bluuebunny/crossref_metadata_2025 huggingface dataset:
168 American mink Genome Sequencing Project
Authors: Miar Younes
Published: September 2024

The long-term goal of American Mink (Neogale vison) Genome Sequencing Project is to develop novel genomics tools to study the genome biology and evolution of mink. This research agenda is organized around three major goals: 1) development of first chromosome-level genome assembly with high quality for American mink to help understanding the biology and evolution of the order Carnivora, 2) designing the first mink single nucleotide polymorphism (SNP) genotyping array for genomic discovery in mink, and 3) using genomics to understand the genetic architecture of economically important traits in mink. An initial draft of the genome assembly is generated using 2,884,047 PacBio long reads. Integration of Hi-C data into the initial draft led to an assembly with 183 scaffolds and scaffold N50 of 220 Mb. This gap-free genome assembly of American mink (ASM_NN_V1) has a length of 2.68 Gb in which about 98.6% of the whole genome is covered by 15 chromosomes. Significant improvements are observed in genome contiguity, the number of scaffolds, and annotation compared with the first draft of mink genome assembly. A custom genotyping array is developed using the developed mink reference genome and DNA panel composed of 100 whole-genome sequences data of American mink from five color-types. This Affymetrix Mink 70K SNP array created 70,000 SNPs, which is sufficient for conducting genomic studies in the mink research program and beyond. This project would facilitate the discovery of genomic regions, markers and genetic networks underlying economically important traits in American mink, which will contribute novel insights into the genetic architecture of key traits and is a critical step to implement genomic selection in mink breeding programs. The results of this research have the potential to impact the mink industry, especially in North America, and improve the overall performance of the mink industry.
161 Development, deployment, and calibration of genomic selection tools to improve performance traits for Canadian beef cattle
Authors: Li Changxi , Basarab John A , Valente Tiago , Plastow Graham , Stothard Paul , Wang Yining , Vinsky Michael
Published: September 2024

Genomic selection has the potential to accelerate the genetic improvement rate for difficult/expensive to measure traits such as feed efficiency and fertility traits in beef cattle. To develop genomic selection tools for Canadian beef cattle, we collected or sourced phenotypic data of feed efficiency along with other traits including carcass merit, female feed intake and fertility related traits, and their genotypes from both research and commercial herds. The phenotypic data were consolidated and recorded for contemporary groups, leading to the development of data sets including 11,292 beef cattle with residual feed intake, dry matter intake, average daily gain, metabolic body weight, 7,299 to 8,081 cattle with carcass merit traits, and 1,802 to 2,792 cows with feed intake and fertility traits after quality controls. Genotype data of the animals from various single nucleotide polymorphisms (SNP) panels were merged to the same allele format of 50K, and then imputed to 770K SNPs, and eventually to whole genome sequence variants. The refined Canadian beef cattle data sets have not only allowed us to investigate genetic architectures of the beef performance traits but also enabled the development of genomic selection tools including molecular breeding values and multiple trait selection indexes with a moderate to moderately high accuracy for the traits through a cross-validation of within reference data set. The genomic selection tools have been successfully deployed to over 10,415 breeding candidates submitted by Canadian beef producers through multiple demonstration projects. The average accuracy of the molecular breeding values and multiple trait selection index of the commercial beef cattle ranged from 0.38 to 0.49 for feed efficiency and carcass merit traits, and from 0.26 to 0.38 for female feed intake and fertility traits. Current research is focusing on calibrating the genomic selection tools with larger data sets and with more advanced genomic prediction methods.
434 Strategies for improving the efficiency of rumen function
Authors: Gruninger Robert J , O’Hara Eóin , Terry Stephanie A , Payne Nikita A , Dubois Megan M , McAllister Tim A , Ribeiro Jr Gabriel O
Published: September 2024

Ruminants are unique amongst livestock, having the ability to convert low cost and low-quality feedstuffs that cannot be consumed by humans, or non-ruminant animals, into high quality protein. Unfortunately, the low digestibility of these feeds also promotes reduced intake and performance, which limits their inclusion in ruminant diets. Variation in the ability of cattle to digest feed has also been considered one of the main factors affecting feed efficiency. In an extensive grazing system, greater feed intake and digestibility of forages are directly related to the performance of cattle fed. Development of technologies to enhance feed intake and digestibility of forage-based diets within the rumen is essential to increase their utilization in ruminant diets. Data will be presented from past, and current, efforts to understand inter-animal variability in feed digestibility, the linkages between the rumen microbiome and feed digestion efficiency, and to develop enzymes, and chemical pretreatment technologies that will enhance the digestion of lignocellulose in the rumen.
218 Comparison between vegetation indices to estimate biomass in cereal rye
Authors: Fernandes Pedro Henrique Jota , Xiong Yijie , Davies-Jenkins Shelby L , Zhao Biquan , Drewnoski Mary E
Published: September 2024

