Copy number variation of individual cattle genomes using next-generation sequencing

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising similar to 55.6-Mbp sequence-476 of which (similar to 38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (similar to 52%, chi(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.

Oviposition behavior of Ceratitis capitata wiedemann (Diptera: Tephritidae): Association between oviposition preference and larval performance in individual females

The oviposition preference and larval performance of females of Ceratitis capitata (Wiedemann) were examined. Wild or laboratory-reared females were tested for oviposition preference in relation to papaya fruit in different stages of ripeness, as well as to two different fruits: papaya and apple. The results demonstrated that both laboratory-reared and wild females preferred ripe papaya fruit compared to unripe fruit for oviposition, and that ripe papaya was the best for larval performance. When oviposition preference was tested with different fruits (papaya and apple), both wild and laboratory-reared larvae developed better in papaya. However, only wild females showed a preference for oviposition on papaya as opposed to apple. Laboratory-reared females showed no oviposition preference on fruits that resulted in better larval performance.

Histochemistry and protein profile of the mandibular glands of workers of the ant Atta sexdens rubropilosa (Hymenoptera: Formicidae)

Insect mandibular glands are always associated to the mandibles; they are part of the salivary glandular system. The mandibular glands are composed by a reservoir associated to the secretory cells, with each secretory cell connected to the reservoir by means of individual canaliculi. These glands play an important role in the production of pheromones, which are compounds involved in defense, communication, and reproduction of the colony. Mandibular glands of soldiers and major and minor workers of the ant Atta sexdens rubropilosa were processed for different histochemical tests, total protein content, and protein electrophoretic profile determination. The histochemical tests detected the presence of lipids, DNA/RNA, polysaccharides, and proteins at different regions of the gland. The protein electrophoretic profiles showed that the total protein content as well as the number of peptides of each caste follow a progressive order in relation to the size of the individual. Thus, we suggest that the production of secretion is directly linked to the task that the individual performs in the colony.

Papillary cystadenoma of the minor salivary gland of the lower lip

A case report of the papillary cystadenoma from minor salivary gland in lower lip of a 54-year-old man is described.

Spontaneous eye blink analysis in the normal individual

Purpose: Spontaneous eye blink activity in the primary eye position and its relationship to age and gender were assessed using digital image processing techniques to quantify blink opening and closing time. Methods: One hundred-and-eighty healthy volunteers (90 males and 90 females), divided into the age groups 0-3, 4-12, 13-20, 21-40, 41-60 and ≥60 years old, were evaluated prospectively. They were videotaped digitally in a standard setting and the images were transferred to a personal computer (Macintosh 400) and processed with the iMovie software. Blink opening and closing time were measured at 30 frames/second. The data were then subjected to statistical analysis. Results: The closing time was significantly longer than the opening time for all ages and both genders. Elderly individuals (≥41 years old) and women had significantly longer closing times. Conclusion: Image processing techniques made possible the observation of differences in spontaneous eye blink opening and closing time in relation to age and gender. Copyright © 2005 Taylor & Francis LLC.

Effects of olive oil and its minor constituents on serum lipids, oxidative stress, and energy metabolism in cardiac muscle

Recent lines of evidence suggest that the beneficial effects of olive oil are not only related to its high content of oleic acid, but also to the antioxidant potential of its polyphenols. The aim of this work was determine the effects of olive oil and its components, oleic acid and the polyphenol dihydroxyphenylethanol (DPE), on serum lipids, oxidative stress, and energy metabolism on cardiac tissue. Twenty four male Wistar rats, 200 g, were divided into the following 4 groups (n = 6): control (C), OO group that received extra-virgin olive oil (7.5 mL/kg), OA group was treated with oleic acid (3.45 mL/kg), and the DPE group that received the polyphenol DPE (7.5 mg/kg). These components were administered by gavage over 30 days, twice a week. All animals were provided with food and water ad libitum The results show that olive oil was more effective than its isolated components in improving lipid profile, elevating high-density lipoprotein, and diminishing low-density lipoprotein cholesterol concentrations. Olive oil induced decreased antioxidant Mn-superoxide dismutase activity and diminished protein carbonyl concentration, indicating that olive oil may exert direct antioxidant effect on myocardium. DPE, considered as potential antioxidant, induced elevated aerobic metabolism, triacylglycerols, and lipid hydroperoxides concentrations in cardiac muscle, indicating that long-term intake of this polyphenol may induce its undesirable pro-oxidant activity on myocardium. © 2006 NRC Canada.

Electrical properties of individual and small ensembles of InAs/InP nanostructures

We investigate electrical properties of InAs/InP semiconductor nanostructures by conductive atomic force microscopy (C-AFM) and current measurements at low temperatures in processed devices. Different conductances and threshold voltages for current onset were observed for each type of nanostructure. In particular, the extremity of the wire could be compared to a dot with similar dimensions. The processed devices were used in order to access the in-plane conductance of an assembly of a reduced number of nanostructures. Here, fluctuations on I-V curves at low temperatures (<40 K) were observed. At these low temperatures and for a suitable range of applied voltages, random telegraph noise (RTN) in the current was observed for devices with dots. These fluctuations can be associated to electrons trapped in dots, as suggested by numerical simulations. A crossover from a semiconductor-like to a metallic transport behavior is also observed for similar parameters. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA.

