Association of bGH and Pit-1 gene variants with milk production traits in dairy Gyr bulls

The objective of this study was to obtain genetic marker information in the Gyr breed by analyzing bGH and Pit-1 gene polymorphisms and to verify their association with milk production traits. One sample including 40 Gyr bulls were genotyped at two bGH gene restriction sites (bGH- AluI and bGH-MspI) and at one restriction site in the Pit-1 gene (Pit-1 HinfI). The bGH-MspI(-) allele was favorable for fat milk percentage. The heterozigous Pit-1 HinfI (+/-) bulls were superior for fat milk production, in relation to homozigous Pit-1 HinfI (+/+). The Pit-1 and bGH genes are strong candidates in the dairy cattle QTL search, and zebuine populations are promising samples for this purpose.

Statistical significance of quantitative PCR.

BACKGROUND: PCR has the potential to detect and precisely quantify specific DNA sequences, but it is not yet often used as a fully quantitative method. A number of data collection and processing strategies have been described for the implementation of quantitative PCR. However, they can be experimentally cumbersome, their relative performances have not been evaluated systematically, and they often remain poorly validated statistically and/or experimentally. In this study, we evaluated the performance of known methods, and compared them with newly developed data processing strategies in terms of resolution, precision and robustness. RESULTS: Our results indicate that simple methods that do not rely on the estimation of the efficiency of the PCR amplification may provide reproducible and sensitive data, but that they do not quantify DNA with precision. Other evaluated methods based on sigmoidal or exponential curve fitting were generally of both poor resolution and precision. A statistical analysis of the parameters that influence efficiency indicated that it depends mostly on the selected amplicon and to a lesser extent on the particular biological sample analyzed. Thus, we devised various strategies based on individual or averaged efficiency values, which were used to assess the regulated expression of several genes in response to a growth factor. CONCLUSION: Overall, qPCR data analysis methods differ significantly in their performance, and this analysis identifies methods that provide DNA quantification estimates of high precision, robustness and reliability. These methods allow reliable estimations of relative expression ratio of two-fold or higher, and our analysis provides an estimation of the number of biological samples that have to be analyzed to achieve a given precision.

DnaSP v5: A software for comprehensive analysis of DNA polymorphism data

DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.

Threading libraries performance when applied to image acquisition and processing in a forensic application

Peer-reviewed

Milk yield and reproductive performance of dairy heifers and cows supplemented with polyunsaturated fatty acids

The objective of this work was to determine productive and fertility responses of Holstein-Friesian heifers and cows to supplementation with extruded linseed and soybean as sources of polyunsaturated fatty acids (PUFAs). Supplementation had a positive effect on profitability, with significant increases in milk yield in supplemented cows, but not in heifers. Treatments had no effect on milk fat content, but higher milk protein contents were observed with supplementation. A higher conception rate was found for supplemented heifers, but not for cows. Fat sources containing PUFAs are recommended for dairy cattle supplementation, since they improve fertility in heifers and milk yield in cows.

Conception rate of artificially inseminated Holstein cows affected by cloudy vaginal mucus, under intense heat conditions

The objective of this work was to obtain prevalence estimates of cloudy vaginal mucus in artificially inseminated Holstein cows raised under intense heat, in order to assess the effect of meteorological conditions on its occurrence during estrus and to determine its effect on conception rate. In a first study, an association was established between the occurrence of cloudy vaginal mucus during estrus and the conception rate of inseminated cows (18,620 services), raised under intense heat (mean annual temperature of 22°C), at highly technified farms, in the arid region of northern Mexico. In a second study, data from these large dairy operations were used to assess the effect of meteorological conditions throughout the year on the occurrence of cloudy vaginal mucus during artificial insemination (76,899 estruses). The overall rate of estruses with cloudy vaginal mucus was 21.4% (16,470/76,899; 95% confidence interval = 21.1-21.7%). The conception rate of cows with clean vaginal mucus was higher than that of cows with abnormal mucus (30.6 vs. 22%). Prevalence of estruses with cloudy vaginal mucus was strongly dependent on high ambient temperature and markedly higher in May and June. Acceptable conception rates in high milk-yielding Holstein cows can only be obtained with cows showing clear and translucid mucus at artificial insemination.

