Hereditary breast cancer next-generation sequencing (NGS) panel evaluation in the south region of Brazil: a novel BRCA2 candidate pathogenic variant is reported.

In this article, we delineate a loosely selected cohort comprising patients with a history of early-onset breast cancer and/or a familial occurrence of cancer. The aim of this study was to gain insights into the presence of breast cancer-related gene variants in a population from a micro-region in southern Brazil, specifically the Metropolitan Region of Curitiba. This area exhibits a highly genetically mixed population, mirroring the general characteristics of the Brazilian people. Comprehensive next-generation sequencing (NGS) multigene panel testing was conducted, involving the evaluation of twelve patients. Two pathogenic variants and one candidate pathogenic variant were identified: BRCA2:c.8878C>T, p.Gln2960Ter; CHEK2:c.1100delAG>A, p.Thr367Metfs*15 and BRCA2:c.3482dupG>GA, p.Asp1161Glufs*3, a novel variant, previously unpublished, is reported.

Hexanoic acid: a new potential substitute for copper-based agrochemicals against citrus canker.

AIMS: The aim of the study is to evaluate hexanoic acid (HA) as an alternative to manage citrus canker. METHODS AND RESULTS: The minimal growth inhibitory concentration of HA against Xanthomonas citri subsp. citri was determined at 2·15 mmol l-1 using a respiratory activity assay. Growth curves at different pH values showed that growth inhibition was not due to media acidification induced by HA. The germination rate and root elongation of Lactuca sativa seeds exposed to different concentrations of HA (varying from 0·86 to 5·16 mmol l-1 ) were assessed to screen for phytotoxicity. The acid exhibited low phytotoxicity for L. sativa at 1·29 and 2·58 mmol l-1 . To evaluate the ability of HA to protect citrus against X. citri infection, leaves of Citrus sinensis were sprayed with the acid and subsequently challenged with X. citri. HA at 3·44 mmol l-1 was able to protect citrus against infection, showing a reduction of three orders of magnitude in the number of citrus canker lesions per cm2 when compared to the untreated negative control. CONCLUSION: HA is a potential alternative to copper for citrus canker management. SIGNIFICANCE AND IMPACT OF THE STUDY: HA inhibits X. citri growth, exhibits low phytotoxicity and is an alternative to copper for the protection of citrus plants against bacterial infection.

Behavioral activities of white-lipped peccary (Tayassu pecari, Link, 1795) in a semi-intensive farming system in Brazil / [Atividades comportamentais de queixadas (Tayassu pecari, Link, 1795) em sistema semi-intensivo de criação no Brasil]

This study aimed to describe the main behaviors of white-lipped peccaries (Tayassu pecari) expressed in a semi-intensive production system in Brazil. The behavioral activities of two groups of peccaries allocated in two paddocks were assessed, totaling 17 adult animals and eventual pups in different developmental stages. The animals were visually observed using the ad libitum sampling and scan sample methods during the adaptation and experimental phases, respectively. The animals were evaluated in the morning, afternoon, and at night. The behavioral activities observed by ad libitum sampling comprised feeding, pool contact, moving, staying inside the handling area, resting, mud bathing, mutual rubbing, rubbing, aggression, sexual behavior, copulation, foraging, breastfeeding, sleeping, territorial marking, interactions, birthing, gnawing, and other behaviors. All behaviors observed by the ad libitum sampling method were confirmed in the experimental period by scan sample, except for territorial marking and birthing. The effects of time of day were statistically significant (p <0.05) for eating, pool contact, movement, staying inside the handling area, resting, mud bathing and sleeping. These results contribute to the understanding of instinctive animal habits and to the development of nutritional, environmental and health management protocols that meet the requirements of peccaries.(AU)

