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The dairy cow model 'Molly' is a mixed discrete event-continuous system model that simulates feeding, metabolism and lactation of dairy cows. Decades of model development have resulted in a valuable tool in dairy science. Due to the deprecation of the ACSL (Advanced Continuous Simulation Language) programming language, Molly has been translated into C++. This paper describes the translation process and discusses the advantages of the new implementation, one of which is the ability to run Molly within RStudio, a popular integrated development environment (IDE) for data science. [ABSTRACT FROM AUTHOR]

Making dairy farming more cost-effective and reducing nitrogen environmental pollution could be reached through a reduced input of dietary protein, provided productivity is not compromised. This could be achieved through balancing dairy rations for essential amino acids (EAA) rather than their aggregate, the metabolizable protein (MP). This review revisits the estimations of the major true protein secretions in dairy cows, milk protein yield (MPY), metabolic fecal protein (MFP), endogenous urinary loss and scurf and associated AA composition. The combined efficiency with which MP (Eff MP ) or EAA (Eff AA ) is used to support protein secretions is calculated as the sum of true protein secretions (MPY + MFP + scurf) divided by the net supply (adjusted to remove the endogenous urinary excretion: MP adj and AA adj ). Using the proposed protein and AA secretions, EffMP and EffAA were predicted through meta-analyses (807 treatment means) and validated using an independent database (129 treatment means). The effects of MPadj or AAadj, plus digestible energy intake (DEI), days in milk (DIM) and parity (primiparous v. multiparous), were significant in all models. Models using (MPadj, MPadj × MPadj, DEI and DEI × DEI) or (MPadj/DEI and MPadj/DEI × MPadj/DEI) had similar corrected Akaike's information criterion, but the model using MPadj/DEI performed better in the validation database. A model that also included this ratio was, therefore, used to fitting equations to predict EffAA. These equations predicted well EffAA in the validation database except for Arg which had a strong slope bias. Predictions of MPY from predicted EffMP based on MPadj/DEI, MPadj/DEI × MPadj/DEI, DIM and parity yielded a better fit than direct predictions of MPY based on MPadj, MPadj × MPadj, DEI, DIM and parity. Predictions of MPY based on each EffAA yielded fairly similar results among AA. It is proposed to ponder the mean of MPY predictions obtained from each EffAA by the lowest prediction to retain the potential limitation from AA with the shortest supply. Overall, the revisited estimations of endogenous urinary excretion and MFP, revised AA composition of protein secretions and inclusion of a variable combined EffAA (based on AAadj/DEI, AAadj/DEI × Aadj/DEI, DIM and parity) offer the potential to improve predictions of MPY, identify which AA are potentially in short supply and, therefore, improve the AA balance of dairy rations. [ABSTRACT FROM AUTHOR]

Two studies were undertaken to assess the effects of individual essential AA supplementation of a proteindeficient diet on lactational performance in mice using litter growth rates as a response variable. The first study was designed to establish a dietary protein response curve, and the second to determine the effects of Leu, Ile, Met, and Thr supplementation of a protein-deficient diet on lactational performance. In both studies, dams were fed test diets from parturition through d 17 of lactation, when the studies ended. Mammary tissue was collected on d 17 from mice on the second experiment and analyzed for mammalian target of rapamycin (mTOR) pathway signaling. Supplementation with Ile, Leu, or Met independently increased litter weight gain by 11, 9, and 10%, respectively, as compared with the protein-deficient diet. These responses were supported by independent phosphorylation responses for mTOR and eIF4E binding protein 1 (4eBP1). Supplementation of Ile, Leu, and Met increased phosphorylation of mTOR by 55, 34, and 47%, respectively, as compared with the protein-deficient diet. Phosphorylation of 4eBP1 increased in response to Ile and Met supplementation by 60 and 40%, respectively. Supplementation of Ile and Met increased phosphorylation of Akt/protein kinase B (Akt) by 41 and 59%, respectively. This work demonstrated that milk production responds nonlinearly to protein supply, and milk production and the mTOR pathway responded independently to supplementation of individual AA. The former demonstrates that a linear breakpoint model is an inappropriate description of the responses, and the latter demonstrates that no single factor limits AA for lactation. Incorporation of a multiple-limiting AA concept and nonlinear responses into milk protein response models will help improve milk yield predictions and allow derivation of diets that will increase postabsorptive N efficiency and reduce N excretion by lactating animals. [ABSTRACT FROM AUTHOR]

