Carbonic anhydrase activity in primary sensory neurons. II. Influence of environmental factors on the phenotypic expression of the enzyme in dissociated cultures of chicken dorsal root ganglion cells.

Neuronal subpopulations of dorsal root ganglion (DRG) cells in the chicken exhibit carbonic anhydrase (CA) activity. To determine whether CA activity is expressed by DRG cells maintained in in vitro cultures, dissociated DRG cells from 10-day-old chick embryos were cultured on a collagen substrate. The influence exerted by environmental factors on the enzyme expression was tested under various conditions of culture. Neuron-enriched cell cultures and mixed DRG-cell cultures (including numerous non-neuronal cells) were performed either in a defined medium or in a horse serum-supplemented medium. In all the tested conditions, subpopulations of cultured sensory neurons expressed CA activity in their cell bodies, while their neurites were rarely stained; in each case, the percentage of CA-positive neurons declined with the age of the cultures. The number and the persistence of neurons possessing CA activity as well as the intensity of the reaction were enhanced by addition of horse serum. In contrast, the expression of the neuronal CA activity was not affected by the presence of non-neuronal cells or by the rise of CO2 concentration. Thus, the appearance and disappearance of neuronal subpopulations expressing CA activity may be decisively influenced by factors contained in the horse serum. The loss of CA-positive neurons with time could result from a cell selection or from genetic repression. Analysis of the time curves does not support a preferential cell death of CA-positive neurons but suggests that the eventual conversion of CA-positive neurons into CA-negative neurons results from a loss of the enzyme activity. These results indicate that the phenotypic expression of cultured sensory neurons is dependent on defined environmental factors.

Influence of environmental factors on the expression of phenotypic characters by chicken dorsal root ganglion cells in culture.

Primary sensory neurons were grown under four conditions of culture. The influence of nonneuronal cells, horse serum or both was studied on the phenotypic expression of certain neuronal subpopulations. The number of neurons expressing acetylcholinesterase, alpha-bungarotoxin-binding sites or a high uptake capacity for glutamine was enhanced by nonneuronal cells. The horse serum increases the neuronal subpopulation exhibiting a carbonic anhydrase activity. Certain phenotypic changes fit conditions consistent with an epigenetic induction rather than a cell selection.

Phenotypic virulence analysis of Pyricularia grisea isolates from Brazilian upland rice cultivars

Phenotypic virulence analysis was made on population of Pyricularia grisea isolates collected from 10 upland cultivars in three distinct rice breeding sites, with the objective of studying the degree of similarity in the phenotypic virulence among the isolates, the composition of races, and their virulence pattern. Sixteen races were identified based on the reaction type on eight standard international differentials, the predominant ones being IB9 and IB41. The virulence frequency was high on IAC47 and IAC165 among medium and early maturing cultivars, respectively. The frequency of isolates virulent was greater on upland rice cultivars (51.1%) than on irrigated rice cultivars (21.8%). Both virulent and avirulent isolates were present in the population of P. grisea to the known genes in the near isogenic lines. Of72test isolates, 94.4% were virulent for genes Pi3 and Pi4a. Thevirulence frequencies were relatively lower in decreasing order on Pi1, Pi4b and Pi2. Thecoefficient of similarity ranged from 0.28 to1.0 among the isolates pertaining to different races, while within the race IB9, it varied from 0.56 to1.0. Considering the coefficient of similarity of 0.81, 72% of isolates of race IB9 exhibited similar pattern of virulence.

Time-Temperature Strength-Reaction Product Relationships in Lime-Bentonite-Water Mixtures, HR-111, 1965