Perfusão cerebral e análise individual automatizada utilizando SPECT em uma população com transtorno obsessivo-compulsivo

Objective: To make individual assessments using automated quantification methodology in order to screen for perfusion abnormalities in cerebral SPECT examinations among a sample of subjects with OCD. Methods: Statistical parametric mapping (SPM) was used to compare 26 brain SPECT images from patients with OCD individually with an image bank of 32 normal subjects, using the statistical threshold of p < 0.05 (corrected for multiple comparisons at the level of individual voxels or clusters). The maps were analyzed, and regions presenting voxels that remained above this threshold were sought. results: Six patients from a sample of 26 OCD images showed abnormalities at cluster or voxel level, considering the criteria described above, which represented 23.07%. However, seven images from the normal group of 32 were also indicated as cases of perfusional abnormality, representing 21.8% of the sample. Conclusion: The automated quantification method was not considered to be a useful tool for clinical practice, for analyses complementary to visual inspection.

Development of sustainable precision farming systems for swine: Estimating realtime individual amino acid requirements in growing-finishing pigs

The objective of this study was to develop and evaluate a mathematical model used to estimate the daily amino acid requirements of individual growing-finishing pigs. The model includes empirical and mechanistic model components. The empirical component estimates daily feed intake (DFI), BW, and daily gain (DG) based on individual pig information collected in real time. Based on DFI, BW, and DG estimates, the mechanistic component uses classic factorial equations to estimate the optimal concentration of amino acids that must be offered to each pig to meet its requirements. The model was evaluated with data from a study that investigated the effect of feeding pigs with a 3-phase or daily multiphase system. The DFI and BW values measured in this study were compared with those estimated by the empirical component of the model. The coherence of the values estimated by the mechanistic component was evaluated by analyzing if it followed a normal pattern of requirements. Lastly, the proposed model was evaluated by comparing its estimates with those generated by the existing growth model (InraPorc). The precision of the proposed model and InraPorc in estimating DFI and BW was evaluated through the mean absolute error. The empirical component results indicated that the DFI and BW trajectories of individual pigs fed ad libitum could be predicted 1 d (DFI) or 7 d (BW) ahead with the average mean absolute error of 12.45 and 1.85%, respectively. The average mean absolute error obtained with the InraPorc for the average individual of the population was 14.72% for DFI and 5.38% for BW. Major differences were observed when estimates from InraPorc were compared with individual observations. The proposed model, however, was effective in tracking the change in DFI and BW for each individual pig. The mechanistic model component estimated the optimal standardized ileal digestible Lys to NE ratio with reasonable between animal (average CV = 7%) and overtime (average CV = 14%) variation. Thus, the amino acid requirements estimated by model are animal- and time-dependent and follow, in real time, the individual DFI and BW growth patterns. The proposed model can follow the average feed intake and feed weight trajectory of each individual pig in real time with good accuracy. Based on these trajectories and using classical factorial equations, the model makes it possible to estimate dynamically the AA requirements of each animal, taking into account the intake and growth changes of the animal. © 2012 American Society of Animal Science. All rights reserved.

Trait contributions to fish community assembly emerge from trophic interactions in an individual-based model

Community ecology seeks to understand and predict the characteristics of communities that can develop under different environmental conditions, but most theory has been built on analytical models that are limited in the diversity of species traits that can be considered simultaneously. We address that limitation with an individual-based model to simulate assembly of fish communities characterized by life history and trophic interactions with multiple physiological tradeoffs as constraints on species performance. Simulation experiments were carried out to evaluate the distribution of 6 life history and 4 feeding traits along gradients of resource productivity and prey accessibility. These experiments revealed that traits differ greatly in importance for species sorting along the gradients. Body growth rate emerged as a key factor distinguishing community types and defining patterns of community stability and coexistence, followed by egg size and maximum body size. Dominance by fast-growing, relatively large, and fecund species occurred more frequently in cases where functional responses were saturated (i.e. high productivity and/or prey accessibility). Such dominance was associated with large biomass fluctuations and priority effects, which prevented richness from increasing with productivity and may have limited selection on secondary traits, such as spawning strategies and relative size at maturation. Our results illustrate that the distribution of species traits and the consequences for community dynamics are intimately linked and strictly dependent on how the benefits and costs of these traits are balanced across different conditions. © 2012 Elsevier B.V.

