NDF is a transcription factor that stimulates elongation by RNA polymerase II.

RNA polymerase II (Pol II) elongation is a critical step in gene expression. Here we found that NDF, which was identified as a bilaterian nucleosome-destabilizing factor, is also a Pol II transcription factor that stimulates elongation with plain DNA templates in the absence of nucleosomes. NDF binds directly to Pol II and enhances elongation by a different mechanism than that used by transcription factor TFIIS. Moreover, yeast Pdp3, which is related to NDF, binds to Pol II and stimulates elongation. Thus, NDF is a Pol II binding transcription elongation factor that is localized over gene bodies and is conserved from yeast to humans.

Effect of alfalfa supplementary change dietary non-fibrous carbohydrate (NFC) to neutral detergent fiber (NDF) ratio on rumen fermentation and microbial function in Gansu alpine fine wool sheep (Ovis aries).

Bodyweight loss and rumen microbial dysfunction of grazing sheep was a challenge for the sheep production industry during cold season, which were considered to correlated with under-roughage-feeding. Alfalfa is a good roughage supplementary for ruminants, which can improve grazing sheep bodyweight-loss and rumen microbial dysfunction during grass-withering period. This study evaluated the effects of alfalfa hay supplementary change dietary non-fibrous carbohydrate/neutral detergent fiber (NFC/NDF) ratios on rumen fermentation and microbial function of Gansu alpine fine wool sheep during extreme cold season. 120 ewes (3-4 yrs) with an average body weight of 28.71 ± 1.22 kg were allocated randomly into three treatments, and fed NFC/NDF of 1.92 (H group), 1.11 (M group), and 0.68 (L group), respectively. This study was conducted for 107 d, including 7 d of adaption to the diets. The rumen fermentation parameters and microbial characteristics were measured after the end of feeding trials. The results showed that the concentrations of sheep body weight, nitrogen components (Total-N, Soluble protein-N and Ammonia-N), blood biochemical indices (LDH, BUN and CHO) and ruminal volatile fatty acids (TVFA and propionate) significantly increased with an increase in the proportion of NFC/NDF ratios (p < .05), and the acetate and acetate/propionat ratio presented a contrary decreasing trend (p < .05). A total of 1018 OTUs were obtained with 97% consistency. Ruminococcus, Ruminococcaceae and Prevotella were observed as the predominant phyla in ruminal fluid microbiota. Higher NFC/NDF ratios with Alfalfa supplementary increased the richness and diversity of ruminal fluid microbiota, and decreased ruminal fluid microbiota beta-diversity. Using clusters of orthologous groups (COG), the ruminal fluid microbiota of alfalfa supplementary feeding showed low immune pathway and high carbohydrate metabolism pathway. In summary, the study suggested that there was an increasing tendency in dietary NFC/NDF ratio of 1.92 in body weight, ruminal fermentation, microbial community composition and fermentation characteristics through developing alfalfa supplementary system.

Effect of acid detergent lignin concentration for diets formulated to be similar in neutral detergent fiber content on energy utilization in lactating Jersey cows.

Lignin is a polyphenolic polymer that is an important factor in limiting fiber digestibility by ruminants. The objective of the current study was to evaluate lignin's effects on whole animal energy utilization in diets similar in NDF content. A low-lignin (LoLig) diet was formulated to contain 32.5% NDF (DM basis) and 9.59% lignin (NDF basis) and the high-lignin (HiLig) diet was formulated to contain 31.0% NDF (DM basis) and 13.3% lignin (NDF basis). These diets were randomly assigned and fed to 12 late-lactation (mean ± SD; 214 ± 14.9 DIM) multiparous Jersey cows (mean ± SD; 435 ± 13.9 kg) in a 2-period crossover design. Cows fed the LoLig treatment consumed more DM than cows on the HiLig diet (mean ± SD; 19.9 vs. 18.7 ± 0.645 kg/d) and the LoLig diet was concurrently of a greater gross energy concentration (mean ± SEM; 4.27 vs. 4.23 ± 0.03 Mcal/kg). As expected, increasing the concentration of lignin resulted in a reduction in total-tract NDF digestibility (45.5% vs. 40.4% ± 0.742%). Increasing lignin also resulted in a reduction in the digestibility of starch (97.7 vs. 96.3 ± 0.420) and CP (65.0 vs. 60.0 ± 0.829). Lignin also decreased the concentration of digestible energy (2.83 vs. 2.63 ± 0.04 Mcal/kg) and ME (2.52 vs. 2.36 ± 0.05 Mcal/kg), but the concentration of NEL was similar (1.81 vs. 1.75 ± 0.06 Mcal/kg). Increasing the concentration of lignin also reduced yields of ECM (33.7 vs. 30.0 ± 0.838 kg/d), milk protein (1.00 vs. 0.843 ± 0.027 kg/d), and milk fat (1.30 vs. 1.19 ± 0.058 kg/d). Decreasing the dietary lignin concentration did not affect daily methane emissions, averaging 391 ± 29.6 L/d. Results of this study indicate that feeding a diet greater in lignin decreases the digestibility of nutrients and provides less energy for production responses and that energy supplied from digestible NDF may be less than predicted by some nutrition models.

