Copyright (c) 2009 University of Nebraska - Lincoln All rights reserved. http://digitalcommons.unl.edu/animalscifacpub Recent documents in Faculty Papers and Publications in Animal Science en-us Fri, 25 Sep 2009 23:49:17 PDT 3600 http://digitalcommons.unl.edu/animalscifacpub/616 http://digitalcommons.unl.edu/animalscifacpub/616 Thu, 24 Sep 2009 13:23:59 PDT Background: Obesity is a particularly complex disease that at least partially involves genetic and environmental perturbations to gene-networks connecting the hypothalamus and several metabolic tissues, resulting in an energy imbalance at the systems level. Results: To provide an inter-tissue view of obesity with respect to molecular states that are associated with physiological states, we developed a framework for constructing tissue-to-tissue coexpression networks between genes in the hypothalamus, liver or adipose tissue. These networks have a scale-free architecture and are strikingly independent of gene-gene coexpression networks that are constructed from more standard analyses of single tissues. This is the first systematic effort to study inter-tissue relationships and highlights genes in the hypothalamus that act as information relays in the control of peripheral tissues in obese mice. The subnetworks identified as specific to tissue-to-tissue interactions are enriched in genes that have obesity-relevant biological functions such as circadian rhythm, energy balance, stress response, or immune response. Conclusions: Tissue-to-tissue networks enable the identification of disease-specific genes that respond to changes induced by different tissues and they also provide unique details regarding candidate genes for obesity that are identified in genome-wide association studies. Identifying such genes from single tissue analyses would be difficult or impossible. Radu Dobrin http://digitalcommons.unl.edu/animalscifacpub/615 http://digitalcommons.unl.edu/animalscifacpub/615 Thu, 24 Sep 2009 13:09:37 PDT Figure S1 shows the connectivity distribution P(k) for GGC networks. Figure S2 shows FDR curves for each tissue in the analysis. Figure S3 shows modules in single tissue GGC networks as detected by the algorithm. Each cluster is marked by the yellow rectangles. Figure S4 shows single tissue module enrichment. Each panel has the following structure: top, P-values from FET for cis-eQTL blue bars over- and red bars under-enriched; middle, percentage overlap between module and genes with cis-eQTL; bottom, percentage overlap between each module and genes on each chromosome. The scale is between green and black where green represents 0% overlap and black 100% overlap. Figure S5 shows connectivity distribution for TTC networks. In each panel we show connectivity distribution for both types of genes in the TTC networks as follows: (a) blue for adipose, red for hypothalamus; (b) blue for hypothalamus, red for liver; (c) blue for adipose, red for liver. Figure S6 shows FDR curves for the TTC networks. Figure S7 shows a representation for the AH TTC network. Figure S8 shows a representation for the HL TTC Network. Figure S9 shows a representation for the AL TTC network. Figure S10 shows the number of network partition versus edge removal time. In black we show total number of subnetworks at each edge removal step; in blue we show number of 'open' subnetworks from where we can potentially remove edges. The number is obtained by subtracting from the total number of subnetworks in the partition the subnetworks defined as 'closed'. Figure S11 shows TTC network partitioning. For each of the TTC networks we have highlighted the subnetworks obtained through partitioning. Each color represents a subnetwork. The AH and HL networks are much more modular than the AL network. Figure S12 shows TTC network enrichment. Each panel has the following structure: top, P-values from FET for cis-eQTL over- (blue bars) and under-enriched (red bars); middle, percentage overlap between module and genes with cis-eQTLs; bottom, percentage overlap between each module and genes on each chromosome. The scale is between green and black where green represents 0% overlap and black 100% overlap. Figure S13 shows the TTC network backbones. Node color and symbols match the description from Figures 6, 7 and 8 in the main section of the paper. Each backbone contains the most robust links from the TTC network. Table T1 lists clinical trait descriptions. Table T2 lists microarray probe annotations. Table T3 lists the probes selected for single tissue analysis. Table T4 lists the adipose single tissue modules. Table T5 lists the hypothalamus single tissue modules. Table T6 lists the liver single tissue modules. Table T7 lists the AH TTC network. Table T8 lists the