Occurrence of mycobacteria in bovine milk samples from both individual and collective bulk tanks at farms and informal markets in the southeast region of Sao Paulo, Brazil

Background: Mycobacterium spp. is one of the most important species of zoonotic pathogens that can be transmitted from cattle to humans. The presence of these opportunistic, pathogenic bacteria in bovine milk has emerged as a public-health concern, especially among individuals who consume raw milk and related dairy products. To address this concern, the Brazilian control and eradication program focusing on bovine tuberculosis, was established in 2001. However, bovine tuberculosis continues to afflict approximately 1,3 percent of the cattle in Brazil. In the present study, 300 samples of milk from bovine herds, obtained from both individual and collective bulk tanks and informal points of sale, were cultured on Löwenstein-Jensen and Stonebrink media. Polymerase chain reaction (PCR)-based tests and restriction-enzyme pattern analysis were then performed on the colonies exhibiting phenotypes suggestive of Mycobacterium spp., which were characterized as acid-fast bacilli.Results: Of the 300 bovine milk samples that were processed, 24 were positively identified as Mycobacterium spp.Molecular identification detected 15 unique mycobacterial species: Mycobacterium bovis, M. gordonae, M. fortuitum, M. intracellulare, M. flavescens, M. duvalii, M. haemophilum, M. immunogenum, M. lentiflavum, M. mucogenicum, M. novocastrense, M. parafortuitum, M. smegmatis, M. terrae and M. vaccae. The isolation of bacteria from the various locations occurred in the following proportions: 9 percent of the individual bulk-tank samples, 7 percent of the collective bulk-tank samples and 8 percent of the informal-trade samples. No statistically significant difference was observed between the presence of Mycobacterium spp. in the three types of samples collected, the milk production profiles, the presence of veterinary assistance and the reported concerns about bovine tuberculosis prevention in the herds.Conclusion: The microbiological cultures associated with PCR-based identification tests are possible tools for the investigation of the presence of Mycobacterium spp. in milk samples. Using these methods, we found that the Brazilian population may be regularly exposed to mycobacteria by consuming raw bovine milk and related dairy products. These evidences reinforces the need to optimize quality programs of dairy products, to intensify the sanitary inspection of these products and the necessity of further studies on the presence of Mycobacterium spp. in milk and milk-based products. © 2013 Franco et al.; licensee BioMed Central Ltd.

Small particles in Pluto's environment: Effects of the solar radiation pressure

Impacts of micrometeoroids on the surfaces of the plutonian small satellites Nix and Hydra can generate dust particles. Even in this region so far from the Sun these tiny ejected particles are under the effects of the solar radiation pressure. In this work, we investigate the orbital evolution of the escaping ejecta from both the small satellites under the effects of the radiation pressure combined with the gravitational effects of Pluto, Charon, Nix and Hydra. The mass production rate of micron-sized dust particles generated by micrometeoroids hitting the satellites is obtained, and numerical simulations are performed to derive the lifetime of the ejecta. These pieces of information allow us to estimate the optical depth of a putative ring, which extends from the orbits of Nix to Hydra. The ejected particles, between the orbits of Nix and Hydra, form a wide ring of about 16 000 km. Collisions with the massive bodies and escape from the system are mainly determined by the effects of the solar radiation pressure. This is an important loss mechanism, removing 30 per cent of the initial set of 1 μm-sized particles in 1 yr. The surviving particles form a ring too faint to be detectable with the derived maximum optical depth of 4 × 10-11. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

How individual movement response to habitat edges affects population persistence and spatial spread

How individual-level movement decisions in response to habitat edges influence population-level patterns of persistence and spread of a species is a major challenge in spatial ecology and conservation biology. Here, we integrate novel insights into edge behavior, based on habitat preference and movement rates, into spatially explicit growth-dispersal models. We demonstrate how crucial ecological quantities (e.g., minimal patch size, spread rate) depend critically on these individual-level decisions. In particular, we find that including edge behavior properly in these models gives qualitatively different and intuitively more reasonable results than those of some previous studies that did not consider this level of detail. Our results highlight the importance of new empirical work on individual movement response to habitat edges. © 2013 by The University of Chicago.

Acute toxicity and environmental risk of teflubenzuron to Daphnia magna, Poecilia reticulata and Lemna minor in the absence and presence of sediment

This study aimed to estimate the acute toxicity of teflubenzuron (1-(3,5-dichloro-2,4-difluorophenyl)-3-(2,6-difluorobenzoyl)urea) (TFB) for Daphnia magna, Lemna minor and Poecilia reticulata, in the absence and presence of sediment; evaluate the effect of sediment on the TFB bioavailability; and to classify this insecticide according to its environmental poisoning risk for agricultural and aquaculture uses. The tests of TFB acute toxicity were conducted in static system in a completely randomized design with increasing TFB concentrations, and a control group. The TFB has been classified according to the estimated values of EC50 and LC50 by its acute toxicity and environmental risk. The sediment significantly reduced toxicity and bioavailability of TFB in water column. Therefore, the insecticide can be classified as being highly toxic to Daphnia magna, which means the agricultural and aquacultural uses of TFB pose a high risk of environmental toxicity to non-target organisms. However, it was practically non-toxic to L. minor and P. reticulata. © 2013 Copyright Taylor and Francis Group, LLC.