Effects of offering free-choice hay for the first 5 days postpartum on productivity, serum inflammatory markers, gut permeability, and colon gene expression in fresh dairy cows.

The objective of the present study was to evaluate the effects of offering free-choice hay to cows during the first 5 d immediately after calving on feed intake, milk yield, plasma metabolites, serum inflammatory markers, rumination, gut permeability, and colon gene expression. It was hypothesized that cows offered free-choice hay would have lower gut permeability, lower inflammation, and higher milk production, compared with cows not offered hay. Thirty-two multiparous cows were fed a closeup total mixed ration (TMR; 21.5% starch, 32.1% forage neutral detergent fiber [NDF] on a dry matter basis) until calving. In the postpartum period, all cows were fed a fresh cow TMR (26.8% starch and 23.4% forage NDF) from calving until 21 DIM, and were assigned randomly to receive 1 of 2 treatments as follows: (1) free-choice timothy hay (61.6% NDF; 9.6% crude protein), offered outside of the TMR in a separate manger, for the first 5 d postpartum (FCH; n = 20), or 2) no free-choice hay (NH; n = 12). The FCH cows tended to have lower serum haptoglobin concentration on d 3, compared with NH (0.95 vs. 1.52 mg/mL). Within the FCH group, cows with greater hay intake had a smaller increase in serum amyloid A from d 1 to 3 after calving (r = 0.37), and tended to have a smaller increase in serum haptoglobin concentration (r = 0.36). Cows in the FCH group had a lower ratio of starch intake (kg) to forage NDF intake (kg) on d 1 and 2, compared with NH (0.91 vs. 1.14 ± 0.03), and cows that had a lower starch:forage NDF ratio tended to have a smaller increase in serum haptoglobin concentration from d 1 to 3 after calving (r = 0.32). Cows in the FCH group had lower TMR dry matter intake (DMI; 15.0 vs. 17.1 ± 0.93 kg/d) and lower total DMI (TMR + hay DMI; 15.9 vs. 17.1 ± 0.87 kg/d), from d 1 to 5 when free-choice hay was offered, compared with NH. However, the hay treatment did not affect plasma energy metabolite concentration, gut permeability, colon gene expression, milk yield, rumination time, or change in body weight or body condition score. Overall, these findings suggest that offering free-choice hay for the first 5 d after calving may reduce serum inflammatory marker concentration, but milk yield may not increase, due to lower intake.

Symposium review: Effects of carbohydrate digestion on feed intake and fuel supply.

Carbohydrates are the primary energy source for lactating dairy cows, and dairy diets are usually formulated for certain concentrations of forage neutral detergent fiber (NDF) and starch due to their direct effects on dry matter intake and milk production. Forage NDF exerts greater filling effects in the rumen than other dietary components and can limit maximum voluntary feed intake of lactating dairy cows. Since an analytical method for NDF was developed more than a half century ago, it has been used widely to characterize forages and diets for dairy cows. However, because NDF is a chemical measurement varying in its digestibility, in vitro digestibility measurements were developed as a biological approach to assess forage quality. Research efforts over the last several decades led to the development of forage cultivars or hybrids with enhanced in vitro NDF digestibility, such as brown midrib, and management practices considering differences in NDF digestibility of forages. In addition, in vitro NDF digestibility and undigested NDF are commonly measured in commercial labs, and estimated rates of digestion are used in dynamic models in an effort to improve the accuracy and precision of diet formulation. Starch digestion in the rumen also varies among starch sources, being affected by grain type, extent of processing, and conservation method. The site and rate of starch digestion affect dry matter intake and nutrient partitioning in dairy cows by modifying temporal supply of fuel. In addition, dietary starch content and its fermentability can affect digestion rates of starch itself and NDF in the rumen. Previous research has increased our understanding of dietary carbohydrates, but its application for diet formulations requires integrated approaches accounting for factors affecting the filling effects of forage NDF, starch digestion, and temporal fuel supply.

