Ras farnesyltransferase inhibitors suppress the phenotype resulting from an activated ras mutation in Caenorhabditis elegans.

Attachment of Ras protein to the membrane, which requires farnesylation at its C terminus, is essential for its biological activity. A promising pharmacological approach of antagonizing oncogenic Ras activity is to develop inhibitors of farnesyltransferase. We use Caenorhabditis elegans vulval differentiation, which is controlled by a Ras-mediated signal transduction pathway, as a model system to test previously identified farnesyltransferase inhibitors. We show here that two farnesyltransferase inhibitors, manumycin and gliotoxin, suppress the Multivulva phenotype resulting from an activated let-60 ras mutation, but not the Multivulva phenotype resulting from mutations in the lin-1 gene or the lin-15 gene, which act downstream and upstream of let-60 ras, respectively, in the signaling pathway. These results are consistent with the idea that the suppression of the Multivulva phenotype of let-60 ras by the two inhibitors is specific for Ras protein and that the mutant Ras protein might be more sensitive than wild-type Ras to the farnesyltransferase inhibitors. This work suggests that C. elegans vulval development could be a simple and effective in vivo system for evaluation of farnesyltransferase inhibitors against Ras-activated tumors.

Identification of a DNA transformation gene required for com101A+ expression and supertransformer phenotype in Haemophilus influenzae.

DNA sequencing, RNA mapping, and protein expression experiments revealed the presence of a gene, tfoX+, encoding a 24.9-kDa polypeptide, that is transcribed divergently from a common promoter region with the Haemophilus influenzae rec-1+ gene. H. influenzae strains mutant for tfoX failed to bind transforming DNA and were transformation deficient. Primer extension experiments utilizing in vivo total RNA from precompetent and competent H. influenzae cells demonstrated that transcription of tfoX+ increased immediately upon competence induction, suggesting that tfoX+ is an early competence gene. Similar experiments showed that the expression of the late competence-specific gene, com101A+, was tfoX+ dependent. Moreover, expression of plasmid-borne tfoX+ in H. influenzae resulted in constitutive competence. The addition of cyclic adenosine monophosphate (cAMP) to strains carrying a tfoX::lacZ operon fusion resulted in an immediate increase in beta-galactosidase activity that correlated with an increase in genetic transformability. Collectively, our results suggest that TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes.

Investigação de mecanismos genéticos e epigenéticos em distúrbios do crescimento humano

Parcela considerável de pacientes com distúrbios de crescimento não têm a causa de seus quadros clínicos estabelecida, incluindo aproximadamente 50% dos pacientes com diagnóstico clínico de síndrome de Silver−Russell (SRS) e 10-20% dos pacientes com síndrome de Beckwith-Wiedemann (BWS). O objetivo deste estudo foi investigar as causas genéticas e epigenéticas de distúrbios de crescimento, de etiologia desconhecida, numa contribuição para o entendimento de mecanismos que regulam o crescimento. O estudo compreendeu: (1) a investigação de microdesequilíbrios cromossômicos, por aCGH; (2) a análise do perfil de expressão alelo-específica de genes sujeitos a imprinting (IG), por pirossequenciamento (PSQ) ou sequenciamento de Sanger; (3) a investigação do padrão de metilação global em pacientes com restrição de crescimento, utilizando microarray de metilação. A casuística constituiu-se de 41 pacientes não aparentados, com distúrbios de crescimento, de etiologia desconhecida: (1) 25, com hipótese diagnóstica de SRS; (2) seis, com restrição de crescimento intrauterino e peso ao nascimento abaixo do 10º percentil, associados a outros sinais clínicos; (3) sete, com hipótese diagnóstica de BWS; e (4) três, com macrossomia pré-natal ou pós-natal, associada a outros sinais. A investigação de microdesequilíbrios cromossômicos foi realizada em 40 pacientes. Foram detectadas 58 variantes raras em 30/40 pacientes (75%): 40 foram consideradas provavelmente benignas (18 pacientes, 45%), 12, com efeito patogênico desconhecido (11 pacientes, 27,5%), duas, provavelmente patogênicas (um paciente, 2,5%) e quatro, patogênicas (três pacientes, 7,5%). Essas frequências são comparáveis àquelas descritas em estudos que investigaram CNV em grupos de pacientes com distúrbios de crescimento e outras alterações congênitas, incluindo SRS, e mostram a importância da investigação de microdesequilíbrios cromossômicos nesses pacientes. A diversidade dos microdesequilíbrios cromossômicos identificados é reflexo da heterogeneidade clínica das casuísticas. Neste estudo, muitos dos pacientes com hipótese diagnóstica de SRS e BWS apresentavam sinais clínicos atípicos, explicando a ausência neles das alterações (epi)genéticas que causam essas síndromes. A identificação de CNV características de outras síndromes reflete a sobreposição de sinais clínicos com BWS e SRS. A análise do perfil de expressão alelo-específica de IG foi realizada em um subgrupo de 18 pacientes com restrição de crescimento. Trinta IG com função em proliferação celular, crescimento fetal ou neurodesenvolvimento foram inicialmente selecionados. Após seleção de SNP transcritos com alta frequência na população, genotipagem de pacientes, genitores e indivíduos controle, determinação da expressão dos IG em sangue periférico e seu padrão de expressão (mono ou bialélico), 13 IG, expressos no sangue, tiveram a expressão alelo-específica avaliada, sete deles por PSQ e seis por sequenciamento de Sanger. Alterações no perfil de expressão de dois genes, de expressão normalmente paterna, foram detectadas em 4/18 pacientes (22%). Este estudo é o primeiro a utilizar pirossequenciamento e sequenciamento de Sanger na avaliação do perfil de expressão alelo-específica de IG, em pacientes com restrição de crescimento. Apesar de terem limitações, ambas as técnicas mostraram-se robustas e revelaram alterações de expressão alélica interessantes; entretanto, a relação dessas alterações com o quadro clínico dos pacientes permanece por esclarecer. A investigação da metilação global do DNA foi realizada em subgrupo de 21 pacientes com restrição de crescimento e em 24 indivíduos controle. Dois tipos de análise foram realizados: (1) análise diferencial de grupo e (2) análise diferencial individual. Na primeira análise, em que foi comparado o padrão de metilação do grupo de pacientes com quadro clínico sugestivo de SRS (n=16) com o do grupo controle (n=24), não houve indicação de hipo ou hipermetilação global no grupo SRS. Na segunda análise, foi comparado o padrão de metilação de cada um dos 21 pacientes com restrição de crescimento e dos 24 indivíduos controle, com o padrão de metilação do grupo controle. O número médio de CpG hipermetilados e de segmentos diferencialmente metilados (SDM) foi significativamente maior nos pacientes. Foram identificados 82 SDM hipermetilados, estando 57 associados a gene(s) (69,5%), em 16 pacientes, e 51 SDM hipometilados, 41 deles associados a gene(s) (80,4%), em 10 pacientes. A análise de ontologia genética dos 61 genes associados aos SDM hipo ou hipermetilados nos pacientes destacou genes que atuam no desenvolvimento e na morfogênese do sistema esquelético e de órgãos fetais, e na regulação da transcrição gênica e de processos metabólicos. Alterações de metilação em genes que atuam em processos de proliferação e diferenciação celulares e crescimento foram identificadas em 9/20 dos pacientes (45%), sugerindo implicação clínica. Não foi detectada alteração epigenética comum aos pacientes com diagnóstico clínico de SRS, explicável provavelmente pela heterogeneidade clínica. A investigação de metilação global, utilizando microarray, produziu novos dados que podem contribuir para a compreensão de mecanismos moleculares que influenciam o crescimento pré- e pós-natal. Na translocação aparentemente equilibrada - t(5;6)(q35.2;p22.3)dn, detectada em paciente com suspeita clínica de SRS, a interrupção de um gene, pela quebra no cromossomo 6, pode ser a causa do quadro clínico; alternativamente, a translocação pode ter impactado a regulação de genes de desenvolvimento localizados próximos aos pontos de quebra. A análise de expressão em sangue periférico mostrou que os níveis de cDNA do gene, interrompido pelo ponto de quebra da translocação, estavam reduzidos à metade. Além de sinais típicos da SRS, a paciente apresentava algumas características clínicas sugestivas de displasia cleidocraniana. Assim, a translocação t(5;6) pode ter alterado a interação de genes de desenvolvimento e seus elementos reguladores, levando à desregulação de sua expressão espaço-temporal, e resultando num fenótipo atípico, com características sobrepostas de mais de uma síndrome genética

