SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements

Selenoproteins are a diverse group of proteinsusually misidentified and misannotated in sequencedatabases. The presence of an in-frame UGA (stop)codon in the coding sequence of selenoproteingenes precludes their identification and correctannotation. The in-frame UGA codons are recodedto cotranslationally incorporate selenocysteine,a rare selenium-containing amino acid. The developmentof ad hoc experimental and, more recently,computational approaches have allowed the efficientidentification and characterization of theselenoproteomes of a growing number of species.Today, dozens of selenoprotein families have beendescribed and more are being discovered in recentlysequenced species, but the correct genomic annotationis not available for the majority of thesegenes. SelenoDB is a long-term project that aims toprovide, through the collaborative effort of experimentaland computational researchers, automaticand manually curated annotations of selenoproteingenes, proteins and SECIS elements. Version 1.0 ofthe database includes an initial set of eukaryoticgenomic annotations, with special emphasis on thehuman selenoproteome, for immediate inspectionby selenium researchers or incorporation into moregeneral databases. SelenoDB is freely available athttp://www.selenodb.org.

A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins

Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3′UTR of selenoprotein mRNAs, and trans-acting factors. Among these, the SECIS Binding Protein 2 (SBP2) is central to the mechanism. SBP2 has been so far functionally characterized only in rats and humans. In this work, we report the characterization of the Drosophila melanogaster SBP2 (dSBP2). Despite its shorter length, it retained the same selenoprotein synthesis-promoting capabilities as the mammalian counterpart. However, a major difference resides in the SECIS recognition pattern: while human SBP2 (hSBP2) binds the distinct form 1 and 2 SECIS RNAs with similar affinities, dSBP2 exhibits high affinity toward form 2 only. In addition, we report the identification of a K (lysine)-rich domain in all SBP2s, essential for SECIS and 60S ribosomal subunit binding, differing from the well-characterized L7Ae RNA-binding domain. Swapping only five amino acids between dSBP2 and hSBP2 in the K-rich domain conferred reversed SECIS-binding properties to the proteins, thus unveiling an important sequence for form 1 binding.

FGF signaling controls caudal hindbrain specification through Ras-ERK1/2 pathway

Background: During early steps of embryonic development the hindbrain undergoes a regionalization process along the anterior-posterior (AP) axis that leads to a metameric organization in a series of rhombomeres (r). Refinement of the AP identities within the hindbrain requires the establishment of local signaling centers, which emit signals that pattern territories in their vicinity. Previous results demonstrated that the transcription factor vHnf1 confers caudal identity to the hindbrain inducing Krox20 in r5 and MafB/Kreisler in r5 and r6, through FGF signaling [1].Results: We show that in the chick hindbrain, Fgf3 is transcriptionally activated as early as 30 min after mvHnf1 electroporation, suggesting that it is a direct target of this transcription factor. We also analyzed the expression profiles of FGF activity readouts, such as MKP3 and Pea3, and showed that both are expressed within the hindbrain at early stages of embryonic development. In addition, MKP3 is induced upon overexpression of mFgf3 or mvHnf1 in the hindbrain, confirming vHnf1 is upstream FGF signaling. Finally, we addressed the question of which of the FGF-responding intracellular pathways were active and involved in the regulation of Krox20 and MafB in the hindbrain. While Ras-ERK1/2 activity is necessary for MKP3, Krox20 and MafB induction, PI3K-Akt is not involved in that process.Conclusion: Based on these observations we propose that vHnf1 acts directly through FGF3, and promotes caudal hindbrain identity by activating MafB and Krox20 via the Ras-ERK1/2 intracellular pathway.

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

Background: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results: Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://ibi.imim.es/osirisform.html. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://ibi.imim.es/OSIRISv1.2.html webcite) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion: OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.

Robust volume-targeted balanced steady-state free-precession coronary magnetic resonance angiography in a breathhold at 3.0 Tesla: a reproducibility study.