Lysine supply is potentially limiting for milk production in dairy cows. The availability of Lys to the mammary gland and other tissues is a function of the quantity of metabolizable Lys supplied and Lys catabolism by the liver. Likewise, Lys catabolism may be influenced by Lys supply. This study evaluated the effect of increased postruminal Lys supply on the expression of aminoadipate semialdehyde synthase (AASS, a committing step in Lys catabolism in the liver) and ornithine transcarbamoylase and argininosuccinate synthase (key urea cycle enzymes that are responsive to protein supply). Eight multiparous peak Holstein cows were used in a replicated 4 × 4 Latin square. Cows were fed a Lys-limiting ration and infused postruminally with 0, 9, 27, or 63 g/d of Lys. The study consisted of 10 d of pretreatment followed by 10 d of Lys infusion. On the last day of each period, liver and milk samples were collected for mRNA analysis, and blood samples were collected for analysis of amino acids and Lys metabolites. Milk protein percent increased by 5.9%, plasma Lys increased by 74%, and α-aminoadipic acid increased by 51% with postruminal infusion of 63 g/d Lys compared with 0 g/d. Expression of AASS, ornithine transcarbamoylase, and argininosuccinate synthase mRNA in liver did not differ with postruminal infusion of Lys. Milk fat globule mRNA for major milk proteins and AASS were not affected by Lys infusion. Postruminal infusion of Lys resulted in an 86% greater increase in AASS mRNA in the liver compared with mammary mRNA. These changes suggest that hepatic Lys metabolism is not responsive to Lys supply at the transcription level, and that the availability of Lys to extrahepatic tissue may be determined by hepatic Lys metabolism. [ABSTRACT FROM AUTHOR]

The National Animal Nutrition Program "National Research Support Project 9" supports efforts in livestock nutrition, including the National Research Council's committees on the nutrient requirements of animals. Our objective was to review the status of experimentation and data reporting in animal nutrition literature and to provide suggestions for the advancement of animal nutrition research and the ongoing improvement of field-applied nutrient requirement models. Improved data reporting consistency and completeness represent a substantial opportunity to improve nutrition-related mathematical models. We reviewed a body of nutrition research; recorded common phrases used to describe diets, animals, housing, and environmental conditions; and proposed equivalent numerical data that could be reported. With the increasing availability of online supplementary material sections in journals, we developed a comprehensive checklist of data that should be included in publications. To continue to improve our research effectiveness, studies utilizing multiple research methodologies to address complex systems and measure multiple variables will be necessary. From the current body of animal nutrition literature, we identified a series of opportunities to integrate research focuses (nutrition, reproduction and genetics) to advance the development of nutrient requirement models. From our survey of current experimentation and data reporting in animal nutrition, we identified 4 key opportunities to advance animal nutrition knowledge: (1) coordinated experiments should be designed to employ multiple research methodologies; (2) systems-oriented research approaches should be encouraged and supported; (3) publication guidelines should be updated to encourage and support sharing of more complete data sets; and (4) new experiments should be more rapidly integrated into our knowledge bases, research programs and practical applications. [ABSTRACT FROM AUTHOR]

