Correlated geometric models of order k and its application to intensive care unit and leprosy data.

Geometric models are used to analyse the discrete time until the occurrence of an event of interest (success or consecutive successes). In two real data sets, named leprosy and intensive care unit (ICU), the events correspond, respectively, to abandoning the clinical treatment of leprosy, where abandonment corresponds to four consecutive patient absences from treatment, and the patient's discharge from the ICU. The distribution proposed in this article, called the correlated geometric distribution of order k (or correlated k-order geometric distribution), k≥1 , consists of including a correlation parameter in the geometric distribution of order k, thus considering the dependence between patient responses until the occurrence of the event. This model proves to be a better option for real data analysis where the effect of individual correlation is considered. The model is applied to real leprosy data to estimate the treatment abandonment probability. Bayesian methods are used to determine the parameter estimators of the models and to evaluate regression models. The covariates are related to the probability of the event by an appropriate link function chosen by Bayesian selection criteria. A diagnostic analysis evaluates the models fit by posterior randomized quantile residuals and influential observations by ψ -divergence measures. This methodology is illustrated by simulation studies and real ICU admission data analysis. Studies show a good fit of the proposed model. Real data analyses also find that the probabilities of the event of interest can be overestimated or underestimated when modeled without considering the effect of dependency on the model.

Type I multivariate zero-inflated COM-Poisson regression model.

In this paper, we present the Type I multivariate zero-inflated Conway-Maxwell-Poisson distribution, whose development is based on the extension of the Type I multivariate zero-inflated Poisson distribution. We developed important properties of the distribution and present a regression model. The AIC and BIC criteria are used to select the best fitted model. Two real data sets have been used to illustrate the proposed model. Moreover, we conclude by stating that the Type I multivariate zero-inflated Conway-Maxwell-Poisson distribution produces a better fitted model for multivariate count data with excess of zeros.

Production and performance of sugarcane seeds (caryopses) from different hybridizations involving RB92579.

A major challenge in sugarcane breeding program is the obtaining of enough number of seeds (caryopses) for the development of new improved cultivars. Genotypes differ in their function as pollen recipient and pollen donor, which also affect the seed performance. Thus, the aim of this study was to verify the production and performance of sugarcane seeds from different hybridizations involving RB92579 as pollen recipient and pollen donor. Twelve bi-parental crossings were carried out involving RB92579 and other different genotypes randomly chosen. Seed production potential was evaluated by percentage of fertile spikelets and caryopsis fresh weight. The seed physiological potential was determined by evaluating germination and vigor (index of germination rate, number of normal seedlings per gram of fuzz, and seedling dry weight). The results showed better performance for RB92579 as pollen donor for all characteristics studied. Therefore, RB92579 sugarcane cultivar should be used as pollen donor during hybridizations, condition that permits a greater production and physiological performance of seeds for the sugarcane breeding programs.

Quadruplex PCR assay for identification of Corynebacterium pseudotuberculosis differentiating biovar Ovis and Equi.

BACKGROUND: Corynebacterium pseudotuberculosis is classified into two biovars, nitrate-negative biovar Ovis which is the etiologic agent of caseous lymphadenitis in small ruminants and nitrate-positive biovar Equi, which causes abscesses and ulcerative lymphangitis in equines. The aim of this study was to develop a quadruplex PCR assay that would allow simultaneous detection and biovar-typing of C. pseudotuberculosis. METHODS: In the present study, genomes of C. pseudotuberculosis strains were used to identify the genes involved in the nitrate reduction pathway to improve a species identification three-primer multiplex PCR assay. The nitrate reductase gene (narG) was included in the PCR assay along with the 16S, rpoB and pld genes to enhance the diagnosis of the multiplex PCR at biovar level. RESULTS: A novel quadruplex PCR assay for C. pseudotuberculosis species and biovar identification was developed. The results of the quadruplex PCR of 348 strains, 346 previously well-characterized clinical isolates of C. pseudotuberculosis from different hosts (goats, sheep, horse, cattle, buffalo, llamas and humans), the vaccine strain 1002 and the type strain ATCC 19410T, were compared to the results of nitrate reductase identification by biochemical test. The McNemar's Chi-squared test used to compare the two methods used for C. pseudotuberculosis biovar identification showed no significant difference (P = 0.75) [95% CI for odds ratio (0.16-6.14)] between the quadruplex PCR and the nitrate biochemical test. Concordant results were observed for 97.13% (338 / 348) of the tested strains and the kappa value was 0.94 [95% CI (0.90-0.98)]. CONCLUSIONS: The ability of the quadruplex assay to discriminate between C. pseudotuberculosis biovar Ovis and Equi strains enhances its usefulness in the clinical microbiology laboratory.