Accurate forage mass estimation can lead to improved pasture management, but it requires a significant investment of time on the ground sampling. The use of satellite images has potential to reduce the time needed and thus, expediting decision-making processes. Satellite measure various spectral wavelengths of light reflected by plants (i.e., reflectance), and using satellite images, various vegetation indices (VI) can be calculated, such as the Normalized Difference Vegetation Index (NDVI), the Enhanced Vegetation Index (EVI), the Green Normalized Difference Vegetation Index (GNDVI), and the Spectral Feature Depth Vegetation Index (SFDVI). Each of these indices shows different vegetation properties via mathematical combinations of reflectance in two or more spectral wavelengths. For example, NDVI is calculated by reflectance in red and near infrared wavelengths, which is an effective VI to quantify vegetation greenness and vigor. This study aimed to compare the mentioned VI to evaluate their ability in estimating cereal rye (Secala cereale) mass and to compare them with a traditional method of biomass measurement, which relies on the standing height of the forage. From May 2 to 23, 2023, forage mass was measured in 18 paddocks (1.6 ha/paddock). Mass in the paddock was estimated by clipping four randomly located frames (0.49 m2) to ground level. The standing height of the forage was collected from 20 random points, measured in 0.625 cm increments, within each paddock. The forage mass of the paddocks measured from the clipped forage ranged from 212 to 3,382 kg/ha. PlanetScope satellite images from the day of forage mass sampling were obtained using the Planet Explorer platform. This satellite data was chosen due to its high spatial resolution (3 x 3 m2/pixel) and highly available data (theoretically daily). The four VI were calculated from images in QGIS software. A linear regression of each index against the forage mass estimated from the average of the clipped forage, was conducted in SAS using PROC REG. There was a significant (P < 0.01) correlation between each VI with the forage mass. The adjusted R2 was 0.60, 0.58, 0.41, 0.78 and 0.76 for NDVI, EVI, GNDVI, SFDVI and standing height, respectively. The root mean square error (RMSE) was 518, 528, 629, 379, and 396 for NDVI, EVI, GNDVI, SFDVI, and standing height, respectively. All VI exhibited moderately promising results in cereal rye mass estimation. In particular, SFDVI proved to be superior with the greatest adjusted R² and least RMSE, followed by the traditional method of estimating forage mass by standing height. This comparable result between the use of SFDVI from satellite images and traditional ground measurement indicates that the use of VI, SFDVI, specifically in our study, from satellite images can be an effective means for a fast cereal rye mass estimation.
221 Multivariate statistics as a quick tool to screen perennial forages for forage value
Authors: Azuhnwi Blasius N , Omokanye Akim
Published: September 2024

Perennial forages seeded as straight grasses and legumes or in mixtures make a valuable contribution as feed for the beef cattle industry in Alberta. With new varieties constantly being released, there is need to quickly screen these for their forage value. Principal component analysis (PCA) is a multivariate analysis which can simplify a large dataset by identifying and representing patterns in fewer dimensions or factors. In total, 23 and 20 perennial straight grass and legume varieties respectively, and 15 commercial mixes were seeded as a complete randomized block design on small plots with 4 replicates on May 31, 2021 at Debolt, Alberta. Plots were harvested on July 12 and September 15, 2022 as first and second cut, respectively. The harvested biomass was weighed, and a sub-sample was air-dried to determine forage dry matter (DM). Dried forage samples were submitted for various forage quality analyses. A PCA was conducted on the correlation matrix of the data set of forage DM yield and quality. The Kaiser-Meyer-Olkin (KMO) measure and Bartlett’s test of sphericity verified the sampling adequacy (KMO = 0.71 and P > 0.001 respectively) for the analysis. The first three principal components (PC) had eigenvalues over Kaiser’s criterion of 1 and in combination explained 81 % of the variance (Table 1). Most of the legumes were greater in crude protein, yielded greater in forage DM, macro minerals (Ca, Mg and P) and micro minerals (Zn, Fe and Cu) compared with grasses and mixtures (Figure 1). Among the legumes, the following alfalfa varieties exhibited high forage value (i.e. combined both forage yield and quality): Peace Alfalfa, PV Ultima Alfalfa, Alfalfa Dalton, Algonquin, AC Yellow Head, Trueman Alfalfa. Noteworthy are the 3 non-alfalfa species (birdsfoot trefoil, sainfoin and cicer milkvetch) which loaded on the opposite quadrant to most of the alfalfa varieties. The grass varieties were more dispersed on the multivariate space of the first two PC thus exhibiting the inherent variability in forage value of the grass collection. A few grass species nonetheless distinguished themselves in terms of greater forage yield and quality and include AC Saltlander, Richard Timothy, Rocky Mountain Fescue and Hybrid Bromegrass. Most of the grasses were high in fiber and loaded primarily opposite to the positive forage value attributes. The mixtures loaded similarly to the grasses with a couple loading close to the legumes but most close to the grasses, revealing their high fiber content. The mixtures which loaded close to the legumes were legume-dominated mixtures such as Alfalfa/Sainfoin Mix, All LegumeMix, HayMix and LegumeMaster Mix which had between 90 to 100% legumes. PCA proved to be a useful tool in distinguishing treatments with high forage value as these corresponded with widely used varieties in Alberta.