The interrelation of curing time, curing temperature, strength, and reactions in lime-bentonite-water mixtures was examined. Samples were molded at constant density and moisture content and then cured for periods of from 1 to 56 days at constant temperatures that ranged from 5C to 60C. After the appropriate curing time the samples were tested for unconfined compressive strength. The broken samples were then analyzed by x-ray diffractometer and spectrophotometer to determine the identity of the reaction products present after each curing period. It was found that the strength gain of lime-clay mixtures cured at different temperatures is due to different phases of the complex reaction, lime & clay to CSH(gel) to CSH(II) to CSH(I) to tobermorite. The farther the reaction proceeds, the higher the strength. There was also evidence of lattice substitutions in the structure of the calcium silicate hydrates at curing temperatures of 50C and higher. No consistent relationship between time, temperature, strength, and the S/A ration of reaction products existed, but in order to achieve high strengths the apparent C/S ration had to be less than two. The curing temperature had an effect on the strength developed by a given amount of reacted silica in the cured lime-clay mixture, but at a given curing temperature the cured sample that had the largest amount of reacted silica gave the highest strength. Evidence was found to indicate that during the clay reaction some calcium is indeed adsorbed onto the clay structure rather than entering into a pozzolanic reaction. Finally, it was determined that it is possible to determine the amount of silica and alumina in lime-clay reaction products by spectrophotometric analysis with sufficient accuracy for comparison purposes. The spectrophotometric analysis techniques used during the investigation were simple and were not time consuming.

LiveCount Assay: concomitant measurement of cytolytic activity and phenotypic characterisation of CD8(+) T-cells by flow cytometry.

Tumour immunologists strive to develop efficient tumour vaccination and adoptive transfer therapies that enlarge the pool of tumour-specific and -reactive effector T-cells in vivo. To assess the efficiency of the various strategies, ex vivo assays are needed for the longitudinal monitoring of the patient's specific immune responses providing both quantitative and qualitative data. In particular, since tumour cell cytolysis is the end goal of tumour immunotherapy, routine immune monitoring protocols need to include a read-out for the cytolytic efficiency of Ag-specific cells. We propose to combine current immune monitoring techniques in a highly sensitive and reproducible multi-parametric flow cytometry based cytotoxicity assay that has been optimised to require low numbers of Ag-specific T-cells. The possibility of re-analysing those T-cells that have undergone lytic activity is illustrated by the concomitant detection of CD107a upregulation on the surface of degranulated T-cells. To date, the LiveCount Assay provides the only possibility of assessing the ex vivo cytolytic activity of low-frequency Ag-specific cytotoxic T-lymphocytes from patient material.

Systematic and biogeographic relationships of the Japanese white-toothed shrew (Crocidura dsinezumi)

To assess the zoogeographic and phylogenetic relationships of C. dsinezumi, its systematic position has been investigated through electrophoretic comparisons. These comparisons comprise typical Indomalayan and Palaearctic species, including C. russula, the supposed sister taxon of the Japanese white-toothed shrew. The range of measured genetic distances that separate dsinezumi from the other shrews (Nei's D = 0.232-0.406) is typical for interspecific comparisons among Crocidura taxa. Our results reinforce morphologic considerations that suggest C. dsinezumi be treated as a valid species. Phylogenetic relationships deduced from a cladistic treatment of allozyme data refute the possibility that the western Palaearctic C. russula is the sister taxon of C. dsinezumi. Zoogeographic interpretation of the genetic results indicates that the Southeast Asian representatives constitute a clade distinct from one that includes the Palaearctic species. However, C. dsinezumi is difficult to assign to either clade due to many intermediate or plesiomorphic electrophoretic characters. Unlike the major karyologic and biochemical separation that divides Afrotropical and Palaearctic species, the subdivision between Palaearctic and Indomalayan Crocidura is not correlated with any trend in karyotypic evolution. It also is shown that the Eurasiatic species of Crocidura possessing 2n = 40 chromosomes (including C. dsinezumi) do not represent a particular clade, but probably share a plesiomorphic character. Further analysis of other Indian or Asiatic species is needed to test whether the Palaearctic versus Indomalayan separation is due to real zoogeographic barriers or whether it is the result of limited samples.

Predicting the mating system from phenotypic correlations between life-history and sperm quality traits in the Alpine whitefish Coregonus zugensis

The mating behavior and reproductive strategies of Alpine whitefish like Coregonus zugensis (Nusslin) are poorly understood, probably because they spawn in deep water where direct observations are difficult. In this study, we interpret life-history and sperm quality traits of fish that we caught from their spawning place. We found that males invest heavily into gonadal tissue (up to 5.6% of their body weight), which is, in comparison to other fish, consistent with external fertilization, distinct pairing and moderate to high communal spawning, or no pairing and low to moderate communal spawning. Sperm competition theory and recent experimental studies on other salmonids predict that males optimize ejaculate characteristics in relation to the costs of sperm and the level of competition they have to expect: dominant males are predicted to invest less into ejaculate quality and to have slower spermatozoa than subdominant males. We found that spermatozoa of older males are slower than those of younger males. Moreover, older males have larger breeding tubercles, a secondary sexual trait that has, in some previous studies, been found to be linked to good condition and to good genetic quality. Our results suggest that C. zugensis has age-linked reproductive strategies, that multimale spawning is common, i.e., that sperm competition plays a significant role, and that older males are on average dominant over younger males at the spawning place.

