A comparative genomics study of the microbiome and freshwater resistome in Southern Pantanal.

This study explores the resistome and bacterial diversity of two small lakes in the Southern Pantanal, one in Aquidauana sub-region, close to a farm, and one in Abobral sub-region, an environmentally preserved area. Shotgun metagenomic sequencing data from water column samples collected near and far from the floating macrophyte Eichhornia crassipes were used. The Abobral small lake exhibited the highest diversity and abundance of antibiotic resistance genes (ARGs), antibiotic resistance classes (ARGCs), phylum, and genus. RPOB2 and its resistance class, multidrug resistance, were the most abundant ARG and ARGC, respectively. Pseudomonadota was the dominant phylum across all sites, and Streptomyces was the most abundant genus considering all sites.

MiR-612, miR-637, and miR-874 can Regulate VEGFA Expression in Hepatocellular Carcinoma Cell Lines.

MicroRNAs (miRNAs) are short non-coding RNA molecules acting as important posttranscriptional gene and protein expression regulators in cancer. The study goal was to examine VEGFA (vascular endothelial growth factor A) expression in hepatocellular carcinoma (HCC) cell lines upon transfection miR-612, miR-637, or miR-874. Methods: MiR-612 mimics, miR-637 mimics, or miR-874 inhibitors were transfected using Lipofectamine RNAiMax in both HCC cell lines, HepG2 and HuH-7. Real-time PCR, Western blotting, and ELISA methods were used to evaluate VEGFA regulation by the miRNAs. Results: Gene and protein expression levels of VEGFA were down-expressed in both cell lines, HepG2 and HuH-7, transfected with miR-612 or miR-637. Transfection with miR-874 inhibitor showed an increase in VEGFA gene expression in HepG2 and HuH-7 cell lines; however, no regulation was observed on VEGFA protein expression by miR-874 inhibition. Correlation analysis between miRNAs and VEGFA protein expression showed that miR-637 and miR-874 expression present inversely correlated to VEGFA protein expression. Conclusions: VEGFA was down-regulated in response to hsa-miR-612 or hsa-miR-637 overexpression; however, the modulation of VEGFA by miR-874 was observed only at the gene expression and thus, needs further investigation.

An improved approximation algorithm for the reversal and transposition distance considering gene order and intergenic sizes.

BACKGROUND: In the comparative genomics field, one of the goals is to estimate a sequence of genetic changes capable of transforming a genome into another. Genome rearrangement events are mutations that can alter the genetic content or the arrangement of elements from the genome. Reversal and transposition are two of the most studied genome rearrangement events. A reversal inverts a segment of a genome while a transposition swaps two consecutive segments. Initial studies in the area considered only the order of the genes. Recent works have incorporated other genetic information in the model. In particular, the information regarding the size of intergenic regions, which are structures between each pair of genes and in the extremities of a linear genome. RESULTS AND CONCLUSIONS: In this work, we investigate the SORTING BY INTERGENIC REVERSALS AND TRANSPOSITIONS problem on genomes sharing the same set of genes, considering the cases where the orientation of genes is known and unknown. Besides, we explored a variant of the problem, which generalizes the transposition event. As a result, we present an approximation algorithm that guarantees an approximation factor of 4 for both cases considering the reversal and transposition (classic definition) events, an improvement from the 4.5-approximation previously known for the scenario where the orientation of the genes is unknown. We also present a 3-approximation algorithm by incorporating the generalized transposition event, and we propose a greedy strategy to improve the performance of the algorithms. We performed practical tests adopting simulated data which indicated that the algorithms, in both cases, tend to perform better when compared with the best-known algorithms for the problem. Lastly, we conducted experiments using real genomes to demonstrate the applicability of the algorithms.

Cytotoxicity of Methotrexate Conjugated to Glycerol Phosphate Modified Superparamagnetic Iron Oxide Nanoparticles.

