Central

    Yu, Hui; Zhang, Victor Wei

    2015-01-01

    Determining the exact genetic causes for a patient and providing definite molecular diagnoses are core elements of precision medicine. Individualized patient care is often limited by our current knowledge of disease etiologies and commonly used phenotypic-based diagnostic approach. The broad and incompletely understood phenotypic spectrum of a disease and various underlying genetic heterogeneity also present extra challenges to our clinical practice. With the rapid adaptation of new sequence technology in clinical setting for diagnostic purpose, phenotypic expansions of disease spectrum are becoming increasingly common. Understanding the underlying molecular mechanisms will help us to integrate genomic information into the workup of individualized patient care and make better clinical decisions. PMID:26137492

  19. Surface proteins of Bordetella pertussis: comparison of virulent and avirulent strains and effects of phenotypic modulation.

    PubMed Central

    Armstrong, S K; Parker, C D

    1986-01-01

    The surface proteins of several Bordetella strains and their modulated derivatives were examined by surface radioiodination, cell fractionation, and Western blotting. A surface protein with a high Mr, missing in a mutant lacking the filamentous hemagglutinin, was identified in virulent Bordetella pertussis and Bordetella parapertussis cells and was absent in avirulent B. pertussis strains. The electrophoretic profiles of lipopolysaccharide and the 40,000-Mr anion-selective porin were not determinants which correlated with phase variation or phenotypic modulation. At least three envelope proteins (91,000, 32,000, and 30,000 molecular weight) were found only in virulent B. pertussis strains and were absent or diminished in the avirulent phase and most phenotypically modulated strains. Two transposon-induced mutants unable to produce hemolysin, dermonecrotic toxin, pertussis toxin, and filamentous hemagglutinin also lacked these three envelope proteins, confirming that virulence-associated envelope proteins were genetically regulated with other virulence-associated traits. Images PMID:2876957

  20. A Grand Challenge. 2. Phenotypic Profiling of a Natural Product Library on Parkinson's Patient-Derived Cells.

    PubMed

    Vial, Marie-Laure; Zencak, Dusan; Grkovic, Tanja; Gorse, Alain-Dominique; Mackay-Sim, Alan; Mellick, George D; Wood, Stephen A; Quinn, Ronald J

    2016-08-26

    Harnessing the inherent biological relevance of natural products requires a method for the recognition of biological effects that may subsequently lead to the discovery of particular targets. An unbiased multidimensional profiling method was used to examine the activities of natural products on primary cells derived from a Parkinson's disease patient. The biological signature of 482 natural products was examined using multiparametric analysis to investigate known cellular pathways and organelles implicated in Parkinson's disease such as mitochondria, lysosomes, endosomes, apoptosis, and autophagy. By targeting several cell components simultaneously the chance of finding a phenotype was increased. The phenotypes were then clustered using an uncentered correlation. The multidimensional phenotypic screening showed that all natural products, in our screening set, were biologically relevant compounds as determined by an observed phenotypic effect. Multidimensional phenotypic screening can predict the cellular function and subcellular site of activity of new compounds, while the cluster analysis provides correlation with compounds with known mechanisms of action. This study reinforces the value of natural products as biologically relevant compounds. PMID:27447544

  1. Central nervous system phenotypes in craniosynostosis

    PubMed Central

    Aldridge, Kristina; Marsh, Jeffrey L; Govier, Daniel; Richtsmeier, Joan T

    2002-01-01

    Though reduction in the number of cranial elements through loss of a suture is a recognized trend in vertebrate evolution, the premature closure of cranial sutures in humans, craniosynostosis, is considered a pathological condition. Previous research on craniosynostosis has focused primarily on the skeletal phenotype, but the intimate relationship between the developing central nervous system (CNS) and skull is well documented. We investigate the morphology of the CNS in patients with isolated craniosynostosis through an analysis of cortical and subcortical features using 3-D magnetic resonance images (MRI). Results show that a distinct CNS phenotype can be defined for specific diagnostic categories. Many differences in CNS morphology observed in the patient samples may be anticipated based on skeletal morphology, but others are not reflected in the skull. We propose a developmental approach to determining the cause of premature suture fusion, which includes investigation of the craniofacial complex as a system, rather than study of isolated tissues. PMID:12171474

