Non-random reef use by fishes at two dominant zones in a tropical, algal-dominated coastal reef

Habitat use and the processes which determine fish distribution were evaluated at the reef flat and reef crest zones of a tropical, algal-dominated reef. Our comparisons indicated significant differences in the majority of the evaluated environmental characteristics between zones. Also, significant differences in the abundances of twelve, from thirteen analyzed species, were observed within and between-sites. According to null models, non-random patterns of species co-occurrences were significant, suggesting that fish guilds in both zones were non-randomly structured. Unexpectedly, structural complexity negatively affected overall species richness, but had a major positive influence on highly site-attached species such as a damselfish. Depth and substrate composition, particularly macroalgae cover, were positive determinants for the fish assemblage structure in the studied reef, prevailing over factors such as structural complexity and live coral cover. Our results are conflicting with other studies carried out in coral-dominated reefs of the Caribbean and Pacific, therefore supporting the idea that the factors which may potentially influence reef fish composition are highly site-dependent and variable.

Genetic diversity and population structure of pumas (Puma concolor) in southeastern Brazil: implications for conservation in a human-dominated landscape

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Non invasive methods for genetic analysis applied to ecological and behavioral studies in Latino-America

Documenting the presence and abundance of the neotropical mammals is the first step for understanding their population ecology, behavior and genetic dynamics in designing conservation plans. The combination of field research with molecular genetics techniques are new tools that provide valuable biological information avoiding the disturbance in the ecosystems, trying to minimize the human impact in the process to gather biological information. The objective of this paper is to review the available non invasive sampling techniques that have been used in Neotropical mammal studies to apply to determine the presence and abundance, population structure, sex ratio, taxonomic diagnostic using mitochondrial markers, and assessing genetic variability using nuclear markers. There are a wide range of non invasive sampling techniques used to determine the species identification that inhabit an area such as searching for tracks, feces, and carcasses. Other useful equipment is the camera traps that can generate an image bank that can be valuable to assess species presence and abundance by morphology. With recent advances in molecular biology, it is now possible to use the trace amounts of DNA in feces and amplify it to analyze the species diversity in an area, and the genetic variability at intraspecific level. This is particularly helpful in cases of sympatric and cryptic species in which morphology failed to diagnose the taxonomic status of several species of brocket deer of the genus Mazama.

Non-additive genetic effects on weights and performance of a Brazilian Bos taurus x Bos indicus beef composite

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Non-destructive genetic sampling in fish. An improved method for DNA extraction from fish fins and scales

DNA-based studies have been one of the major interests in conservation biology of endangered species and in population genetics. As species and population genetic assessment requires a source of biological material, the sampling strategy can be overcome by non-destructive procedures for DNA isolation. An improved method for obtaining DNA from fish fins and scales with the use of an extraction buffer containing urea and further DNA purification with phenol-chloroform is described. The methodology combines the benefits of a non-destructive DNA sampling and its high efficiency. In addition, comparisons with other methodologies for isolating DNA from fish demonstrated that the present procedure also becomes a very attractive alternative to obtain large amounts of high-quality DNA for use in different molecular analyses. The DNA samples, isolated from different fish species, have been successfully used on random amplified polymorphic DNA (RAPD) experiments, as well as on amplification of specific ribosomal and mitochondrial DNA sequences. The present DNA extraction procedure represents an alternative for population approaches and genetic studies on rare or endangered taxa.

Delimiting genetic units in Neotropical toads under incomplete lineage sorting and hybridization

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Molecular analysis of the Von Hippel-Lindau (VHL) gene in a family with non-syndromic pheochromocytoma: the importance of genetic testing

Dois pacientes índices da família analisada neste estudo foram submetidos a adrenalectomia bilateral devido a feocromocitoma. Foi, então, realizado o estudo genético dos pacientes e de sete parentes de primeiro grau. Os dois pacientes com feocromocitoma e dois outros membros assintomáticos da família apresentaram a mutação c496G>T no exon 3 do gene VHL. A família perdeu seguimento médico. Três anos após a realização da avaliação genética, a irmã dos pacientes, portadora da mutação, foi encaminhada para o nosso serviço após uma gestação complicada por pré-eclampsia. Ela referia paroxismos sugestivos de feocromocitoma, mas as metanefrinas urinárias eram negativas. Entretanto, a tomografia computadorizada de abdômen evidenciou uma massa adrenal que também se contrastou na cintilografia com metaiodobenzilguanidina (MIBG). Esse estudo mostra que a análise molecular do paciente índice pode levar à identificação de parentes assintomáticos portadores da mutação. Além disso, mesmo com as metanefrinas urinárias negativas, a identificação de uma mutação específica levou a um aumento da suspeita e detecção de feocromocitoma na irmã dos afetados pela doença.

