With increased production of genomic data since the advent of next-generation sequencing (NGS), there has been a need to develop new bioinformatics tools and areas, such as comparative genomics. In ...comparative genomics, the genetic material of an organism is directly compared to that of another organism to better understand biological species. Moreover, the exponentially growing number of deposited prokaryote genomes has enabled the investigation of several genomic characteristics that are intrinsic to certain species. Thus, a new approach to comparative genomics, termed pan-genomics, was developed. In pan-genomics, various organisms of the same species or genus are compared. Currently, there are many tools that can perform pan-genomic analyses, such as PGAP (Pan-Genome Analysis Pipeline), Panseq (Pan-Genome Sequence Analysis Program) and PGAT (Prokaryotic Genome Analysis Tool). Among these software tools, PGAP was developed in the Perl scripting language and its reliance on UNIX platform terminals and its requirement for an extensive parameterized command line can become a problem for users without previous computational knowledge. Thus, the aim of this study was to develop a web application, known as PanWeb, that serves as a graphical interface for PGAP. In addition, using the output files of the PGAP pipeline, the application generates graphics using custom-developed scripts in the R programming language. PanWeb is freely available at http://www.computationalbiology.ufpa.br/panweb.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
This study developed a computational tool with a graphical interface and a web-service that allows the identification of phage regions through homology search and gene clustering. It uses G+C content ...variation evaluation and tRNA prediction sites as evidence to reinforce the presence of prophages in indeterminate regions. Also, it performs the functional characterization of the prophages regions through data integration of biological databases. The performance of PhageWeb was compared to other available tools (PHASTER, Prophinder, and PhiSpy) using Sensitivity (Sn) and Positive Predictive Value (PPV) tests. As a reference for the tests, more than 80 manually annotated genomes were used. In the PhageWeb analysis, the Sn index was 86.1% and the PPV was approximately 87%, while the second best tool presented Sn and PPV values of 83.3 and 86.5%, respectively. These numbers allowed us to observe a greater precision in the regions identified by PhageWeb while compared to other prediction tools submitted to the same tests. Additionally, PhageWeb was much faster than the other computational alternatives, decreasing the processing time to approximately one-ninth of the time required by the second best software. PhageWeb is freely available at http://computationalbiology.ufpa.br/phageweb.
We report phase transitions in blue phase-forming liquid crystals (LCs) that are triggered by exposure to toluene vapours. Specifically, we reveal that room-temperature cholesteric phase mixtures of ...MLC-2142 and S-811 form blue phases (BP I, II and III) with increasing vapour pressure of toluene. To probe the mechanism underlying this observation, we investigated the phase behaviour of mixtures of BP-forming LCs containing a range of non-volatile aromatic compounds (e.g. pyrene). We interpret our observations to indicate that the principal effect of small aromatic compounds is to decrease the energy penalty associated with the formation of disclination lines in BPs. We also conclude that the absorption of toluene into the BP-forming LCs lowers the energy required for the formation of disclination cores in the BP phase, thus allowing the elastically favoured double-twist cylinders to form at lower temperatures. We demonstrate that BP-forming LCs containing pyrene can be used to detect toluene at concentrations below 200 ppm at room temperature. Overall, these results guide the design of LC-based materials that respond to VOCs at concentrations relevant to occupational settings.
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BFBNIB, GIS, IJS, KISLJ, NUK, PNG, UL, UM, UPUK
Zoonotic tuberculosis is a disease of public health importance worldwide, especially in developing countries. The present study aimed to investigate the role played by Mycobacterium bovis and other ...mycobacteria as etiologic agents of bubaline tuberculosis (TB) in the Brazilian Amazon region.
Granulomatous lesions suggestive of TB obtained from 109 buffaloes (n =109) during sanitary inspection at slaughter were subjected to histopathological evaluation, immunohistochemical (IHC) detection of Mycobacterium antigens, and to molecular tests (PCR) to detect hsp65, IS6110 and RD4 genes, which are specific to Mycobacterium spp., Mycobacterium tuberculosis Complex (MTBC) and M. bovis, respectively.
PCR results indicated Mycobacterium infection in 87.2% of the cases, of which 69.5% were positive for M. bovis, 27.4% belonged to MTBC, and 3.1% were probably non-TB mycobacteria. There was good agreement between the genus-specific molecular technique and the histopathological analysis. This high frequency of TB cases caused by non-M. bovis suggests a diversified scenario of mycobacteria associated with bubaline TB in the Brazilian Amazon region.
The results reinforce the need of discussing the inclusion of more accurate techniques in examinations carried out by Inspection Services in Brazil.
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Astrocytoma is the most common type of primary brain tumor. The risk factors for astrocytoma are poorly understood; however, germline genetic variants account for 25% of the risk of developing ...gliomas. In this study, we assessed the risk of astrocytoma associated with variants in
AGT
, known by its role in angiogenesis,
TP53
, a well-known tumor suppressor and the DNA repair gene
MGMT
in a Mexican population. A case–control study was performed in 49 adult Mexican patients with grade II–IV astrocytoma. Sequencing of exons and untranslated regions of
AGT
,
MGMT
, and
TP53
from was carried in an Ion Torrent platform. Individuals with Mexican Ancestry from the 1000 Genomes Project were used as controls. Variants found in our cohort were then assessed in a The Cancer Genome Atlas astrocytoma pan-ethnic validation cohort. Variants rs1926723 located in
AGT
(OR 2.74, 1.40–5.36 95% CI), rs7896488 in
MGMT
(OR 3.43, 1.17–10.10 95% CI), and rs4968187 in
TP53
(OR 2.48, 1.26–4.88 95% CI) were significantly associated with the risk of astrocytoma after multiple-testing correction. This is the first study where the
AGT
rs1926723 variant,
TP53
rs4968187, and
MGMT
rs7896488 were found to be associated with the risk of developing an astrocytoma.
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EMUNI, FZAB, GEOZS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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