BACKGROUND: Transient balanced steady-state free-precession (bSSFP) has shown substantial promise for noninvasive assessment of coronary arteries but its utilization at 3.0 T and above has been hampered by susceptibility to field inhomogeneities that degrade image quality. The purpose of this work was to refine, implement, and test a robust, practical single-breathhold bSSFP coronary MRA sequence at 3.0 T and to test the reproducibility of the technique. METHODS: A 3D, volume-targeted, high-resolution bSSFP sequence was implemented. Localized image-based shimming was performed to minimize inhomogeneities of both the static magnetic field and the radio frequency excitation field. Fifteen healthy volunteers and three patients with coronary artery disease underwent examination with the bSSFP sequence (scan time = 20.5 ± 2.0 seconds), and acquisitions were repeated in nine subjects. The images were quantitatively analyzed using a semi-automated software tool, and the repeatability and reproducibility of measurements were determined using regression analysis and intra-class correlation coefficient (ICC), in a blinded manner. RESULTS: The 3D bSSFP sequence provided uniform, high-quality depiction of coronary arteries (n = 20). The average visible vessel length of 100.5 ± 6.3 mm and sharpness of 55 ± 2% compared favorably with earlier reported navigator-gated bSSFP and gradient echo sequences at 3.0 T. Length measurements demonstrated a highly statistically significant degree of inter-observer (r = 0.994, ICC = 0.993), intra-observer (r = 0.894, ICC = 0.896), and inter-scan concordance (r = 0.980, ICC = 0.974). Furthermore, ICC values demonstrated excellent intra-observer, inter-observer, and inter-scan agreement for vessel diameter measurements (ICC = 0.987, 0.976, and 0.961, respectively), and vessel sharpness values (ICC = 0.989, 0.938, and 0.904, respectively). CONCLUSIONS: The 3D bSSFP acquisition, using a state-of-the-art MR scanner equipped with recently available technologies such as multi-transmit, 32-channel cardiac coil, and localized B0 and B1+ shimming, allows accelerated and reproducible multi-segment assessment of the major coronary arteries at 3.0 T in a single breathhold. This rapid sequence may be especially useful for functional imaging of the coronaries where the acquisition time is limited by the stress duration and in cases where low navigator-gating efficiency prohibits acquisition of a free breathing scan in a reasonable time period.

A comparative phenotypic study of kallmann syndrome patients carrying monoallelic and biallelic mutations in the prokineticin 2 or prokineticin receptor 2 genes.

Context: Both biallelic and monoallelic mutations in PROK2 or PROKR2 have been found in Kallmann syndrome (KS). Objective: The objective of the study was to compare the phenotypes of KS patients harboring monoallelic and biallelic mutations in these genes. Design and Patients: We studied clinical and endocrine features that reflect the functioning of the pituitary-gonadal axis, and the nonreproductive phenotype, in 55 adult KS patients (42 men and 13 women), of whom 41 had monoallelic mutations and 14 biallelic mutations in PROK2 or PROKR2. Results: Biallelic mutations were associated with more frequent cryptorchidism (70% vs. 34%, P < 0.05) and microphallus (90% vs. 28%, P < 0.001) and lower mean testicular volume (1.2 +/- 0.4 vs. 4.5 +/- 6.0 ml; P < 0.01) in male patients. Likewise, the testosterone level as well as the basal FSH level and peak LH level under GnRH-stimulation were lower in males with biallelic mutations (0.2 +/- 0.1 vs. 0.7 +/- 0.8 ng/ml; P = 0.05, 0.3 +/- 0.1 vs. 1.8 +/- 3.0 IU/liter; P < 0.05, and 0.8 +/- 0.8 vs. 5.2 +/- 5.5 IU/liter; P < 0.05, respectively). Nonreproductive, nonolfactory anomalies were rare in both sexes and were never found in patients with biallelic mutations. The mean body mass index of the patients (23.9 +/- 4.2 kg/m(2) in males and 26.3 +/- 6.6 kg/m(2) in females) did not differ significantly from that of gender-, age-, and treatment-matched KS individuals who did not carry a mutation in PROK2 or PROKR2. Finally, circadian cortisol levels evaluated in five patients, including one with biallelic PROKR2 mutations, were normal in all cases. Conclusion: Male patients carrying biallelic mutations in PROK2 or PROKR2 have a less variable and on average a more severe reproductive phenotype than patients carrying monoallelic mutations in these genes. Nonreproductive, nonolfactory clinical anomalies associated with KS seem to be restricted to patients with monoallelic mutations.

Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation

Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.

Analysis of meiotic recombination in 22q11.2, a region that frequently undergoes deletions and duplications

Background: The 22q11.2 deletion syndrome is the most frequent genomic disorder with an estimated frequency of 1/4000 live births. The majority of patients (90%) have the same deletion of 3 Mb (Typically Deleted Region, TDR) that results from aberrant recombination at meiosis between region specific low-copy repeats (LCRs). Methods: As a first step towards the characterization of recombination rates and breakpoints within the 22q11.2 region we have constructed a high resolution recombination breakpoint map based on pedigree analysis and a population-based historical recombination map based on LD analysis. Results: Our pedigree map allows the location of recombination breakpoints with a high resolution (potential recombination hotspots), and this approach has led to the identification of 5 breakpoint segments of 50 kb or less (8.6 kb the smallest), that coincide with historical hotspots. It has been suggested that aberrant recombination leading to deletion (and duplication) is caused by low rates of Allelic Homologous Recombination (AHR) within the affected region. However, recombination rate estimates for 22q11.2 region show that neither average recombination rates in the 22q11.2 region or within LCR22-2 (the LCR implicated in most deletions and duplications), are significantly below chromosome 22 averages. Furthermore, LCR22-2, the repeat most frequently implicated in rearrangements, is also the LCR22 with the highest levels of AHR. In addition, we find recombination events in the 22q11.2 region to cluster within families. Within this context, the same chromosome recombines twice in one family; first by AHR and in the next generation by NAHR resulting in an individual affected with the del22q11.2 syndrome. Conclusion: We show in the context of a first high resolution pedigree map of the 22q11.2 region that NAHR within LCR22 leading to duplications and deletions cannot be explained exclusively under a hypothesis of low AHR rates. In addition, we find that AHR recombination events cluster within families. If normal and aberrant recombination are mechanistically related, the fact that LCR22s undergo frequent AHR and that we find familial differences in recombination rates within the 22q11.2 region would have obvious health-related implications.

Defining the Effect of the 16p11.2 Duplication on Cognition, Behavior, and Medical Comorbidities.

IMPORTANCE: The 16p11.2 BP4-BP5 duplication is the copy number variant most frequently associated with autism spectrum disorder (ASD), schizophrenia, and comorbidities such as decreased body mass index (BMI). OBJECTIVES: To characterize the effects of the 16p11.2 duplication on cognitive, behavioral, medical, and anthropometric traits and to understand the specificity of these effects by systematically comparing results in duplication carriers and reciprocal deletion carriers, who are also at risk for ASD. DESIGN, SETTING, AND PARTICIPANTS: This international cohort study of 1006 study participants compared 270 duplication carriers with their 102 intrafamilial control individuals, 390 reciprocal deletion carriers, and 244 deletion controls from European and North American cohorts. Data were collected from August 1, 2010, to May 31, 2015 and analyzed from January 1 to August 14, 2015. Linear mixed models were used to estimate the effect of the duplication and deletion on clinical traits by comparison with noncarrier relatives. MAIN OUTCOMES AND MEASURES: Findings on the Full-Scale IQ (FSIQ), Nonverbal IQ, and Verbal IQ; the presence of ASD or other DSM-IV diagnoses; BMI; head circumference; and medical data. RESULTS: Among the 1006 study participants, the duplication was associated with a mean FSIQ score that was lower by 26.3 points between proband carriers and noncarrier relatives and a lower mean FSIQ score (16.2-11.4 points) in nonproband carriers. The mean overall effect of the deletion was similar (-22.1 points; P < .001). However, broad variation in FSIQ was found, with a 19.4- and 2.0-fold increase in the proportion of FSIQ scores that were very low (≤40) and higher than the mean (>100) compared with the deletion group (P < .001). Parental FSIQ predicted part of this variation (approximately 36.0% in hereditary probands). Although the frequency of ASD was similar in deletion and duplication proband carriers (16.0% and 20.0%, respectively), the FSIQ was significantly lower (by 26.3 points) in the duplication probands with ASD. There also were lower head circumference and BMI measurements among duplication carriers, which is consistent with the findings of previous studies. CONCLUSIONS AND RELEVANCE: The mean effect of the duplication on cognition is similar to that of the reciprocal deletion, but the variance in the duplication is significantly higher, with severe and mild subgroups not observed with the deletion. These results suggest that additional genetic and familial factors contribute to this variability. Additional studies will be necessary to characterize the predictors of cognitive deficits.