  2. Commentary: behavioral phenotype.

    PubMed

    Oitzl, Melly S

    2008-01-01

    PTSD arises by definition as a direct consequence of the experience of an acute severe stressor. The formation of traumatic memory and its extinction, sympathetic and adrenocortical stress systems activity in relation to individual vulnerability form the core of animal models for PTSD. PMID:18037010

  3. Determination of spring modulus for several types of elastomeric materials (O-rings) and establishment of an open database for seals

    SciTech Connect

    McMurtry, W.M.; Hohnstreiter, G.F.

    1995-12-31

    Seals that provide the containment system interface between the packaging body and closure must function in high and low temperature environments, under dynamic and static loading conditions, and with different types of contained media. It is one of the most critical elements in the container since the container fails to meet regulations if the seal does not function properly. A research and testing program for seal materials was initiated at Sandia in 1988 with the goal of characterizing the behavior of seal materials commonly used in packages conditions as specified in the regulations (NRC IOCFR Part 71) and American National Standards Institute (ANSI) 14.5. The performance of elastomeric seals in undeformed closures at both high and low temperatures has been investigated (Bronowski 1995). Work has begun with this program to determine the response of elastomeric seals to fast acting dynamic deformations`` in the closure. The response of elastomeric o-ring seals during closure movements due to long-term deformations has already been characterized. What has not been well characterized are short-term closure movements with durations of only a few milliseconds that result in the so called ``burp`` release. Methods for generating this type of response in a repeatable manner had not been developed and standard leak detection equipment does not have a fast enough response time to measure these transient events. One factor which affects the length of the burp is the ability of the o-ring to quickly close the gap to prevent a significant leak. The dynamic characteristics of the elastomeric o-ring material including the dynamic spring modulus and internal damping are directly related to its ability to quickly close the gap. A set of tests designed to determine the dynamic properties for various material types and durometers (hardness) of elastomers that were both lubricated and dry at ambient temperature were conducted.

  4. Microstructural alterations in trigeminal neuralgia determined by diffusion tensor imaging are independent of symptom duration, severity, and type of neurovascular conflict.

    PubMed

    Lutz, Juergen; Thon, Niklas; Stahl, Robert; Lummel, Nina; Tonn, Joerg-Christian; Linn, Jennifer; Mehrkens, Jan-Hinnerk

    2016-03-01

    OBJECT In this prospective study diffusion tensor imaging (DTI) was used to evaluate the influence of clinical and anatomical parameters on structural alterations within the fifth cranial nerve in patients with trigeminal neuralgia (TN) due to neurovascular compression. METHODS Overall, 81 patients (40 men and 41 women; mean age 60 ± 5 years) with typical TN were included who underwent microsurgical decompression. Preoperative 3.0-T high-resolution MRI and DTI were analyzed in a blinded fashion. The respective fractional anisotropy (FA) and apparent diffusion coefficient values were compared with the clinical, imaging, and intraoperative data. This study was approved by the institutional review board, and written informed consent was obtained from all patients. RESULTS DTI analyses revealed significantly lower FA values within the vulnerable zone of the affected trigeminal nerve compared with the contralateral side (p = 0.05). The DTI analyses also included 3 patients without clear evidence of neurovascular conflict on preoperative MRI. No differences were seen between arterial and venous compression. Lower FA values were found 5 months after symptom onset; however, no correlation was found with the duration of symptoms or severity of compression. CONCLUSIONS DTI analysis allows the quantification of structural alterations, even in those patients without any discernible neurovascular contact on MRI. Moreover, our findings support the hypothesis that both the arteries and veins can cause structural alterations that lead to TN. These aspects can be useful for making treatment decisions. PMID:26406792

  5. [Determination of silver and cerium in the liver and the kidney from a severely burned infant treated with silver sulfadiazine and cerium nitrate].