Genetic and non-genetic effects on calf vigor at birth and preweaning mortality in nellore calves

The objective of the present study was to evaluate the genetic and non-genetic effects that influencevigor at birth and preweaning mortality in Nellore calves. A total of 11,727 records of births that occurred between 1978 and 2006, offspring of 363 sires, were analyzed. Poor calf vigor at birth (VB) and preweaning mortality divided into stillbirth (SB), early mortality (EM) and total mortality (TM) were analyzed as binary variables. Generalized linear models were used for the evaluation of non-genetic effects and generalized linear mixed models for genetic effects (sire and animal models). The incidences were 4.75% for VB, 2.66% for SB, 5.28% for EM, and 7.99% for TM. Birth weight was the effect that most influenced the traits studied. Calves weighing less than 22kg(females) and less than 24kg (males) were at a higher risk of low vigor and preweaning mortality. Preweaning mortality was higher among calves born from cows aged .3 and .11 years at calving compared with cows aged 7 to 10 years. Male calves presented less vigor and higher preweaning mortality than female calves. Selection for postweaning weight did not influence preweaning mortality. The heritability estimates ranged between 0.01 and 0.09 for VB, 0.00 and 0.27 for SB, 0.03 and 0.17 for EM and 0.02 and 0.10 for TM. Stillbirth should be included as a selection criterion in breeding programs of Nellore cattle, alone or as part of a selection index, aiming to reduce preweaning mortality. © 2013 Sociedade Brasileira de Zootecnia.

An approach to implement data fusion techniques in wireless sensor networks using genetic machine learning algorithms

Wireless Sensor Networks (WSNs) can be used to monitor hazardous and inaccessible areas. In these situations, the power supply (e.g. battery) of each node cannot be easily replaced. One solution to deal with the limited capacity of current power supplies is to deploy a large number of sensor nodes, since the lifetime and dependability of the network will increase through cooperation among nodes. Applications on WSN may also have other concerns, such as meeting temporal deadlines on message transmissions and maximizing the quality of information. Data fusion is a well-known technique that can be useful for the enhancement of data quality and for the maximization of WSN lifetime. In this paper, we propose an approach that allows the implementation of parallel data fusion techniques in IEEE 802.15.4 networks. One of the main advantages of the proposed approach is that it enables a trade-off between different user-defined metrics through the use of a genetic machine learning algorithm. Simulations and field experiments performed in different communication scenarios highlight significant improvements when compared with, for instance, the Gur Game approach or the implementation of conventional periodic communication techniques over IEEE 802.15.4 networks. © 2013 Elsevier B.V. All rights reserved.

Genetic Instability Persists in Non-Neoplastic Urothelial Cells from Patients with a History of Urothelial Cell Carcinoma

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Clinico-genetic aspects of a pediatric non-neurofibromatosis type 1 malignant triton tumor with loss of chromosome X

Malignant triton tumor (MTT) is an aggressive peripheral nerve sheath tumor with rhabdomyoblastic differentiation. Less than 100 cases have been described, being mostly male children with type 1 neurofibromatosis. We report a 6-year-old female with MTT and no diagnostic criteria for neurofibromatosis type 1. Cytogenetic analysis showed a 46,X,-X[4]/46,XX[16] karyotype. She underwent a transfemoral amputation and chemotherapy and is free of disease 15 months after diagnosis. The few cytogenetic studies of MTT described in the literature have been inconclusive. Further cytogenetic analyses are needed to understand the role of chromosome X monosomy in the pathogenesis of this rare tumor. Pediatr Blood Cancer 2012; 59: 13201323. (C) 2012 Wiley Periodicals, Inc.

