SignificanceUS agriculture was modeled to determine impacts of removing farmed animals on food supply adequacy and greenhouse gas (GHG) emissions. The modeled system without animals increased total food production (23%), altered foods available for domestic consumption, and decreased agricultural US GHGs (28%), but only reduced total US GHG by 2.6 percentage units. Compared with systems with animals, diets formulated for the US population in the plants-only systems had greater excess of dietary energy and resulted in a greater number of deficiencies in essential nutrients. The results give insights into why decisions on modifications to agricultural systems must be made based on a description of direct and indirect effects of change and on a dietary, rather than an individual nutrient, basis.

The initiation and maintenance of lactation are complex phenomena governed by biochemical and endocrine processes in the mammary gland (MG). Although DNA-based approaches have been used to study the onset of lactation, more comprehensive RNA-based techniques may be critical in furthering our understanding of gene alterations that occur to support lactation in the bovine MG. To further determine how gene profiles vary during lactation compared with the dry period, RNA-seq transcriptomic analysis was used to identify differentially expressed genes (DEG) in bovine MG tissues from animals that were lactating and not lactating. A total of 881 DEG (605 upregulated and 276 downregulated) were identified in MG of 3 lactating Chinese Holstein dairy cows versus the 3 dry cows. The subcellular analysis showed that the upregulated genes were most abundantly located in "integral to membrane" and "mitochondrion," and the top number of downregulated genes existed in "nucleus" and "cytoplasm." The functional analysis indicated that the DEG were primarily associated with the support of lactation processes. The genes in higher abundance were most related to "metabolic process," "oxidation-reduction process," "transport" and "signal transduction," protein synthesis-related processes (transcription, translation, protein modifications), and some MG growth-associated processes (cell proliferation/cycle/apoptosis). The downregulated genes were mainly involved in immune-related processes (inflammatory/immune/defense responses). The KEGG analysis suggested that protein synthesis-related pathways (such as protein digestion and absorption; protein processing in endoplasmic reticulum; and glycine, serine, and threonine metabolism) were highly and significantly enriched in the bovine MG of lactating cows compared to dry cows. The results suggested that the dry cows had decreased capacity for protein synthesis, energy generation, and cell growth but enhanced immune response. Collectively, this reduced capacity in dry cows supports the physiological demands of the next lactation and the coordinated metabolic changes that occur to support these demands. A total of 51 identified DEG were validated by RT-PCR, and consistent results were found between RT-PCR and the transcriptomic analysis. This work provides a profile of gene-associated changes that occur during lactation and can be used to facilitate further investigation of the mechanisms underlying lactation in dairy cows.

The objective was to summarize the literature and derive equations that relate the chemical composition of diet and rumen characteristics to the intestinal supply of microbial nitrogen (MicN), efficiency of microbial protein synthesis (EMPS), and flow of nonammonia nonmicrobial N (NANMN). In this study, 619 treatment means from 183 trials were assembled for dairy cattle sampled from the duodenum or omasum. Backward elimination multiple regression was used to derive equations to estimate flow of nitrogenous components over a large range of dietary conditions. An intercept shift for sample location revealed that omasal sampling estimated greater MicN flow relative to duodenal sampling, but sample location did not interact with any other variables tested. The ruminal outflow of MicN was positively associated with dry matter intake (DMI) and with dietary starch percentage at a decreasing rate (quadratic response). Also, MicN was associated with DMI and rumen-degraded starch and neutral detergent fiber (NDF). When rumen measurements were included, ruminal pH and ammonia-N were negatively related to MicN flow along with a strong positive association with ruminal isovalerate molar proportion. When evaluating these variables with EMPS, isovalerate interacted with ammonia such that the slope for EMPS with increasing isovalerate increased as ammonia-N concentration decreased. A similar equation with isobutyrate confirms the importance of branched-chain volatile fatty acids to increase growth rate and therefore assimilation of ammonia-N into microbial protein. The ruminal outflow of NANMN could be predicted by dietary NDF and crude protein percentages, which also interacted. This result is probably associated with neutral detergent insoluble N contamination of NDF in certain rumen-undegradable protein sources. Because NANMN is calculated by subtracting MicN, sample location was inversely related compared with the MicN equation, and omasal sampling underestimated NANMN relative to duodenal sampling. As in the MicN equation, sampling location did not interact with any other variables tested for NANMN. Equations derived from dietary nutrient composition are robust across dietary conditions and could be used for prediction in protein supply-requirement models. These empirical equations were supported by more mechanistic equations based on the ruminal carbohydrate degradation and ruminal variables related to dietary rumen degradable protein.