    PubMed

    Hirakawa, K

    1983-02-01

    Silver and cerium in the liver and the kidney from severely burned infant were analyzed by neutron activation method. The patient was treated topically with cerium nitrate/silver sulfadiazine cream and cerium nitrate solution for 3 months. Then, the treatment with these drugs was stopped because of abdominal distention. The patient died 1 month after the cessation of the treatment with these drugs. The tissue specimens, blank liver sample and reference standards were irradiated with TRIGA MARK II Reactor of Rikkyo University. About 1 month after the irradiation, the activities were measured with a Ge(Li) detector coupled to a 4096 channel pulse height analyzer. A large amount of silver was detected both in the liver and in the kidney and a trace of cerium only in the liver. A considerable amount of silver was detected in the liver and its quantity was about 1600 times more than that of normal livers reported by Hamilton, Minski and Cleary (1972-73). Neither silver nor cerium were detected in the blank liver. These results suggest that prolonged topical chemotherapy of cerium nitrate/silver sulfadiazine cream and cerium nitrate solution for the extensive burn injuries causes considerable absorption of silver and cerium into the liver and the kidney. PMID:6867381

  6. Effect of reducing the topographical altitude of the Tibetan Plateau on a severe winter drought in eastern China as determined using RAMS

    NASA Astrophysics Data System (ADS)

    Meng, Chunchun; Ma, Yaoming; Han, Cunbo; Gou, Peng

    2016-05-01

    Regional Atmospheric Modeling System (RAMS) was applied to the study of the effect of the topographical altitude of the Tibetan Plateau (TP) on a severe drought event which took place in eastern China from November 2008 to January 2009. Two simulations of this drought event were conducted: a control simulation (CNTRL run) using original model settings and a sensitive simulation (TOPO run), where no change other than to reduce the TP topography by 50 %. The results show that the CNTRL simulation validates RAMS by reproducing this drought event fairly accurately. However, as part of the TOPO simulation, the total heat flux showed a decrease over most parts of the TP, latent heat flux underwent a significant increase over the southeastern TP, contrary to sensible heat, and a universal decrease over eastern China; this led to an increase in precipitation over the southeastern TP and a decrease in precipitation over eastern China. The decrease of total heat flux over the TP is collocated with an anomalous anticyclonic circulation from the TP to the coasts of southeastern China. Changes in atmospheric circulation and low-level water vapor transport pathways were consistent with changes in precipitation. In general, reducing the topographical altitude of the TP worsens drought in eastern China and moreover causes a significant decrease in precipitation over southern China.

  7. Application of chemometrics in determination of the acid dissociation constants (pKa) of several benzodiazepine derivatives as poorly soluble drugs in the presence of ionic surfactants.