HL TTC network. Table T9 lists the AL TTC network. Table T10 lists the AH subnetworks. Table T11 lists the HL subnetworks. Table T12 lists the AL subnetworks. Table T13 provides the AH network backbone. Table T14 provides the HL network backbone. Table T15 provides the AL network backbone. Table T16 lists the adipose cis-eQTL genes. Table T17 lists the hypothalamus cis-eQTL genes. Table T18 lists the liver cis-eQTL genes. Radu Dobrin http://digitalcommons.unl.edu/animalscifacpub/614 http://digitalcommons.unl.edu/animalscifacpub/614 Thu, 24 Sep 2009 13:01:34 PDT The Cornell-Penn-Miner (CPM) Dairy is an applied mathematical nutrition model that computes dairy cattle requirements and the supply of energy and nutrients based on characteristics of the animal, the environment and the physicochemical composition of the feeds under diverse production scenarios. The CPM Dairy was designed as a steady-state model to use rates of degradation of feed carbohydrate and protein and the rate of passage to estimate the extent of ruminal fermentation, microbial growth, and intestinal digestibility of carbohydrate and protein fractions in computing energy and protein post-rumen absorption, and the supply of metabolizable energy and protein to the animal. The CPM Dairy version 3.0 (CPM Dairy 3.0) includes an expanded carbohydrate fractionation scheme to facilitate the characterization of individual feeds and a sub-model to predict ruminal metabolism and intestinal absorption of long chain fatty acids. The CPM Dairy includes a non-linear optimization algorithm that allows for least-cost formulation of diets while meeting animal performance, feed availability and environmental restrictions of modern dairy cattle production. When the CPM Dairy 3.0 was evaluated with data of 228 individual lactating dairy cows containing appropriate information including observed dry matter intake, the linear regression between observed and model-predicted milk production values indicated the model was able to account for 79.8% of the variation. The concordance correlation coefficient (CCC) was high (rc=0.89) without a significant mean bias (0.52 kg/d; P=0.12). The accuracy estimated by the CCC was 0.997. The root of mean square error of prediction (MSEP) was 5.14 kg/d (0.16 of the observed mean) and 87.3% of the MSEP was due to random errors, suggesting little systematic bias in predicting milk production of high-producing dairy cattle. Based upon these evaluations, it was concluded the CPM Dairy 3.0 model adequately predicts milk production at the farm level when appropriate animal characterization, feed composition and feed intake are provided; however, further improvements are needed to account for individual animal variation. L. O, Tedeschi http://digitalcommons.unl.edu/animalscifacpub/613 http://digitalcommons.unl.edu/animalscifacpub/613 Tue, 28 Jul 2009 12:33:10 PDT The ability to predict the effects of extreme climatic variables on livestock is important in terms of welfare and performance. An index combining temperature and humidity (THI) has been used for more than 4 decades to assess heat stress in cattle. However, the THI does not include important climatic variables such as solar load and wind speed (WS, m/s). Likewise, it does not include management factors (the effect of shade) or animal factors (genotype differences). Over 8 summers, a total of 11,669 Bos taurus steers, 2,344 B. taurus crossbred steers, 2,142 B. taurus × Bos indicus steers, and 1,595 B. indicus steers were used to develop and test a heat load index (HLI) for feedlot cattle. A new HLI incorporating black globe (BG) temperature (°C), relative humidity (RH, decimal form), and WS was initially developed by using the panting score (PS) of 2,490 Angus steers. The HLI consists of 2 parts based on a BG temperature threshold of 25°C: HLIBG>25 = 8.62 + (0.38 × RH) + (1.55 × BG) − (0.5 × WS) + e(2.4−WS), and HLIBG<25 = 10.66 + (0.28 × RH) + (1.3 × BG) − WS, where e is the base of the natural logarithm. A threshold HLI above which cattle of different genotypes gain body heat was developed for 7 genotypes. The threshold for unshaded black B. taurus steers was 86, and for unshaded B. indicus (100%) the threshold was 96. Threshold adjustments were developed for factors such as coat color, health status, access to shade, drinking water temperature, and manure management. Upward and downward adjustments are possible; upward adjustments occur when cattle have access to shade (+3 to +7) and downward adjustments occur when cattle are showing clinical signs of disease (−5). A related measure, the accumulated heat load (AHL) model, also was developed after the development of the HLI. The AHL is a measure of the animal's heat load balance and