Non-inflammatory destructive periodontal disease: a clinical, microbiological, immunological and genetic investigation

Periodontitis comprises a group of multifactorial diseases in which periodontopathogens accumulate in dental plaque and trigger host chronic inflammatory and immune responses against periodontal structures, which are determinant to the disease outcome. Although unusual cases of non-inflammatory destructive periodontal disease (NIDPD) are described, their pathogenesis remains unknown. A unique NIDPD case was investigated by clinical, microbiological, immunological and genetic tools. The patient, a non-smoking dental surgeon with excessive oral hygiene practice, presented a generalized bone resorption and tooth mobility, but not gingival inflammation or occlusion problems. No hematological, immunological or endocrine alterations were found. No periodontopathogens (A. actinomycetemcomitans, P. gingivalis, F. nucleatum and T. denticola) or viruses (HCMV, EBV-1 and HSV-1) were detected, along with levels of IL-1 beta and TNF-alpha in GCF compatible with healthy tissues. Conversely ALP, ACP and RANKL GCF levels were similar to diseased periodontal sites. Genetic investigation demonstrated that the patient carried some SNPs, as well HLA-DR4 (*0404) and HLA-B27 alleles, considered risk factors for bone loss. Then, a less vigorous and diminished frequency of toothbrushing was recommended to the patient, resulting in the arrest of alveolar bone loss, associated with the return of ALP, ACP and RANKL in GCF to normality levels. In conclusion, the unusual case presented here is compatible with the previous description of NIDPD, and the results that a possible combination of excessive force and frequency of mechanical stimulation with a potentially bone loss prone genotype could result in the alveolar bone loss seen in NIDPD.

Permutation classes, sorting algorithms, and lattice paths

A permutation is said to avoid a pattern if it does not contain any subsequence which is order-isomorphic to it. Donald Knuth, in the first volume of his celebrated book "The art of Computer Programming", observed that the permutations that can be computed (or, equivalently, sorted) by some particular data structures can be characterized in terms of pattern avoidance. In more recent years, the topic was reopened several times, while often in terms of sortable permutations rather than computable ones. The idea to sort permutations by using one of Knuth’s devices suggests to look for a deterministic procedure that decides, in linear time, if there exists a sequence of operations which is able to convert a given permutation into the identical one. In this thesis we show that, for the stack and the restricted deques, there exists an unique way to implement such a procedure. Moreover, we use these sorting procedures to create new sorting algorithms, and we prove some unexpected commutation properties between these procedures and the base step of bubblesort. We also show that the permutations that can be sorted by a combination of the base steps of bubblesort and its dual can be expressed, once again, in terms of pattern avoidance. In the final chapter we give an alternative proof of some enumerative results, in particular for the classes of permutations that can be sorted by the two restricted deques. It is well-known that the permutations that can be sorted through a restricted deque are counted by the Schrӧder numbers. In the thesis, we show how the deterministic sorting procedures yield a bijection between sortable permutations and Schrӧder paths.

Vitamin D time profile based on the contribution of non-genetic and genetic factors in HIV-infected individuals of European ancestry

BACKGROUND Vitamin D deficiency is prevalent in HIV-infected individuals and vitamin D supplementation is proposed according to standard care. This study aimed at characterizing the kinetics of 25(OH)D in a cohort of HIV-infected individuals of European ancestry to better define the influence of genetic and non-genetic factors on 25(OH)D levels. These data were used for the optimization of vitamin D supplementation in order to reach therapeutic targets. METHODS 1,397 25(OH)D plasma levels and relevant clinical information were collected in 664 participants during medical routine follow up visits. They were genotyped for 7 SNPs in 4 genes known to be associated with 25(OH)D levels. 25(OH)D concentrations were analyzed using a population pharmacokinetic approach. The percentage of individuals with 25(OH)D concentrations within the recommended range of 20-40ng/ml during 12 months of follow up and several dosage regimens were evaluated by simulation. RESULTS A one-compartment model with linear absorption and elimination was used to describe 25(OH)D pharmacokinetics, while integrating endogenous baseline plasma concentrations. Covariate analyses confirmed the effect of seasonality, body mass index, smoking habits, the analytical method, darunavir/r and the genetic variant in GC (rs2282679) on 25(OH)D concentrations. 11% of the interindividual variability in 25(OH)D levels was explained by seasonality and other non-genetic covariates and 1% by genetics. The optimal supplementation for severe vitamin D deficient patients was 300000 IU two times per year. CONCLUSIONS This analysis allowed identifying factors associated with 25(OH)D plasma levels in HIV-infected individuals. Improvement of dosage regimen and timing of vitamin D supplementation is proposed based on those results.