High-performance payload data handling system for Gaia

Gaia is the most ambitious space astrometry mission currently envisaged and is a technological challenge in all its aspects. We describe a proposal for the payload data handling system of Gaia, as an example of a high-performance, real-time, concurrent, and pipelined data system. This proposal includes the front-end systems for the instrumentation, the data acquisition and management modules, the star data processing modules, and the payload data handling unit. We also review other payload and service module elements and we illustrate a data flux proposal.

DnaSP Version 5. DNA Sequence Polymorphism

DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguadé (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.

Data-division-specific robustness and power of randomization tests for ABAB designs

This study deals with the statistical properties of a randomization test applied to an ABAB design in cases where the desirable random assignment of the points of change in phase is not possible. In order to obtain information about each possible data division we carried out a conditional Monte Carlo simulation with 100,000 samples for each systematically chosen triplet. Robustness and power are studied under several experimental conditions: different autocorrelation levels and different effect sizes, as well as different phase lengths determined by the points of change. Type I error rates were distorted by the presence of autocorrelation for the majority of data divisions. Satisfactory Type II error rates were obtained only for large treatment effects. The relationship between the lengths of the four phases appeared to be an important factor for the robustness and the power of the randomization test.

A Computer program for estimating population size by the removal method

A BASIC computer program (REMOVAL) was developed to compute in a VAXNMS environment all the calculations of the removal method for population size estimation (catch-effort method for closed populations with constant sampling effort). The program follows the maximum likelihood methodology,checks the failure conditions, applies the appropriate formula, and displays the estimates of population size and catchability, with their standard deviations and coefficients of variation, and two goodness-of-fit statistics with their significance levels. Data of removal experiments for the cyprinodontid fish Aphanius iberus in the Alt Emporda wetlands are used to exemplify the use of the program

Prediction of free-stall occupancy rate in dairycattle barns through fuzzy sets

The goal of this study was to develop a fuzzy model to predict the occupancy rate of free-stalls facilities of dairy cattle, aiding to optimize the design of projects. The following input variables were defined for the development of the fuzzy system: dry bulb temperature (Tdb, °C), wet bulb temperature (Twb, °C) and black globe temperature (Tbg, °C). Based on the input variables, the fuzzy system predicts the occupancy rate (OR, %) of dairy cattle in free-stall barns. For the model validation, data collecting were conducted on the facilities of the Intensive System of Milk Production (SIPL), in the Dairy Cattle National Research Center (CNPGL) of Embrapa. The OR values, estimated by the fuzzy system, presented values of average standard deviation of 3.93%, indicating low rate of errors in the simulation. Simulated and measured results were statistically equal (P>0.05, t Test). After validating the proposed model, the average percentage of correct answers for the simulated data was 89.7%. Therefore, the fuzzy system developed for the occupancy rate prediction of free-stalls facilities for dairy cattle allowed a realistic prediction of stalls occupancy rate, allowing the planning and design of free-stall barns.

Fireweed (Senecio madagascariensis) poisoning in cattle

In a dairy cattle herd in southern Brazil, 7 out of 554 cattle were affected and died due to Senecio madagascariensis poisoning. Clinical, pathological, and epidemiological findings in the affected cattle were indistinguishable from those usually seen in poisoning caused by other Senecio species. The plant invaded extensive areas in heavily stocked paddocks. Senecio madagascariensis had been spreading in this farm for the last three years, with no control strategy, because neither the farmers nor the local veterinarian knew about the potential risks of this Sernecio species.

