SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Background The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. Results In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Conclusion Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net

A novel approach for honey pollen profile assessment using an electronic tongue and chemometric tools

Nowadays the main honey producing countries require accurate labeling of honey before commercialization, including floral classification. Traditionally, this classification is made by melissopalynology analysis, an accurate but time-consuming task requiring laborious sample pre-treatment and high-skilled technicians. In this work the potential use of a potentiometric electronic tongue for pollinic assessment is evaluated, using monofloral and polyfloral honeys. The results showed that after splitting honeys according to color (white, amber and dark), the novel methodology enabled quantifying the relative percentage of the main pollens (Castanea sp., Echium sp., Erica sp., Eucaliptus sp., Lavandula sp., Prunus sp., Rubus sp. and Trifolium sp.). Multiple linear regression models were established for each type of pollen, based on the best sensors sub-sets selected using the simulated annealing algorithm. To minimize the overfitting risk, a repeated K-fold cross-validation procedure was implemented, ensuring that at least 10-20% of the honeys were used for internal validation. With this approach, a minimum average determination coefficient of 0.91 ± 0.15 was obtained. Also, the proposed technique enabled the correct classification of 92% and 100% of monofloral and polyfloral honeys, respectively. The quite satisfactory performance of the novel procedure for quantifying the relative pollen frequency may envisage its applicability for honey labeling and geographical origin identification. Nevertheless, this approach is not a full alternative to the traditional melissopalynologic analysis; it may be seen as a practical complementary tool for preliminary honey floral classification, leaving only problematic cases for pollinic evaluation.This work was co-financed by FCT/MEC and FEDER under Programme PT2020 (Project UID/EQU/50020/2013); and under the strategic funding of UID/BIO/04469/2013 unit

Síndrome da sela parcialmente vazia associada a deficiência do eixo gonadotrófico: relato de caso

Empty thoracic saddle is a diagnosis made by Magnetic Resonance Imaging, which defines it as partial when less than 50% of the saddle is filled with cerebrospinal fluid (CSF) and the pituitary gland has a thickness ≥ 3 mm or total when more than 50% of the saddle is filled with cerebrospinal fluid. that 50% of the saddle is filled with CSF and the thickness of the gland is ≤ 2 mm in diameter. Associated with this condition, with prevalence of 8 to 35% in the general population, a high incidence of pituitary dysfunction was documented. This study aims to report the case of a male patient with hypogonadotrophic hypogonadism associated with the partially empty Sella. Coming from Coronel Mota Hospital, Boa Vista / RR, in follow-up at the Endocrinology outpatient clinic for diabetes control and thyroid nodule follow-up, the patient complains of reduced libido and erectile dysfunction. Magnetic resonance imaging (MRI), after identifying the low hormonal levels in the laboratory tests, confirming the clinical suspicion of hypogonadism, showed a hypophysis with a height of up to 0.3 cm, characterizing a partially empty túrcica saddle. It was then decided to treat the patient with testosterone replacement. Conclusion: Although the diagnosis of this syndrome is most frequently observed incidentally, the association with hormonal disorders makes it necessary to routinely screen for these changes in asymptomatic patients so that treatment is early, avoiding complications in the short and long term.A sela túrcica vazia é um diagnóstico realizado através do exame de Ressonância Magnética que a define como parcial quando menos de 50% da sela é preenchida com líquido cefalorraquidiano (LCR) e a glândula pituitária tem espessura ≥ 3 mm ou total quando mais do que 50% da sela é preenchida com LCR e a espessura da glândula tem ≤ 2 mm de diâmetro. Associada a essa condição, com prevalência de 8 a 35% na população geral, uma alta incidência de disfunção pituitária foi documentada. O presente trabalho tem como objetivo relatar o caso de um paciente masculino com hipogonadismo hipogonadotrófico associado à Sela parcialmente vazia. Proveniente do hospital Coronel Mota, Boa Vista/RR, em acompanhamento no ambulatório de Endocrinologia para controle de diabetes e seguimento de nódulos da tireoide, o paciente queixa-se de redução da libido e disfunção erétil. A Ressonância Magnética solicitada após identificados os baixos níveis hormonais nos exames laboratoriais, confirmando a suspeita clínica de hipogonadismo, evidenciou hipófise com altura de até 0,3 cm, caracterizando uma sela túrcica parcialmente vazia. Foi optado, então, pelo tratamento do paciente com reposição de testosterona. Conclusão: Apesar do diagnóstico dessa síndrome ser evidenciado incidentalmente na maioria das vezes, a associação com distúrbios hormonais torna necessário o rastreio rotineiro dessas alterações nos portadores assintomáticos para que o tratamento seja precoce, evitando-se complicações a curto e longo prazo

Molecular Genetic Variability, Population Structure and Mating System in Tropical Forages

Microsatellite (SSR) markers were developed for the following tropical forage species, using accessions available from the plant genetic resources (PGR) collections held by EMBRAPA (Brazilian Agricultural Research Corporation): Brachiaria brizantha, B. humidicola, Panicum maximum, Paspalum spp., Stylosanthes capitata, S. guianensis, S. macrocephala, Calopogonium mucunoides and Centrosema spp. The markers were used to analyse population structure and genetic diversity, evolution and origin of the genetic variability in the centre of origin, mating systems and genetic resources in EMBRAPA’s germplasm bank. The results shed light on the amount of genetic variation within and between populations, revealed the need in some cases for further plant collection to adequately represent the species in PGR collections, allowed us to assemble core collections (subsets of the total collections) that should contain most of the available diversity and (in the case of the legumes) showed the need to avoid unwanted outcrossing when regenerating conserved material. The data will allow plant breeders to better select accessions for hybrid production, discriminate between genotypes and use marker-assisted selection in breeding programs. Our results will also underpin the construction of genetic maps, mapping of genes of agronomic interest and numerous other studies on genetic variability, population structure, gene flow and reproductive systems for the tropical forage species studied in this work

Enxaqueca em 746 pacientes com esclerose múltipla

Enxaqueca piora o sofrimento do paciente que tem esclerose múltipla (EM). ID-migraine é uma ferramenta útil para seleção de pacientes com enxaqueca e Migraine Disability Assessment (MIDAS) é um questionário que avalia o impacto da doença. O objetivo do presente estudo foi avaliar a presença e impacto de enxaqueca em pacientes com EM. Métodos: Pacientes diagnosticados com EM e tratados em clínicas especializadas foram convidados a responder um questionário online se também apresentassem cefaleia. Resultados: O estudo incluiu 746 participantes com cefaleia e EM que preencheram completamente as respostas. Foram 625 mulheres e 121 homens, sendo 69% dos pacientes com idade entre 20 e 40 anos. Enxaqueca foi identificada em 404 pacientes (54,1%) e moderado a grave impacto da doença foi observado em 68,3% dos casos. Conclusão: Enxaqueca é uma cefaleia primária frequente e incapacitante relatada por pacientes com EM.Migraine adds to the burden of patients suffering from multiple sclerosis (MS). The ID-migraine is a useful tool for screening migraine, and the Migraine Disability Assessment questionnaire can evaluate disease burden. The aim of the present study was to assess the presence and burden of migraine in patients with MS. Methods: Patients diagnosed with MS attending specialized MS units were invited to answer an online survey if they also experienced headache. Results: The study included 746 complete responses from patients with MS and headache. There were 625 women and 121 men, and 69% of all the patients were aged between 20 and 40 years. Migraine was identified in 404 patients (54.1%) and a moderate-to-high burden of disease was observed in 68.3% of the patients. Conclusion: Migraine is a frequent and disabling type of primary headache reported by patients with MS

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio