The renoprotective effects of soy protein in the aging rat kidney.

Aging is a risk factor for chronic kidney disease (CKD) and is itself associated with alterations in renal structure and function. There are no specific interventions to attenuate age-dependent renal dysfunction and the mechanism(s) responsible for these deficits have not been fully elucidated. In this study, male Fischer 344 rats, which develop age-dependent nephropathy, were feed a casein- or soy protein diet beginning at 16 mon (late life intervention) and renal structure and function was assessed at 20 mon. The soy diet did not significantly affect body weight, but was renoprotective as assessed by decreased proteinuria, increased glomerular filtration rate (GFR) and decreased urinary kidney injury molecule-1 (Kim-1). Renal fibrosis, as assessed by hydroxyproline content, was decreased by the soy diet, as were several indicators of inflammation. RNA sequencing identified several candidates for the renoprotective effects of soy, including decreased expression of Twist2, a basic helix-loop-helix transcription factor that network analysis suggest may regulate the expression of several genes associated with renal dysfunction. Twist2 expression is upregulated in the aging kidney and the unilateral ureteral obstruction of fibrosis; the expression is limited to distal tubules of mice. Taken together, these data demonstrate the renoprotective potential of soy protein, putatively by reducing inflammation and fibrosis, and identify Twist2 as a novel mediator of renal dysfunction that is targeted by soy.

Occurrence of enrofloxacin in overflows from animal lot and residential sewage lagoons and a receiving-stream.

Enrofloxacin (ENRO), a fluoroquinolone, was quantified in overflows from an animal lot and residential sewage lagoons and in a receiving-stream (Gans Creek). The concentrations of ENRO in samples was determined by high-performance liquid chromatography - tandem mass spectrometry. In total, ninety samples including duplicates were analyzed during several monthly sampling campaigns. The samples collected represented the residential sewage lagoon overflow (RLO), animal lot lagoon overflow (ALLO), the combined overflows (RLO and ALLO), and Gans Creek (upstream, midstream and downstream positions). The frequency of detection of ENRO was 90% for RLO and 100% for both ALLO and Gans Creek. The highest concentration of ENRO (0.44 µg/L) was found in ALLO sample collected during high precipitation. ENRO levels found in RLO samples ranged from < LOQ to 259 ng/L and the highest value observed also coincided with high flow. The levels of ENRO found in Gans Creek ranged from 17-216 ng/L. A preliminary ecotoxicological assessment was conducted through calculation of the risk quotients (RQs) for organisms based on the ratio of the measured environmental concentrations in this study to the predicted-no-effect-concentrations (acute and chronic effect) data. From the RQs, high risks were observed for Microcystis aeruginosa (cyanobacteria; RQ = 4.4); Anabaena flosaquae (cyanobacteria; RQ = 1.3); and Lemna minor (aquatic vascular plant; RQ = 2.0). The long-term effects of mixtures of PHCs on Gans Creek watershed are probable.

Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle.

BACKGROUND: Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations. RESULTS: Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE ≥ 1.0%) and a nominal P-value threshold (P ≤ 5e-05). Lead SNPs with PVE ≥ 2.0% were considered putative evidence of large-effect QTL (n = 52), whereas those with PVE ≥ 1.0% but < 2.0% were considered putative evidence for moderate-effect QTL (n = 35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained). CONCLUSIONS: Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs ≤ 3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species.

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity.

By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level. Using a new network bi-partition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure.

QTLs associated with dry matter intake, metabolic mid-test weight, growth and feed efficiency have little overlap across 4 beef cattle studies.

BACKGROUND: The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyses using 50 K and 770 K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford and Simmental×Angus) with phenotypes for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake. RESULTS: A total of 5, 6, 11 and 10 significant QTL (defined as 1-Mb genome windows with Bonferroni-corrected P-value<0.05) were identified for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake, respectively. The identified QTL were population-specific and had little overlap across the 4 populations. The pleiotropic or closely linked QTL on BTA 7 at 23 Mb identified in the Angus population harbours a promising candidate gene ACSL6 (acyl-CoA synthetase long-chain family member 6), and was the largest effect QTL associated with dry matter intake and mid-test body weight explaining 10.39% and 14.25% of the additive genetic variance, respectively. Pleiotropic or closely linked QTL associated with average daily gain and mid-test body weight were detected on BTA 6 at 38 Mb and BTA 7 at 93 Mb confirming previous reports. No QTL for residual feed intake explained more than 2.5% of the additive genetic variance in any population. Marker-based estimates of heritability ranged from 0.21 to 0.49 for residual feed intake across the 4 populations. CONCLUSIONS: This GWAS study, which is the largest performed for feed efficiency and its component traits in beef cattle to date, identified several large-effect QTL that cumulatively explained a significant percentage of additive genetic variance within each population. Differences in the QTL identified among the different populations may be due to differences in power to detect QTL, environmental variation, or differences in the genetic architecture of trait variation among breeds. These results enhance our understanding of the biology of growth, feed intake and utilisation in beef cattle.

Effect of varying dietary starch and fiber levels and inoculum source (mule deer vs. dairy cow) on simulated rumen fermentation characteristics.

