Downstream analysis of genomic and transcriptomic sequence data is often executed by functional annotation that can be performed by various bioinformatics tools and biological databases. However, a ...full fast integrated tool is not available for such analysis. Besides, the current available software is not able to produce analytic lists of annotations and graphs to help users in evaluating the output results. Therefore, we present the Gene Ontology Functional Enrichment Annotation Tool (GO FEAT), a free web platform for functional annotation and enrichment of genomic and transcriptomic data based on sequence homology search. The analysis can be customized and visualized as per users' needs and specifications. GO FEAT is freely available at http://computationalbiology.ufpa.br/gofeat/ and its source code is hosted at https://github.com/fabriciopa/gofeat .
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Vibrio cholerae is the causal organism of the cholera epidemic, which is mostly prevalent in developing and underdeveloped countries. However, incidences of cholera in developed countries are also ...alarming. Because of the emergence of new drug-resistant strains, even though several generic drugs and vaccines have been developed over time, Vibrio infections remain a global health problem that appeals for the development of novel drugs and vaccines against the pathogen. Here, applying comparative proteomic and reverse vaccinology approaches to the exoproteome and secretome of the pathogen, we have identified three candidate targets (ompU, uppP and yajC) for most of the pathogenic Vibrio strains. Two targets (uppP and yajC) are novel to Vibrio, and two targets (uppP and ompU) can be used to develop both drugs and vaccines (dual targets) against broad spectrum Vibrio serotypes. Using our novel computational approach, we have identified three peptide vaccine candidates that have high potential to induce both B- and T-cell-mediated immune responses from our identified two dual targets. These two targets were modeled and subjected to virtual screening against natural compounds derived from Piper betel. Seven compounds were identified first time from Piper betel to be highly effective to render the function of these targets to identify them as emerging potential drugs against Vibrio. Our preliminary validation suggests that these identified peptide vaccines and betel compounds are highly effective against Vibrio cholerae. Currently we are exhaustively validating these targets, candidate peptide vaccines, and betel derived lead compounds against a number of Vibrio species.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
This work presents a formalization in PVS of the computational theory for a computational model given as a class of partial recursive functions called PVS0. The model is built over basic operators, ...which, when restricted to constants, successor, projections, greater-than, and bijections from tuples of naturals to naturals, results in a proven (formalized) Turing complete model. Complete formalizations of the Recursion theorem and Rice’s theorem are discussed in detail. Other relevant results, such as the undecidability of the Halting problem and the fixed-point theorem, were also fully formalized.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
This paper presents a formalization of several termination criteria for first-order recursive functions. The formalization, which is developed in the Prototype Verification System (PVS), includes the ...specification and proof of equivalence of semantic termination, Turing termination, size change principle, calling context graphs, and matrix-weighted graphs. These termination criteria are defined on a computational model that consists of a basic functional language called PVS0, which is an embedding of recursive first-order functions. Through this embedding, the native mechanism for checking termination of recursive functions in PVS could be soundly extended with semi-automatic termination criteria such as calling contexts graphs.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Antibiotic resistance is one of the biggest health challenges of our time. We are now facing a post-antibiotic era in which microbial infections, currently treatable, could become fatal. In this ...scenario, antimicrobial peptides such as bacteriocins represent an alternative solution to traditional antibiotics because they are produced by many organisms and can inhibit bacteria, fungi, and/or viruses. Herein, we assessed the antimicrobial activity and biotechnological potential of 54
strains isolated from bovine mastitis. Deferred plate antagonism assays revealed an inhibition spectrum focused on species of the genus
-namely,
,
,
, and
. Three genomes were successfully sequenced, allowing for their taxonomic confirmation via a multilocus sequence analysis (MLSA). Virulence potential and antibiotic resistance assessments showed that strain LGMAI_St_08 is slightly more pathogenic than the others. Moreover, the
gene was identified in the three strains. This gene is associated with resistance against erythromycin, azithromycin, and spiramycin. Assessments for secondary metabolites and antimicrobial peptides detected the bacteriocin zoocin A. Finally, comparative genomics evidenced high similarity among the genomes, with more significant similarity between the LGMAI_St_11 and LGMAI_St_14 strains. Thus, the current study shows promising antimicrobial and biotechnological potential for the
strains.
