Additional morphological characters and a new host for Aceria gymnoscuta Navia & Flechtmann (Acari, Eriophyidae)

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

Morphological study of the thorax of the five nymphal instars of Triatoma arthurneivai Lent & Martins (Hemiptera, Reduviidae, Triatominae)

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

Characterization of the external female genitalia of six species of Triatominae (Hemiptera: Reduviidade) by scanning electron microscopy

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

Ramificação e distribuição dos nervos frênicos no músculo diafragma do gato doméstico

The ramification and the distribution of the phrenic nerves right and left had been studied in 30 muscles diaphragms of unknown breed adult domestic cats, 7 males and 23 females, and were fixed in 10% buffered formalin solution. After fixation and dissection, it was observed that the phrenic nerves ramified for the respective carnous parts of the muscle diaphragm, pars lumbalis, costalis and sternalis, and had finished in higher frequency in dorsolateral trunk and ventral branch (63.33%). We observed the following arrangements: dorsal, ventral and lateral branches (25.0%); dorsal branch and ventrolateral trunk (6.66%); dorsolateral and ventrolateral trunks (3.33%); dorsolateral trunk, lateral and ventral branches (1.66%). The phrenic nerves had distributed symmetrically in 11 samples (36.66%), only showing the termination in dorsolateral trunk and ventral branch. The dorsal branches supplied pars lumbalis (73.33% to right and 56.66% to the left) and pars costalis (13.33% to right and 10.0% to the left). The right dorsal branch supplied the crus mediale dexter of the right pillar (100.0%) and the left dorsal branch supplied the crus mediale sinister of the right pillar and the left pillar (100.0%). The lateral branches supply pars lumbalis (23.33% to right and 33.33% to the left), pars costalis (96.66% to right and 100.0% to the left) and pars sternalis (3.33% only to the right). The ventral branches supplied the ventral region of pars costalis (46.66 % to right and 43.33% to the left) and pars sternalis (96.66% to right and 100.0% to the left). Four female animals (13.33%) had shown fibers crossing proceeding from the left ventral branch for right antimere had been that in one of these samples (3.33%) occurred connection between the left ventral branch and the right.

A new species of milk frog of the genus trachycephalus tschudi (anura, hylidae) from the amazonian rainforest

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Two-stage rumenostomy in buffaloes

Background: Rumenostomy may be performed for therapeutic and digestibility research purposes in bovines, small ruminants and camelids. Several studies requires romenostomy in buffaloes in order to sample ruminal content for laboratorial assays. However, complications and outcome of rumenostomy was poorly studied in buffaloes. Therefore, the aim of the current study was to describe a two-stage rumenostomy technique in buffaloes, focused on intra and post-operative period.Materials, Methods & Results: Nine Murrah buffaloes were submitted to a 36-h and 12-h of food and water fastening. The animals were given acepromazine and maintained in standing position. Flank local anesthesia was carried out. A circular skin incision was carried out in the center of the left flank, followed by divulsion of the external and internal obliques and transversus abdominus muscles, and incision of the peritoneum. Subsequently, a segment of the dorsal aspect of the rumen was grasped and pulled through the flank incision. The rumen was attached to the peritoneum and skin incision margins in four points (dorsal, ventral, cranial and caudal). Additional simple interrupted sutures attaching the rumen serosa to the skin were applied subsequently. Four additional interrupted horizontal mattress sutures were applied equidistantly, taking bites only in the skin and rumen serosa. Following 12 h, the second stage was carried out. The buffaloes were prepared and restrained as performed for the first stage. A circular flap was excised from the exteriorized rumen and the silicone romenostomy cannula was placed. Clinical parameters, postoperative recovery, weight and behavioral pain scale were assessed. Positioning and anesthesia regimen were adequate for the achievement of the procedure. However, two animals fell in the restraint chute during the first surgical stage. Mild ischemia of the exteriorized rumen segment was observed on the second surgical stage, which resulted in less hemorrhage and enhanced cannula positioning. Complete cicatrization and permanent adhesion of the rumen to the skin were achieved. No ruminal leakage to the abdominal cavity occurred. No signs of pain were reported. There were few cases of laxity of the romenostomy opening leading to drop of cannula, myiasis on the margin of the stoma site and few cases of mild ruminal content leakage on the long-term assessment.Discussion: Restraint in standing position was considered adequate, although lateral recumbence constitutes another option. However, higher risk of contamination and technical difficulties in placing the cannulas are expected if lateral recumbence is considered. In other trials using acepromazine, no accidental recumbence occurred. Xylazine was also indicated for chemical restraint of buffaloes. It is known that flexible cannulas provide better anatomic adjustment and adaptation as well as being effective for sampling ruminal content, as seen in the current study. Ruminal leakage is one of the most frequent complications of romenostomy, which may affect animal's welfare. The animals in the current study presented no variations on the body score, even though on those presenting cannula loosening or ruminal content leakage. Moreover, no significant changes of the ruminal content parameters were noticed. Myiasis was also reported following ruminal surgical interventions, which were mainly attributed to extensive breeding. Loss of the cannula, subcutaneous emphysema and suture dehiscence are common complications of romenostomy. Nonetheless, none of those complications were found on the current study. Thus, romenostomy was feasible and efficient for sampling and performing assays of the ruminal content in buffaloes.