Identification of Gut Microbiota Affecting Fiber Digestibility in Pigs.

Dietary fiber plays an important role in porcine gut health and welfare. Fiber is degraded by microbial fermentation in the intestine, and most gut microbiota related to fiber digestibility in pigs are worth pursuing. The aim of this study was to identify gut microbiota associated with the apparent total tract digestibility (ATTD) of neutral detergent fiber (NDF) and of acid detergent fiber (ADF) in pigs. Large phenotypic variations in the ATTD of NDF and of ADF were separately found among 274 Suhuai pigs. Microbial community structures were significantly different between high and low fiber digestibility groups. Fourteen genera separately dominated the communities found in the high ATTD (H-AD) of NDF and ADF samples and were in very low abundance in the low ATTD (L-AD) of NDF and ADF samples. In conclusion, norank_f__Bacteroidales_S24-7_group (p < 0.05), Ruminococcaceae_UCG-005 (p < 0.05), unclassified_f__Lachnospiraceae (p < 0.05), Treponema_2 (p < 0.01), and Ruminococcaceae_NK4A214_group (p < 0.01) were the main genera of gut microbiota affecting the ATTD of NDF in pigs. Christensenellaceae_R-7_group (p < 0.01), Treponema_2 (p < 0.05), Ruminococcaceae_NK4A214_group (p < 0.05), Ruminococcaceae_UCG-002 (p < 0.05), and [Eubacterium]_coprostanoligenes_group (p < 0.05) were the main genera of gut microbiota affecting the ATTD of ADF in pigs. The most important functions of the above different potential biomarkers were: carbohydrate transport and metabolism, general function prediction only, amino acid transport and metabolism, cell wall/membrane/envelope biogenesis, translation, transcription, replication, energy production and conversion, signal transduction mechanisms, and inorganic ion transport and metabolism. The most important metabolic pathways of the above different potential biomarkers were: membrane transport, carbohydrate metabolism, amino acid metabolism, replication and repair, translation, cell motility, energy metabolism, poorly characterized, nucleotide metabolism, metabolism of cofactors and vitamins, and cellular processes and signaling.

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. III: Relation with solid passage rate and pH on prokaryotic fatty acid profile and community in continuous culture.

Our objectives were to evaluate potential interactions in culture conditions that influence how exogenously dosed branched-chain VFA (BCVFA) would be recovered as elongated fatty acids (FA) or would affect bacterial populations. A 2 × 2 × 2 factorial arrangement of treatments evaluated 3 factors: (1) without versus with BCVFA (0 vs. 2 mmol/d each of isobutyrate, isovalerate, and 2-methylbutyrate; each dose was partially substituted with 13C-enriched tracers before and during the collection period); (2) high versus low pH (ranging diurnally from 6.3 to 6.8 vs. 5.7 to 6.2); and (3) low versus high particulate-phase passage rate (kp; 2.5 vs. 5.0%/h) in continuous cultures administered a 50:50 forage:concentrate diet twice daily. Samples of effluent were collected and composited before harvesting bacteria from which FA and DNA were extracted. Profiles and enrichments of FA in bacteria were evaluated by gas chromatography and isotope-ratio mass spectrometry. The 13C enrichment in bacterial FA was calculated as percentage recovery of dosed 13C-labeled BCVFA. Dosing BCVFA increased the even-chain iso-FA, preventing the reduced concentration at higher kp and potentially as a physiological response to decreased pH. However, decreasing pH decreased recovery of 13C in these even-chain FA, suggesting greater reliance on isobutyrate produced from degradation of dietary valine. The iso-FA were decreased, whereas anteiso-FA and 16:0 increased with decreasing pH. Thus, 2-methylbutyrate still appeared to be important as a precursor for anteiso-FA to counter the increased rigidity of bacterial membranes that had more saturated straight-chain FA when pH decreased. Provision of BCVFA stimulated the relative sequence abundance of Fibrobacter and Treponema, both of which require isobutyrate and 2-methylbutyrate. Numerous bacterial community members were shifted by low pH, including increased Prevotella and genera within the phylum Proteobacteria, at the expense of members within phylum Firmicutes. Because of relatively few interactions with pH and kp, supplementation of BCVFA can stimulate neutral detergent fiber degradability via key fibrolytic bacteria across a range of conditions. Decreasing pH shifted bacterial populations and their FA composition, suggesting that further research is needed to distinguish pH from dietary changes.