Cetuximab chemotherapy resistance: Insight into the homeostatic evolution of head and neck cancer (Review).

The complex evolution of genetic alterations in cancer that occurs in vivo is a selective process involving numerous factors and mechanisms. Chemotherapeutic agents that prevent the growth and spread of cancer cells induce selective pressure, leading to rapid artificial selection of resistant subclones. This rapid evolution is possible because antineoplastic drugs promote alterations in tumor­cell metabolism, thus creating a bottleneck event. The few resistant cells that survive in this new environment obtain differential reproductive success that enables them to pass down the newly selected resistant gene pool. The present review aims to summarize key findings of tumor evolution, epithelial­mesenchymal transition and resistance to cetuximab therapy in head and neck squamous cell carcinoma.

First report of trans-A2B-corrole derived from a lapachone derivative: photophysical, TD-DFT and photobiological assays.

In this work, the synthesis, characterization and photophysical assays of a new trans-A2B-corrole derivative from the naturally occurring quinone are described. ß-Lapachone is a naturally occurring quinoidal compound that provides highly fluorescent heterocyclic compounds such as lapimidazoles. The new trans-A2B-corrole compound was obtained from the reaction between 2,3,4,5,6-(pentafluorophenyl)dipyrromethane and the lapimidazole bearing an aldehyde group. The dyad was characterized by high-resolution mass spectrometry (HRMS), NMR spectroscopy (1H, COSY 2D, HMBC, 19F), FT-IR, UV-vis, steady-state and time-resolved fluorescence, electrochemical studies (CV), TD-DFT analysis and photobiological experiments, in which includes aggregation, stability in solution, photostability and partition coefficients assays. Finally, ROS generation assays were performed using 1,3-diphenylisobenzofuran (DPBF) method and the presented compound showed significant photostability and singlet oxygen production.

Probiogenomics of Leuconostoc Mesenteroides Strains F-21 and F-22 Isolated from Human Breast Milk Reveal Beneficial Properties.

Bacteria of the Leuconostoc genus are Gram-positive bacteria that are commonly found in raw milk and persist in fermented dairy products and plant food. Studies have already explored the probiotic potential of L. mesenteroides, but not from a probiogenomic perspective, which aims to explore the molecular features responsible for their phenotypes. In the present work, probiogenomic approaches were applied in strains F-21 and F-22 of L. mesenteroides isolated from human milk to assess their biosafety at the molecular level and to correlate molecular features with their potential probiotic characteristics. The complete genome of strain F-22 is 1.99 Mb and presents one plasmid, while the draft genome of strain F-21 is 1.89 Mb and presents four plasmids. A high percentage of average nucleotide identity among other genomes of L. mesenteroides (≥ 96%) corroborated the previous taxonomic classification of these isolates. Genomic regions that influence the probiotic properties were identified and annotated. Both strains exhibited wide genome plasticity, cell adhesion ability, proteolytic activity, proinflammatory and immunomodulation capacity through interaction with TLR-NF-κB and TLR-MAPK pathway components, and no antimicrobial resistance, denoting their potential to be candidate probiotics. Further, the strains showed bacteriocin production potential and the presence of acid, thermal, osmotic, and bile salt resistance genes, indicating their ability to survive under gastrointestinal stress. Taken together, our results suggest that L. mesenteroides F-21 and F-22 are promising candidates for probiotics in the food and pharmaceutical industries.

Whole-genome sequence of Corynebacterium pseudotuberculosis strain Cp162, isolated from camel.

Corynebacterium pseudotuberculosis is a pathogen of great veterinary and economic importance, since it affects livestock, mainly sheep and goats, worldwide, together with reports of its presence in camels in several Arabic, Asiatic, and East and West African countries, as well as Australia. In this article, we report the genome sequence of Corynebacterium pseudotuberculosis strain Cp162, collected from the external neck abscess of a camel in the United Kingdom.

Complete genome sequence of Corynebacterium pseudotuberculosis strain Cp267, isolated from a llama.

In this work we report the genome of Corynebacterium pseudotuberculosis strain 267, isolated from a llama. This pathogen is of great veterinary and economic importance, as it is the cause of caseous lymphadenitis in several livestock species around the world and causes significant losses due to the high cost of treatment.

Complete genome sequence of Corynebacterium pseudotuberculosis strain 1/06-A, isolated from a horse in North America.

Corynebacterium pseudotuberculosis causes disease in several animal species, although distinct biovars exist that appear to be restricted to specific hosts. In order to facilitate a better understanding of the differences between biovars, we report here the complete genome sequence of the equine pathogen Corynebacterium pseudotuberculosis strain 1/06-A.

Complete genome sequences of Corynebacterium pseudotuberculosis strains 3/99-5 and 42/02-A, isolated from sheep in Scotland and Australia, respectively.