    PubMed

    Shayesteh, Tavakol Heidary; Radmehr, Moojan; Khajavi, Farzad; Mahjub, Reza

    2015-03-10

    In this study, the acid dissociation constants (pKa) of some benzodiazepine derivatives including chlordiazepoxide, clonazepam, lorazepam, and oxazepam in aqueous micellar solution were determined spectrophotometrically at an ionic strength of 0.1M at 25°C. The effect of cetyl trimethylammonium bromide (CTAB) as a cationic and sodium n-dodecyl sulfate(SDS) as an anionic surfactant on the absorption spectra of benzodiazepine drugs at different pH values were studied. The acidity constants of all related species are estimated by considering the surfactant concept and the application of chemometric methods using the whole spectral fitting of the collected data to an established factor analysis model. DATAN® software (Ver. 5.0, Multid Analyses AB, and Goteborg, Sweden) was applied to determine the acidity constants. In this study, a simple and fast method to determine the ionization constant (pKa) of poorly soluble drugs was developed using surfactants. The acidity constant (i.e. pKa) for chlordiazepoxide, clonazepam, lorazepam, and oxazepam were reported as 4.62, pKa1 value of 1.52 and pKa2 value of 10.51, pKa1 value of 1.53 and pKa2 value of 10.92 and pKa1 value 1.63 and pKa2 value of 11.21 respectively. The results showed that the peak values in the spectrophotometric absorption spectra of drugs are influenced by the presence of anionic and cationic surfactants. According to the results, by changing the SDS concentration from 0 to 0.05M, the pKa of chlordiazepoxide was increased to 5.9, the pKa1 of lorazepam was decreased to 0.1 while the pKa2 was increased to 11.5. Increase in SDS concentration has not shown significant alteration in pKa of clonazepam and oxazepam. Results indicate that by Changing the CTAB concentration from 0 to 0.05M, the pKa of chlordiazepoxide was reduced to 4.4, the pKa1 of clonazepam was decreased to 0.1 and the pKa2 was decreased to 9.1, the pKa1 of lorazepam was decreased to 0.4 and the pKa2 was decreased to 9.4, the pKa1 of oxazepam was

  8. Capturing phenotypes for precision medicine.

    PubMed

    Robinson, Peter N; Mungall, Christopher J; Haendel, Melissa

    2015-10-01

    Deep phenotyping followed by integrated computational analysis of genotype and phenotype is becoming ever more important for many areas of genomic diagnostics and translational research. The overwhelming majority of clinical descriptions in the medical literature are available only as natural language text, meaning that searching, analysis, and integration of medically relevant information in databases such as PubMed is challenging. The new journal Cold Spring Harbor Molecular Case Studies will require authors to select Human Phenotype Ontology terms for research papers that will be displayed alongside the manuscript, thereby providing a foundation for ontology-based indexing and searching of articles that contain descriptions of phenotypic abnormalities-an important step toward improving the ability of researchers and clinicians to get biomedical information that is critical for clinical care or translational research. PMID:27148566

  9. Finding Our Way through Phenotypes

    PubMed Central

    Deans, Andrew R.; Lewis, Suzanna E.; Huala, Eva; Anzaldo, Salvatore S.; Ashburner, Michael; Balhoff, James P.; Blackburn, David C.; Blake, Judith A.; Burleigh, J. Gordon; Chanet, Bruno; Cooper, Laurel D.; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T. Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E.; Dumontier, Michel; Franz, Nico M.; Friedrich, Frank; Gkoutos, George V.; Haendel, Melissa; Harmon, Luke J.; Hayamizu, Terry F.; He, Yongqun; Hines, Heather M.; Ibrahim, Nizar; Jackson, Laura M.; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J.; Le Novère, Nicolas; Lundberg, John G.; Macklin, James; Mast, Austin R.; Midford, Peter E.; Mikó, István; Mungall, Christopher J.; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J.; Richter, Stefan; Robinson, Peter N.; Ruttenberg, Alan; Schulz, Katja S.; Segerdell, Erik; Seltmann, Katja C.; Sharkey, Michael J.; Smith, Aaron D.; Smith, Barry; Specht, Chelsea D.; Squires, R. Burke; Thacker, Robert W.; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D.; Vogt, Lars; Wall, Christine E.; Walls, Ramona L.; Westerfeld, Monte; Wharton, Robert A.; Wirkner, Christian S.; Woolley, James B.; Yoder, Matthew J.; Zorn, Aaron M.; Mabee, Paula