Development of a mathematical model to predict pool sizes and rates of digestion of 2 pools of digestible neutral detergent fiber and an undigested neutral detergent fiber fraction within various forages.

The digestion of neutral detergent fiber treated with amylase and sodium sulfite and ash corrected (aNDFom) has been described as a single digestible pool and a fraction undigested in ruminants. Further, most models that predict rate and extent of digestion of aNDFom in the rumen assume first-order processes, in which the rates of digestion and passage are proportional to the pool size of aNDFom consumed and digested. Data exist demonstrating that the undigested fraction of aNDFom is not well described by a fixed coefficient and varies by maturity and agronomic growing conditions of the plant. Thus, our objective was to improve the prediction of digestible aNDFom (pdNDF) and to quantify, using a minimum number of fermentation time points, 2 pools of digestible aNDFom, pdNDF1 and pdNDF2, and their respective rates. Based on fermentations from 0 to 240 h among 34 forages (grasses, conventional and brown midrib corn silages, and alfalfas), 3 pools were described by aNDFomt = pdNDF1 × e-k1(t-L) + pdNDF2 × e-k2(t-L) + uNDF, where aNDFomt is the residue at time t; L is the lag; k1 is the rate of digestion of pdNDF1; k2 is the rate of digestion of pdNDF2; and uNDF the unavailable NDF on an aNDFom basis. A nonlinear estimation allowed the computation of the pool size and respective digestion rates. Using 3 time points from the digestion curve, 30, 120, and 240 h, as the fermentation endpoints to represent uNDF, we optimized the same model in Vensim (Ventana Simulation Environment; Ventana Systems Inc., Belmont, MA) to obtain rates and pool sizes of aNDFom. In addition, the same optimization was also performed with 2 timepoints and a forage type-specific range for uNDF. Parameters (with and without uNDF) obtained per forage using Vensim were compared by fitting kinetics data from the nonlinear calculations, using coefficients of determination and residual mean squares at convergence for ranking purposes for the whole equation and mean squared prediction errors for specific parameters. The highest coefficient of determination (0.98) and lowest mean square prediction error [0.0927 (NDF-1)2] were obtained when using 48, 120, and 240 h of aNDFom residues or when using 30 and 120 h and a range for the forage-specific uNDFom. Correlations were in all cases consistently high for all kinetic parameters, ranging from 0.76 to 0.99. Results demonstrated that an adequate description of the heterogeneity of aNDFom disappearance was possible without multiple fermentation time points. The equation was fit to all data generated; however, because of the variable nature of pool sizes and rates, forage-specific equations should be developed for better estimations of the forage specific pool sizes and uNDF estimation. This study further describes the heterogeneous nature of aNDFom disappearance and provides an approach for estimating the individual pool sizes and rates of digestion for application for diet formulation.

Effects of silencing TT8 and HB12 on in vitro nutrients degradation and VFA production in relation to molecular structures of alfalfa (Medicago sativa).

BACKGROUND: Transparent Testa8 (TT8) and Homeobox12 (HB12) are two transcriptional factors in plant phenylpropanoid pathways and were reported to be positively related to lignin content. Alfalfa with silenced TT8 (TT8i) and HB12 (HB12i) was therefore generated using the RNA interference (RNAi) technique. Although lignin was found to be high in HB12i, such gene-silencing of alfalfa resulted in nutrient profiles that might be suitable for grazing. To extend the nutritional evaluation of transformed alfalfa, ground samples of 11 HB12i, 5 TT8i and 4 wild type (WT) were incubated in rumen fluid : buffer solution for 0, 2, 4, 8, 12, 24 and 48 h at 39 °C. Dry matter (DM) and neutral detergent fiber (NDF) degradations at each time point, and production of volatile fatty acids (VFA) at 4, 12, 24 and 48 h were analyzed, as well as degradation and production kinetics. The correlations and regressions between nutritive profiles and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectral parameters were determined. RESULTS: Both transformed genotypes had lower DM degradation and HB12i had lower VFA production compared with WT. Structural carbohydrate (STC) parameters were found to be negatively correlated with DM degradation and VFA production. The kinetics of DM degradation and VFA production were predicted from spectral parameters with good estimation power. CONCLUSION: Silencing of HB12 and TT8 affected fermentation characteristics of alfalfa and some fermentation characteristics were predictable from spectral parameters using ATR-FTIR spectroscopy. © 2019 Society of Chemical Industry.