Phenotypic plasticity in salmonid embryos : characterizing pathogen-induced stress effects on heritable variation in traits and reaction norms

Les pressions écologiques peuvent varier tant en nature qu'en intensité dans le temps et l'espace. C'est pourquoi, un phénotype unique ne peut pas forcément conférer la meilleure valeur sélective. La plasticité phénotypique peut être un moyen de s'accommoder de cette situation, en augmentant globalement la tolérance aux changements environnementaux. Comme pour tout trait de caractère, une variation génétique doit persister pour qu'évoluent les traits plastiques dans une population donnée. Cependant, les pressions extérieures peuvent affecter l'héritabilité, et la direction de ces changements peut dépendre du caractère en question, de l'espèce mais aussi du type de stress. Dans la présente thèse, nous avons cherché à élucider les effets des pressions pathogéniques sur les phénotypes et la génétique quantitative de plusieurs traits plastiques chez les embryons de deux salmonidés, la palée (Coregonus palaea), et la truite de rivière (Salmo trutta). Les salmonidés se prêtent à de telles études du fait de leur extraordinaire variabilité morphologique, comportementale et des traits d'histoire de vie. Par ailleurs, avec le déclin des salmonidés dans le monde, il est important de savoir combien la variabilité génétique persiste dans les normes de réaction afin d'aider à prédire leur capacité à répondre aux changements de leur milieu. Nous avons observé qu'une augmentation de la croissance des communautés microbiennes symbiotiques entraînait une mortalité accrue et une éclosion précoce chez la palée, et dévoilait la variance génétique additive pour ces deux caractères (Chapitres 1-2). Bien qu'aucune variation génétique n'ait été trouvée pour les normes de réaction, nous avons observé une variabilité de la plasticité d'éclosion. Néanmoins, on a trouvé que les temps d'éclosion étaient corrélés entre les environnements, ce qui pourrait limiter l'évolution de la norme de réaction. Le temps d'éclosion des embryons est lié à la taille des géniteurs mâles, ce qui indique des effets pléiotropiques. Dans le Chapitre 3, nous avons montré qu'une interaction triple entre la souche bactérienne {Pseudomonas fluorescens}, l'état de dévelopement de l'hôte ainsi que ses gènes ont une influence sur la mortalité, le temps d'éclosion et la taille des alevins de la palée. Nous avons démontré qu'une variation génétique subsistait généralement dans les normes de réaction des temps d'éclosion, mais rarement pour la taille des alevins, et jamais pour la mortalité. Dans le même temps, nous avons exhibé que des corrélations entre environnements dépendaient des caractères phénotypiques, mais contrairement au Chapitre 2, nous n'avons pas trouvé de preuve de corrélations transgénérationnelles. Le Chapitre 4 complète le chapitre précédent, en se plaçant du point de vue moléculaire, et décrit comment le traitement d'embryons avec P. fluorescens s'est traduit par une régulation négative d'expression du CMH-I indépendemment de la souche bactérienne. Nous avons non seulement trouvé une variation génétique des caractères phénotypiques moyens, mais aussi de la plasticité. Les deux derniers chapitres traitent de l'investigation, chez la truite de rivière, des différences spécifiques entre populations pour des normes de réaction induites par les pathogènes. Dans le Chapitre 5, nous avons illustré que le métissage entre des populations génétiquement distinctes n'affectait en rien la hauteur ou la forme des normes de réaction d'un trait précoce d'histoire de vie suite au traitement pathogénique. De surcroît, en dépit de l'éclosion tardive et de la réduction de la taille des alevins, le traitement n'a pas modifié la variation héritable des traits de caractère. D'autre part, dans le Chapitre 6, nous avons démontré que le traitement d'embryons avec des stimuli contenus dans l'eau de conspécifiques infectés a entraîné des réponses propre à chaque population en terme de temps d'éclosion ; néanmoins, nous avons observé peu de variabilité génétique des normes de réaction pour ce temps d'éclosion au sein des populations. - Ecological stressors can vary in type and intensity over space and time, and as such, a single phenotype may not confer the highest fitness. Phenotypic plasticity can act as a means to accommodate this situation, increasing overall tolerance to environmental change. As with any trait, for plastic traits to evolve in a population, genetic variation must persist. However, environmental stress can alter trait heritability, and the direction of this shift can be trait, species, and stressor-dependent. In this thesis, we sought to understand the effects of pathogen stressors on the phenotypes and genetic architecture of several plastic traits in the embryos of two salmonids, the whitefish (Coregonus palaea), and the brown trout (Salmo trutta). Salmonids lend themselves to such studies because their extraordinary variability in morphological, behavioral, and life-history traits. Also, with declines in salmonids worldwide, knowing how much genetic variability persists in reaction norms may help predict their ability to respond to environmental change. We found that increasing growth of symbiotic microbial communities increased mortality and induced hatching in whitefish, and released additive genetic variance for both traits (Chapters 1-2). While no genetic variation was found for survival reaction norms, we did find variability in hatching plasticity. Nevertheless, hatching time was correlated across environments, which could constrain evolution of the reaction norm. Hatching time in the induced environment was also correlated to sire size, indicating pleiotropic effects. In Chapter 3 we report that a three-way interaction between bacterial strain (Pseudomonas fluorescens), host developmental stage, and host genetics impacted mortality, hatching time, and hatchling size in whitefish. We also showed that genetic variation generally persisted in hatching age reaction norms, but rarely for hatchling length, and never for mortality. At the same time, we demonstrated that cross-environmental correlations were trait-dependent, and unlike Chapter 2, we found no evidence of cross-generational correlations. Chapter 4 expands on the previous chapter, moving to the molecular level, and describes how treatment of embryos with P. fluorescens resulted in strain-independent downregulation of MHC class I. Genetic variation was evident not only in trait means, but also in plasticity. In the last two chapters, we investigated population level differences in pathogen- induced reaction norms in brown trout. In Chapter 5, we found that interbreeding between genetically distinct populations did not affect the elevation or shapes of the reaction norms of early life-history traits after pathogen challenge. Moreover, despite delaying hatching and reducing larval length, treatment produced no discernable shifts in heritable variation in traits. On the other hand, in Chapter 6, we found that treatment of embryos with water-borne cues from infected conspecifics elicited population-specific responses in terms of hatching time; however, we found little evidence of genetic variability in hatching reaction norms within populations. We have made considerable progress in understanding how pathogen stressors affect various early life-history traits in salmonid embryos. We have demonstrated that the effect of a particular stressor on heritable variation in these traits can vary according to the trait and species under consideration, in addition to the developmental stage of the host. Moreover, we found evidence of genetic variability in some, but not all reaction norms in whitefish and brown trout.

