Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells.

Gene transfer in eukaryotic cells and organisms suffers from epigenetic effects that result in low or unstable transgene expression and high clonal variability. Use of epigenetic regulators such as matrix attachment regions (MARs) is a promising approach to alleviate such unwanted effects. Dissection of a known MAR allowed the identification of sequence motifs that mediate elevated transgene expression. Bioinformatics analysis implied that these motifs adopt a curved DNA structure that positions nucleosomes and binds specific transcription factors. From these observations, we computed putative MARs from the human genome. Cloning of several predicted MARs indicated that they are much more potent than the previously known element, boosting the expression of recombinant proteins from cultured cells as well as mediating high and sustained expression in mice. Thus we computationally identified potent epigenetic regulators, opening new strategies toward high and stable transgene expression for research, therapeutic production or gene-based therapies.

Comparison of carcass composition by parts and tissues between cocks and capons

The effect of caponisation on carcass composition by parts and tissues was examined. Twenty-eight castrated and twenty male Penedesenca Negra chicks reared under free-range conditions were slaughtered at 28 weeks of age. The birds were castrated at 4 or 8 weeks. The left sides of the carcasses were quartered (wing, breast, thigh and drumstick), and the parts dissected into the tissue components (skin, subcutaneous fat, intermuscular fat, muscle, bone and tendons). Capons showed more abdominal, intermuscular and subcutaneous fat than the cocks, both at the same slaughter age and at the same weight. The breast and thigh were heavier in the capons than in the cocks. However, the whole muscle mass in the breast was increased by caponisation. This favourable effect was achieved at the expense of decreasing the carcass yield. The age of castration up to 8 weeks did not affect the carcass composition of the parts and tissues.

RNA interference is ineffective as a routine method for gene silencing in chick embryos as monitored by fgf8 silencing.

The in vivo accessibility of the chick embryo makes it a favoured model system for experimental developmental biology. Although the range of available techniques now extends to miss-expression of genes through in ovo electroporation, it remains difficult to knock out individual gene expression. Recently, the possibility of silencing gene expression by RNAi in chick embryos has been reported. However, published studies show only discrete quantitative differences in the expression of the endogenous targeted genes and unclear morphological alterations. To elucidate whether the tools currently available are adequate to silence gene expression sufficiently to produce a clear and specific null-like mutant phenotype, we have performed several experiments with different molecules that trigger RNAi: dsRNA, siRNA, and shRNA produced from a plasmid coexpressing green fluorescent protein as an internal marker. Focussing on fgf8 expression in the developing isthmus, we show that no morphological defects are observed, and that fgf8 expression is neither silenced in embryos microinjected with dsRNA nor in embryos microinjected and electroporated with a pool of siRNAs. Moreover, fgf8 expression was not significantly silenced in most isthmic cells transformed with a plasmid producing engineered shRNAs to fgf8. We also show that siRNA molecules do not spread significantly from cell to cell as reported for invertebrates, suggesting the existence of molecular differences between different model systems that may explain the different responses to RNAi. Although our results are basically in agreement with previously reported studies, we suggest, in contrast to them, that with currently available tools and techniques the number of cells in which fgf8 gene expression is decreased, if any, is not sufficient to generate a detectable mutant phenotype, thus making RNAi useless as a routine method for functional gene analysis in chick embryos.

Effect of feed fat by-products with trans fatty acids and heated oil on cholesterol and oxycholesterols in chicken

Chicken is the most widely consumed meat all over the world due to chickens being easy to rear, their fast growth rate and the meat having good nutritional characteristics. The main objective of this paper was to study the effects of dietary fatty by-products in low, medium and high levels of oxidized lipids and trans fatty acids (TFAs) on the contents of cholesterol and oxycholesterols in meat, liver, and plasma of chickens. A palm fatty acid distillate, before and after hydrogenation, and a sunflower-olive oil blend (70/30, v/v) before and after use in a commercial frying process were used in feeding trials after adding 6% of the fats to the feeds. Highly oxidized lipid and TFA feeds significantly increased the contents of cholesterol and oxycholesterols in all tissues of chicken (0.01 < p <= 0.05). The contents of oxycholesterols in chicken meat, liver and plasma obtained from TFA feeding trials varied between 17 and 48 μg/100 g in meat, 19-42 μg/100 g in liver and 105-126 μg/dL in plasma. In contrast, in the oxidized lipid feeding trials, oxycholesterols varied between 13 and 75 μg/100 g in meat, 30-58 μg/100 g in liver and 66-209 μg/dL in plasma. Meat from chickens fed with feeds containing high levels of TFAs or oxidized lipids may contribute to higher ingestion of cholesterol and oxycholesterols by humans.