Here, we report the whole-genome sequences of two ovine-pathogenic Corynebacterium pseudotuberculosis isolates: strain 3/99-5, which represents the first C. pseudotuberculosis genome originating from the United Kingdom, and 42/02-A, the second from Australia. These genome sequences will contribute to the objective of determining the global pan-genome of this bacterium.

Evaluation of neurodevelopmental effects on rats exposed prenatally to sulfentrazone.

Although some studies have pointed to embryo/fetal toxicity at treatment levels that were not maternally toxic, knowledge about the potential toxic effects of the herbicide sulfentrazone is still limited. Since the results of these studies have raised some concern, the present work studied the effects of sulfentrazone maternal exposure on the physical and neurobehavioral endpoints in the development of rat pups. To accomplish that, the effects of the herbicide sulfentrazone (25 and 50mg/kg) were examined at two different developmental stages in rats: during the first 6 days of gestation, or in the organogenesis period (6-15 days). After parturition, pups were tested in a developmental test battery including measures of growth, maturational milestones, and neurobehavioral development. Maternal exposure to the herbicide resulted in significant alterations of the postnatal age at which the developmental milestones of ear and eye opening and testes descent were observed. There was a reduced weight gain rate in pups and their mothers when treated during the gestational period at the highest dose tested. Also, the functional state of the rat pup nervous system at different stages of postnatal development showed some neurodevelopmental delays in righting reflex, negative geotaxis, grip response, and motor coordination-locomotion and rearing (21-90 days of life) in the treated groups. Herbicide genotoxicity was investigated in fresh leukocytes both in mothers and pups using the comet assay: the data did not show any significant genotoxic effect induced by the herbicide. The findings of this study emphasize that sulfentrazone maternal exposure may lead to some neuromuscular and behavioral deficits in nursing pups.

Neurodevelopmental effects of perinatal fenarimol exposure on rats.

Knowledge about the potential toxic effects of fenarimol, a widely used fungicide, is still limited. Fenarimol is an aromatase inhibitor and therefore can affect estrogen/androgen levels in vivo in rodents. In view of these facts, the aim of the present work was to study the effects of fenarimol maternal exposure during different critical phases in the development of central nervous system in rat pups, on early physical and neurobehavioral endpoints essential to their development. For that, the effects of the fungicide fenarimol (150 and 300 mg/kg) were examined at three different developmental stages in the rat: during the first 6 days of gestation, prenatal (15-21 days), or first 6 days of lactation. Three categories of the impact of fenarimol on neonatal growth and neurobehavioral development of offspring were assessed: (1) physical, (2) reflex and strength, and (3) motor coordination. Findings on the pups' physical development did not indicate any significant alterations of the postnatal age at which specific developmental milestones were observed (pinna detachment, development of the fur, eruption of the incisor teeth, opening of the ears and eyes and testes descent). However, there was a reduced rate of weight gain in pups of mothers treated during lactation related to the earlier testing time periods (1-23 days of life). The study of the functional state of the rat pup nervous systems at different stages of postnatal development revealed some neurodevelopmental delays in righting reflex, climbing and grip response and locomotion (20-90 days of life) in the treated groups. Taken together, findings of this study emphasize that, as a result of fenarimol maternal exposure, some neuromuscular and behavioral deficits in nursing pups may occur principally during the last gestational period and lactation. These results could be the basis for further studies on molecular actions of fenarimol in order to predict better the biological consequences of this fungicide.

Exploration of Nitrate Reductase Metabolic Pathway in Corynebacterium pseudotuberculosis.

Based on the ability of nitrate reductase synthesis, Corynebacterium pseudotuberculosis is classified into two biovars: Ovis and Equi. Due to the presence of nitrate reductase, the Equi biovar can survive in absence of oxygen. On the other hand, Ovis biovar that does not have nitrate reductase is able to adapt to various ecological niches and can grow on certain carbon sources. Apart from these two biovars, some other strains are also able to carry out the reduction of nitrate. The enzymes that are involved in electron transport chain are also identified by in silico methods. Findings about pathogen metabolism can contribute to the identification of relationship between nitrate reductase and the C. pseudotuberculosis pathogenicity, virulence factors, and discovery of drug targets.

Electrophysiological characterization and molecular identification of the Phoneutria nigriventer peptide toxin PnTx2-6.

A cDNA with 403 nucleotides encoding the precursor of the toxin PnTx2-6 was cloned and sequenced. Subsequent analysis revealed that the precursor begins with a signal peptide and a glutamate-rich propeptide. The succeeding peptide confirmed the reported sequence of PnTx2-6. The purified toxin exerted complex effects on Na(+) current of frog skeletal muscle. There was a marked decrease of the inactivation kinetics, and a shift to hyperpolarizing potentials of both the Na(+) conductance and the steady-state inactivation voltage dependences, along with a reduction of the current amplitude. The concentration dependence of the modified current suggests a K(D) of 0.8 microM for the toxin-channel complex.