The objectives of the current study were to compare and model feed intake responses to ambient temperature across species and to assess opportunities to use cross-species (CS) data to parameterize models when species-specific (SS) data were limited. Literature searches were conducted to identify studies reporting intake during thermal stress compared with thermoneutral (TN) conditions. The resulting data set comprised 614 treatment means from 108 studies on livestock responses to thermal stress. An analysis of variance was conducted with the CS data set to identify the effects of species, temperature and species by temperature interactions on intake as (fractional feed intake; FFI). Four models were derived from the CS data set and root mean squared prediction error (RMSPE) and concordance correlation coefficients (CCC) of these models were compared with models of the same form derived from SS data sets. Models used explanatory variables for (1) duration of exposure; (2) mean temperature; (3) minimum and maximum temperatures; or (4) difference between minimum and maximum temperatures. An additional model accounting for temperature and stage of production was derived from the SS data. Analysis of variance demonstrated that the species by temperature interaction did not have a significant effect on FFI. Across species, intake decreased with temperature. Notably, all species demonstrated a constant decrease in intake across the TN zone indicating the previous assumption of constant intake during thermoneutrality may be not fully valid. When compared on a SS basis, SS-derived models had marginally lower RMSPE and higher CCC when compared with models derived from the CS data sets. The model fit with production data had the lowest RMSPE and highest CCC within the study. When compared over temperature ranges with minimal data available in some species (e.g., cold stress), using CS models often resulted in decreased RMSPE and improved CCC when compared with SS models. Although fitting models based on SS data allows for incorporating unique covariates, like level of production, fitting responses based on CS data can help to improve model estimates when knowledge gaps exist. [ABSTRACT FROM PUBLISHER]

This experiment was designed to investigate the effects of different concentrations (0.00, 0.10, 0.15, 0.20, 0.25, and 0.30 g/L) of dried Cordyceps militaris mushroom on in vitro anaerobic ruminal microbe fermentation and methane production using soluble starch as a substrate. Ruminal fluids were collected from Korean native cattle, mixed with phosphate buffer (1:2), and incubated anaerobically at 38°C for 3, 6, 9, 12, 24, 36, 48, and 72 h. The addition of C. militaris significantly increased total volatile fatty acid and total gas production. The molar proportion of acetate was decreased and that of propionate was increased, with a corresponding decrease in the acetate:propionate ratio. As the concentration of C. militaris increased from 0.10 to 0.30 g/L, methane and hydrogen production decreased. The decrease in methane accumulation relative to the control was 14.1, 22.0, 24.9, 39.7, and 40.9% for the 0.10, 0.15, 0.20, 0.25, and 0.30 g/L treatments, respectively. Ammonia-N concentration and numbers of live protozoa decreased linearly with increasing concentrations of C. militaris. The pH of the medium significantly decreased at the highest level of C. militaris compared with the control. In conclusion, C. militaris stimulated mixed ruminal microorganism fermentation and inhibited methane production in vitro. Therefore, C. militaris could be developed as a novel compound for antimethanogenesis. [ABSTRACT FROM AUTHOR]

The Molly cow model represents nutrient digestion and metabolism based on a mechanistic representation of the key biological elements. Digestive parameters were derived ad hoc from literature observations or were assumed. Preliminary work determined that several of these parameters did not represent the true relationships. The current work was undertaken to derive ruminal and postruminal digestive parameters and to use a meta-approach to assess the effects of interactions among nutrients and identify areas of model weakness. Model predictions were compared with a database of literature observations containing 233 treatment means. Mean square prediction errors were assessed to characterize model performance. Ruminal pH prediction equations had substantial mean bias, which caused problems in fiber digestion and microbial growth predictions. The pH prediction equation was reparameterized simultaneously with the several ruminal and postruminal digestion parameters, resulting in more realistic parameter estimates for ruminal fiber digestion, and moderate reductions in prediction errors for pH, neutral detergent fiber, acid detergent fiber, and microbial N outflow from the rumen; and postruminal digestion of neutral detergent fiber, acid detergent fiber, and protein. Prediction errors are still large for ruminal ammonia and outflow of starch from the rumen. The gain in microbial efficiency associated with fat feeding was found to be more than twice the original estimate, but in contrast to prior assumptions, fat feeding did not exert negative effects on fiber and protein degradation in the rumen. Microbial responses to ruminal ammonia concentrations were half saturated at 0.2 mM versus the original estimate of 1.2 mM. Residuals analyses indicated that additional progress could be made in predicting microbial N outflow, volatile fatty acid production and concentrations, and cycling of N between blood and the rumen. These additional corrections should lead to an even more robust representation of the effects of dietary nutrients on ruminal metabolism and nutrient absorption, of animal performance, and the environmental impact of dairy production. [ABSTRACT FROM AUTHOR]