Evolution of dosage compensation under sexual selection differs between X and Z chromosomes.

Complete sex chromosome dosage compensation has more often been observed in XY than ZW species. In this study, using a population genetic model and the chicken transcriptome, we assess whether sexual conflict can account for this difference. Sexual conflict over expression is inevitable when mutation effects are correlated across the sexes, as compensatory mutations in the heterogametic sex lead to hyperexpression in the homogametic sex. Coupled with stronger selection and greater reproductive variance in males, this results in slower and less complete evolution of Z compared with X dosage compensation. Using expression variance as a measure of selection strength, we find that, as predicted by the model, dosage compensation in the chicken is most pronounced in genes that are under strong selection biased towards females. Our study explains the pattern of weak dosage compensation in ZW systems, and suggests that sexual selection plays a major role in shaping sex chromosome dosage compensation.

Effect of magnesium sulphate and L-tryptophan and genotype on the feed intake, behaviour and meat quality of pigs

Sixty-nine entire male pigs with different halothane genotype (homozygous halothanepositive – nn-, n=36; and homozygous halothane negative – NN-, n=33) were fed with a supplementation of magnesium sulphate (Mg) and/or L-tryptophan (Trp) in the diet for 5days before slaughter. Animals were housed individually and were submitted to stressful ante mortem conditions (mixed in the lorry according to treatments and transported 1h on rough roads). Individual feed intake was recorded during the 5-day treatment. At the abattoir, pig behaviour was assessed in the raceway to the stunning system and during the stunning period by exposure to CO2. Muscle pH, colour, water holding capacity, texture and cathepsin activities were determined to assess meat quality. The number of pigs with an individual feed intake lower than 2kg/day was significantly different among diets (P<0.05; Control: 8.7%; Mg&Trp: 43.5%; Trp:17.4%) and they were considered to have inadequate supplement intake. During the antemortem period, 15.2% of pigs included in the experiment died, and this percentagedecreased to 8.7% in those pigs with a feed intake > 2kg/day, all of them from thestress-sensitive pigs (nn). In general, no differences were observed in the behaviour ofpigs along the corridor leading to the stunning system and inside the CO2 stunningsystem. During the stunning procedure, Trp diet showed shorter periods of muscularexcitation than control and Mg&Trp diets. The combination of a stressful ante mortemtreatment and Mg&Trp supplementation led to carcasses with high incidence of severeskin lesions. Different meat quality results were found when considering all pigs orconsidering only those with adequate supplement intake. In this later case, Trp increased pH45 (6.15) vs Control diet (5.96) in the Longissimus thoracis (LT) muscle (P<0.05) and pH at 24h (Trp: 5.59 vs C: 5.47) led to a higher incidence of dark, firm and dry (DFD) traits in SM muscle (P<0.05). Genotype affected negatively all the meat quality traits. Seventy-five percent of LT and 60.0% of the SM muscles from nn pigs wereclassified as pale, soft and exudative (PSE), while none of the NN pigs showed these traits (P<0.0001). No significant differences were found between genotypes on the incidence of DFD meat. Due to the negative effects observed in the Mg&Trp group in feed intake and carcass quality, the utilization of a mixture of magnesium sulphate and tryptophan is not recommended

Alusöljyvahingossa kuolleiden eläinten turvallinen käsittely

Diplomityö on osa Kymenlaakson ammattikorkeakoulun SÖKÖ II-hanketta, missä tehdään toimintamalli suuren öljyntorjuntaoperaation koordinointiin rannikon öljytorjunnasta vastaaville viranomaisille. Työn tavoitteena oli selvittää alusöljyvahingossa kuolleiden eläinten sekä eläinten keräilystä ja hoidosta syntyvien jätteiden käsittelymenetelmät ja soveltuvat käsittelylaitokset. Lisäksi tavoitteena oli selvittää kuolleiden eläinten välivarastointialueen tekniset vaatimukset ja öljyiselle eläinjätteelle soveltuva kuljetuskalusto. Työn teoriaosuudet toteutettiin kirjallisten lähteiden ja asiantuntijahaastatteluiden avulla. Tärkeäksi osaksi työtä muodostui kustannuslaskelma, missä laskettiin kuolleiden eläinten keräilystä aina loppukäsittelyyn asti muodostuvat kustannukset. Työn teoriaosuudet loivat pohjan kustannuslaskelmalle. Kuolleiden eläinten loppukäsittelyyn valittiin kolme eri laitosta ja kolme eri käsittelytekniikkaa, mitkä ovat: rumpu-uuni, siirrettävä termodesorptio ja renderöinti. Kuolleet eläimet kannattaa keskitetysti kerätä ja kuljettaa yhdelle alueelle, missä suoritetaan kuolleiden eläinten välivarastointi kylmäkonteissa ja tilastointi sekä elävien eläinten pesu ja hoito. Kustannuslaskelman perusteella siirrettävä termodesorptiolaitos on halvin käsittelyvaihtoehto, mutta kustannuserot muihin laitoksiin ovat pienet. Koko kuolleiden eläinten turvallisen käsittelyn kustannukset ovat alle promillen koko suuren öljyvahingon kustannuksista. Loppukäsittelylaitosta valittaessa on käsittelykustannuksia tärkeämpää selvittää laitoksen sen hetkinen jätteenkäsittelytilanne ja vapaa käsittelykapasiteetti kuolleille eläimille.