Predicting nutrient digestibility in high-producing dairy cows.

Our objective was to determine the effects of dry matter intake (DMI), body weight (BW), and diet characteristics on total tract digestibilities of dry matter, neutral detergent fiber, and starch (DMD, NDFD, and StarchD, respectively) in high-producing dairy cows. Our database was composed of 1,942 observations from 662 cows in 54 studies from Michigan, Ohio, and Georgia. On average, cows ate 23 ± 4.5 kg of dry matter/d, weighed 669 ± 79 kg, and produced 38 ± 10 kg of milk/d. Diets were 31 ± 5% neutral detergent fiber, 27 ± 6% starch, 2.6 ± 1.2% fatty acids, and 17 ± 1.4% crude protein. Digestibility means were 66 ± 6, 42 ± 11, and 93 ± 5% for DMD, NDFD, and StarchD, respectively. Forage sources included corn silage, alfalfa, and grasses. Corn source was classified by its ruminal fermentability. Data were analyzed using a mixed effects model, including diet chemical composition, forage source, and corn source, all expressed as percentage of dry matter, except for DMI, which was expressed as percentage of BW (DMI%BW); location and 2-way interactions were fixed effects. Cow, block, period, treatment, and study were included as random effects. Best fitting candidate models were generated using backward and stepwise regression methods. Additionally, the simplest model was generated using only DMI and location as fixed effects and all random effects. Candidate models were cross-validated across studies, and the resulting predictive correlation coefficients across studies (PC) and root mean square error of prediction (RMSEP) were compared by t-test. For each nutrient, the digestibility model that resulted in the highest PC and lowest RMSEP was determined to be the best fitting model. We observed heterogeneous coefficients among the different locations, suggesting that specific location factors influenced digestibilities. The overall location-averaged best fitting prediction equations were: DMD = 69 - 0.83 × DMI%BW (PC = 0.22, RMSEP = 5.39); NDFD = 53 + 0.26 × grass %DM - 0.59 × starch %DM + 3.06 × DMI%BW - 0.46 × DMI%BW2 (PC = 0.53, RMSEP = 9.70); and StarchD = 96 + 0.19 × HFERM%DM - 0.12 × starch %DM - 1.13 × DMI%BW (PC = 0.34, RMSEP = 4.77); where HFERM%DM is highly-fermentable corn source as percentage of DM. Our results confirm that digestibility is reduced as DMI increases, albeit at a lower rate than that reported in National Research Council. Furthermore, dietary starch depresses NDFD. Whereas DMD can be predicted based on DMI only, the best predictions for NDFD and StarchD require diet characteristics in addition to DMI.

Technical note: Near infrared reflectance spectroscopy to predict fecal indigestible neutral detergent fiber for dairy cows.

In vitro and in situ procedures performed to estimate indigestible neutral detergent fiber (iNDF) in forage or fecal samples are time consuming, costly, and limited by intrinsic factors. In contrast, near infrared reflectance spectroscopy (NIRS) has become widely recognized as a valuable tool for accurately determining chemical composition and digestibility parameters of forages. The aim of this study was to build NIRS calibrations and equations for fecal iNDF. In total, 1,281 fecal samples were collected to build a calibration data set, but only 301 were used to develop equations. Once dried, samples were ground and chemically analyzed for crude protein, ash, amylase and sodium sulfite-treated NDF corrected for ash residue (aNDFom), acid detergent fiber, acid detergent lignin, and in vitro digestion at 240 h to estimate iNDF (uNDF240). Each fecal sample was scanned using a NIRSystem 6500 instrument (Perstorp Analytical Inc., Silver Spring, MD). Spectra selection was performed, resulting in 301 sample spectra used to develop regression equations with good accuracy and low standard error of prediction. The standard error of calibration (SEC), cross validation (SECV), and coefficients of determination for calibration (R2) and for cross validation (1 - VR, where VR = variance ratio) were used to evaluate calibration and validation results. Moreover, the ratio performance deviation (RPD) and ratio of the range of the original data to SECV (range/SECV; range error ratio, RER) were also used to evaluate calibration and equation performance. Calibration data obtained on fiber fractions aNDFom (R2 = 0.92, 1 - VR = 0.87, SEC = 1.48, SECV = 1.89, RPD = 2.80, and RER = 20.19), uNDF240 (R2 = 0.92, 1 - VR = 0.86, SEC = 1.65, SECV = 2.24, RPD = 2.57, and RER = 14.30), and in vitro rumen aNDFom digestibility at 240 h (R2 = 0.90, 1 - VR = 0.85, SEC = 2.68, SECV = 3.43, RPD = 2.53, and RER = 14.0) indicated the predictive equations had good predictive value.