Extração/pré-concentração de íons cobre no ponto nuvem explorando a formação de complexos com DMIT [4,5-dimercapto-1,3-ditiol-2-tionato]

The present study proposes a method for cloud point preconcentration of copper ions at pH 2.0 based on complexes formed with [4,5-dimercapto-1,3-dithyol-2-thionate] and subsequent determination by flame atomic absorption spectrometry (FAAS). Under optimal analytical conditions, the method provided limits of detection of 0.84 and 0.45 µg L-1, by preconcentrating 12.0 and 24.0 mL of sample, respectively. The method was applied for copper determination in water samples, synthetic saliva, guarana powder, tea samples and soft drinks and the accuracy was assessed by analyzing the certified reference materials Dogfish Liver (DOLT-4) and Lobster Hepatopancreas (TORT-2).

Spectrophotometric determination of arsenic in soil samples using 2-(5-bromo-2-pyridylazo)-5-di-ethylaminophenol (Br-PADAP)

In this paper, a new, simple and sensitive method for arsenic determination in soil is proposed. This is based on the reduction of silver (I) and iron (III) ions by arsine followed by a complexation reaction of iron (II) with the spectrophotometric reagent Br-PADAP 2-(5-bromo-2-pyridylazo)-5-di-ethylaminophenol. Arsenic determination with a Sandell's sensitivity of 3.1 10-4 cm-2, linear range from 0.1 µg ml-1 to 2.0 µg ml-1 (r560 = 0.9995), molar absorptivity of 2.45 10(5) l mol-1 cm-1 and a concentration detection limit of 1.4 ng ml-1 (3s) were obtained using a 10 ml sample volume. Selectivity was increased with the use of EDTA as a masking agent. The proposed method was applied for arsenic determination in the presence of several ions amounts in digested soil samples. The results revealed that antimony (III), mercury (II), germanium (IV), platinum (IV) interferes at all analyzed proportions. The interferences can be easily removed by the use of EDTA. Precision and accuracy obtained were satisfactory with a R.S.D. < 5 %. Recovery of arsenic in soil samples varied from 95.55 to 102.70 % with a mean of 99.63 %. These results demonstrated that the proposed method is applicable for arsenic analysis in different soil samples.

Electrochemical properties of Cu4[PhN3C6H4N3(H)Ph]4(µ-O)2, a tetranuclear Copper(II) complex with 1-phenyltriazenido-2-phenyltriazene-benzene as ligand

Bis-(µ2-oxo)-tetrakis{[1-feniltriazene-1,3-diil)-2-(phenyltriazenil)benzene copper(II) is a tetranuclear complex which shows four Cu(II) ions coordinated by four 1,2-bis(phenyltriazene)benzene bridged ligands, with one diazoaminic deprotonated chain, and two O2- ligands. The complex reduces at E1/2 = -0.95 V vs Fc+/Fc, a two electrons process. Cyclic voltammetric and spectroelectrochemical studies showed a reversible process. When immobilized on carbon paste electrode, the complex electrocatalyses the reduction of O2 dissolved on aqueous solution at -0.3 V vs SCE potential. The obtained current shows linearity with O2 concentration.