Spatial variability of air dry bulb temperature and black globe humidity index in a broiler house during the heating phase

The air dry-bulb temperature (t db),as well as the black globe humidity index (BGHI), exert great influence on the development of broiler chickens during their heating phase. Therefore, the aim of this study was to analyze the structure and the magnitude of the t db and BGHI spatial variability, using geostatistics tools such as semivariogram analysis and also producing kriging maps. The experiment was conducted in the west mesoregion of the states of Minas Gerais in 2010, in a commercial broiler house with heating system consisting of two furnaces that heat the air indirectly, in the firsts 14 days of the birds' life. The data were registered at intervals of five minutes in the period from 8 a.m. to 10 a.m. The variables were evaluated by variograms fitted by residual maximum likelihood (REML) testing the Spherical and Exponential models. Kriging maps were generated based on the best model used to fit the variogram. It was possible to characterize the variability of the t db and BGHI, which allowed observing the spatial dependence by using geostatistics techniques. In addition, the use of geostatistics and distribution maps made possible to identify problems in the heating system in regions inside the broiler house that may harm the development of chicks.

Estimating the most important criteria for hatching eggs as function of broiler breeders age

This research aimed to compare two female broiler breeder ages during the incubation period regarding management using the Analytic Hierarchy Process method (AHP). This method is characterized by the possibility of analyzing a multicriteria problem and assists a decision making. This study was carried out on a commercial hatchery located in São Paulo, Brazil. Two ages of broiler breeder (42 and 56 weeks) were compared relative to production rate. Production index data were the same in both ages and were submitted to multicriteria decision analysis using the AHP method. The results indicate that broiler breeders of 42 weeks presented better performance than those of 56 week-old. The setter phase (incubation) is more critical than the hatcher. The AHP method was efficient for this analysis and can serve as a methodological basis for future studies to improve the hatchability of broilers eggs.

Nutrient loss in composting of agroindustrial residues

The management of composting may influence the characteristics of the produced compounds. The experiment used three frequencies of plowing, combined with the conditions: with and without coverage of the composting patio, with and without the use of commercial inoculant, resulting in 12 furrows, installed on the Experimental Center of Agricultural Engineering (NEEA), of the STATE UNIVERSITY OF WEST PARANÁ (UNIOESTE), Campus of Cascavel city - state of Paraná (PR), in Brazil. The waste and quantities used in kg were: corn cob (7.5); hatchery residue (5); floater sludge (31); ash (1); wheat cleaning residue (120); wheat pre-cleaning residue (120); corn peel (7.5); solid fraction of wash trucks used to transport chickens (2); solid fraction of pig manure (1) and coal (5), totaling 300kg of natural matter. The aim of this study was to evaluate the influence of plowings, patio coverage and inoculation in losses of N, P, K, Ca, Mg, Na, Cu, Zn, Mn, Fe. The furrows plowed three times a week in the first month showed significant higher losses of N (p<0.05). The coverage of the composting patio influenced significantly the losses of N, K, Mg and Na (p<0.05). The produced compounds had a high agronomic value in relation to macro and micronutrients. It is recommended the use of patio coverage and plowing twice a week in the first month and once a week in the subsequent months for a compound with higher concentrations of nutrients.

Identification of acoustic parameters for broiler welfare estimate

Estimates of broiler welfare have subjective character. Nowadays, researchers seek non-invasive features or indicators that may describe this condition in animal production. The aim of this study was to identify acoustic parameters to estimate broiler welfare using the following five vocalization acoustic parameters: energy, spectral centroid, bandwidth, first formant, and second formant. The database that generated the model was obtained from a field experiment with 432 broilers, which half were Cobb® and half, Ross® breed, from day 21 to 42, containing bird vocalizations under either welfare or stress conditions. The results of the experiment generated responses to the tested conditions of gender, genetic strain, and welfare. The proposed model was based on the specific response of mean weights for each situation of stress and well-being. From the results, a model was developed to estimate the welfare condition of broilers from the registered information linked to their vocalization.