    2015-01-01

    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. PMID:25562316

  10. Epigenetics in heart failure phenotypes.

    PubMed

    Berezin, Alexander

    2016-12-01

    Chronic heart failure (HF) is a leading clinical and public problem posing a higher risk of morbidity and mortality in different populations. HF appears to be in both phenotypic forms: HF with reduced left ventricular ejection fraction (HFrEF) and HF with preserved left ventricular ejection fraction (HFpEF). Although both HF phenotypes can be distinguished through clinical features, co-morbidity status, prediction score, and treatment, the clinical outcomes in patients with HFrEF and HFpEF are similar. In this context, investigation of various molecular and cellular mechanisms leading to the development and progression of both HF phenotypes is very important. There is emerging evidence that epigenetic regulation may have a clue in the pathogenesis of HF. This review represents current available evidence regarding the implication of epigenetic modifications in the development of different HF phenotypes and perspectives of epigenetic-based therapies of HF. PMID:27335803

  11. Capturing phenotypes for precision medicine

    PubMed Central

    Robinson, Peter N.; Mungall, Christopher J.; Haendel, Melissa

    2015-01-01

    Deep phenotyping followed by integrated computational analysis of genotype and phenotype is becoming ever more important for many areas of genomic diagnostics and translational research. The overwhelming majority of clinical descriptions in the medical literature are available only as natural language text, meaning that searching, analysis, and integration of medically relevant information in databases such as PubMed is challenging. The new journal Cold Spring Harbor Molecular Case Studies will require authors to select Human Phenotype Ontology terms for research papers that will be displayed alongside the manuscript, thereby providing a foundation for ontology-based indexing and searching of articles that contain descriptions of phenotypic abnormalities—an important step toward improving the ability of researchers and clinicians to get biomedical information that is critical for clinical care or translational research. PMID:27148566

  12. Finding our way through phenotypes.

    PubMed

    Deans, Andrew R; Lewis, Suzanna E; Huala, Eva; Anzaldo, Salvatore S; Ashburner, Michael; Balhoff, James P; Blackburn, David C; Blake, Judith A; Burleigh, J Gordon; Chanet, Bruno; Cooper, Laurel D; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E; Dumontier, Michel; Franz, Nico M; Friedrich, Frank; Gkoutos, George V; Haendel, Melissa; Harmon, Luke J; Hayamizu, Terry F; He, Yongqun; Hines, Heather M; Ibrahim, Nizar; Jackson, Laura M; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J; Le Novère, Nicolas; Lundberg, John G; Macklin, James; Mast, Austin R; Midford, Peter E; Mikó, István; Mungall, Christopher J; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J; Richter, Stefan; Robinson, Peter N; Ruttenberg, Alan; Schulz, Katja S; Segerdell, Erik; Seltmann, Katja C; Sharkey, Michael J; Smith, Aaron D; Smith, Barry; Specht, Chelsea D; Squires, R Burke; Thacker, Robert W; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D; Vogt, Lars; Wall, Christine E; Walls, Ramona L; Westerfeld, Monte; Wharton, Robert A; Wirkner, Christian S; Woolley, James B; Yoder, Matthew J; Zorn, Aaron M; Mabee, Paula

    2015-01-01

    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. PMID:25562316

  13. Determination of cocaine and its major metabolite benzoylecgonine in several matrices obtained from deceased individuals with presumed drug consumption prior to death.