Objetivou-se descrever os principais comportamentos que os queixadas (Tayassu pecari) expressam em sistema de produção semi-intensivo no Brasil, bem como suas diferenças de frequências comportamentais em função do período do dia. Foram avaliadas as atividades comportamentais de dois grupos de queixadas alocados em dois piquetes, totalizando 17 animais adultos e eventuais filhotes em diferentes estágios comportamentais. Na fase adaptativa e experimental os animais foram observados visualmente pelos métodos ad libitum e scan sample, respectivamente. Os animais foram avaliados nos períodos da manhã, tarde e noite. As atividades comportamentais observadas pelo método ad libitum foram alimentação, contato com a piscina, movimentação, interior do brete de manejo, descanso, lameando, esfregação mútua, esfregar-se, agressão, comportamento sexual, cópula, fuçando, amamentação, dormindo, marcando território, interações, manilha, parição, roendo e outros comportamentos. Todos os comportamentos observados pelo método ad libitum foram confirmados no período experimental scan sample, exceto para as variáveis marcando território e parição. O efeito do período do dia foi estatisticamente significativo (P<0,05) sobre as frequências dos comportamentos alimentação, contato com a piscina, movimentação, interior do brete de manejo, descanso, lameando e dormindo. Os resultados contribuem para a compreensão dos hábitos instintivos dos animais e, com isso, colaborar com a elaboração de protocolos de manejo nutricional, ambiental e sanitário, buscando-se suprir as necessidades dos queixadas. Futuras pesquisas envolvendo queixadas em cativeiro fomentarão os estudos voltados aos aspectos biológicos, conservacionistas e produtivos.(AU)

Identification of the transcriptionally active cytochrome P450 repertoire in Coffea arabica.

Cytochrome P450s (P450s) comprise a gene superfamily encoding enzymes that are involved in diverse plant metabolic pathways that produce primary and secondary metabolites such as phenylpropanoids, terpenoids, nitrogen-containing compounds, and plant hormones. They comprise one of the most diverse gene families in plant evolution. Although there are many studies that aim to characterize P450s in plants, there is no report on the characterization of this superfamily in Coffea arabica, where they might be related to plant tolerance to biotic and abiotic stresses, as well as aroma-related compounds. In this study, we report the characterization and annotation of 87 putative P450s from C. arabica obtained from the Brazilian Coffee Genome Project and describe their transcriptional pattern in different tissues and coffee organs. To validate our approach, we measured the transcriptional profile of the CaCYP81D8_1 gene by quantitative polymerase chain reaction in leaves, flowers, and fruits. This study is the first effort to present and analyze the P450 superfamily in C. arabica, which may assist in understanding the chemical diversity of coffee secondary metabolites.

CoffeebEST: an integrated resource for Coffea spp expressed sequence tags.

Coffee is one of the most important commodities in the world, and its production relies mainly on two species, Coffea arabica and Coffea canephora. Although there are diverse transcriptome datasets available for coffee trees, few research groups have exploited the potential knowledge contained in these data, especially with respect to fruit and seed development. Here, we present a comparative analysis of the transcriptomes of Coffea arabica and Coffea canephora with a focus on fruit development using publicly available expressed sequence tags (ESTs). Most of the fruit and seed EST data has been obtained from C. canephora. Therefore, we performed a fruit EST analysis of the 5 developmental stages of this species (18, 22, 30, 42, and 46 weeks after flowering) comprising 29,009 sequences. We compared C. canephora fruit ESTs to reference unigenes of C. canephora (7710 contigs and 8955 singletons) and C. arabica (15,656 contigs and 16,351 singletons). Additional analyses included functional annotation based on Gene Onthology, as well as an annotation using PlantCyc, a curated plant protein database. The Coffee Bean EST (CoffeebEST) is a public database available at http://bioinfo-02.cp.utfpr.edu.br/. This database represents an additional resource for the coffee scientific community, offering a user-friendly collection of information for non-specialists in coffee molecular biology to support experimental research on comparative and functional genomics.

Construction and characterization of a BAC library from the Coffea arabica genotype Timor Hybrid CIFC 832/2.

Most of the world's coffee production originates from Coffea arabica, an allotetraploid species with low genetic diversity and for which few genomic resources are available. Genomic libraries with large DNA fragment inserts are useful tools for the study of plant genomes, including the production of physical maps, integration studies of physical and genetic maps, genome structure analysis and gene isolation by positional cloning. Here, we report the construction and characterization of a Bacterial Artificial Chromosome (BAC) library from C. arabica Timor Hybrid CIFC 832/2, a parental genotype for several modern coffee cultivars. The BAC library consists of 56,832 clones with an average insert size of 118 kb, which represents a dihaploid genome coverage of five to sixfold. The content of organellar DNA was estimated at 1.04 and 0.5 % for chloroplast and mitochondrial DNA, respectively. The BAC library was screened for the NADPH-dependent mannose-6-phosphate reductase gene (CaM6PR) with markers positioned on four linkage groups of a partial C. arabica genetic map. A mixed approach using PCR and membrane hybridization of BAC pools allowed for the discovery of nine BAC clones with the CaM6PR gene and 53 BAC clones that were anchored to the genetic map with simple sequence repeat markers. This library will be a useful tool for future studies on comparative genomics and the identification of genes and regulatory elements controlling major traits in this economically important crop species.