Tables and Figures 2.pdf
394 Cover crops for efficient grazing systems
Authors: Suazo Sofia A , Pereira Jose D , Mullenix Kim , Smith W Brandon , Dillard S Leanne L
Published: September 2024

Grazing of cool-season cover crops provides a sustainable solution for extending the grazing season while potentially reducing the environmental impact of conventional row-crop farming practices. The primary objective of this study was to evaluate how different mixtures of cover crops affect stocker performance when grazed. The study was conducted across 18 paddocks that were sown with grass [‘Coker’ oat (Avena sativa)], grass + legume [‘Dixie’ crimson clover (Trifolium incarnatum)], or grass + legume + brassica [‘Turnip’ brassica (Brassica rapa subsp.; rapa)] at the Wiregrass Research and Extension Center in Headland, AL. These paddocks were randomly assigned to either grazed or un-grazed conditions (n = 3). In this study, yearling beef steers with an average body weight (BW) of 266 ± 44 kg were grazed in paddocks using the put and take method to maintain a forage allowance of 1 kg dry matter per kilogram of BW. Forage samples were collected biweekly to analyze biomass, botanical composition, and forage nutritive value. Grazing occurred from January 17 to March 22, 2023 (65 d). Steer BW were recorded at the beginning and end of the grazing season to calculate average daily gain. The data were subjected to analysis as a two-way ANOVA using Glimmix in SAS 9.4 (SAS Institute, Cary, NC), harvest date was considered a repeated measure. No treatment × grazing interaction was observed on forage yield performance [average (AVG) forage yield kg DM/ha; P = 0.460]. In addition, no difference was observed among the different cover crop mixtures (AVG forage yield kg DM/ha; P = 0.670). Grazed paddocks had a greater crude protein when compared with ungrazed paddocks (Grazed vs. Ungrazed %; P = 0. 017). However, there was no effect of cover crop mixture on crude protein (CP) concentration (AVG CP %; P = 0.670 for treatment effect). These results indicate that cool-season annual cover crops can provide sufficient forage yield and quality to support sufficient animal gains, even during the relatively short grazing season. Incorporating cover crops not only improves agricultural sustainability but can also enhance the resilience and long-term health of the agroecosystem.
369 Unlocking the mysteries of cow and calf grazing behavior on rugged rangeland pastures using GPS and accelerometer sensor technology
Authors: Sprinkle Jim E , Sullivan Landon , Jensen Kevin S , Ellison Melinda J , Hall John B , Willmore Carmen M , Sagers Joseph , Yelich Joel V , Glaze James B , Brennan Jameson R , Lewis Ronald M , Taylor Joshua B , Murdoch Brenda M , Stegemiller Morgan R , Tolleson Douglas R , Clark Pat , Roberts-Lew Meghan , Lamb Jim
Published: September 2024

Studies were undertaken to assess low residual feed intake (RFI; efficient, EFF) and high RFI (inefficient, INE) cattle grazing behavior and performance on sagebrush steppe rangeland in Idaho. Global positioning system (GPS) and 3-axis accelerometers were used. As nonlactating 2-yr-old cattle grazed dormant forage, INE cattle lost more body weight (BW; P < 0.05) than EFF cattle. Subsequent research revealed that INE cattle tended (P = 0.07) to spend more time search-grazing than did EFF. Lactating cattle were evaluated during late spring and summer over 2 yr while grazing pastures with slopes approaching 60%, but mostly 5 to 25%. When temperatures were mild in late spring, INE cattle grazed 1.7 h/d more than EFF cattle (P < 0.05), starting earlier and grazing later into the morning. As summer temperatures increased, no differences in morning grazing occurred (P > 0.10), but INE cattle started grazing later in the afternoon (P < 0.05) than did EFF cattle. On days when cattle were in mild heat load (MHL), INE cows spent more time resting at lower elevations (P < 0.05). Inefficient cattle appeared to engage in more (P < 0.10) search-grazing than did EFF cattle. In a 4-d spring and summer forage intake study in 2016 with the same cows, no differences (P > 0.10) occurred for either forage intake or harvest rate. Treatment groups had similar (P > 0.10) milk production, BW and body condition. A genome-wide association study identified genetic markers associated with terrain use during MHL, but not RFI efficiency. In a 2021-2022 study evaluating 3- to 8-yr-old lactating EFF and INE cows and their calves, both INE cows and calves tended to rise earlier (P < 0.10) in the morning to start grazing when grazing flatter meadows in July 2022. This relationship did not hold true on steeper pastures, though INE cows tended (P = 0.08) to graze later into the morning. Daily activity was strongly correlated with MHL in July 2022. When the effects of MHL were removed by wind and cooler temperatures, INE cows walked 1.5 h/d more (P < 0.01) than EFF cows with their calves accompanying them. On days with increasing heat load, EFF cows tended to walk more (P < 0.10) than INE cows. On the day following the long travel day for INE cows, calves from INE cows remained a greater distance (P < 0.01) from their dams at lower elevations (- 290 m) than did calves from EFF cows (+ 0.1 m). Calves from EFF cows utilized more south facing slopes (P < 0.05) than did calves from INE cows in July of both years. The EFF cows and their calves appear to tolerate > MHL than do INE cows and calves.
368 Applying physics and math to describe chemistry and biology at the plant/animal interface
Authors: Tolleson Douglas R
Published: September 2024