Light emitting diode (LED) use in artificial lighting for broiler chicken production

Light emitting diode (LED) has been used in commercial poultry industry by presenting superior energy savings and providing feasibility on production process. The objective of this research was to evaluate performance and carcass yield of broiler chickens exposed to different LED colors compared with fluorescent lamps. For that, two experiments (E1 and E2) were performed and 2,646 Cobb® chickens were used. In experiment E1, male birds were exposed to 20 lux artificial lighting with red, yellow, blue, and white LED bulbs; and fluorescent bulb. In experiment E2, male and female birds were exposed to 15 lux artificial lighting with red and blue LED bulbs; and fluorescent bulb. Cumulative weight gain (kg), feed intake (kg), feed conversion, hot carcass weight (kg), carcass yield (%), and breast and thigh + drumstick yield (%) were used as response variables. Results showed no difference (p > 0.05) among treatments for performance, carcass yield, and cut yield in experiment E1. In experiment E2 there was only difference between genders (p < 0.05) and males showed higher total weight gain, feed intake, hot carcass weight and thigh + drumstick yield. Different LED color use had same effect as fluorescent lights on broiler performance and carcass yield.

Impact of different light sources on broiler rearing environment

Broiler production is highly dependent on the use of artificial light. The light source may affect the effectiveness of housing conditions due to increasing ambient temperature and concentration of noxious gases. This research aimed to evaluate the effects of different bulb types on the thermal, aerial, and acoustic environment of broiler aviaries. The experiment was carried out at a commercial broiler farm in Dourados, Mato Grosso do Sul State, Brazil. Three aviaries were used, and two flocks of male broilers from Cobb® genetic strain were reared from the first day to slaughter. Each aviary was equipped with a different light source, comprising the adopted treatments (A1 - incandescent light bulb, control; A2 - sodium vapor light bulb; A3 - fluorescent light bulb). The aviaries were divided into nine quadrants, and the environmental data (ambient dry bulb temperature and relative humidity), litter surface temperature, CO2 and NH3 concentrations, and bird sound pressure behavior were recorded in each quadrant. The aviary with incandescent light presented higher air and litter temperatures, and concentration of gases than the other tested alternatives. It also presented higher level of sound pressure in the second week of the growing period; however, from this period up to slaughter, there was no effect of the light source on the results of broiler sound pressure level.

Integrated multivariate analysis to evaluate effects of pre-slaughter handling on pork quality

The aim of this study was to investigate the effect of pre-slaughter handling on the occurrence of PSE (Pale, Soft, and Exudative) meat in swine slaughtered at a commercial slaughterhouse located in the metropolitan region of Dourados, Mato Grosso do Sul, Brazil. Based on the database (n=1,832 carcasses), it was possible to apply the integrated multivariate analysis for the purpose of identifying, among the selected variables, those of greatest relevance to this study. Results of the Principal Component Analysis showed that the first five components explained 89.28% of total variance. In the Factor Analysis, the first factor represented the thermal stress and fatiguing conditions for swine during pre-slaughter handling. In general, this study indicated the importance of the pre-slaughter handling stages, evidencing those of greatest stress and threat to animal welfare and pork quality, which are transport time, resting period, lairage time before unloading, unloading time, and ambience.

Poultry carcass decomposition and physicochemical analysis of compounds in different Composter types

This study aimed to assess five composter types in poultry carcasses decomposition and to perform a physicochemical analysis of the compounds obtained. Composter types used were six-hole brick, wood, screen, windrow with three PVC pipes with six holes and windrow with three PVC pipes with 10 holes. Composting was followed by four periods using wood shaving like substrate with one bird carcass placed in each composter. Pile turning was performed every 10 days and temperature in each layer was measured on 1st, 7th, 14th, 19th and 29th day, at 3 p.m., as well as room temperature. Temperature during pile turning was also measured at five points per layer and carcass weighing performed to calculate decomposition percentage. Physicochemical parameters evaluated in substrates were moisture, ash, phosphorus, potassium, nitrogen, pH, organic carbon and C/N ratio, up to 30 days. Data were analyzed by repeated measures model, using MIXED method of SAS software. All values of final physicochemical composition of substrates were found according to values of IN-25, except nitrogen. The composter types were efficient in decomposition of poultry carcasses.