is determined by the duration of exposure above the threshold HLI. The THI and THI-hours (hours above a THI threshold) were compared with the HLI and AHL. The relationships between tympanic temperature and the average HLI and THI for the previous 24 h were R2 = 0.67, P < 0.001, and R2 = 0.26, P < 0.001, respectively. The R2 for the relationships between HLI or AHL and PS were positive (0.93 and 0.92 for HLI and AHL, respectively, P < 0.001). The R2 for the relationship between THI and PS was 0.61 (P < 0.001), and for THI-hours was 0.37 (P < 0.001). The HLI and the AHL were successful in predicting PS responses of different cattle genotypes during periods of high heat load. J. B. Gaughan http://digitalcommons.unl.edu/animalscifacpub/612 http://digitalcommons.unl.edu/animalscifacpub/612 Tue, 28 Jul 2009 12:32:50 PDT Three studies were conducted to evaluate the effects of supplemental fat and salt (sodium chloride) on DMI, daily water intake (DWI), body temperature, and respiration rate (RR) in Bos Taurus beef cattle. In Exp. 1 and 2, whole soybeans (SB) were used as the supplemental fat source. In Exp. 3, palm kernel meal and tallow were used. Experiment 1 (winter) and Exp. 2 (summer) were undertaken in an outside feedlot. Experiment 3 was conducted in a climate-controlled facility (mean ambient temperature = 29.9°C). In Exp. 1, three diets, 1) control; 2) salt (control + 1% sodium chloride); and 3) salt-SB (control + 5% SB + 1% sodium chloride), were fed to 144 cattle (BW = 327.7 kg), using a replicated 3 × 3 Latin square design. In Exp. 2, 168 steers (BW = 334.1 kg) were used. In Exp. 2, the same dietary treatments were used as in Exp. 1, and a 5% SB dietary treatment was included in an incomplete 3 × 4 Latin square design. In Exp. 3, three diets, 1) control; 2) salt (control + 0.92% NaCl); and 3) salt-fat (control + 3.2% added fat + 0.92% NaCl) were fed to 12 steers (BW = 602 kg) in a replicated Latin square design. In Exp. 1, cattle fed the salt-SB diet had elevated (P < 0.05) tympanic temperature (TT; 38.83°C) compared with cattle fed the control (38.56°C) or salt (38.50°C) diet. In Exp. 2, cattle fed the salt and salt-SB diets had less (P < 0.05) DMI and greater (P < 0.05) DWI than cattle in the control and SB treatments. Cattle fed the salt-SB diet had the greatest (P < 0.05) TT (38.89°C). Those fed only the salt diet or only the SB diet had the least (P < 0.05) TT, at 38.72 and 38.78°C, respectively. Under hot conditions (Exp. 3), DMI of steers fed the salt and salt-fat diets declined by approximately 40% compared with only 24% for the control cattle. During hot conditions, DWI was greatest (P < 0.05) for steers on the salt-fat diet. These steers also had the greatest (P < 0.05) mean rectal temperature (40.03 ± 0.1°C) and RR (112.7 ± 1.7 breaths/min). The RR of steers on the control diet was the least (P < 0.05; 98.3 ± 1.7 breaths/min). Although added salt plus fat decreased DMI under hot conditions, these data suggest that switching to diets containing the combination of added salt and fat can elevate body temperature, which would be a detriment in the summer but a benefit to the animal during winter. Nevertheless, adding salt plus fat to diets resulted in increased DWI under hot conditions. Diet ingredients or the combination of ingredients that can be used to regulate DMI may be useful to limit large increases in DMI during adverse weather events. J. B. Gaughan http://digitalcommons.unl.edu/animalscifacpub/611 http://digitalcommons.unl.edu/animalscifacpub/611 Tue, 28 Jul 2009 12:32:45 PDT To assess the efficacy of growth-promoting agents among seasons, triiodothyronine (T3), thyroxine (T4), plasma urea nitrogen (PUN), IGF-I, and tympanic temperature (TT) were measured in summer and winter studies. Heifers (n = 9/pen) were allotted to 12 pens in both December and June. Pens were assigned to 1 of 6 growth promotant treatments: control (no growth promotant), estrogenic implant (E), trenbolone acetate implant (TBA), E + TBA (ET), melengestrol acetate (MGA), and ET + MGA (ETM). Blood samples were collected from 4 heifers per pen per study on d 0, 28, 56, and 84 via jugular puncture. Near the midpoint of both studies, TT were obtained from the heifers. There was a season by sample day interaction for all blood metabolites (P < 0.05). During the winter, IGF-I levels peaked on d 28, whereas T3, T4, and PUN peaked on d 56. In the summer, IGF-I levels increased from d 0 to 28 and remained elevated throughout the study. Season by growth promotant interactions (P < 0.05) indicated that in the winter ET increased T3, whereas TBA alone decreased both T3 and T4, compared with control, or ET, and ETM treatment groups. Across seasons, treatments ET and ETM increased (P < 