Towards the Design of a Textile Chemical Ontology

The main goal of this paper is to present the initial version of a Textile Chemical Ontology, to be used by textile professionals with the purpose of conceptualising and representing the banned and harmful chemical substances that are forbidden in this domain. After analysing different methodologies and determining that “Methontology” is the most appropriate for the purposes, this methodology is explored and applied to the domain. In this manner, an initial set of concepts are defined, together with their hierarchy and the relationships between them. This paper shows the benefits of using the ontology through a real use case in the context of Information Retrieval. The potentiality of the proposed ontology in this preliminary evaluation encourages extending the ontology with a higher number of concepts and relationships, and validating it within other Natural Language Processing applications.

Increased frequency of the autism broader phenotype in mothers transmitting etiological CNVs to sons affected by Autism Spectrum Disorder (ASD)

Introduction: Autism Spectrum Disorder (ASD) is a frequent and complex neurodevelopmental disorder, characterized by impairments in social communication and repetitive behaviors and with a high male to female ratio: ~4:1. Genetic factors, including rare Copy Number Variants (CNVs), have a substantial impact in ASD risk 1, and are associated with specific phenotypic manifestations 2. Recent studies reported that rare inherited CNVs are enriched in mothers of ASD children compared with mothers of controls and are preferentially transmitted from mothers to ASD children suggesting a sex bias in CNV transmission; further, the imbalanced transmission of small pathogenic CNVs from unaffected mothers to their sons with ASD has been described 3, 4. An increased prevalence of autism - like personality traits is found in unaffected relatives of ASD children, suggesting a genetic liability of a broader autism phenotype (BAP) 5. The BAP in parents of autistic children can be assessed by the Social Responsiveness Scale (SRS) 6 and Broad Autism Phenotype Questionnaire (BAPQ) 7 reports . The SRS is 65 - item questionnaire to identify sub - clinical social impairments and interpersonal behaviour in individuals . The BAPQ is a 36 - item questionnaire measures social aloofness, rigid personality, and pragmatic language deficits in both parents and children.

Frequency of MELAS main mutation in a phenotype-targeted young ischemic stroke patient population

Mitochondrial diseases, predominantly mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS), may occasionally underlie or coincide with ischemic stroke (IS) in young and middle-aged individuals. We searched for undiagnosed patients with MELAS in a target subpopulation of unselected young IS patients enrolled in the Stroke in Young Fabry Patients study (sifap1). Among the 3291 IS patients aged 18-55 years recruited to the sifap1 study at 47 centers across 14 European countries, we identified potential MELAS patients with the following phenotypic features: (a) diagnosed cardiomyopathy or (b) presence of two of the three following findings: migraine, short stature (≤165 cm for males; ≤155 cm for females), and diabetes. Identified patients' blood samples underwent analysis of the common MELAS mutation, m.3243A>G in the MTTL1 gene of mitochondrial DNA. Clinical and cerebral MRI features of the mutation carriers were reviewed. We analyzed blood samples of 238 patients (177 with cardiomyopathy) leading to identification of four previously unrecognized MELAS main mutation carrier-patients. Their clinical and MRI characteristics were within the expectation for common IS patients except for severe hearing loss in one patient and hyperintensity of the pulvinar thalami on T1-weighted MRI in another one. Genetic testing for the m.3243A>G MELAS mutation in young patients with IS based on phenotypes suggestive of mitochondrial disease identifies previously unrecognized carriers of MELAS main mutation, but does not prove MELAS as the putative cause.