This paper presents a novel term structure of interest rate (TSIR) model with stochastic volatility and jumps (SVJ) that combines the market framework proposed by Brace et al. (1997) with the ...string-shock framework of Santa-Clara and Sornette (2001). In this model, the factors’ variance is estimated through the eigendecomposition of a variance–covariance matrix obtained with a measure of market volatility derived from out-of-the-money option prices and historical correlations of interest rates traded in the futures market. The stochastic evolution of the factors’ variance is governed by the 4/2 model developed by Grasselli (2017), including jumps. A novel method is employed to estimate the parameters of the SVJ model that minimizes the distance between the sample moments and the moments of a gamma distribution. The empirical application of the model in the Brazilian derivatives market demonstrates its effectiveness in accurately capturing the volatility smile of interest rate options.
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•Introduces a new TSIR model with stochastic volatility and jumps.•Proposes a novel methodology to estimate the time-varying variance–covariance matrix.•Proposes a novel methodology to estimate parameters of the stochastic volatility model.•The model capture the volatility smile of IDI options in the Brazilian financial market.•Analyzes the predictive power of interest rate futures and the options market.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Multidrug-resistant bacteria are of critical importance and a problem for human health and food preservation; the discovery of new antimicrobial substances to control their proliferation is part of ...the solution. This work reports on 57 antagonistic Aeromonas strains, of which 38 strains were antagonistic towards problematic human pathogens. The genome of the most antagonistic strain was sequenced and identified as Aeromonas allosaccharophila. Its genome was fully annotated and mined for genes that might explain that activity. Strain AE59-TE was antagonistic toward clinically relevant gram-negative and gram-positive multidrug-resistant bacteria, including Klebsiella pneumoniae KPC, Escherichia coli ESBL, Salmonella typhimurium, and Staphylococcus aureus MRSA. Strain AE59-TE2 was identified by multilocus sequence analysis. Genome mining identified four genes homologous to the bacteriocin, zoocin A from Streptococcus equi and a gene 98% similar to cvpA linked to colicin V production. A. allosaccharophila strain AE59-TE2 produced antimicrobial activity against a broad range of bacteria, including important gram-negative bacteria, not typically targeted by bacteriocins. Herewere described novel zoocin genes that are promising for industrial applications in the food and health sectors. Interesting and important antagonistic activity is described combined with the first detailed genomic analysis of the species Aeromonas allosaccharophila.
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is a Gram-negative bacterial species that causes disease in fish and is nowadays increasingly recurrent in enteric infections of humans. This study was performed to characterize newly sequenced ...isolates by comparing them with complete genomes deposited at the NCBI (National Center for Biotechnology Information). Nine isolates from fish, environments, and humans from the São Francisco Valley (Petrolina, Pernambuco, Brazil) were sequenced and compared with complete genomes available in public databases to gain insight into taxonomic assignment and to better understand virulence and resistance profiles of this species within the One Health context. One local genome and four NCBI genomes were misidentified as
. A total of 239 virulence genes were identified in the local genomes, with most encoding adhesion, motility, and secretion systems. In total, 60 genes involved with resistance to 22 classes of antibiotics were identified in the genomes, including
and
. The results suggest that the use of methods such as ANI is essential to avoid misclassification of the genomes. The virulence content of
from local isolates is similar to those complete genomes deposited at the NCBI. Genes encoding colistin resistance are widespread in the species, requiring greater attention for surveillance systems.
Objective
The aim of this study was to evaluate and compare alterations in gene expression using two distinct immortalization methods (hTERT and HPV16‐E6/E7) in ameloblastoma cell lines.
Materials ...and Methods
A primary cell culture derived from human ameloblastoma (AME‐1) was established and immortalized by two different methods using a transfection processes to hTERT and HPV‐E6/E7. The RNA‐seq was used to verify which immortalization method had less influence on gene expression. It was performed in four steps: extraction and collection of mRNA, PCR amplification, comparison with the human reference genome, and analysis of differential expression. The genes with differentiated expression were identified and mapped.
Results
RNA‐seq revealed genetic alterations in ameloblastoma cell lines after the immortalization process, including increased expression of tumor genes like MYC, E2F1, BRAF, HRAS, and HTERT, and a decrease in tumor suppressor genes like P53, P21, and Rb.
Conclusions
It is possible to affirm that cell immortalization is not an inert method regarding gene regulation mechanisms and the hTERT method (AME‐TERT) presented fewer changes in gene expression levels.
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CMK, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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