PnTx3-6 a spider neurotoxin inhibits K+-evoked increase in [Ca2+](i) and Ca2+-dependent glutamate release in synaptosomes.

The present experiments investigated the effect of a neurotoxin purified from the venom of the spider Phoneutria nigriventer. This toxic component, P. nigriventer toxin 3-6 (PnTx3-6), abolished Ca(2+)-dependent glutamate release with an IC(50) of 74.4nM but did not alter Ca(2+)-independent secretion of glutamate when brain cortical synaptosomes were depolarized by KCl (33mM). This effect was most likely due to interference with the entry of calcium through voltage activated calcium channels (VACC), reducing the increase in the intrasynaptosomal free calcium induced by membrane depolarization with an IC(50) of 9.5nM. We compared the alterations induced by PnTx3-6 with the actions of toxins known to block calcium channels coupled to exocytosis. Our results indicate that PnTx3-6 inhibition of glutamate release and intrasynaptosomal calcium involves P/Q type calcium channels and this toxin can be a valuable tool in the investigation of calcium channels.

Analysis of fatty acids released by crotoxin in rat brain synaptosomes.

Crotoxin, the main toxin of Crotalus durissus terrificus venom, exerts its lethal effect by blocking neurotransmission at the neuromuscular junction level through a triphasic mechanism. This effect seems to depend on its phospholipasic activity, suggesting that the mechanism of neurotransmission blockage may be related to fatty acids release in specific sites of the nervous terminal. In this work, we purified the fatty acids released by crotoxin's activity and this outline was compared with other phospholipases A(2), including CB, a subunit of crotoxin. Our results show a higher release of palmitate and arachidonate by crotoxin when compared to other phospholipases A(2). Since palmitate has a role in protein acylation processes and arachidonate participates in signal transduction events, these mechanisms may be related to the neurotoxic actions of crotoxin.

A generalized approach to the modeling of the species-area relationship.

This paper proposes a statistical generalized species-area model (GSAM) to represent various patterns of species-area relationship (SAR), which is one of the fundamental patterns in ecology. The approach enables the generalization of many preliminary models, as power-curve model, which is commonly used to mathematically describe the SAR. The GSAM is applied to simulated data set of species diversity in areas of different sizes and a real-world data of insects of Hymenoptera order has been modeled. We show that the GSAM enables the identification of the best statistical model and estimates the number of species according to the area.

Genome Sequence of Lactococcus lactis subsp. lactis NCDO 2118, a GABA-Producing Strain.

Lactococcus lactis subsp. lactis NCDO 2118 is a nondairy lactic acid bacterium, a xylose fermenter, and a gamma-aminobutyric acid (GABA) producer isolated from frozen peas. Here, we report the complete genome sequence of L. lactis NCDO 2118, a strain with probiotic potential activity.

The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains.

Corynebacterium pseudotuberculosis is a facultative intracellular pathogen and the causative agent of several infectious and contagious chronic diseases, including caseous lymphadenitis, ulcerative lymphangitis, mastitis, and edematous skin disease, in a broad spectrum of hosts. In addition, Corynebacterium pseudotuberculosis infections pose a rising worldwide economic problem in ruminants. The complete genome sequences of 15 C. pseudotuberculosis strains isolated from different hosts and countries were comparatively analyzed using a pan-genomic strategy. Phylogenomic, pan-genomic, core genomic, and singleton analyses revealed close relationships among pathogenic corynebacteria, the clonal-like behavior of C. pseudotuberculosis and slow increases in the sizes of pan-genomes. According to extrapolations based on the pan-genomes, core genomes and singletons, the C. pseudotuberculosis biovar ovis shows a more clonal-like behavior than the C. pseudotuberculosis biovar equi. Most of the variable genes of the biovar ovis strains were acquired in a block through horizontal gene transfer and are highly conserved, whereas the biovar equi strains contain great variability, both intra- and inter-biovar, in the 16 detected pathogenicity islands (PAIs). With respect to the gene content of the PAIs, the most interesting finding is the high similarity of the pilus genes in the biovar ovis strains compared with the great variability of these genes in the biovar equi strains. Concluding, the polymerization of complete pilus structures in biovar ovis could be responsible for a remarkable ability of these strains to spread throughout host tissues and penetrate cells to live intracellularly, in contrast with the biovar equi, which rarely attacks visceral organs. Intracellularly, the biovar ovis strains are expected to have less contact with other organisms than the biovar equi strains, thereby explaining the significant clonal-like behavior of the biovar ovis strains.