Monitoring the diet consumed by grazing animals and relating that to health and performance is a task dating back to the origins of herding and pastoralism. Visual assessment of plants and animals by knowledgeable individuals has and will likely continue to be the most common manner of obtaining this information. It is part of the culture of livestock rearing and so even with the advent of modern analytical methods, adoption may be slow until the demographics of the industry change toward practitioners who have grown up with technology as part of their culture. Recent discussion within the rangeland profession has revolved around the art and science of grazing management, and thus grazing animal nutrition. These two skill sets are not mutually exclusive. I contend that art is the skilled application of science. With respect to the science, near infrared spectroscopy (NIRS) has been applied to determine the chemical content of feeds and forages. Fecal NIRS has been used to determine diet quality and composition in herbivores and results of this analysis can generate inputs to nutritional balance software that subsequently project animal performance. As described in the title, this presentation will involve a discussion of physics, math, chemistry, and biology. Regarding physics, the absorbance and reflection of near infrared energy by a population of chemical bonds ultimately described mathematically via multivariate statistics. Statistics that quantify the relationships between spectra and reference methods. Chemistry in this application quantifies constituents of interest in plant tissue consumed which are related to biology by way of intake, digestion, metabolism, and elimination of said grazed material. When projections of grazing animal performance are merged with landscape scale remotely sensed vegetation indices, the result is a powerful decision support system, provided by science, that facilitates the skill of the grazier; the artist if you will.
279 Estimating the impact of genomic selection for thermotolerance and in utero heat stress on piglet body weight from birth to bacon
Authors: Sullivan Caitlyn R , Brito Luiz F , Schinckel Allan P , Byrd MaryKate H , Hernandez Rick O , Diggs Shelby L , Maltecca Christian , Tiezzi Francesco , Johnson Jay S
Published: September 2024

The maternal response to heat stress (HS) has detrimental effects on swine offspring in the form of in utero heat stress (IUHS). Long-term effects of IUHS include reduced postnatal growth performance and lean muscle deposition. As such, developing mitigation strategies that reduce IUHS is essential to maximize economic return. Therefore, the study objective was to investigate whether genomic selection for HS tolerance (TOL) or HS sensitivity (SEN) would impact the postnatal growth of IUHS and in utero thermoneutral (IUTN) pigs from birth to market. We hypothesized that the IUHS pigs born to TOL dams would have improved growth relative to IUHS pigs born to SEN dams, but overall, IUHS pigs would have reduced growth compared with IUTN pigs. Pregnant gilts (n = 15 TOL and 13 SEN) were exposed to thermoneutral (TN; 17-20ºC; n = 7 TOL and 6 SEN) or heat stress (HS; cycling 26 to 36ºC; n = 8 TOL and 7 SEN) conditions from d 6 to 70 of gestation, and then all gilts were exposed to TN conditions until farrowing. Thirty-six offspring (barrows) were selected to represent each possible treatment combination: TOL+IUTN (n = 9), TOL+IUHS (n = 9), SEN+IUTN (n = 9), and SEN+IUHS (n = 9). Barrows were group-housed and fed a corn-soybean based diet that was provided with water ad libitum. Body weight (BW) of all barrows was measured at d 1, 21, 28, 35, 42, 49, 56, 84, 105, 126, 147, 168, and 189 of life to evaluate growth from birth (d 1) to market (d 189). Data were analyzed using the PROC GLIMMIX procedure of SAS with pig as the experimental unit and random effects being pen and litter. Body weights for each treatment group were fitted to a generalized Michaelis-Menten (GMM) function using the Nonlinear MIXED procedure of SAS with pig specific random effects for mature BW. On d 1, 126, and 168, IUHS pigs tended to have reduced BW (P < 0.10; 1.19 ± 0.07, 58.37 ± 4.94, 91.18 ± 7.26 kg, respectively) when compared with IUTN pigs (1.32 ± 0.07, 68.95 ± 4.94, 106.25 ± 7.26 kg, respectively). Overall, final BW was reduced (P = 0.04) for IUHS (111.08 ± 7.91 kg) versus IUTN (128.79 ± 7.91 kg) pigs, and estimated days to a market weight of 125 kg tended to be greater (P = 0.06) for IUHS (219.8 ± 10.8 d) versus IUTN (188.1 ± 10.21 d) barrows. The GMM model predicted that IUHS+TOL and IUTN+TOL barrows had different shaped BW growth curves with decreased age to achieve one-half of their predicted mature BW than IUHS+SEN and IUTN+SEN barrows. In conclusion, IUHS resulted in reduced growth rates overall; however, TOL improved some aspects of growth.
283 Investigating molecular changes in juvenile rainbow trout muscle hyperplasia and hypertrophy over time
Authors: Udoka Aliute Nkoyo S , Kronlein Niklas , Griggs Logan , Schrimsher Aubrey , Duckett Susan K
Published: September 2024