A systematic study was carried out to evaluate the uptake and cytotoxicity of methotrexate (MTX) conjugated to superparamagnetic iron oxide nanoparticles (SPIONs) modified with glycerol phosphate (Glyc) and phosphorylethanolamine (PEA), using MCF-7 cancer cell line as model. The ligand shell composition was controlled in such a way to get SPIONs with nine different surface functionalization and up to three co-conjugated ligands but the very iron oxide core, in order to test and compare uptake and cytotoxicity, and verify possible additive effects. Folic acid (FA), the non-toxic analogue of MTX, was also explored as ligand for SPIONs. Glyc was shown to enhance dramatically the cellular uptake despite the high negative zeta potentials, whereas PEA, FA and MTX was found to have a much lower effect on the cellular uptake. Also, a significant ten times lowering of IC50 was observed for the co-conjugated MTX in the SPION-Glyc/PEA/MTX as compared to the free drug, whereas the analogue SPION-Glyc/PEA/FA nanoparticles exhibited no significant cytotoxicity. In short, the conjugation of MTX to SPIONs enhanced dramatically its cytotoxicity and decreased the IC50 value against MCF-7 tumor cells as compared to the free drug, probably due to the enhanced uptake of SPIONs as a result of their surface modification with Glyc/PEA, demonstrating that SPION-Glyc/PEA is a good nanocarrier for co-conjugated methotrexate.

Differential expression of angiogenesis-related miRNAs and VEGFA in cirrhosis and hepatocellular carcinoma.

INTRODUCTION: Liver cirrhosis (LC) is a heterogeneous liver disease, the last stage of liver fibrosis, and the major risk factor for hepatocellular carcinoma (HCC). Our study aimed to evaluate the expression of microRNAs and the endothelial vascular growth factor (VEGFA) gene in LC and HCC. MATERIAL AND METHODS: The sample group consisted of 46 tissue samples: 21 of LC, 15 of HCC, and 10 of non-tumoural and non-cirrhotic liver tissue (control group). MiRNAs were chosen based on a mirDIP prediction database as regulators of the VEGFA gene. Gene expression of VEGF and miRNAs was quantified by real-time quantitative polymerase chain reaction. VEGFA protein expression was evaluated by ELISA. RESULTS: VEGFA gene expression was significantly overexpressed in LC compared to the control group (p < 0.0001). Hsa-miR-206 (p = 0.0313) and hsa-miR-637 (p = 0.0156) were down-expressed in LC. In HCC, hsa-miR-15b (p = 0.0010), hsa-miR-125b (p = 0.0010), hsa-miR-423-3p (p = 0.0010), hsa-miR-424 (p = 0.0313), hsa-miR-494 (p < 0.0001), hsa-miR-497 (p < 0.0001), hsa-miR-612 (p = 0.0078), hsa-miR-637 (p < 0.0001), and hsa-miR-1255b (p = 0.0156) presented down-expression. CONCLUSIONS: Overexpression of VEGFA in LC suggests impairment of angiogenesis in this tissue. The differential expression of microRNAs in LC and HCC observed in our study can lead to the evaluation of possible biomarkers for these diseases.

Super short operations on both gene order and intergenic sizes.

BACKGROUND: The evolutionary distance between two genomes can be estimated by computing a minimum length sequence of operations, called genome rearrangements, that transform one genome into another. Usually, a genome is modeled as an ordered sequence of genes, and most of the studies in the genome rearrangement literature consist in shaping biological scenarios into mathematical models. For instance, allowing different genome rearrangements operations at the same time, adding constraints to these rearrangements (e.g., each rearrangement can affect at most a given number of genes), considering that a rearrangement implies a cost depending on its length rather than a unit cost, etc. Most of the works, however, have overlooked some important features inside genomes, such as the presence of sequences of nucleotides between genes, called intergenic regions. RESULTS AND CONCLUSIONS: In this work, we investigate the problem of computing the distance between two genomes, taking into account both gene order and intergenic sizes. The genome rearrangement operations we consider here are constrained types of reversals and transpositions, called super short reversals (SSRs) and super short transpositions (SSTs), which affect up to two (consecutive) genes. We denote by super short operations (SSOs) any SSR or SST. We show 3-approximation algorithms when the orientation of the genes is not considered when we allow SSRs, SSTs, or SSOs, and 5-approximation algorithms when considering the orientation for either SSRs or SSOs. We also show that these algorithms improve their approximation factors when the input permutation has a higher number of inversions, where the approximation factor decreases from 3 to either 2 or 1.5, and from 5 to either 3 or 2.