Avaliação espectrofotométrica das formas CR+3, CRO4-2 e CR2O7-2

Um estudo espectrofotométrico de especiação das formas Cr+3, CrO4-2 e Cr2O7-2 foi realizado em amplo intervalo de pH de 2,0 a 12,0 em solução tampão Britton-Robinson. Os espectros de absorção das regiões ultra-violeta e visível são bem caracterizados, apresentando bandas nas duas regiões espectrais. A relação de absorbância versus concentração, para cada espécie química, permitiu conhecer o coeficiente de absortividade molar das entidades químicas.

Efeito de subdoses de 2,4-D na produtividade do algodão e suscetibilidade da cultura em função de seu estádio de desenvolvimento

O objetivo deste trabalho foi avaliar o efeito de subdoses de 2,4-D no desenvolvimento e produtividade da cultura do algodoeiro. Dois experimentos foram conduzidos utilizando-se da variedade IAPAR-95 e o sistema de avaliação por meio de testemunhas duplas. No primeiro experimento, as aplicações foram realizadas no estádio F1 (início do florescimento), aplicando-se dosagens de 0,84; 1,68; 3,36; 6,72; 13,44 e 26,88 g de equivalente ácido (e.a.) por hectare, equivalentes a derivas de 0,125; 0,25; 0,5; 1,0; 2,0 e 4,0% da dose de 670 g e.a. ha-1. No segundo experimento, os tratamentos foram constituídos pela combinação em esquema fatorial de duas doses (6,72 e 13,44 g e.a. ha-1) e três épocas de aplicação (C1, C3/C4 e C6), visando a avaliar a variação da sensibilidade do algodão ao 2,4-D em função de seu estádio de desenvolvimento. Os resultados evidenciaram que doses maiores que 3,36 g e.a. ha-1 (0,50%) aplicadas na fase de florescimento afetaram de forma significativa a produtividade, que a queda dos botões florais foi o sintoma mais importante para a redução da produtividade. No segundo experimento, observou-se que a sensibilidade do algodão caiu drasticamente em função do estádio de desenvolvimento. O único tratamento que provocou queda significativa de produtividade foi a dose de 13,44 g e.a. ha-1 (2,0%) aplicada no estádio C1. Dessa forma, a partir do momento em que as maçãs começam a se formar, a sensibilidade da cultura cai substancialmente.

Efeito de subdoses de 2,4-D na produtividade de fumo e suscetibilidade da cultura em função de seu estádio de desenvolvimento

O presente trabalho teve como objetivo determinar os efeitos de subdoses do herbicida 2,4-D na cultura do fumo. Os experimentos foram conduzidos a campo durante o ano de 2003, no município de Santa Isabel do Ivaí - PR, utilizando-se de fumo tipo Virgínia. No primeiro experimento, foram aplicadas, no estádio de pré-florescimento, doses de 0,84; 1,68; 3,36; 6,72; 13,44 e 26,88 g e.a. ha-1 de 2,4-D, equivalentes à deriva de 0,125; 0,25; 0,5; 1,0; 2,0 e 4,0% de produtos comerciais aplicados a 1,0 L ha-1 (670 g e.a. ha-1). Para o segundo experimento, os tratamentos foram constituídos pela combinação em esquema fatorial de duas doses (6,72 e 13,44 g e.a. ha-1, equivalentes a 1,0 e 2,0% de deriva) e três épocas de aplicação após o transplante para o campo. Nenhum sintoma visual marcante de fitotoxicidade foi observado dentro da faixa de doses avaliada. Visualmente, alguns dos possíveis efeitos atribuídos à fitotoxicidade ocasionada pela deriva de 2,4-D na cultura do fumo podem estar associados à utilização de antibrotantes. Nenhuma das doses aplicadas no primeiro experimento afetou a produtividade da cultura, nem o aspecto e qualidade das folhas, tendo o fumo tolerado até 4,0% de deriva avaliada. Resultados obtidos no segundo experimento confirmaram esses dados, constatando-se que níveis de deriva de até 2,0% (13,44 g e.a. ha-1), aplicados em três fases após o transplante das mudas para o campo, não causaram qualquer efeito negativo sobre a produtividade da cultura.