Farmed rainbow trout require specific cold, freshwater habitations to maximize overall growth for future release and general production. The growth and development of muscle tissue in rainbow trout are critical factors in understanding and maximizing the production and quality of farmed fish. Unlike mammals, rainbow trout can undergo muscle hyperplasia and hypertrophy throughout its lifetime, which only adds to its muscle growth potential as a species. This study aimed to investigate the growth patterns and gene expression changes in red, pink, and white muscle tissue over time in farmed rainbow trout. Twenty rainbow trout were harvested at 6 and 7 mo of age from the Walhalla State Hatchery (SC), and red, pink, and white muscle samples were collected in RNAlater for RNA extraction and downstream gene expression analysis. General growth pattern changes were assessed through measurements of wet body weight, wet length, empty carcass weight, and filet weight, while gene expression changes were examined using quantitative polymerase chain reaction (RT-qPCR). Genes such as PAX7A, PAX7B, MYOG, MYOD, IGF1, and IGF2B were investigated to illuminate dynamic changes in the muscle tissue of rainbow trout. These genes are associated with myogenic regulatory factors involved in muscle growth and development. Water and ambient temperature were captured to monitor potential temperature effects. Wet weight (g) and left filet weight (g) increased (P < 0.05) over the 30-d period. PAX7A, PAX7B, and MYOG were all downregulated (P < 0.05) in red and pink muscle in comparison to the previous 30 d. White muscle displayed no differences (P > 0.05) in expression of PAX7A, PAX7B, and MYOG. IGF1 gene expression in red, pink and white muscle were downregulated (P < 0.05) over the 30 d. MYOD had a very low expression in comparison with other target genes during these age points. These findings highlight the dynamic nature of muscle growth in rainbow trout and the importance of red and pink muscle dynamics. Understanding the molecular mechanisms underlying muscle growth and gene expression changes over time can inform strategies to optimize fish growth and meat quality in aquaculture systems. Further investigation is needed to elucidate the specific regulatory pathways involved in muscle development and their potential applications in fish farming.
282 Effects of granddam poor maternal nutrition during gestation on second generation offspring oxidative status in circulation and skeletal muscle
Authors: Reiter Amanda S , Kawaida Mia Y , Tillquist Nicole M , Govoni Kristen E , Zinn Steven A , Reed Sarah A
Published: September 2024

Poor maternal nutrition (under- or over-feeding) during gestation negatively impacts antioxidant activity and oxidative stress markers in first generation (F1) offspring. To determine if these alterations persist into subsequent generations, multiparous Dorset ewes (F0; n = 46) pregnant with twins were fed 100% (CON), 60% (RES), or 140% (OVER) of total nutrient requirements (NRC) from d 30 of gestation until parturition. At 16 to 19 mo of age, F1 ewes (n = 37) were maintained on a control diet and bred to generate second generation offspring (F2; CON-F2, RES-F2, OVER-F2 corresponding to F0 diet). At 112 and 224 d of age, plasma samples were collected from F2 offspring, and at d 284 semitendinosus (STN) samples were collected from rams at necropsy and muscle biopsies in ewes. Data were analyzed in SAS using PROC MIXED where significance was determined at P ≤ 0.05. Circulating superoxide dismutase (SOD) activity was decreased by 21% and 25% in RES-F2 and OVER-F2 offspring, respectively, compared with CON-F2 (P < 0.0001). Plasma SOD activity was 17% less at d 224 than d 112 (P < 0.0001). Ewes had 9% greater circulating SOD activity compared with rams (P = 0.03). Muscle SOD activity was 31% and 35% greater in CON-F2 compared with RES-F2 and OVER-F2 offspring, respectively (P ≤ 0.003). Rams had 26% greater STN SOD activity than ewes (P = 0.006). Plasma glutathione peroxidase (GPx) activity was 14% greater in CON-F2 than RES-F2 and OVER-F2 offspring (P ≤ 0.003). Circulating GPx activity was 14% less at d 224 than d 112 (P < 0.0001). Muscle GPx activity was 39% and 35% greater in CON-F2 offspring compared with RES-F2 and OVER-F2, respectively (P < 0.0001). Ewes had 11% and 16% greater GPx activity in circulation and STN, respectively, than rams (P ≤ 0.005). Plasma concentrations of malondialdehyde (MDA) were 18% and 10% greater in RES-F2 and OVER-F2 offspring, respectively, than CON-F2 (P = 0.004). Circulating MDA concentrations were 20% greater at d 224 compared with d 112 (P < 0.0001). Concentrations of MDA in STN were increased in RES-F2 and OVER-F2 offspring by 36% and 50%, respectively, compared with CON-F2 (P ≤ 0.006). Ewes had 87% greater concentrations of MDA in STN compared with rams (P < 0.0001). Circulating protein carbonyl (PC) concentrations were 16% greater in RES-F2 offspring than CON-F2 and OVER-F2 (P ≤ 0.04). Plasma PC concentrations were 9% greater at d 224 compared with d 112 (P = 0.04). The concentrations of PC in STN were 81% and 69% greater in RES-F2 and OVER-F2 rams, respectively, compared with CON-F2 rams (P ≤ 0.0001). Alterations in oxidative status persist into the F2 generation and may impact muscle growth and metabolism.
426 Effects of maternal nutritional restriction on beef cattle fetal metabolism
Authors: Odhiambo John F , Elder Kasey , Lemley Caleb O
Published: September 2024