0.05) IGFI and decreased (P < 0.05) PUN. However, E, TBA, and MGA alone had no effect on IGF-I or PUN concentrations. The maximum TT was greater (P < 0.01) in the summer than in the winter, whereas the minimum TT was lower (P < 0.01) in the summer. Mean TT did not differ among growth-promoting treatments. However, in the summer and over both seasons, the maximum TT was lower (P < 0.05) in E-, MGA-, and ETM-treated heifers. Although limited growth promotant by season interactions existed, changes in blood metabolite levels resulting from the use of growth promotants do not appear to influence seasonal changes in body temperature as measured by TT. Terry L. Mader http://digitalcommons.unl.edu/animalscifacpub/610 http://digitalcommons.unl.edu/animalscifacpub/610 Tue, 28 Jul 2009 12:21:12 PDT Heat stress in cattle results in millions of dollars in lost revenue each year due to production losses, and in extreme cases, death. Death losses are more likely to result from animals vulnerable to heat stress. A study was conducted to determine risk factors for heat stress in feedlot heifers. Over two consecutive summers, a total of 256 feedlot heifers (32/ breed/ year) of four breeds were observed. As a measure of stress, respiration rates and panting scores were taken twice daily (morning and afternoon) on a random sample of 10 heifers/ breed. Weights, condition scores, and temperament scores were taken on 28-day intervals during the experiment. Health history from birth to slaughter was available for every animal used in this study. It was found that at temperatures above 25 °C, dark-hided animals were 25% more stressed than light-colored; a history of respiratory pneumonia increased stress level by 10.5%; each level of fatness increased stress level by approximately 10%; and excitable animals had a 3.2% higher stress level than calm animals. Not only did the stress level increase with these risk factors, but average daily gain was reduced. The Charolais cattle gained significantly more than all other breeds of cattle tested. Calm cattle gained 5% more than excitable cattle. Finally, cattle treated for pneumonia gained approximately 8% slower than non-treated cattle. The results of this study have not only revealed heat stress risk factors of breed (color), condition score (fatness), temperament, and health history (treated or not treated for pneumonia), but have also shown the effectiveness of using respiration rate as an indicator of heat stress. Tami M. Brown-Brandl http://digitalcommons.unl.edu/animalscifacpub/609 http://digitalcommons.unl.edu/animalscifacpub/609 Tue, 28 Jul 2009 12:21:09 PDT Ten years of calving records were examined from Bos taurus crossbred cows (mean of 182 cows/ yr) to quantify the effects of environmental conditions during the breeding season on pregnancy rate. Estimated breeding dates were determined by subtracting 283 d from the calving date. Relationships were determined between the proportion of cows bred during the periods from the beginning of the breeding season until d 21, 42, and 60 of the breeding season and the corresponding environmental variables. Weather data were compiled from a weather station located approximately 20 km from the research site. Average daily temperature and relative humidity were used to calculate daily temperature-humidity index (THI). Daily averages for each environmental variable were averaged for each period. Minimum temperature (MNTP) and THI for the first 21 and 42 d of the breeding season were negatively associated (P < 0.001) with pregnancy rate. For the 0- to 21-d, 0- to 42-d, and 0- to 60-d breeding periods, respective r2 for average temperatures were 0.32, 0.37, and 0.11, whereas r2 for MNTP were 0.45, 0.40, and 0.10 and r2 for THI were 0.38, 0.41, and 0.11, respectively, for the same breeding periods. The negative associations of temperature and THI with pregnancy rate are most pronounced during the first 21 d of the breeding season, with a −3.79 and −2.06% change in pregnancy rate for each unit of change in MNTP and THI, respectively. A combination of environmental variables increased the R2 to 0.67. In this analysis, windspeed was found to be positively associated with pregnancy rate in all equations and increased the R2 in all breeding periods. Optimum MNTP for the 0- to 21-d, 0- to 42-d, and 0- to 60- d breeding periods was 12.6, 13.5, and 14.9°C, respectively. For the 0- to 60-d breeding period, optimum THI was 68.0, whereas the THI threshold, the calculated level at which cattle will adapt, was found to be 72.9. Reductions in pregnancy rate are likely when the average MNTP and THI equal or exceed 16.7°C and 72.9, respectively, and for Bos Taurus beef cows that are pasture bred during a 60-d spring-summer