Production of dairy cows fed distillers dried grains with solubles in low- and high-forage diets.

The objective of the study was to investigate the effects of dietary forage and distillers dried grains with solubles (DDGS) concentration on the performance of lactating dairy cows. Twelve Holstein cows were blocked by parity and milk production and assigned to replicated 4 × 4 Latin squares with a 2 × 2 factorial arrangement of treatments. Diets were formulated to contain low forage [LF; 17% forage neutral detergent fiber (NDF)] or high forage (HF; 24.5% forage NDF) and DDGS at 0 or 18% of diet dry matter. The forage portion of the diet consisted of 80% corn silage and 20% alfalfa hay (dry matter basis). A portion of the ground corn and all of the expeller soybean meal and extruded soybeans from 0% DDGS diets were replaced with DDGS to formulate 18% DDGS diets. Overall, we found no interactions of forage × DDGS concentrations for any of the production measures. We observed no effect of diet on dry matter intake. Milk yield was greater when cows were fed LF diets compared with HF diets (43.3 vs. 41.5 kg/d). Milk fat concentration (3.03 vs. 3.38%) was lower for cows fed LF diets compared with HF diets, whereas protein concentration (3.11 vs. 2.98%) and yield (1.34 vs. 1.24 kg/d) were greater for cows fed LF diets compared with HF diets. Yields of fat, total solids, energy-corrected milk, and feed efficiency were not affected by diets. Cows partitioned equally for milk, maintenance, and body reserves. Replacing starch from ground corn and protein from soybean feeds with DDGS at either 17 or 24.5% of forage NDF concentration in the diet was cost-effective and did not affect the production performance of lactating dairy cows.

Effects of partial replacement of maize in the diet with crude glycerin and/or soyabean oil on ruminal fermentation and microbial population in Nellore steers.

The objective of this study was to determine whether a combination of crude glycerin (CG) and soyabean oil (SO) could be used to partially replace maize in the diet of Nellore steers while maintaining optimum feed utilisation. Eight castrated Nellore steers fitted with ruminal and duodenal cannulas were used in a double 4×4 Latin square design balanced for residual effects, in a factorial arrangement (A×B), when factor A corresponded to the provision of SO, and factor B to the provision of CG. Steers feed SO and CG showed similar DM intake, DM, organic matter and neutral-detergent fibre digestibility to that of steers fed diets without oil and without glycerine (P>0·05). Both diets with CG additions reduced the acetate:propionate ratio and increased the proportion of iso-butyrate, butyrate, iso-valerate and valerate (P<0·05). Steers fed diets containing SO had less total N excretion (P<0·001) and showed greater retained N expressed as % N intake (P=0·022). SO and CG diet generated a greater ruminal abundance of Prevotella, Succinivibrio, Ruminococcus, Syntrophococcus and Succiniclasticum. Archaea abundance (P=0·002) and total ciliate protozoa were less in steers fed diets containing SO (P=0·011). CG associated with lipids could be an energy source, which is a useful strategy for the partial replacement of maize in cattle diets, could result in reduced total N excretion and ruminal methanogens without affecting intake and digestibility.

Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology.

The National Drug File - Reference Terminology (NDF-RT) is a large and complex drug terminology consisting of several classification hierarchies on top of an extensive collection of drug concepts. These hierarchies provide important information about clinical drugs, e.g., their chemical ingredients, mechanisms of action, dosage form and physiological effects. Within NDF-RT such information is represented using tens of thousands of roles connecting drugs to classifications. In previous studies, we have introduced various kinds of Abstraction Networks to summarize the content and structure of terminologies in order to facilitate their visual comprehension, and support quality assurance of terminologies. However, these previous kinds of Abstraction Networks are not appropriate for summarizing the NDF-RT classification hierarchies, due to its unique structure. In this paper, we present the novel Ingredient Abstraction Network (IAbN) to summarize, visualize and support the audit of NDF-RT's Chemical Ingredients hierarchy and its associated drugs. A common theme in our quality assurance framework is to use characterizations of sets of concepts, revealed by the Abstraction Network structure, to capture concepts, the modeling of which is more complex than for other concepts. For the IAbN, we characterize drug ingredient concepts as more complex if they belong to IAbN groups with multiple parent groups. We show that such concepts have a statistically significantly higher rate of errors than a control sample and identify two especially common patterns of errors.