This study measured starch and fiber digestion and microbial fermentation of three commercial exotic animal feeds using mule deer (MD) or dairy cow (DC) rumen inoculum. Diets were formulated to provide either high starch/low fiber (based on neutral detergent fiber fraction; NDF) with either alfalfa (diet A) or grain and oilseed byproducts (diet B) as the major fiber sources or low starch/high NDF (diet C). An initial batch culture incubation was run with diets inoculated with each rumen inoculum (n = 6; N = 36) over a 48 hr period with samples taken at different hour points for ammonia, pH, lactate, and volatile fatty acids (VFA). A second experiment was conducted where two continuous culture incubations (MD or DC) were run with six single-flow polycarbonate fermentation vessels per dietary treatment. Diets were fed two times a day over an 8-day period and sampled for ammonia, pH, and VFA before and after feeding on the last 3 days. On day 8, fermenter and effluent contents were collected and analyzed for nitrogen, dry matter digestibility (DMD), and organic matter digestibility (OMD). OMD was greater in MD (P = 0.02) and DMD tended to do the same (P = 0.06), but there were no differences due to diet (P > 0.05). Ammonia concentration was greater in DC (P < 0.01), and diets A and B had greater concentrations than diet C (P < 0.01). The greater digestibility, higher acetate:propionate (A:P) ratio and increased lactate levels prior to feeding likely led to diet C having a lower pH than diet A (6.59 vs. 6.66, respectively; P < 0.01) and led the tendency of A to be lower than C after feeding (P = 0.08). A:P ratio was greater in DC than MD before and after feeding (P < 0.01) and was greater in diet C than diets A or B (P < 0.01). Total VFA production tended to be greater in diets B and C in DC (P = 0.06). Rumen fluid source did affect fermentation. Increasing fiber level did not negatively affect fermentation and may increase OMD by removal of negative associative affects by starch on cellulolytic bacteria.

Activity-based metagenomic screening and biochemical characterization of bovine ruminal protozoan glycoside hydrolases.

The rumen, the foregut of herbivorous ruminant animals such as cattle, functions as a bioreactor to process complex plant material. Among the numerous and diverse microbes involved in ruminal digestion are the ruminal protozoans, which are single-celled, ciliated eukaryotic organisms. An activity-based screen was executed to identify genes encoding fibrolytic enzymes present in the metatranscriptome of a bovine ruminal protozoan-enriched cDNA expression library. Of the four novel genes identified, two were characterized in biochemical assays. Our results provide evidence for the effective use of functional metagenomics to retrieve novel enzymes from microbial populations that cannot be maintained in axenic cultures.

Use of lignin extracted from different plant sources as standards in the spectrophotometric acetyl bromide lignin method.

A nongravimetric acetyl bromide lignin (ABL) method was evaluated to quantify lignin concentration in a variety of plant materials. The traditional approach to lignin quantification required extraction of lignin with acidic dioxane and its isolation from each plant sample to construct a standard curve via spectrophotometric analysis. Lignin concentration was then measured in pre-extracted plant cell walls. However, this presented a methodological complexity because extraction and isolation procedures are lengthy and tedious, particularly if there are many samples involved. This work was targeted to simplify lignin quantification. Our hypothesis was that any lignin, regardless of its botanical origin, could be used to construct a standard curve for the purpose of determining lignin concentration in a variety of plants. To test our hypothesis, lignins were isolated from a range of diverse plants and, along with three commercial lignins, standard curves were built and compared among them. Slopes and intercepts derived from these standard curves were close enough to allow utilization of a mean extinction coefficient in the regression equation to estimate lignin concentration in any plant, independent of its botanical origin. Lignin quantification by use of a common regression equation obviates the steps of lignin extraction, isolation, and standard curve construction, which substantially expedites the ABL method. Acetyl bromide lignin method is a fast, convenient analytical procedure that may routinely be used to quantify lignin.

Biofortification of soybean meal: immunological properties of the 27 kDa γ-zein.

Legumes, including soybeans ( Glycine max ), are deficient in sulfur-containing amino acids, which are required for the optimal growth of monogastric animals. This deficiency can be overcome by expressing heterologous proteins rich in sulfur-containing amino acids in soybean seeds. A maize 27 kDa γ-zein, a cysteine-rich protein, has been successfully expressed in several crops including soybean, barley, and alfalfa with the intent to biofortify these crops for animal feed. Previous work has shown that the maize 27 kDa zein can withstand digestion by pepsin and elicit an immunogenic response in young pigs. By use of sera from patients who tested positive by ImmunoCAP assay for elevated IgE to maize proteins, specific IgE binding to the 27 kDa γ-zein is demonstrated. Bioinformatic analysis using the full-length and 80 amino acid sliding window FASTA searches identified significant sequence homology of the 27 kDa γ-zein with several known allergens. Immunoblot analysis using human serum that cross-reacts with maize seed proteins also revealed specific IgE-binding to the 27 kDa γ-zein in soybean seed protein extracts containing the 27 kDa zein. This study demonstrates for the first time the allergenicity potential of the 27 kDa γ-zein and the potential that this protein has to limit livestock performance when used in soybeans that serve as a biofortified feed supplement.