Physically effective neutral detergent fiber (peNDF) is the fraction of neutral detergent fiber (NDF) that stimulates chewing activity and contributes to the floating mat of large particles in the rumen. Multiplying dietary NDF by particle size has been used as an estimate of peNDF. In re-evaluating the concept of peNDF, we compared the use of peNDF as dietary NDF × particle size with the use of individual NDF and particle size descriptors (physically adjusted NDF; paNDF) when used with other physical and chemical diet descriptors to predict dry matter (DM) intake (DMI), rumination time, and ruminal pH in lactating dairy cows. The purpose is to ultimately use these equations to estimate diet adequacy to maintain ruminal conditions. Each response variable had 8 models in a 2 (peNDF, paNDF) × 2 (diet, diet and ruminal factors) × 2 (DM, as fed basis) factorial arrangement. Particle size descriptors were those determined with the Penn State Particle Separator. Treatment means (n = 241) from 60 publications were used in backward elimination multiple regression to derive models of response variables. When available, peNDF terms entered equations. Models containing peNDF terms had similar or lower unadjusted concordance correlation coefficients (an indicator of similar or lower accuracy and precision) than did models without peNDF terms. The peNDF models for rumen pH did not differ substantially from paNDF models. This suggests that peNDF can account for some variation in ruminal pH; however, overt advantages of peNDF were not apparent. Significant variables that entered the models included estimated mean particle size; as fed or DM proportions retained on 19- and 8-mm sieves of the Penn State Particle Separator; DMI; dietary concentrations of forage; forage NDF; CP; starch; NDF; rumen-degraded starch and rumen-degraded NDF; and the interaction terms of starch × mean particle size, acid detergent fiber/NDF, and rumination time/DMI. Many dietary factors beyond particle size and NDF were identified as influencing the response variables. In conclusion, these results appear to justify the development of a modeling approach to integrate individual physical and chemical factors to predict effects on factors affecting rumen conditions.

Several attempts have been made to quantify microbial protein flow from the rumen; however, few studies have evaluated tradeoffs between empirical equations (microbial N as a function of diet composition) and more mechanistic equations (microbial N as a function of ruminal carbohydrate digestibility). Although more mechanistic approaches have been touted because they represent more of the biology and thus might behave more appropriately in extreme scenarios, their precision is difficult to evaluate. The objective of this study was to derive equations describing starch, neutral detergent fiber (NDF), and organic matter total-tract and ruminal digestibilities; use these equations as inputs to equations predicting microbial N (MicN) production; and evaluate the implications of the different calculation methods in terms of their precision and accuracy. Models were evaluated based on root estimated variance σˆe and concordance correlation coefficients (CCC). Ruminal digestibility of NDF was positively associated with DMI and concentrations of NDF and CP and was negatively associated with concentration of starch and the ratio of acid detergent fiber to NDF (CCC=0.946). Apparent ruminal starch digestibility was increased by omasal sampling (compared with duodenal sampling), was positively associated with forage NDF and starch concentrations, and was negatively associated with wet forage DMI and total dietary DMI (CCC=0.908). Models were further evaluated by calculating fit statistics from a common data set, using stochastic simulation, and extreme scenario testing. In the stochastic simulation, variance in input variables were drawn from a multi-variate random normal distribution reflective of input measurement errors and predicting MicN while accounting for the measurement errors. Extreme scenario testing evaluated each MicN model against a data subset. When compared against an identical data set, predicting MicN empirically had the lowest prediction error, though differences were slight (σˆe 23.3% vs. 23.7 or 24.3%), and highest concordance (0.52 vs. 0.48 or 0.44) of any approach. Minimal differences were observed between empirical MicN prediction (σˆe 25.3%; CCC 0.530) and MicN prediction (σˆe 25.3%; CCC 0.532) from rumen carbohydrate digestibility in the stochastic analysis or extreme scenario testing. Despite the hypothesized benefits of a more mechanistic prediction approach, few differences between the calculation approaches were identified.