Cellular respiration is the metabolic process that breaks down glucose by use of oxygen to produce ATP. It consists of three main steps: glycolysis, the TCA cycle and oxidative phosphorylation. Oxidative phosphorylation provides most of the ATP for body functions. If oxidative phosphorylation is downregulated, then cellular metabolism will be disrupted. The objective of this study was to identify the cellular pathways impacted by maternal nutrient restriction in beef cattle. A total of 36 fetuses were examined: 18 fetuses from dams that were given either a restricted (RES) or an adequate (ADQ) diet from d 160 to 240 of gestation. At d 240 of gestation, dams underwent Cesarean section for fetal removal, morphometrics, blood and tissue collection. Liver tissue samples were sequenced via Illumina platforms and analyzed by DESeq2, while the screening threshold was set at |log2(FoldChange)| >= 1 and padj <= 0.05. Enrichment analysis of the differential expressed genes (DEGs) was performed by annotating genes to biological processes (Gene Ontology terms) and metabolic pathways (KEGG pathways). Genes with an adjusted P-value ≤ 0.05 were assigned as differentially expressed. Morphometrics data was evaluated by mixed procedures of SAS and significant was declared at P < 0.10. There was a significant group effect of the fetal necropsy weights (25.5 ± 0.55 vs 23.0 ± 0.60, kg, for ADQ and RES respectively, P < 0.02). Further, there was a significant group effect on the fetal liver weights (485.20 ± 29.19 vs 394.90 ± 29.19 g, for ADQ and RES, respectively, P < 0.07). RES fetuses exhibited 704 uniquely expressed genes compared with ADQ fetuses that showed 304 uniquely expressed genes. However, 13,145 genes were co-expressed by RES and ADQ Fetuses. A total of 2,327 genes were identified as differentially regulated between the groups. Of these 1,106 genes were up-regulated and 1,221 are down-regulated in RES vs. ADQ fetuses. KEGG pathway enrichment analysis showed downregulation of key enzymes involved in oxidative phosphorylation specifically in complexes I, II, III and IV. Thus, downregulation of oxidative phosphorylation is a potential mechanism by which maternal restriction retards fetal growth and development as seen in this project. Funded by NIFA CBG # 2021-38821-34599.
170 Understanding how zinc and manganese interact with the hormones found in anabolic implants to alter growth of bovine satellite cells
Authors: Thornton-Kurth Kara J , Alberto Anthony F , Hansen Stephanie L
Published: September 2024

It has been well established in both in vitro and in vivo models that the hormones found in anabolic implants [estradiol (E2) and trenbolone acetate (TBA)] positively impact skeletal muscle growth. Previous research has demonstrated that treating primary bovine satellite cells (BSC) with E2 or TBA results in increases in proliferation and protein synthesis and decreases in protein degradation, leading to enhanced skeletal muscle growth. This improved skeletal muscle growth occurs through partially defined pathways, but many unknowns remain. More recently, research has emerged demonstrating that strategic supplementation of specific trace minerals (TM) may further augment the positive effects of E2 and TBA on skeletal muscle growth. There are many ways through which the complex signaling pathways induced by the hormones found in anabolic implants may interact with TM to further enhance skeletal muscle growth. Zinc (Zn) and manganese (Mn) are two of the TM that we have recently investigated. Zinc is the most utilized metal in biological processes and supports animal growth through critical roles in the functions of IGF-1, GH, and DNA synthesis. Manganese is an essential TM providing catalytic activity to enzymes involved in protein glycosylation, nitrogen metabolism, and antioxidant capacity. However, additional research is needed to determine if hormones and TM interact to impact growth of skeletal muscle, specifically. As such, the goal of recent research that has been conducted by our group is to utilize an in vitro primary BSC model to determine whether hormones and TM interact to alter differentiation and protein synthesis. Preliminary research from our group assesses the impacts of varying, physiological concentrations of Zn or Mn on differentiation and protein synthesis of primary BSC cultures that have also been treated with or without the hormones found in anabolic implants. These preliminary findings demonstrate that while there seems to be no interaction between Zn and hormones in differentiating BSC, supplemental Zn on the higher end of physiologically relevant concentrations has a positive effect on signaling pathways involved in growth, protein turnover, skeletal muscle differentiation, and mineral transporters. However, it appears that Zn and Mn each interact with hormones to positively augment protein synthesis in primary BSC cultures. A deeper understanding of the relationship these TM and others may have with hormones will allow for more strategic supplementation practices that can potentially improve skeletal muscle growth.
171 Examining the role of vitamin E in ruminant livestock growth and production
Authors: Reichhardt Caleb C
Published: September 2024

Vitamin E is necessary for health, growth, and reproduction in livestock. However, vitamin E requirements and supplement strategies for optimal livestock production and performance are poorly understood, and the role that it plays in skeletal muscle growth has not been thoroughly explored. Ideal vitamin E requirements for optimal skeletal muscle growth have yet to be identified in beef cattle or sheep. Because skeletal muscle growth is important for meat production in livestock, a more thorough understanding of postnatal skeletal muscle growth and the relationship with vitamin E is necessary. The goal of this presentation is to discuss what we currently understand about vitamin E and the relationship it has with skeletal muscle growth in ruminant livestock. This presentation will discuss previous research relating to vitamin E supplementation in beef cattle and sheep, and the resulting impacts on growth and production. Additionally, emerging research using both in vivo and in vitro methods to further explore the relationship between vitamin E and skeletal muscle growth and production of beef cattle and sheep will be presented.
57 In vitro degradation kinetics of protein and starch from equine feedstuffs (corn, beet pulp, oat hulls, soybean meal, whey, timothy, and alfalfa hay)
Authors: Cargo-Froom Cara L , Nosworthy Matthew , Darani Priska , Darani Sharifa , Cieslar Scott , Ellis Jennifer L
Published: September 2024