Prediction of cross-recognition of peptide-HLA A2 by Melan-A-specific cytotoxic T lymphocytes using three-dimensional quantitative structure-activity relationships.

The cross-recognition of peptides by cytotoxic T lymphocytes is a key element in immunology and in particular in peptide based immunotherapy. Here we develop three-dimensional (3D) quantitative structure-activity relationships (QSARs) to predict cross-recognition by Melan-A-specific cytotoxic T lymphocytes of peptides bound to HLA A*0201 (hereafter referred to as HLA A2). First, we predict the structure of a set of self- and pathogen-derived peptides bound to HLA A2 using a previously developed ab initio structure prediction approach [Fagerberg et al., J. Mol. Biol., 521-46 (2006)]. Second, shape and electrostatic energy calculations are performed on a 3D grid to produce similarity matrices which are combined with a genetic neural network method [So et al., J. Med. Chem., 4347-59 (1997)] to generate 3D-QSAR models. The models are extensively validated using several different approaches. During the model generation, the leave-one-out cross-validated correlation coefficient (q (2)) is used as the fitness criterion and all obtained models are evaluated based on their q (2) values. Moreover, the best model obtained for a partitioned data set is evaluated by its correlation coefficient (r = 0.92 for the external test set). The physical relevance of all models is tested using a functional dependence analysis and the robustness of the models obtained for the entire data set is confirmed using y-randomization. Finally, the validated models are tested for their utility in the setting of rational peptide design: their ability to discriminate between peptides that only contain side chain substitutions in a single secondary anchor position is evaluated. In addition, the predicted cross-recognition of the mono-substituted peptides is confirmed experimentally in chromium-release assays. These results underline the utility of 3D-QSARs in peptide mimetic design and suggest that the properties of the unbound epitope are sufficient to capture most of the information to determine the cross-recognition.