Two studies were undertaken to assess the effects of individual essential AA supplementation of a protein-deficient 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.

Evaluation of ration balancing systems such as the National Research Council (NRC) Nutrient Requirements series is important for improving predictions of animal nutrient requirements and advancing feeding strategies. This work used a literature data set (n = 550) to evaluate predictions of total-tract digested neutral detergent fiber (NDF), fatty acid (FA), crude protein (CP), and nonfiber carbohydrate (NFC) estimated by the NRC (2001) dairy model. Mean biases suggested that the NRC (2001) lactating cow model overestimated true FA and CP digestibility by 26 and 7%, respectively, and under-predicted NDF digestibility by 16%. All NRC (2001) estimates had notable mean and slope biases and large root mean squared prediction error (RMSPE), and concordance (CCC) ranged from poor to good. Predicting NDF digestibility with independent equations for legumes, corn silage, other forages, and nonforage feeds improved CCC (0.85 vs. 0.76) compared with the re-derived NRC (2001) equation form (NRC equation with parameter estimates re-derived against this data set). Separate FA digestion coefficients were derived for different fat supplements (animal fats, oils, and other fat types) and for the basal diet. This equation returned improved (from 0.76 to 0.94) CCC compared with the re-derived NRC (2001) equation form. Unique CP digestibility equations were derived for forages, animal protein feeds, plant protein feeds, and other feeds, which improved CCC compared with the re-derived NRC (2001) equation form (0.74 to 0.85). New NFC digestibility coefficients were derived for grain-specific starch digestibilities, with residual organic matter assumed to be 98% digestible. A Monte Carlo cross-validation was performed to evaluate repeatability of model fit. In this procedure, data were randomly subsetted 500 times into derivation (60%) and evaluation (40%) data sets, and equations were derived using the derivation data and then evaluated against the independent evaluation data. Models derived with random study effects demonstrated poor repeatability of fit in independent evaluation. Similar equations derived without random study effects showed improved fit against independent data and little evidence of biased parameter estimates associated with failure to include study effects. The equations derived in this analysis provide interesting insight into how NDF, starch, FA, and CP digestibilities are affected by intake, feed type, and diet composition.

The relationships between postruminal casein infusion and production variables and concentrations of plasma AA and blood urea were evaluated using multilevel mixed-effects models derived from literature data collected in dairy cows. The data set contained 147 treatment means [i.e., 66 controls (CTL) and 81 casein-infused (CAS) means]. Each CAS mean was paired with its corresponding CTL mean to create 81 mean differences (CAS minus CTL), which were analyzed as absolute and percentage-based units (i.e., percentage increase or decrease in CAS relative to CTL). The primary variable of interest was the difference in estimated metabolizable protein (MP) supply (ΔMP) between CAS and CTL. The other explanatory variables were based on levels in CTL: MP supply, MP balance, the ratio of duodenal microbial protein (MCP) to MP supply (MCPMP), the stage of lactation (early or mid/late) and the type of forage (grass/legume- or corn silage-based). The MP supply and MP balance influenced negatively the relationship between ΔMP and the response of true protein yield. Responses of milk urea, blood urea, and plasma urea cycle AA concentrations were associated positively with ΔMP, indicating that a large amount of infused AA was catabolized to urea. Responses of plasma essential AA concentrations were related positively to ΔMP. The relative effect of ΔMP was highest for responses of plasma His concentration in cows fed grass/legume-based diets and at high MCPMP ratios. This relationship suggests that positive responses of plasma His concentrations are associated with diets relying heavily on microbial protein synthesis (high MCP), low in crude protein (low estimated MP supply), or both. The relationship between ΔMP and responses of plasma group 2 AA (Ile, Leu, Lys, and Val) concentrations was approximately 2 times greater than that for group 1 AA (His, Met, and Phe+Tyr) at mean MCPMP and MP supply. This could reflect the low hepatic removal group 2 AA compared with group 1 AA in dairy cows. Collectively, these results provide novel information on how dietary and cow conditions may alter responses to protein supplementation.