Meaningful progress can be made in the field of equine nutrition through improved feed characterization and the development of in vitro nutritional models to describe nutrient degradation. The objective of this study was to assess at which time point macronutrient degradation reached plateau when equine feedstuffs were digested using a static two-step enzymatic digest. Prior to addition of any enzymes, 10 g of each ingredient was weighed in triplicate into digestion vessels and hydrated with 50 mL water. To initiate gastric digestion, 60 mL of 0.1M hydrochloric acid-pepsin solution (pH 2) was added to the digestion vessels and incubated for 2 h at 39℃ under constant mixing. The liquid fractions of the digestions were sampled at 0, 5, 10, 20, 30 60, 90 and 120 min. Post-gastric digestion, samples were neutralized with 1 M sodium hydroxide and raised to a pH of 6.8. To initiate small intestinal digestion, 42 mL of a pancreatin-phosphate buffer (pH of 6.8) was added to the digestion vessels and incubated for 18 h at 39℃ under constant mixing. The liquid fractions of the digestions were sampled at 0, 5, 10, 20, 30 60, 90, 120, 150, 180 min and thereafter hourly up until the end of digestion (1,020 min). Liquid samples were analyzed for glucose via GOPOD kit to determine starch degradation and crude protein via combustion (LECO) and o-phthalaldehyde assay to determine protein degradation. A modified Chapmans-Richard (first order kinetics) model was fit to the time point data to determine the immediately soluble fraction, the degradable fraction, the degradation rate (Kd) of the degradable fraction, and the undegradable fraction (from the plateau point) of each ingredient. The rate and plateau were estimated for each ingredient by nonlinear regression procedures, that included a boundary of ≤ 100% for the plateaus (Table 1). Corn did not reach a plateau for glucose released; as such, the kinetic model could not be fit to the data points. The ingredients with the greatest and least rates of starch degradation were alfalfa hay (5.36 %/min) and oat hulls (0.11 %/min), respectively. The ingredients with the greatest and least rates of protein degradation were oat hulls (0.379 %/min) and whey (0.004 %/min), respectively. These preliminary results will be used to adjust the in vitro protocol used herein, as it is part of a larger project aiming to characterize the degradation of a wider collection of equine feedstuffs, with these degradation parameter profiles being used as inputs to a mechanistic digestion model. This combination of in vitro techniques and modelling will be advantageous in optimizing equine nutrition.
73 Awardee Talk: Recent updates in dark-cutting beef color research
Authors: Ramanathan Ranjith , Harr Keayla M , Kiyimba Frank , Pfeiffer Morgan , Mafi Gretchen G
Published: September 2024

Meat color is an important sensory property influencing purchasing decisions and the value of the product during grading. Any deviation from a bright red color, especially in beef, leads to economic losses. Dark-cutting beef is a color deviation in which beef fails to have a bright red color. The dark-cutting condition has a worldwide occurrence. The dark-cutting condition in the US results in $210 million annually. The current talk will focus on recent advances in basic and applied research in dark-cutting beef color. The proteomics and metabolomics research showed that glycolytic proteins and metabolites are less abundant in dark-cutting beef than normal-pH beef. Interestingly, dark-cutting beef has greater mitochondrial protein content than normal-pH beef. Although the mechanistic basis for increased mitochondrial content is unclear, we speculate that higher energy demand pre-slaughter contributes to increased mitochondrial biogenesis. This metabolic alteration plays a critical role in detriments of substrate metabolism in dark-cutting beef muscles, contributing to aberrant postmortem pH decline. In recent research, we compared metabolomic and lipidomic profiles using different shades of dark-cutting beef, such as mild, moderate, and severe, demonstrating that metabolite and lipid profiles vary significantly between normal and severe dark-cutting samples. However, there were not many differences between mild and moderate. Applied research to improve dark-cutting beef has utilized various post-harvest practices such as modified atmospheric packaging, enhancement, nitrite-embedded film, and high-pressure processing. The use of modified atmospheric packaging and antioxidant enhancement reversed the dark color of steaks. Recently, we have demonstrated that high-pressure processing (HPP) of strip loin steaks can reverse dark color when packaged in PVC overwrap. Dark-cutting steaks processed with 300 MPa (megapascal pressure) for 90 sec using chilled water (6 to 10 °C) immediately improved redness and had similar redness as USDA Choice steak on d 3 of retail storage. In addition, dark-cutters maintained a brighter red color than normal-pH USDA Choice during retail display (hence, less loss due to meat discoloration). The trained panelists also noticed no taste, flavor, or tenderness differences between USDA-Choice and dark-cutters applied with 300 MPa. The application of HPP allows aerobic overwrap polyvinyl chloride (PVC) packaging with no use of modified atmosphere packaging (MAP) trays. In summary, understanding the fundamental basis helps to elucidate the etiology of dark-cutting beef occurrence, while applied research helps to improve the value of dark-cutting beef.
80 Empowering informed choices: How computer vision can assist consumers in making decisions about meat quality
Authors: Menezes Guilherme , Junior Dante , Ferreira Rafael , Oliveira Dario , Araujo Julcimara , Duarte Marcio S , Dórea Joao R R
Published: September 2024