    PubMed

    Alvear, Eduardo; von Baer, Dietrich; Mardones, Claudia; Hitschfeld, Antonieta

    2014-03-01

    In the field of forensic toxicology, femoral blood is the most useful sample for the determination and quantification of drugs; however, cases in which blood is unavailable are common. In such cases, validated methodologies for drug determination in alternative matrices can be decisive in the investigation of a case. In particular, when femoral blood is unavailable for analysis for the presence of systemic exposure to cocaine and its principal metabolite, benzoylecgonine, validated methodologies from matrices other than blood that can be obtained in the autopsy room would be useful to the forensic toxicologist in the evaluation of a specific forensic case. To address this issue, we implemented and compared in our study the systematic evaluation of extraction, chromatographic separation, and quantification of cocaine and benzoylecgonine in different biological matrices (right and left cardiac blood, femoral arterial and venous blood, urine, vitreous humor, cerebrospinal fluid, brain accumbens nucleus, brain ventral tegmental area, and liver). The studied matrices were those most likely to be obtained from different autopsy rooms at the time of forensic testing in deceased individuals who are presumed of antemortem drug consumption. Solid phase extraction of analytes from the different matrices was performed using C-8/SCX mixed-phase columns, and gas chromatographic mass spectrometry separation was performed using detection in single-ion monitoring mode. The methodological validation was performed for all the studied matrices, and the results showed similar sensitivity and recoveries without statistical differences between the studied matrices. The methods were applied to evaluate a thanatological case using all the study matrices, showing unequal postmortem distribution of cocaine and benzoylecgonine throughout the different matrices tested. The present work opens the option of applying appropriate methodologies in the analysis of matrices, other than the usual

  14. A study of selective spectrophotometric methods for simultaneous determination of Itopride hydrochloride and Rabeprazole sodium binary mixture: Resolving sever overlapping spectra

    NASA Astrophysics Data System (ADS)

    Mohamed, Heba M.

    2015-02-01

    Itopride hydrochloride (IT) and Rabeprazole sodium (RB) are co-formulated together for the treatment of gastro-esophageal reflux disease. Three simple, specific and accurate spectrophotometric methods were applied and validated for simultaneous determination of Itopride hydrochloride (IT) and Rabeprazole sodium (RB) namely; constant center (CC), ratio difference (RD) and mean centering of ratio spectra (MCR) spectrophotometric methods. Linear correlations were obtained in range of 10-110 μg/μL for Itopride hydrochloride and 4-44 μg/mL for Rabeprazole sodium. No preliminary separation steps were required prior the analysis of the two drugs using the proposed methods. Specificity was investigated by analyzing the synthetic mixtures containing the two cited drugs and their capsules dosage form. The obtained results were statistically compared with those obtained by the reported method, no significant difference was obtained with respect to accuracy and precision. The three methods were validated in accordance with ICH guidelines and can be used for quality control laboratories for IT and RB.

  15. Fluctuation and noise propagation in phenotypic transition cascades of clonal populations

    NASA Astrophysics Data System (ADS)

    Pei, Qi-ming; Zhan, Xuan; Yang, Li-jian; Shen, Jian; Wang, Li-fang; Qui, Kang; Liu, Ting; Kirunda, J. B.; Yousif, A. A. M.; Li, An-bang; Jia, Ya

    2015-07-01

    Quantitative modeling of fluctuations of each phenotype is a crucial step towards a fundamental understanding of noise propagation through various phenotypic transition cascades. The theoretical formulas for noise propagation in various phenotypic transition cascades are derived by using the linear noise approximation of master equation and the logarithmic gain. By virtue of the theoretical formulas, we study the noise propagation in bidirectional and unidirectional phenotypic transition cascades, respectively. It is found that noise propagation in these two phenotypic transition cascades evidently differs: In the bidirectional cascade, a systemic random environment is provided by a correlated global component. The total noise of each phenotype is mainly determined by the intrinsic noise and the transmitted noise from other phenotypes. The intrinsic noise enlarged by interconversion through an added part shows a novel noise propagation mechanism. However, in the unidirectional cascade, the random environment of each downstream phenotype is provided by upstream phenotypes. The total noise of each downstream phenotype is mainly determined by the transmitted noises from upstream phenotypes. The intrinsic noise and the conversion noise can propagate in both bidirectional and unidirectional phenotypic transition cascades.