Gene expression and enzymatic activity of pectin methylesterase during fruit development and ripening in Coffea arabica L.

Coffee quality is directly related to the harvest and post harvest conditions. Non-uniform maturation of coffee fruits, combined with inadequate harvest, negatively affects the final quality of the product. Pectin methylesterase (PME) plays an important role in fruit softening due to the hydrolysis of methylester groups in cell wall pectins. In order to characterize the changes occurring during coffee fruit maturation, the enzymatic activity of PME was measured during different stages of fruit ripening. PME activity progressively increased from the beginning of the ripening process to the cherry fruit stage. In silico analysis of expressed sequence tags of the Brazilian Coffee Genome Project database identified 5 isoforms of PME. We isolated and cloned a cDNA homolog of PME for further characterization. CaPME4 transcription was analyzed in pericarp, perisperm, and endosperm tissues during fruit development and ripening as well as in other plant tissues. Northern blot analysis revealed increased transcription of CaPME4 in the pericarp 300 days after flowering. Low levels of CaPME4 mRNAs were observed in the endosperm 270 days after flowering. Expression of CaPME4 transcripts was strong in the branches and lower in root and flower tissues. We showed that CaPME4 acts specifically during the later stages of fruit ripening and possibly contributes to the softening of coffee fruit, thus playing a significant role in pectin degradation in the fruit pericarp.

Mutator System Derivatives Isolated from Sugarcane Genome Sequence.

Mutator-like transposase is the most represented transposon transcript in the sugarcane transcriptome. Phylogenetic reconstructions derived from sequenced transcripts provided evidence that at least four distinct classes exist (I-IV) and that diversification among these classes occurred early in Angiosperms, prior to the divergence of Monocots/Eudicots. The four previously described classes served as probes to select and further sequence six BAC clones from a genomic library of cultivar R570. A total of 579,352 sugarcane base pairs were produced from these "Mutator system" BAC containing regions for further characterization. The analyzed genomic regions confirmed that the predicted structure and organization of the Mutator system in sugarcane is composed of two true transposon lineages, each containing a specific terminal inverted repeat and two transposase lineages considered to be domesticated. Each Mutator transposase class displayed a particular molecular structure supporting lineage specific evolution. MUSTANG, previously described domesticated genes, are located in syntenic regions across Sacharineae and, as expected for a host functional gene, posses the same gene structure as in other Poaceae. Two sequenced BACs correspond to hom(eo)logous locus with specific retrotransposon insertions that discriminate sugarcane haplotypes. The comparative studies presented, add information to the Mutator systems previously identified in the maize and rice genomes by describing lineage specific molecular structure and genomic distribution pattern in the sugarcane genome. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12042-012-9104-y) contains supplementary material, which is available to authorized users.

New mariner elements in Anastrepha species (Diptera: Tephritidae).

Mariner-like elements (MLE) are members from class II of transposable elements also known as DNA transposons. These elements have a wide distribution among different groups of organisms, including insects, which can be explained by horizontal and vertical gene-transfer. MLE families have been described in tephritid flies and other genera. During screening for Wolbachia bacteria in fruit flies of the genus Anastrepha, we discovered two sequences related to mariner-like elements. Based on these sequences, we designed primers that allowed us to isolate and characterize two new mariner-like elements (Anmar1 and Anmar2) in Anastrepha flies. These elements, which belong to the mellifera and rosa subfamilies have a low nucleotide diversity, and are probably inactive and acquired by vertical transfer. This is the first report of mariner-like transposons in flies found in South America.

Genital mycoplasmas in women attending a family planning clinic in Guiné-Bissau and their susceptibility to antimicrobial agents.