Milk urea nitrogen (MUN) is correlated with N balance, N intake, and dietary N content, and thus is a good indicator of proper feeding management with respect to protein. It is commonly used to monitor feeding programs to achieve environmental goals; however, genetic diversity also exists among cows. It was hypothesized that phenotypic diversity among cows could bias feed management decisions when monitoring tools do not consider genetic diversity associated with MUN. The objective of the work was to evaluate the effect of cow and herd variation on MUN. Data from 2 previously published research trials and a field trial were subjected to multivariate regression analyses using a mixed model. Analyses of the research trial data showed that MUN concentrations could be predicted equally well from diet composition, milk yield, and milk components regardless of whether dry matter intake was included in the regression model. This indicated that cow and herd variation could be accurately estimated from field trial data when feed intake was not known. Milk urea N was correlated with dietary protein and neutral detergent fiber content, milk yield, milk protein content, and days in milk for both data sets. Cow was a highly significant determinant of MUN regardless of the data set used, and herd trended to significance for the field trial data. When all other variables were held constant, a percentage unit change in dietary protein concentration resulted in a 1.1 mg/dL change in MUN. Least squares means estimates of MUN concentrations across herds ranged from a low of 13.6 mg/dL to a high of 17.3 mg/dL. If the observed MUN for the high herd were caused solely by high crude protein feeding, then the herd would have to reduce dietary protein to a concentration of 12.8% of dry matter to achieve a MUN concentration of 12 mg/dL, likely resulting in lost milk production. If the observed phenotypic variation is due to genetic differences among cows, genetic choices could result in herds that exceed target values for MUN when adhering to best management practices, which is consistent with the trend for differences in MUN among herds. [ABSTRACT FROM AUTHOR]

The effect of reticuloruminal epithelial blood flow on the absorption of propionate as a volatile fatty acid (VFA) marker in 8 lactating Holstein cows was studied under washed rumen conditions. The cows were surgically prepared with ruminal cannulas and permanent catheters in an artery and mesenteric, right ruminal, and hepatic portal veins. The experiment was designed with 2 groups of cows: 4 cows adapted to high crude protein (CP) and 4 to low CP. All cows were subjected to 3 buffers: butyric, ammonia, and control in a randomized replicated 3 x 3 incomplete Latin square design. The buffers (30 kg) were maintained in a temporarily emptied and washed rumen for 40 min. The initial concentration of VFA was 84.2 mmol/L. Butyrate was increased from 4 to 36 mmol/L in butyric buffer by replacement of acetate, and ammonia (NH3) was increased from 2.5 to 22.5 mmol/L in ammonia buffer by replacement of NaCl. Increasing amounts of deuterium oxide (D2O) were added to the buffers as the order of buffer sequence increased (6, 12, and 18 g of D2O). Ruminal clearance of D2O was used to estimate epithelial blood flow. To increase accuracy of the epithelial blood flow estimates, data of ruminal liquid marker (Cr-EDTA), and initial and final buffer volumes were fitted to a dynamic simulation model. The model was used to estimate ruminal liquid passages, residual liquid, and water influx (saliva and epithelia water) for each combination of cow and buffer (n = 24). Epithelial blood flow increased 49 ± 11% for butyric buffer compared with control. The ruminal disappearance of propionate (marker VFA) was affected by buffer and followed the same pattern as for epithelial blood flow. The correlation between ruminal disappearance of propionate and epithelial blood flow (r = 0.56) indicates that the removal of propionate can be limited by epithelial blood flow. The ruminal disappearance of propionate increased 30 ± 12% for the butyric compared with ammonia buffer and 12.5 ± 8% when compared with control. The net portal flux of propionate increased 32 ± 6% in butyric compared with control. In conclusion, rumen epithelial blood flow is positively correlated with ruminal disappearance of propionate and affects the kinetics of ruminal VFA absorption. [ABSTRACT FROM AUTHOR]