Clinicopathological Phenotype of Autosomal Recessive Cholesterol Deficiency in Holstein Cattle.

BACKGROUND Cholesterol deficiency (CD), a newly identified autosomal recessive genetic defect in Holstein cattle, is associated with clinical signs of diarrhea, failure to thrive, and hypocholesterolemia. HYPOTHESIS/OBJECTIVES The objective is to describe the clinicopathological phenotype of affected Holstein cattle homozygous for the causative apolipoprotein B gene (APOB) mutation. ANIMALS Six Holstein cattle, 5 calves with a clinical history of chronic diarrhea, and 1 heifer with erosions in the buccal cavity and neurologic symptoms were admitted to the Clinic for Ruminants. METHODS This case review included a full clinical examination, a complete blood count, blood chemistry, and measurements of cholesterol and triglycerides. The animals were euthanized and necropsied. A PCR-based direct gene test was applied to determine the APOB genotype. RESULTS All 6 animals were inbred, could be traced back to the sire Maughlin Storm, and were confirmed homozygous for the APOB mutation. The clinical phenotype included poor development, underweight, and intermittent diarrhea in the calves, and neurologic signs in the heifer included hypermetria and pacing. Hypocholesterolemia and low triglycerides concentrations were present in all animals. The pathological phenotype of all animals was steatorrhea with enterocytes of the small intestine containing intracytoplasmic lipid vacuoles. The peripheral nervous system of the heifer displayed degenerative changes. CONCLUSIONS AND CLINICAL IMPORTANCE Suspicion of CD in Holstein cattle is based on the presence of chronic diarrhea with no evidence of primary infections. Confirmation of the associated APOB gene mutation is needed. Additionally, the heifer demonstrated primarily signs of neurologic disease providing an unexpected phenotype of CD.

The interplay of opposites, : a dialectical ontology.

Mode of access: Internet.

A critique of Jean-Paul Sartre's ontology

Bibliography: p. 127-142.

Metaphysic : in three books, ontology, cosmology, and psychology /

English translation first printed in 1884, 1 v.

.osophy, comprising logic and ontology or general metaphysics.

Mode of access: Internet.

A Knowledge-based System for Intelligent Support in Pharmacogenomics Evidence Assessment: Ontology-driven Evidence Representation, Retrieval, Classification and Interpretation

Thesis (Ph.D.)--University of Washington, 2016-06

Expression of the CD44v2-10 isoform confers a metastatic phenotype: Importance of the heparan sulfate attachment site CD44v3

We expressed the full-length CD44v2-10 isoform in SKHep1 cells, a nonmetastatic human hepatocellular carcinoma cell line that does not express any endogenous CD44v isoforms. In SCID mice, expression of CD44v2-10 by SKHep1 cells had no effect on s.c. primary tumor development but caused pulmonary metastases in 41% (7 of 17) of animals compared with control SKHep1 cells (0 of 16; P < 0.01). CD44v2-10 expression by SKHep1 cells resulted in enhanced heparan sulfate (HS) attachment and an enhanced capacity to bind heparin-binding growth factors. Mutation of the v3 domain to prevent HS attachment and growth factor binding abolished the metastatic phenotype, demonstrating that HS modification of CD44v2-10 plays a critical role in the development of metastases in this model. However, in vitro proliferation, motility, and invasion were not altered by CD44v2-10 expression.