Phenotypic and molecular characterization of the onset of neuropathy in rodent models of diabetes mellitus

Abstract : The principal focus of this work was to study the molecular changes leading to the development of diabetic peripheral neuropathy (DPN). DPN is the most common complication associated with both type I and II diabetes mellitus (DM). This pathology is the leading cause of non-traumatic amputations. Even though the pathological and morphological changes underlying DPN are relatively well described, the implicated molecular mechanisms remain poorly understood. The following two approaches were developed to study the development of DPN in a rodent model of DM type I. As a first approach, we studied the implication of lipid metabolism in DPN phenotype, concentrating on Sterol Response Element Binding Protein (SREBP)-lc which is the key regulator of storage lipid metabolism. We showed that SREBP-1c was expressed in peripheral nerves and that its expression profile followed the expression of genes involved in storage lipid metabolism. In addition, the expression of SREBP-1c in the endoneurium of peripheral nerves was dependant upon nutritional status and this expression was also perturbed in type I diabetes. In line with this, we showed that insulin elevated the expression of SREBP-1c in primary cultured Schwann cells by activating the SREBP-1c promoter. Taken together, these findings reveal that SREBP-1c expression in Schwann cells responds to metabolic stimuli including insulin and that this response is affected in type I diabetes mellitus. This suggests that disturbed SREBP-1c regulated lipid metabolism may contribute to the pathophysiology of DPN. As a second approach, we performed a comprehensive analysis of the molecular changes associated with DPN in the Akital~1~+ mouse which is a model of spontaneous early-onset type I diabetes mellitus. This mouse expresses a mutated non-functional isoform of insulin, leading to hypoinsulinemia and hyperglycaemia. To determine the onset of DPN, weight, blood glucose and motor nerve conduction velocity (MNCV) were measured in Akital+/+ mice during the first three months of life. A decrease in MNCV was evident akeady one week after the onset of hyperglycemia. To explore the molecular changes associated with the development of DPN in these mice, we performed gene expression profiling using sciatic nerve endoneurium and dorsal root ganglia (DRG) isolated from early diabetic male Akita+/+ mice and sex-matched littermate controls. No major transcriptional changes were detected either in the DRG or in the sciatic nerve endoneurium. This experiment indicates that the phenotypic changes observed during the development of DPN are not correlated with major transcriptional alterations, but mainly with alterations at the protein level. Résumé Lors ce travail, nous nous sommes intéressés aux changements moléculaires aboutissant aux neuropathies périphériques dues au diabète (NPD). Les NPD sont la complication la plus commune du diabète de type I et de type II. Cette pathologie est une cause majeure d'amputations. Même si les changements pathologiques et morphologiques associés aux NPD sont relativement bien décrits, les mécanismes moléculaires provoquant cette pathologie sont mal connus. Deux approches ont principalement été utilisées pour étudier le développement des NPD dans des modèles murins du diabète de type I. Nous avons d'abord étudié l'impact du métabolisme des lipides sur le développement des NPD en nous concentrant sur Sterol Response Element Binding Protein (SREBP)-1 c qui est un régulateur clé des lipides de stockage. Nous avons montré que SREBP-1 c est exprimé dans les nerfs périphériques et que son profil d'expression suit celui de gènes impliqués dans le métabolisme des lipides de stockage. De plus, l'expression de SREBP-1c dans l'endoneurium des nerfs périphériques est dépendante du statut nutritionnel et est dérégulée lors de diabète de type I. Nous avons également pu montrer que l'insuline augmente l'expression de SREBP-1c dans des cultures primaires de cellules de Schwann en activant le promoteur de SREBP-1c. Ses résultats démontrent que l'expression de SREBP-1c dans les cellules de Schwann est contrôlée par des stimuli métaboliques comme l'insuline et que cette réponse