Avaliação das doses de cães submetidos a exames radiográficos de pulmão

This study aims to determine surface skin doses in dogs (with suspected pulmonary metastasis) submitted to chest X-rays using the technique of thermoluminescence dosimetry. Twenty seven exams from different dogs were performed at the Faculdade de Medicina Veterinária e Zootecnia da Universidade Estadual Paulista (FMVZ-UNESP/Botucatu). The doses were evaluated using thermoluminescent dosimeters of calcium sulphate doped with dysprosium (CaSO4:Dy) produced by the Instituto de Pesquisas Energéticas e Nucleares (IPEN-CNEN). The pulmonary metastasis exams are carried out in three projections, one dorsal-ventral and two lateral-lateral. During the procedures the projection thicknesses and source-skin surface distances were registered. To simulate the dog phantom the dosimeters were positioned in a cubic simulator (30x30x30 cm) of polymethylmethacrylate (PMMA) filled with water and irradiated according to the parameters of projections with the X-ray energies ranging from 45 to 70 kV. To estimate the surface skin dose the dose-response curves were obtained for X-ray energies of 50 and 70 kV using the diagnostic X-ray beam machine of the Instruments Calibration Laboratory of IPEN for doses of 1.5, 2.0, 2.5, 3.5 and 4.0 mGy. The main difficulty of this work was the dog immobilization that is reflected in poor-quality diagnostic imaging and, consequently, demands the repetition of the exams, which contributes to the increase of the doses received by the animals being studied and the clinical staff. The doses evaluated in this type of procedure are between 0.43 and 4.22 mGy. This research has shown to be extremely important for the assessment of doses involved in veterinary diagnostic radiology procedures, and as a parameter in the individual monitoring of pet’s owners who assist the animal positioning and occupationally exposed workers of the Department of Veterinary Radiology

Fenologia e dendrocronologia de duas espécies de Fabaceae em uma área de cerrado no sudeste do Brasil

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

Morphological variation, advertisement call, and tadpoles of Bokermannohyla nanuzae (Bokermann, 1973), and taxonomic status of B-feioi (Napoli &Caramaschi, 2004) (Anura, Hylidae, Cophomantini)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Using complex networks to quantify consistency in the use of words

In this paper we have quantified the consistency of word usage in written texts represented by complex networks, where words were taken as nodes, by measuring the degree of preservation of the node neighborhood. Words were considered highly consistent if the authors used them with the same neighborhood. When ranked according to the consistency of use, the words obeyed a log-normal distribution, in contrast to Zipf's law that applies to the frequency of use. Consistency correlated positively with the familiarity and frequency of use, and negatively with ambiguity and age of acquisition. An inspection of some highly consistent words confirmed that they are used in very limited semantic contexts. A comparison of consistency indices for eight authors indicated that these indices may be employed for author recognition. Indeed, as expected, authors of novels could be distinguished from those who wrote scientific texts. Our analysis demonstrated the suitability of the consistency indices, which can now be applied in other tasks, such as emotion recognition.