  16. Fluctuation and noise propagation in phenotypic transition cascades of clonal populations.

    PubMed

    Pei, Qi-ming; Zhan, Xuan; Yang, Li-jian; Shen, Jian; Wang, Li-fang; Qui, Kang; Liu, Ting; Kirunda, J B; Yousif, A A M; Li, An-bang; Jia, Ya

    2015-07-01

    Quantitative modeling of fluctuations of each phenotype is a crucial step towards a fundamental understanding of noise propagation through various phenotypic transition cascades. The theoretical formulas for noise propagation in various phenotypic transition cascades are derived by using the linear noise approximation of master equation and the logarithmic gain. By virtue of the theoretical formulas, we study the noise propagation in bidirectional and unidirectional phenotypic transition cascades, respectively. It is found that noise propagation in these two phenotypic transition cascades evidently differs: In the bidirectional cascade, a systemic random environment is provided by a correlated global component. The total noise of each phenotype is mainly determined by the intrinsic noise and the transmitted noise from other phenotypes. The intrinsic noise enlarged by interconversion through an added part shows a novel noise propagation mechanism. However, in the unidirectional cascade, the random environment of each downstream phenotype is provided by upstream phenotypes. The total noise of each downstream phenotype is mainly determined by the transmitted noises from upstream phenotypes. The intrinsic noise and the conversion noise can propagate in both bidirectional and unidirectional phenotypic transition cascades. PMID:26274216

  17. Phenotype Sequencing: Identifying the Genes That Cause a Phenotype Directly from Pooled Sequencing of Independent Mutants

    PubMed Central

    Harper, Marc A.; Chen, Zugen; Toy, Traci; Machado, Iara M. P.; Nelson, Stanley F.; Liao, James C.; Lee, Christopher J.

    2011-01-01

    Random mutagenesis and phenotype screening provide a powerful method for dissecting microbial functions, but their results can be laborious to analyze experimentally. Each mutant strain may contain 50–100 random mutations, necessitating extensive functional experiments to determine which one causes the selected phenotype. To solve this problem, we propose a “Phenotype Sequencing” approach in which genes causing the phenotype can be identified directly from sequencing of multiple independent mutants. We developed a new computational analysis method showing that 1. causal genes can be identified with high probability from even a modest number of mutant genomes; 2. costs can be cut many-fold compared with a conventional genome sequencing approach via an optimized strategy of library-pooling (multiple strains per library) and tag-pooling (multiple tagged libraries per sequencing lane). We have performed extensive validation experiments on a set of E. coli mutants with increased isobutanol biofuel tolerance. We generated a range of sequencing experiments varying from 3 to 32 mutant strains, with pooling on 1 to 3 sequencing lanes. Our statistical analysis of these data (4099 mutations from 32 mutant genomes) successfully identified 3 genes (acrB, marC, acrA) that have been independently validated as causing this experimental phenotype. It must be emphasized that our approach reduces mutant sequencing costs enormously. Whereas a conventional genome sequencing experiment would have cost $7,200 in reagents alone, our Phenotype Sequencing design yielded the same information value for only $1200. In fact, our smallest experiments reliably identified acrB and marC at a cost of only $110–$340. PMID:21364744

  18. Determination of hydraulic properties of the Callovo-Oxfordian argillite at the bure site: Synthesis of the results obtained in deep boreholes using several in situ investigation techniques

    NASA Astrophysics Data System (ADS)