est affectée dans le cas d'un diabète de type I. Ces données suggèrent que la dérégulation de l'expression de SREBP-1c lors du diabète pourrait affecter le métabolisme des lipides et ainsi contribuer à la pathophysiologie des NPD. Comme seconde approche, nous avons réalisé une analyse globale des changements moléculaires associés au développement des NPD chez les souris Akita+/+, un modèle de diabète de type I. Cette souris exprime une forme mutée et non fonctionnelle de l'insuline provoquant une hypoinsulinémie et une hyperglycémie. Afin de déterminer le début du développement de la NPD, le poids, le niveau de glucose sanguin et la vitesse de conduction nerveuse (VCN) ont été mesurés durant les 3 premiers mois de vie. Une diminution de la VCN a été détectée une semaine seulement après le développement de l'hyperglycémie. Pour explorer les changements moléculaires associés avec le développement des NPD, nous avons réalisé un profil d'expression de l'endoneurium du nerf sciatique et des ganglions spinaux isolés à partir de souris Akital+/+ et de souris contrôles Akita+/+. Aucune altération transcriptionnelle majeure n'a été détectée dans nos échantillons. Cette expérience suggère que les changements phénotypiques observés durant le développement des NPD ne sont pas corrélés avec des changements importants au niveau transcriptionnel, mais plutôt avec des altérations au niveau protéique. Résumé : Lors ce travail, nous nous sommes intéressés aux changements moléculaires aboutissant aux neuropathies périphériques dues au diabète (NPD). Les NPD sont la complication la plus commune du diabète de type I et de type II. Cette pathologie est une cause majeure d'amputations. Même si les changements pathologiques et morphologiques associés aux NPD sont relativement bien décrits, les mécanismes moléculaires provoquant cette pathologie sont mal connus. Deux approches ont principalement été utilisées pour étudier le développement des NPD dans des modèles murins du diabète de type I. Nous avons d'abord étudié l'impact du métabolisme des lipides sur le développement des NPD en nous concentrant sur Sterol Response Element Binding Protein (SREBP)-1c qui est un régulateur clé des lipides de stockage. Nous avons montré que SREBP-1 c est exprimé dans les nerfs périphériques et que son profil d'expression suit celui de gènes impliqués dans le métabolisme des lipides de stockage. De plus, l'expression de SREBP-1c dans l'endoneurium des nerfs périphériques est dépendante du statut nutritionnel et est dérégulée lors de diabète de type I. Nous avons également pu montrer que l'insuline augmente l'expression de SREBP-1c dans des cultures primaires de cellules de Schwann en activant le promoteur de SREBP-1c. Ses résultats démontrent que l'expression de SREBP-1c dans les cellules de Schwann est contrôlée par des stimuli métaboliques comme l'insuline et que cette réponse est affectée dans le cas d'un diabète de type I. Ces données suggèrent que la dérégulation de l'expression de SREBP-1c lors du diabète pourrait affecter le métabolisme des lipides et ainsi contribuer à la pathophysiologie des NPD. Comme seconde approche, nous avons réalisé une analyse globale des changements moléculaires associés au développement des NPD chez les souris Akita~~Z~+, un modèle de diabète de type I. Cette souris exprime une forme mutée et non fonctionnelle de l'insuline provoquant une hypoinsulinémie et une hyperglycémie. Afin de déterminer le début du développement de la NPD, le poids, le niveau de glucose sanguin et la vitesse de conduction nerveuse (VCN) ont été mesurés durant les 3 premiers mois de vie. Une diminution de la VCN a été détectée une semaine seulement après le développement de l'hyperglycémie. Pour explorer les changements moléculaires associés avec le développement des NPD, nous avons réalisé un profil d'expression de l'endoneurium du nerf sciatique et des ganglions spinaux isolés à partir de souris Akital+/+ et de souris contrôles Akita+/+. Aucune altération transcriptionnelle majeure n'a été détectée dans nos échantillons. Cette expérience suggère que les changements phénotypiques observés durant le développement des NPD ne sont pas corrélés avec des changements importants au niveau transcriptionnel, mais plutôt avec des altérations au niveau protéique.