Network-based high level data classification

Traditional supervised data classification considers only physical features (e. g., distance or similarity) of the input data. Here, this type of learning is called low level classification. On the other hand, the human (animal) brain performs both low and high orders of learning and it has facility in identifying patterns according to the semantic meaning of the input data. Data classification that considers not only physical attributes but also the pattern formation is, here, referred to as high level classification. In this paper, we propose a hybrid classification technique that combines both types of learning. The low level term can be implemented by any classification technique, while the high level term is realized by the extraction of features of the underlying network constructed from the input data. Thus, the former classifies the test instances by their physical features or class topologies, while the latter measures the compliance of the test instances to the pattern formation of the data. Our study shows that the proposed technique not only can realize classification according to the pattern formation, but also is able to improve the performance of traditional classification techniques. Furthermore, as the class configuration's complexity increases, such as the mixture among different classes, a larger portion of the high level term is required to get correct classification. This feature confirms that the high level classification has a special importance in complex situations of classification. Finally, we show how the proposed technique can be employed in a real-world application, where it is capable of identifying variations and distortions of handwritten digit images. As a result, it supplies an improvement in the overall pattern recognition rate.

The tangential variation of a localized flux-type eigenvalue problem

In this work the differentiability of the principal eigenvalue lambda = lambda(1)(Gamma) to the localized Steklov problem -Delta u + qu = 0 in Omega, partial derivative u/partial derivative nu = lambda chi(Gamma)(x)u on partial derivative Omega, where Gamma subset of partial derivative Omega is a smooth subdomain of partial derivative Omega and chi(Gamma) is its characteristic function relative to partial derivative Omega, is shown. As a key point, the flux subdomain Gamma is regarded here as the variable with respect to which such differentiation is performed. An explicit formula for the derivative of lambda(1) (Gamma) with respect to Gamma is obtained. The lack of regularity up to the boundary of the first derivative of the principal eigenfunctions is a further intrinsic feature of the problem. Therefore, the whole analysis must be done in the weak sense of H(1)(Omega). The study is of interest in mathematical models in morphogenesis. (C) 2011 Elsevier Inc. All rights reserved.

Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

The bovine aristaless-like homeobox 4 (ALX4) as a candidate gene for syndactyly

The ALX4 (aristaless-like homeobox 4) gene encodes a paired-type homeodomain transcriptional activator and plays a major role in anterior-posterior pattern formation during limb development. Here, the cloning, genomic structure and expression of the bovine ortholog of the ALX4 gene are reported. The bovine ALX4 gene consists of four exons and is located on BTA15q28-->q29 in a region syntenic to HSA11p11.2. The transcribed ALX4 mRNA encodes a 397-amino-acid protein showing a paired-type homeodomain and a C-terminal stretch of amino acids known as the OAR- or aristaless domain. The predicted protein shares 92.5% identity to human and mouse ALX4 proteins and all three species share almost complete identity in the conserved domains. ALX4 expression was detected by reverse transcriptase polymerase chain reaction in bovine fetal limb bones. The ALX4 gene was evaluated as a candidate gene for bovine syndactyly which has been mapped on the telomeric region of cattle chromosome 15. Sequencing of the four exons with flanking sequences of the bovine ALX4 gene from a panel of 14 affected animals belonging to German Holstein, German Fleckvieh and crossbreds, and 27 unaffected individuals from German Holstein revealed five silent SNPs within the coding region out of eleven SNPs in total. Four SNPs were polymorphic in the affected animals, but in comparison to the genotyped unaffected individuals the genotype distribution showed no evidence for an association to the phenotype. Therefore our data indicate that the ALX4 gene can probably be excluded as candidate gene for bovine syndactyly in the examined animals.