Surface Topography, Gloss and Flexural Strength of Pressable Ceramic After Finishing-Polishing Protocols.

This study evaluated the effect of different finishing-polishing protocols on surface roughness, gloss, morphology and biaxial flexural strength of pressable fluorapatite glass ceramic. Thirty ceramic discs (12x1 mm) were produced and divided into five groups (n=6): CT: control (glaze); DA: fine grit diamond bur; DG: DA + new glaze layer; DP: DA + felt disk with fine grit diamond paste; DK: DA+ sequential polishing with silicon abrasive instruments, goat hair brush and cotton wheel. The specimens were analyzed for surface roughness (Ra) under profilometry and atomic force microscopy (AFM). Gloss was measured with spectrophotometry and micromorphology with scanning electron microscopy (SEM). Flexural strength was assessed by biaxial flexural strength test. Data were analyzed using one-way ANOVA and Tukey's post hoc test (a=0.05). DK showed the lowest surface roughness values and DA presented the highest in the perfilometer analysis. No significant differences were observed in the AFM for the CT, DG and DK groups, which presented the lower surface roughness; DA and DP had the higher Ra values. The DA, DP and CT showed the lowest surface gloss values, and the reflectance was significantly different from those observed for DK and DG groups. SEM analysis revealed the smoothest surface for DK group, followed by DG and CT groups; DA and DP groups exhibited variable degrees of surface irregularities. No significant differences were observed among groups for the biaxial flexural strength. The polishing protocol used in DK group can be a good alternative for chairside finishing of adjusted pressable fluorapatite glass ceramic surfaces.

Surface topography, gloss and flexural strength of pressable ceramic after finishing-polishing protocols

Abstract This study evaluated the effect of different finishing-polishing protocols on surface roughness, gloss, morphology and biaxial flexural strength of pressable fluorapatite glass ceramic. Thirty ceramic discs (12x1 mm) were produced and divided into five groups (n=6): CT: control (glaze); DA: fine grit diamond bur; DG: DA + new glaze layer; DP: DA + felt disk with fine grit diamond paste; DK: DA+ sequential polishing with silicon abrasive instruments, goat hair brush and cotton wheel. The specimens were analyzed for surface roughness (Ra) under profilometry and atomic force microscopy (AFM). Gloss was measured with spectrophotometry and micromorphology with scanning electron microscopy (SEM). Flexural strength was assessed by biaxial flexural strength test. Data were analyzed using one-way ANOVA and Tukey's post hoc test (a=0.05). DK showed the lowest surface roughness values and DA presented the highest in the perfilometer analysis. No significant differences were observed in the AFM for the CT, DG and DK groups, which presented the lower surface roughness; DA and DP had the higher Ra values. The DA, DP and CT showed the lowest surface gloss values, and the reflectance was significantly different from those observed for DK and DG groups. SEM analysis revealed the smoothest surface for DK group, followed by DG and CT groups; DA and DP groups exhibited variable degrees of surface irregularities. No significant differences were observed among groups for the biaxial flexural strength. The polishing protocol used in DK group can be a good alternative for chairside finishing of adjusted pressable fluorapatite glass ceramic surfaces.

Resumo O objetivo deste estudo foi avaliar o efeito de diferentes protocolos de acabamento e polimento na rugosidade da superfície, brilho, resistência à flexão biaxial e morfologia de cerâmica prensada. Trinta discos de cerâmica (12x1 mm) foram produzidos e divididos em cinco grupos (n=6): CT- controle (glaze); DA- ponta diamantada de granulação fina; DG: DA + nova camada de glaze; DP: DA + disco de feltro com pasta de diamante de granulo fino; DK: DA + polimento sequencial com instrumentos abrasivos de silício, escova de cabra e roda de algodão. Os espécimes foram analisados quanto à rugosidade da superfície (Ra) sob profilometria e microscopia de força atômica (AFM). O brilho foi medido com espectrofotometria e a micromorfologia com microscopia eletrônica de varredura (SEM). A resistência à flexão foi avaliada pelo teste de resistência à flexão biaxial. Os dados foram analisados ​​usando ANOVA um fator e teste post hoc de Tukey (a=0,05). DK mostrou mais baixos valores de rugosidade da superfície e DA apresentou o maior na análise do perfilômetro. Não foram observadas diferenças significativas no AFM para os grupos CT, DG e DK, que apresentaram a menor rugosidade de superfície; DA e DP apresentaram os maiores valores Ra. O DA, DP e CT mostraram valores de brilho superficial mais baixos, e a reflectância foi significativamente diferente da observada para os grupos DK e DG. A análise de SEM revelou a superfície mais homogênea para o grupo DK, seguido de grupos DG e CT; Os grupos DA e DP exibiram graus variáveis de irregularidades da superfície. Não foram observadas diferenças significativas entre os grupos quanto à resistência à flexão biaxial. O protocolo de polimento utilizado no grupo DK pode ser uma boa alternativa para o acabamento em consultório das superfícies de cerâmicas prensadas após ajustes.

Sorting signed circular permutations by super short operations.

BACKGROUND: One way to estimate the evolutionary distance between two given genomes is to determine the minimum number of large-scale mutations, or genome rearrangements, that are necessary to transform one into the other. In this context, genomes can be represented as ordered sequences of genes, each gene being represented by a signed integer. If no gene is repeated, genomes are thus modeled as signed permutations of the form π=(π1π2…πn) , and in that case we can consider without loss of generality that one of them is the identity permutation ιn=(12…n) , and that we just need to sort the other (i.e., transform it into ιn ). The most studied genome rearrangement events are reversals, where a segment of the genome is reversed and reincorporated at the same location; and transpositions, where two consecutive segments are exchanged. Many variants, e.g., combining different types of (possibly constrained) rearrangements, have been proposed in the literature. One of them considers that the number of genes involved, in a reversal or a transposition, is never greater than two, which is known as the problem of sorting by super short operations (or SSOs). RESULTS AND CONCLUSIONS: All problems considering SSOs in permutations have been shown to be in P , except for one, namely sorting signed circular permutations by super short reversals and super short transpositions. Here we fill this gap by introducing a new graph structure called cyclic permutation graph and providing a series of intermediate results, which allows us to design a polynomial algorithm for sorting signed circular permutations by super short reversals and super short transpositions.

Thermodynamic and kinetic characterization of PccH, a key protein in microbial electrosynthesis processes in Geobacter sulfurreducens.

The monoheme c-type cytochrome PccH from Geobacter sulfurreducens, involved in the pathway of current-consumption in biofilms, was electrochemically characterized in detail. Cyclic voltammetry was used to determine the kinetics and thermodynamics properties of PccH redox behavior. Entropy, enthalpy and Gibbs free energy changes associated with the redox center transition between the ferric and the ferrous state were determined, indicating an enhanced solvent exposure. The midpoint redox potential is considerably low for a monoheme c-type cytochrome and the heterogeneous electron transfer constant rate reflects a high efficiency of electron transfer process in PccH. The midpoint redox potential dependence on the pH (redox-Bohr effect) was investigated, over the range of 2.5 to 9.1, and is described by the protonation/deprotonation events of two distinct centers in the vicinity of the heme group with pKa values of 2.7 (pKox1); 4.1 (pKred1) and 5.9 (pKox2); 6.4 (pKred2). Based on the inspection of PccH structure, these centers were assigned to heme propionic acids P13 and P17, respectively. The observed redox-Bohr effect indicates that PccH is able to thermodynamically couple electron and proton transfer in the G. sulfurreducens physiological pH range.