The effects of adding fat to diets of lactating dairy cows on total-tract neutral detergent fiber digestibility: A meta-analysis.

The objective of this meta-analysis was to determine the effects of supplemental fat on fiber digestibility in lactating dairy cattle. Published papers that evaluated the effects of adding fat to the diets of lactating dairy cattle on total-tract neutral detergent fiber digestibility (ttNDFd) and dry matter intake (DMI) were compiled. The final data set included 108 fat-supplemented treatment means, not including low-fat controls, from 38 publications. The fat-supplemented treatment means exhibited a wide range of ttNDFd (49.4% ± 9.3, mean ± standard deviation) and DMI (21.3 kg/d ± 3.5). Observations were summarized as the difference between the treatment means for fat-supplemented diets minus their respective low-fat control means. Additionally, those differences were divided by the difference in diet fatty acid (FA) concentration between the treatment and control diets. Treatment means were categorized by the type of fat supplement. Supplementing 3% FA in the diet as medium-chain fats (containing predominately 12- and 14-carbon saturated FA) or unsaturated vegetable oil decreased ttNDFd by 8.0 and 1.2 percentage units, respectively. Adding 3% calcium salts of long-chain FA or saturated fats increased ttNDFd by 3.2 and 1.3 percentage units, respectively. No other fat supplement type affected ttNDFd. Except for saturated fats and animal-vegetable fats, supplementing dietary fat decreased DMI. When the values for changes in ttNDFd are regressed on changes in DMI there was a positive relationship, though the coefficient of determination is only 0.20. When changes in ttNDFd were regressed on changes in DMI, within individual fat supplement types, there was no relationship within calcium salt supplements. There was a positive relationship between changes in ttNDFd and changes in DMI for saturated fats. Neither relationship suggested that the increased ttNDFd with calcium salts or saturated FA was due to decreased DMI for these fat sources. A subset of the means included measured ruminal neutral detergent fiber digestion. Analysis of this smaller data set did not suggest that ruminal neutral detergent fiber digestibility is depressed by fat supplementation more than ttNDFd. Adding fats, other than those with medium-chain FA, consistently increased digestible energy density of the diet. However, due to reduced DMI, this increased energy density may not result in increased digestible nutrient intake.

Diuron treatment reveals the different roles of two cyclic electron transfer pathways in photosystem II in Arabidopsis thaliana.

Three ecotypes of Arabidopsis thaliana, ecotype Columbia (Wild type, Wt) and two mutants (pgr5 and ndf4), were used to evaluate the effects of diuron on photosynthetic activity of A. thaliana. It was found that diuron adversely affected the fresh weight and chlorophyll content of the plants. Chlorophyll fluorescence studies determined that the pgr5 mutant was more sensitive to diuron than Wt and the ndf4 mutant. Gene expression analysis revealed different roles for the two cyclic electron transfer (CET) pathways, NAD(P)H dehydrogenase (NDH) and proton gradient regulation (PGR5) pathways, in the plant after diuron treatment. For example, a gene in the NDH pathway, lhca5, was activated in the low dose (LD) group in the pgr5 mutant, but was down-regulated in the moderate dose (MD) group, along with two other NDH-related genes (ppl2 and ndhH). In the PGR5 pathway, the pgr5 gene was functional under conditions of increased stress (MD group), and was up-regulated to a greater extent in the ndf4 mutant than that in the Wt and pgr5 mutant. Our results suggest that the PGR5 pathway in plants is more important than the NDH pathway during resistance to environmental stress. Deficiencies in the PGR5 pathway could not be counteracted by the NDH pathway, but deficiencies in the NDH pathway could be overcome by stimulating PGR5.

Effects of fibre digestibility and level of roughage on performance and rumen fermentation of finishing beef cattle.

The objective was to evaluate effects of neutral detergent fibre (NDF) digestibility and level of fresh sugarcane on intake, body fatness, carcass characteristics, and rumen kinetics and fermentation of beef cattle. Forty-eight Nellore young bulls were used in a complete randomized block design with a 2 × 2 factorial arrangement of treatments. Eight rumen-cannulated Nellore steers were used in a replicated 4 × 4 Latin square design. Two sugarcane genotypes divergent for stalk NDF digestibility (NDFD) were used. Experimental diets were formulated with 20 or 40% of sugarcane on a dry matter (DM) basis. High-NDFD genotype associated with the lower level of roughage in the diet promoted greater DM intake, resulting in greater body gain. Sugarcane with high-NDFD increased final body weight, hot carcass weight, and back-fat thickness. Animals receiving the genotype with high NDFD had greater rump-fat thickness only with 40% sugarcane in the diet. Animals receiving the low-NDFD genotype at 20% of the diet had lower NDF passage rate. Rumen pH was greater for diets with greater NDF content. There was greater proportion of butyrate in the rumen of animals receiving diets with greater NDF content. In conclusion, high-NDFD sugarcane increased final body and carcass weight, HCW, and fat thickness. When associated with lower inclusion of roughage in the diet, it can also increase DM intake and body weight gain of beef cattle.