    Distinguin, Marc; Lavanchy, Jean-Marc

    Since 1991, ANDRA ( Agence Nationale pour la gestion des Déchets Radioactifs - National Radioactive Waste Management Agency) has been performing research on the possibility of geologic disposal of high level radioactive waste. In 1999, Andra began constructing an Underground Research Laboratory at Bure, a site located on the border of the Meuse-Haute-Marne departments, 300 km East of Paris. The laboratory is investigating the Callovo-Oxfordian argillite, a 130 m thick middle Jurassic stratum, at a depth of about 420 m. Argillite is a clay-rich sedimentary rock with low-permeability. Between 1994 and 2004, Andra collected from deep boreholes an impressive wealth of data covering a wide range of geosciences. This paper focuses on the hydraulic data related to argillite, including the results from short-term hydraulic packer tests and long-term monitoring of the formation pressures. Three types of tools are used on the site for investigations in deep boreholes. The first one is a conventional packer test tool used in the petroleum industry and adapted for hydrogeological purposes. The main objective is to determinate the permeability of the formation through short-term tests (24-72 h) at about 10 regular intervals. The two other types of tool are permanent monitoring devices. The electromagnetic pressure gauge (EPG) is totally isolated from the surface perturbations. There are no electric or hydraulic lines to the surface and the borehole is cemented. The advantage of this tool is that the formation almost recovers its initial pressure, avoiding disturbances from surface. Although the multi-packer equipment, installed in an open borehole can be affected by surface perturbations, it is used to measure pressure at different isolated levels in the same borehole ( i. e., 11 chambers in one borehole). Evaluations of the formation pressure (freshwater head) and hydraulic conductivity have been performed for all intervals investigated (19 short-term packer tests and 15 long

  19. Phenotypic Heterogeneity of Monogenic Frontotemporal Dementia

    PubMed Central

    Benussi, Alberto; Padovani, Alessandro; Borroni, Barbara

    2015-01-01

    Frontotemporal dementia (FTD) is a genetically and pathologically heterogeneous disorder characterized by personality changes, language impairment, and deficits of executive functions associated with frontal and temporal lobe degeneration. Different phenotypes have been defined on the basis of presenting clinical symptoms, i.e., the behavioral variant of FTD, the agrammatic variant of primary progressive aphasia, and the semantic variant of PPA. Some patients have an associated movement disorder, either parkinsonism, as in progressive supranuclear palsy and corticobasal syndrome, or motor neuron disease (FTD–MND). A family history of dementia is found in 40% of cases of FTD and about 10% have a clear autosomal-dominant inheritance. Genetic studies have identified several genes associated with monogenic FTD: microtubule-associated protein tau, progranulin, TAR DNA-binding protein 43, valosin-containing protein, charged multivesicular body protein 2B, fused in sarcoma, and the hexanucleotide repeat expansion in intron 1 of the chromosome 9 open reading frame 72. Patients often present with an extensive phenotypic variability, even among different members of the same kindred carrying an identical disease mutation. The objective of the present work is to review and evaluate available literature data in order to highlight recent advances in clinical, biological, and neuroimaging features of monogenic frontotemporal lobar degeneration and try to identify different mechanisms underlying the extreme phenotypic heterogeneity that characterizes this disease. PMID:26388768

  20. Molecular mapping of the Edwards syndrome phenotype to two noncontiguous regions on chromosome 18

    SciTech Connect

    Boghosian-Sell, L.; Mewar, R.; Harrison, W.; Shapiro, R.M.; Zackai, E.H.; Carey, J.; Davis-Keppen, L.; Hudgins, L.; Overhauser, J.

    1994-09-01

    In an effort to identify regions on chromosome 18 that may be critical in the appearance of the Edwards syndrome phenotype, the authors have analyzed six patients with partial duplication of chromosome 18. Four of the patients have duplications involving the distal half of 18q (18q21.1-qter) and are very mildly affected. The remaining two patients have most of 18q (18q12.1-qter) duplicated, are severely affected, and have been diagnosed with Edwards syndrome. The authors have employed FISH, using DNA probes from a chromosome 18-specific library, for the precise determination of the duplicated material in each of these patients. The clinical features and the extent of the chromosomal duplication in these patients were compared with four previously reported partial trisomy 18 patients, to identify regions of chromosome 18 that may be responsible for certain clinical features of trisomy 18. The comparative analysis confirmed that there is no single region on 18q that is sufficient to produce the trisomy 18 phenotype and identified two regions on 18q that may work in conjunction to produce the Edwards syndrome phenotype. In addition, correlative analysis indicates that duplication of 18q12.3-q22.1 may be associated with more severe mental retardation in trisomy 18 individuals. 25 refs., 3 figs., 1 tab.