Estudo citogenético de abortos espontâneos / Cytogenetical study on miscarriages

Os abortamentos espontâneos ocorrem por diversas causas, sendo as anomalias cromossômicas do concepto,as mais freqüentes. Assim, o estudo citogenético de seus produtos e genitores, seguido do aconselhamentogenético aos casais participantes, são condutas essenciais. O presente estudo retrospectivo teve comoobjetivo investigar os cariótipos de 574 amostras de produtos de abortamentos espontâneos, bem comosangue periférico de casais com abortamentos espontâneos recorrentes, para estimar a frequência de alteraçõescromossômicas. Os cariótipos foram previamente realizados a partir da cultura de vilosidade coriônica (abortos)e sangue periférico (casais), seguida da técnica de bandeamento G. Concluiu-se que as frequências observadasde alterações cromossômicas entre os abortos (19,69%) e os casais (7,6%) foram concordantes com a literatura,reforçando a importância da análise citogenética nesses casos.

Miscarriages result of several causes, but chromosomal anomalies are the most frequent. Thus, the cytogeneticstudies of its products and of the parents, followed by genetic counseling to involved couples, are crucialconducts. The present retrospective work aimed to investigate the karyotypes of 574 samples of miscarriageproducts, and the peripheral blood of couples involved with recurrent miscarriages in an attempt to estimatethe frequencies of chromosomal alterations. Karyotypes were previously made from the culture of chorionicvilli (miscarriages) and peripheral blood (couples), followed by the technique of G banding. It was concludedthat the observed frequency of abnormal karyotypes among miscarriage products (19.69%) and couples(7.6%) were both consistent with the literature, reinforcing the importance of cytogenetic study in thesecases.

Freqüência das anormalidades cromossômicas: importância para o diagnóstico citogenético / Frequency of chromosomal abnormalities: the significance for cytogenetic diagnosis

As anomalias cromossômicas fazem parte de uma das maiores categorias de doenças genéticas, sendoresponsáveis por diversas malformações congênitas e parte dos insucessos reprodutivos. Este estudo retrospectivo teve como principal objetivo analisar a freqüência de anomalias cromossômicas em 1171indivíduos, encaminhados para exame citogenético, no período de janeiro de 1998 a dezembro de 2007, aoAmbulatório e Laboratório de Genética da Unesp – Bauru. Os cariótipos foram previamente realizados com atécnica de bandeamento G em células obtidas a partir de cultura de linfócitos de sangue periférico. Os resultados mostraram 142 casos de cariótipos anormais, sendo as aneuploidias (45,1%) as mais freqüentes,seguidas pelas alterações estruturais (38,7%) e mosaicismos (16,2%). Concluiu-se que esses resultadosconcordam com a literatura pertinente, sendo de alta relevância o estudo citogenético tanto para diagnósticoem indivíduos malformados ou inférteis, como para esclarecer a etiologia da perda fetal e, assim, alertar à possibilidade de futuras malformações congênitas.

Chromosomal abnormalities are part of a larger category of genetic diseases, and responsible for various congenital malformations and part of the reproductive failures. The mainly objective of this retrospective work was to analyze the frequency of chromosomal abnormalities among 1,171 individuals referred to the Ambulatório e Laboratório de Genética, Unesp-Bauru for cytogenetic examination, from January, 1998 to December, 2007. The G-banding technique was previously used to prepare karyotypes of cells from lymphocyte culture of peripheral blood. The results showed 142 cases of abnormal karyotypes. The most frequent were aneuploidies (45.1%), followed by structural anomalies (38.7%), and mosaicisms (16.2%). It was concluded that these results are consistent with those in the literature, and they are important both for the cytogenetic diagnosis in malformed or infertile individuals, and also to clarify the etiology of fetal loss, and thus alert to the possibility of further congenital malformations.