Influence of ruminal methane on digesta retention and digestive physiology in non-lactating dairy cattle.

Enteric methane (CH4) production is a side-effect of herbivore digestion, but it is unknown whether CH4 itself influences digestive physiology. We investigated the effect of adding CH4 to, or reducing it in, the reticulorumen (RR) in a 4×4 Latin square experiment with rumen-fistulated, non-lactating cows, with four treatments: (i) control, (ii) insufflation of CH4 (iCH4), (iii) N via rumen fistula, (iv) reduction of CH4 via administration of bromochloromethane (BCM). DM intake (DMI), apparent total tract digestibility, digesta mean retention times (MRT), rumen motility and chewing activity, spot breath CH4 emission (CH4exhal, litre/kg DMI) as well as CH4 dissolved in rumen fluid (CH4RRf, µg/ml) were measured. Data were analysed using mixed models, including treatment (or, alternatively, CH4exhal or CH4RRf) and DMI relative to body mass0·85 (rDMI) as covariates. rDMI was the lowest on the BCM treatment. CH4exhal was highest for iCH4 and lowest for BCM treatments, whereas only BCM affected (reduced) CH4RRf. After adjusting for rDMI, CH4RRf had a negative association with MRT in the gastrointestinal tract but not in the RR, and negative associations with fibre digestibility and measures of rumination activity. Adjusting for rDMI, CH4exhal had additionally a negative association with particle MRT in the RR and a positive association with rumen motility. Thus, higher rumen levels of CH4 (CH4exhal or CH4RRf) were associated with shorter MRT and increased motility. These findings are tentatively interpreted as a feedback mechanism in the ruminant digestive tract that aims at mitigating CH4 losses by shortening MRT at higher CH4.

Meta-analysis of postruminal microbial nitrogen flows in dairy cattle. II. Approaches to and implications of more mechanistic prediction.

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.

Validation of an approach to predict total-tract fiber digestibility using a standardized in vitro technique for different diets fed to high-producing dairy cows.

The experimental objective was to validate an in vitro model to predict total-tract neutral detergent fiber (NDF) digestibility in dairy cattle. Twenty-one diets from 7 studies conducted at University of Wisconsin-Madison were analyzed for in vitro fiber digestibility. Forages varied among diets (corn, alfalfa, tall and meadow fescue, and wheat straw silages) and nutrient composition (ranges: NDF = 22.5 to 33.8%; crude protein = 15.8 to 18.9%; nonfiber carbohydrates = 38.0 to 51.0%). Total-tract NDF digestibility (TTNDFD) observed in in vivo trials was determined using different markers as described in the individual studies. The in vitro TTNDFD model predicted total-tract fiber digestibility from the proportion of total NDF potentially digestible (pdNDF), rate of pdNDF degradation, and rate of passage of pdNDF. The model predicted TTNDFD similar to in vivo measurements. The relationship between TTNDFD measured in vivo and TTNDFD predicted by the in vitro assay was significant (R(2) = 0.68). The relationship between in vitro 30-h NDF digestibility values and in vivo total-tract NDF digestibility values was not significant, whereas in vitro 48-h NDF digestibility values were correlated (R(2) = 0.30) with in vivo TTNDFD measurements. Indigestible NDF (iNDF) showed a negative relationship (R(2) = 0.40) with TTNDFD in vivo. Each 1-percentage-unit increase of iNDF resulted in a decrease of 0.96 percentage units of total-tract NDF digestibility; however, iNDF by itself was not a good predictor of TTNDFD because of the difference among the means. This study showed that an in vitro TTNDFD model that uses iNDF, pdNDF, and rates of pdNDF digestion and passage can predict (R(2) = 0.68) total-tract NDF digestibility. Most importantly, we demonstrated the ability to predict total-tract fiber digestibility from a model based on in vitro NDF degradation, which could improve our ability to optimize forage utilization and milk production.