period. J. L. Amundson http://digitalcommons.unl.edu/animalscifacpub/608 http://digitalcommons.unl.edu/animalscifacpub/608 Tue, 28 Jul 2009 12:21:07 PDT Data from 3 summer feedlot studies were utilized to determine the environmental factors that influence heat stress in cattle and also to determine wind speed (WSPD; m∙s-1) and solar radiation (RAD; W∙m-2) adjustments to the temperature-humidity index (THI). Visual assessments of heat stress, based on panting scores (0 = no panting to 4 = severe panting), were collected from 1400 to 1700. Mean daily WSPD, black globe temperature at 1500, and minimums for nighttime WSPD, nighttime black globe THI, and daily relative humidity were found to have the greatest influence on panting score from 1400 to 1700 (R2 = 0.61). From hourly values for THI, WSPD, and RAD, panting score was determined to equal −7.563 + (0.121 × THI) − (0.241 × WSPD) + (0.00082 × RAD) (R2 = 0.49). Using the ratio of WSPD to THI and RAD to THI (−1.992 and 0.0068 for WSPD and RAD, respectively), adjustments to the THI were derived for WSPD and RAD. On the basis of these ratios and the average hourly data for 1400 to 1700, the THI, adjusted for WSPD and RAD, equals [4.51 + THI − (1.992 × WSPD) + (0.0068 × RAD)]. Four separate cattle studies, comparable in size, type of cat- tle, and number of observations to the 3 original studies, were utilized to evaluate the accuracy of the THI equation adjusted for WSPD and RAD, and the relationship between the adjusted THI and panting score. Mean panting score derived from individual observations of black-hided cattle in these 4 studies were 1.22, 0.94, 1.32, and 2.00 vs. the predicted panting scores of 1.15, 1.17, 1.30, and 1.96, respectively. Correlations between THI and panting score in these studies ranged from r = 0.47 to 0.87. Correlations between the adjusted THI and mean panting score ranged from r = 0.64 to 0.80. These adjustments would be most appropriate to use, within a day, to predict THI during the afternoon hours using hourly data or current conditions. In addition to afternoon conditions, nighttime conditions, including minimum WSPD, minimum black globe THI, and minimum THI, were also found to influence heat stress experienced by cattle. Although knowledge of THI alone is beneficial in determining the potential for heat stress, WSPD and RAD adjustments to the THI more accurately assess animal discomfort. Terry L. Mader http://digitalcommons.unl.edu/animalscifacpub/607 http://digitalcommons.unl.edu/animalscifacpub/607 Tue, 07 Jul 2009 09:27:35 PDT A feedlot (Exp. 1) experiment was conducted to evaluate the effects of an essential oil mixture (EOM), experimental essential oil mixture (EXP), tylosin, and monensin (MON) on performance, carcass characteristics, and liver abscesses. A metabolism experiment (Exp. 2) was conducted to evaluate the effects of EOM, EXP, and MON on ruminal fermentation and digestibility in finishing steers. In Exp. 1, 468 yearling steers (398 ± 34 kg initial BW) were used in 50 pens (10 pens/treatment) and received their respective dietary treatments for 115 d. Five dietary treatments were compared in Exp. 1: 1) control, no additives (CON); 2) EOM, 1.0 g/steer daily; 3) EXP, 1.0 g/steer daily; 4) EOM, 1.0 g/steer daily plus tylosin, 90 mg/ steer daily (EOM+T); and 5) monensin, 300 mg/steer daily plus tylosin, 90 mg/steer daily (MON+T). Compared with CON, steers fed MON+T had decreased DMI (P < 0.01), and steers fed EOM+T and MON+T had improved G:F (P ≤ 0.02). Average daily gain was not different among treatments (P > 0.58). There was a trend (P = 0.09) for a treatment effect on 12th-rib fat thickness, which resulted in a significant increase in calculated yield grade for the EOM+T treatment. No other carcass characteristics were affected by treatment (P ≥ 0.10). Prevalence of total liver abscesses was reduced for steers fed tylosin compared with no tylosin (P < 0.05). In Exp. 2, 8 ruminally fistulated steers (399 ± 49 kg initial BW) were assigned randomly to 1 of 4 treatments in a replicated 4 × 4 Latin square designed experiment. Treatments were 1) CON, 2) EOM, 3) EXP, and 4) MON with feeding rates similar to Exp. 1. There were no differences in DMI, OM intake, and apparent total tract DM or OM digestibilities among treatments (P > 0.30). Feed intake patterns were similar among feed additive treatments (P > 0.13). Total VFA (P = 0.10) and acetate (P = 0.06) concentrations tended to be affected by treatment with EOM numerically greater than CON. Average ruminal pH ranged from 5.59 to 5.72 and did not differ among treatments. Addition of a EOM or monensin to a diet containing tylosin improves G:F, but little difference was observed in metabolism or digestibility. N. F. Meyer