Mutations in the human UBR1 gene and the associated phenotypic spectrum.

Johanson-Blizzard syndrome (JBS) is a rare, autosomal recessive disorder characterized by exocrine pancreatic insufficiency, typical facial features, dental anomalies, hypothyroidism, sensorineural hearing loss, scalp defects, urogenital and anorectal anomalies, short stature, and cognitive impairment of variable degree. This syndrome is caused by a defect of the E3 ubiquitin ligase UBR1, which is part of the proteolytic N-end rule pathway. Herein, we review previously reported (n = 29) and a total of 31 novel UBR1 mutations in relation to the associated phenotype in patients from 50 unrelated families. Mutation types include nonsense, frameshift, splice site, missense, and small in-frame deletions consistent with the hypothesis that loss of UBR1 protein function is the molecular basis of JBS. There is an association of missense mutations and small in-frame deletions with milder physical abnormalities and a normal intellectual capacity, thus suggesting that at least some of these may represent hypomorphic UBR1 alleles. The review of clinical data of a large number of molecularly confirmed JBS cases allows us to define minimal clinical criteria for the diagnosis of JBS. For all previously reported and novel UBR1 mutations together with their clinical data, a mutation database has been established at LOVD.

Decision curve analysis revisited: overall net benefit, relationships to ROC curve analysis, and application to case-control studies.

ABSTRACT: BACKGROUND: Decision curve analysis has been introduced as a method to evaluate prediction models in terms of their clinical consequences if used for a binary classification of subjects into a group who should and into a group who should not be treated. The key concept for this type of evaluation is the "net benefit", a concept borrowed from utility theory. METHODS: We recall the foundations of decision curve analysis and discuss some new aspects. First, we stress the formal distinction between the net benefit for the treated and for the untreated and define the concept of the "overall net benefit". Next, we revisit the important distinction between the concept of accuracy, as typically assessed using the Youden index and a receiver operating characteristic (ROC) analysis, and the concept of utility of a prediction model, as assessed using decision curve analysis. Finally, we provide an explicit implementation of decision curve analysis to be applied in the context of case-control studies. RESULTS: We show that the overall net benefit, which combines the net benefit for the treated and the untreated, is a natural alternative to the benefit achieved by a model, being invariant with respect to the coding of the outcome, and conveying a more comprehensive picture of the situation. Further, within the framework of decision curve analysis, we illustrate the important difference between the accuracy and the utility of a model, demonstrating how poor an accurate model may be in terms of its net benefit. Eventually, we expose that the application of decision curve analysis to case-control studies, where an accurate estimate of the true prevalence of a disease cannot be obtained from the data, is achieved with a few modifications to the original calculation procedure. CONCLUSIONS: We present several interrelated extensions to decision curve analysis that will both facilitate its interpretation and broaden its potential area of application.

Genetic diversity and population structure of Brazilian native bovine breeds

Conservation and improvement strategies should be based on the association between genetic and phenotypic characteristics. The objective of this work was to characterize five native Brazilian cattle breeds (Caracu, Crioulo Lageano, Curraleiro, National Polled and Pantaneiro) and two commercial breeds (Holstein and Nellore) using RAPD technique to estimate genetic distances and variability between and within breeds. Genetic relationships were investigated using 22 primers which generated 122 polymorphic bands. Analysis of molecular variance indicated that most of the genetic variation lay among individuals within populations. The genetic variabilities between pairs of breeds were statistically significant. The smallest genetic divergence was between Crioulo Lageano and Curraleiro.The National Polled, although historically considered to be of Bos taurus aquitanicus origin,similar to theCaracu, was grouped together with the other breeds of Bos taurus ibericus origin. Generally, the individual breeds formed distinct clusters except the National Polled. The RAPD technique was capable to distinguish genetically between the breeds studied; the Caracu, Crioulo Lageano, Curraleiro and Pantaneiro may be considered distinct genetic entities thereby proving the uniqueness of the populations; the National Polled has not been able to re-establish itself after its decline in the 1950s, thereby losing its genetic identity.