Consumer perception of meat quality is highly influenced by meat tenderness and juiciness. Artificial intelligence technology, such as computer vision systems (CVS), can be a powerful tool to predict such meat attributes in retail markets and help consumers make informed decisions. This study aimed to develop a CVS using smartphone images to classify beef steaks and pork chops tenderness (1), predicting shear-force (SF) and intramuscular fat (IMF) content (2), and performing a comparative evaluation between consumer assessments and the CVS (3). The dataset for beef steak consisted of 915 images (one image per steak), with 691 in the training set, 82 in the validation set, and 142 in the testing set. For pork, there were 514 images (one image per chop), distributed as 377 in the training set, 80 in the validation set, and 57 in the testing set. We trained deep neural networks (Xception), pretrained on the ImageNet dataset, for image classification and regression. The tenderness of the steaks was categorized based on Warner-Bratzler shear-force (N) as tender, intermediate, and tough. To achieve the third object, 1,000 pairwise comparisons were drawn from the 142 testing set images, where both consumers and the CVS performed predictions on tender and tough meat. The option with the least SF in each pair was identified as the most tender meat, with ground truth established using SF measurements. The same pairs were presented to meat consumers through a survey. For classifying beef as tender and tough, the algorithms demonstrated F1-scores of 68.1% and 70.8%, respectively. However, intermediate meat yielded worse results, with an F1-score of 36.4%. The dataset was subsequently re-categorized into two classes: tender and tough, with all intermediate steaks classified as tough, and resulted in an F1-score of 76.6% for tough meat. For classifying pork chops as tender and tough, the algorithms demonstrated F1-scores of 81.4% and 85.7%, respectively. The intermediate class in pork chops also exhibited worse results, with an F1-score of 24.0%. After re-categorizing the dataset into two classes, the F1-score for classifying pork chops as tough was 83.9%. The regression model predicted SF in beef steak and pork chops with R2 of 0.64 and 0.76, and RMSEP of 16.9 N and 9.15 N, respectively. The regression model, after analyzing with 1,000 pairwise comparisons, accurately predicted the tenderest steak with an accuracy of 76.5%. In contrast, human recognition of meat tenderness achieved an average accuracy of 46.7% for beef steak. To predict IMF in beef steaks and pork chops the model achieved R2 values of 0.61 and 0.54, and RMSEP of 2.6% and 1.22%, respectively. These findings suggest that CVS can provide a more objective method for evaluating meat tenderness and IMF before purchase, potentially enhancing consumer satisfaction.
79 Microbiological effects of control measures during pork production
Authors: Yang Xianqin , Wang Hui , Tran Frances , McAllister Tim A , Stanford Kim
Published: September 2024

The objective of this study was to determine the prevalence of Shiga toxin-producing Escherichia coli (STEC) O157:H7 and efficacy of control measures at a pork processing facility. Outbreaks of E. coli O157:H7 associated with pork, though not common globally, have been reported multiple times in recent years in Alberta. Sampling at a commercial facility processing hogs was carried out at monthly intervals for 11 mo. At the facility, the dressed carcasses are sprayed with 5% lactic acid (LA) and immediately air-chilled after the LA spray. At each sampling time, 14 different types of samples were collected: dirt from the holding pen floor (n = 2), gloves of workers (n = 5), scalding water (n = 1), tonsils (n = 5), cecal material (n = 5), five swabs each from hides of animals after bleeding (HAB), and carcasses after scalding (CAS), before evisceration (CBE), after evisceration (CAE), before LA spray (BLA), after LA spray (ALA), 1h after LA spray (ALA1), 2h after LA spray (ALA2), and after chilling (ACH). All samples were enumerated for total plate count (TPC), Enterobacteriaceae, and E. coli using specific media for each. In addition, an aliquot of each sample was enriched and tested for the presence of the O-antigen gene (rfbE) for E. coli O157 and Shiga toxin-producing gene (stx1/stx2) using real-time PCR. Cultures positive for both rfbE and stx were further plated for the isolation of E. coli O157:H7. Of the 683 enrichment cultures, 12 were positive for both marker genes, from cecal material (n = 2), dirt (n = 4) and HAB (n = 6). However, none of these samples yielded STEC O157 isolates. Of these enrichment cultures, 69, 45 and 32 were positive for stx1, stx2, and both stx genes, respectively. Positive samples were mostly associated with HAB, cecal material and dirt. HAB was most and least contaminated in August/June and December, differing by 1 log unit for TPC (P < 0.05). Enterobacteriaceae and E. coli on HAB were also affected by month of sampling (P < 0.05), but this temporal trend differed from TPC (Table). The numbers for TPC, Enterobacteriaceae, and E. coli all decreased (P < 0.05) as the stage of carcass processing progressed. The overall reduction of TPC and E. coli was 7 and 5 log units, respectively. Scalding, LA spray and air chilling all reduced (P < 0.05) the numbers of indicator bacteria on carcasses. Of the 55 samples each collected from BLA, ALA, ALA1, ALA2, and ACH, 36, 13, 2, 1 and 0 were positive for E. coli, respectively. In conclusion, pork processing environments can be contaminated with STEC from hides, feces and holding pen, but levels of STEC O157 appear to be low. Scalding, LA spray and air chilling can be effective measures to reduce the risk of bacterial contamination of pork.