A study on the prevalence of genital mycoplasmas and their susceptibility to the most common antimicrobial agents used for treating the infection was conducted on 94 women attending a family planning clinic in Guiné-Bissau. Fifty-four women (57.4%) were positive for Mycoplasma hominis and/or Ureaplasma urealyticum. M. hominis and U. urealyticum separately isolated from infected women yielded frequencies of 31.5 and 27.8%, respectively, the remainder were infected with both species. No strain was found to be resistant to all three commonly employed antibiotics for the management of these infections (erythromycin, tetracycline and ofloxacin), although multiple resistance to two antibiotics was frequent, especially when both genital mycoplasmas were present. Some 90.7 and 24.1% of all isolates were resistant to erythromycin and tetracycline, respectively. No resistance was observed to ofloxacin, although 50% of the strains had intermediate resistance. The high prevalence of genital mycoplasmas in women attending a family planning clinic in Guiné-Bissau, as demonstrated in this study, appears to be associated with trichomonosis and bacterial vaginosis. These infections were also found to be highly resistant to erythromycin and tetracycline and to have intermediate resistance to ofloxacin. However, further studies are necessary to establish the burden of infection due to antibiotic resistant genital mycoplasmas.

Ureaplasma urealyticum biovar determination in women attending a family planning clinic in Guiné-Bissau, using polymerase chain reaction of the multiple-banded antigen gene.

Although Ureaplasma urealyticum is commonly found in the genital tract of asymptomatic women, it has been suggested that only certain subgroups of this microorganism are disease associated. Vaginal specimens were collected to determine the distribution of U. urealyticum biovars and to estimate their possible association with age, absence of lactobacilli, and tetracycline resistance. Of the 94 women studied, 40 (43%) carried U. urealyticum and were biotyped by polymerase chain reaction (PCR). Twenty-nine (73%) strains presented with parvo biovar, 10 (25%) with T960 biovar, and one (2.5%) with both biovars. Parvo biovar was predominant in all age groups and appears to be more frequent in women 20-25 years of age (41%), whereas T960 was common in women 30-35 years of age (22%). In this study, U. urealyticum was not associated with changes in vaginal flora, although the inverse apparently was true for Mycoplasma hominis. However, T960 biovar was more associated with the loss of lactobacilli than was parvo biovar. The number of T960 biovar strains that presented tetracycline (40%) or multiple (100%) resistance was higher than that of parvo biovar strains (27% and 69%, respectively).

Contextual interference effects with skilled baseball players.

The learning benefits of contextual interference have been frequently demonstrated in different settings using novice learners. The purpose of the present study was to test such effects with skilled athletic performers. Scheduling differences for biweekly additional ("extra") batting-practice sessions of a collegiate baseball team were examined. 30 players (ns = 10) were blocked on skill and then randomly assigned to one of three groups. The random and blocked groups received 2 additional batting-practice sessions each week for 6 wk. (12 sessions), while the control group received no additional practice. The extra sessions consisted of 45 pitches, 15 fastballs, 15 curveballs, and 15 change-up pitches. The random group received these pitches in a random order, while the blocked group received all 15 of one type, then 15 of the next type, and finally 15 of the last type of pitch in a blocked fashion. All subjects received a pretest of 45 randomly presented pitches of the three varieties. After 6 wk. of extra batting practice, all subjects received two transfer tests, each of 45 trials; one was presented randomly and one blocked. The transfer tests were counterbalanced across subjects. Pretest analysis showed no significant differences among groups. On both the random and blocked transfer tests, however, the random group performed with reliably higher scores than the blocked group, who performed better than the control group. When comparing the pretest to the random transfer test, the random group improved 56.7%, the blocked group 24.8%, and the control group only 6.2%.(ABSTRACT TRUNCATED AT 250 WORDS)

Directly observed 15N NMR spectra of uniformly enriched proteins.

The proteins cytochrome c2, cytochrome c', and ribulosebisphosphate carboxylase/oxygenase from Rhodospirillum rubrum were enriched in 15N by growth of the organism on 15NH4Cl. The proteins were purified to homogeneity and studied by 15N NMR. Longitudinal and transverse relaxation times as well as the nuclear Overhauser effects were determined for various groups of the proteins which vary in molecular weight from 13,000 to 114,000. The values of these parameters for the amide resonances or for groups thought to be rigid were consistent with the molecular weights of the proteins. Relaxation times of the amino-terminal alpha-amino groups and the side chain nitrogen atoms of arginine and lysine were consistent with much more rapid motion. Nitrogen atoms having bound protons were generally found to be decoupled from the protons by chemical exchange. Demonstrable 1H-15N coupling was taken as an indication that exchange was hindered, either by hydrogen bonding interactions or by inaccessibility of the group to solvent. Histidine side chain nitrogen atoms, which experience a large chemical shift upon protonation/deprotonation, were often found to be broadened beyond detectability by chemical exchange and tautomerization. Strategies for improving sensitivity and for obtaining specific peak assignments are also discussed.