Metabolic evaluation of dairy cows submitted to three different strategies to decrease the effects of negative energy balance in early postpartum

In early lactation dairy cattle suffer metabolic alterations caused by negative energy balance, which predisposes to fatty liver and ketosis. The aim of this study was to evaluate the metabolic condition of high yielding dairy cows subjected to three treatments for preventing severe lipomobilization and ketosis in early lactation. Fifty four multiparous Holstein cows yielding >30 L/day were divided into four groups: control (CN= no treatment), glucose precursor (PG= propylene-glycol), hepatic protector (Mp= Mercepton®), and energy supplement with salts of linolenic and linoleic faty acids (Mg-E= Megalac-E®). Treatments were administrated randomly at moment of calving until 8 weeks postpartum. Blood samples were collected on days 1, 7, 14, 21, 28, 35, 42 and 49 postpartum. Body condition score (BCS) was evaluated at the same periods and milk yield was recorded at 2nd, 4th, 5th, 6th, 7th, and 8th weeks of lactation. Concentrations of non-esterified fatty acids (NEFA), albumin, AST, ß-hydroxybutyrate (BHBA), cholesterol, glucose, total protein, urea and triglycerides were analyzed in blood samples. Cut-off points for subclinical ketosis were defined when BHBA >1.4 mmol/L and NEFA >0.7 mmol/L. General occurrence of subclinical ketosis was 24% during the period. An ascendant curve of cholesterol and glucose was observed from the 1st to the 8th week of lactation, while any tendency was observed with BHBA and NEFA, although differences among treatments were detected (p<0.05). BCS decreased from a mean of 3.85 at 1st week to 2.53 at 8th week of lactation (p=0.001). Milk yield was higher in the Mg-E group compared with the other treatment groups (p<0.05) Compared with the CN group, the treatments with Mp and PG did not show significant differences in blood biochemistry and milk yield. Cows receiving PG and Mg-E showed higher values of BHBA and NEFA (P<0.05), indicating accentuated lipomobilization. Supplementation with Mg-E also resulted in significant higher concentrations of cholesterol, BHBA, urea, AST and lower values of glycemia. This performance may be explained by the highest milk yield observed with this treatment. Treatments with PG and Mp did not improve milk yield, compared with control cows, but did not show metabolic evidence of ketosis, fat mobilization or fatty liver. These results suggest that treatment with Mg-E improves milk production but induces a higher negative energy balance leading to moderated lipomobilization and ketone bodies production, increasing the risk of fatty liver.

Molecular epidemiology and extended-spectrum β-lactamases production of Klebsiella pneumoniae isolated from three dairy herds

The objectives of this study were to isolate Klebsiella pneumoniae from different sources in three dairy cattle herds, to use the pulsed-field gel electrophoresis (PFGE) to measure genotypic similarities between isolates within a dairy herd, to verify the production of extended-spectrum β-lactamases (ESBLs) by the double-disk synergy test (DDST), and to use the PCR to detect the main ESBLs subgroups genes. Three dairy farms were selected based on previous mastitis outbreaks caused by K. pneumoniae. Milk samples were collected from lactating cows and from the bulk tank. Swabs were performed in different locations, including milking parlors, waiting room, soil, animal's hind limbs and rectum. K. pneumoniae was isolated from 27 cases of intramammary infections (IMI) and from 41 swabs. For farm A isolates from IMI and bulk tank were considered of the same PGFE subtype. One isolate from a bulk tank, three from IMI cases and four from environmental samples were positive in the DDST test. All eight DDST positive isolates harbored the bla shv gene, one harbored the bla tem gene, and three harbored the bla ctx-m gene, including the bulk tank isolate. Our study confirms that ESBL producing bacteria is present in different locations in dairy farms, and may be responsible for IMI. The detection of ESBLs on dairy herds could be a major concern for both public and animal health.

Developing sustainable research data management services: an institutional collaboration

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014