Maize 27 kDa gamma-zein is a potential allergen for early weaned pigs.

Soybean and maize are extensively used in animal feed, primarily in poultry, swine, and cattle diets. Soybean meal can affect pig performance in the first few weeks following weaning and elicit specific antibodies in weaned piglets. Though maize is a major component of pig feed, it is not known if any of the maize proteins can elicit immunological response in young pigs. In this study, we have identified a prominent 27 kDa protein from maize as an immunodominant protein in young pigs. This protein, like some known allergens, exhibited resistance to pepsin digestion in vitro. Several lines of evidence identify the immunodominant 27 kDa protein as a gamma-zein, a maize seed storage protein. First, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of different solubility classes of maize seed proteins revealed the presence of an abundant 27 kDa protein in the prolamin (zein) fraction. Antibodies raised against the purified maize 27 kDa gamma-zein also reacted against the same protein recognized by the young pig serum. Additionally, matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of the peptides generated by trypsin digestion of the immunodominant 27 kDa protein showed significant homology to the maize 27 kDa gamma-zein. Since eliminating the allergenic protein will have a great impact on the nutritive value of the maize meal and expand its use in the livestock industry, it will be highly desirable to develop maize cultivars completely lacking the 27 kDa allergenic protein.

Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle.

BACKGROUND: Molecular estimates of breeding value are expected to increase selection response due to improvements in the accuracy of selection and a reduction in generation interval, particularly for traits that are difficult or expensive to record or are measured late in life. Several statistical methods for incorporating molecular data into breeding value estimation have been proposed, however, most studies have utilized simulated data in which the generated linkage disequilibrium may not represent the targeted livestock population. A genomic relationship matrix was developed for 698 Angus steers and 1,707 Angus sires using 41,028 single nucleotide polymorphisms and breeding values were estimated using feed efficiency phenotypes (average daily feed intake, residual feed intake, and average daily gain) recorded on the steers. The number of SNPs needed to accurately estimate a genomic relationship matrix was evaluated in this population. RESULTS: Results were compared to estimates produced from pedigree-based mixed model analysis of 862 Angus steers with 34,864 identified paternal relatives but no female ancestors. Estimates of additive genetic variance and breeding value accuracies were similar for AFI and RFI using the numerator and genomic relationship matrices despite fewer animals in the genomic analysis. Bootstrap analyses indicated that 2,500-10,000 markers are required for robust estimation of genomic relationship matrices in cattle. CONCLUSIONS: This research shows that breeding values and their accuracies may be estimated for commercially important sires for traits recorded in experimental populations without the need for pedigree data to establish identity by descent between members of the commercial and experimental populations when at least 2,500 SNPs are available for the generation of a genomic relationship matrix.

Nutrient composition of plants consumed by black and white ruffed lemurs, Varecia variegata, in the Betampona Natural Reserve, Madagascar.

The purpose of this study was to quantify the concentrations of crude protein, fat, ash, neutral detergent fiber, acid detergent fiber, lignin, nonstructural carbohydrates, and gross energy in plant foods consumed by wild black and white ruffed lemurs (Varecia variegata). Calcium, phosphorous, magnesium, potassium, sodium, iron, zinc, copper, manganese, molybdenum, and selenium concentrations were also determined. A total of 122 samples from 33 plant families and more than 60 species were collected and analyzed for their nutritional content. The specific nutrient needs of black and white ruffed lemurs are unknown, but quantifying the nutritional composition of the foods they consume in the wild will help nutritionists and veterinarians formulate more appropriate diets for captive ruffed lemurs. This information will also supply information on how man-induced habitat changes affect the nutritional composition of foods consumed by free-ranging lemurs.

All three subunits of soybean beta-conglycinin are potential food allergens.

Soybeans are recognized as one of the "big 8" food allergens. IgE antibodies from soybean-sensitive patients recognize more than 15 soybean proteins. Among these proteins only the alpha-subunit of beta-conglycinin, but not the highly homologous alpha'- and beta-subunits, has been shown to be a major allergenic protein. The objective of this study was to examine if the alpha'- and beta-subunits of beta-conglycinin can also serve as potential allergens. Immunoblot analysis using sera collected from soybean-allergic patients revealed the presence of IgE antibodies that recognized several soy proteins including 72, 70, 52, 34, and 21 kDa proteins. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) analysis of trypsin-digested 72, 70, and 52 kDa proteins indicated that these proteins were the alpha'-, alpha-, and beta-subunits of beta-conglycinin, respectively. Additionally, purified alpha'-, alpha-, and beta-subunits of beta-conglycinin were recognized by IgE antibodies present in the soybean-allergic patients. The IgE reactivity to the beta-subunit of beta-conglycinin was not abolished when this glycoprotein was either deglycosylated using glycosidases or expressed as a recombinant protein in Escherichia coli . The results suggest that in addition to the previously recognized alpha-subunit of beta-conglycinin, the alpha'- and beta-subunits of beta-conglycinin also are potential food allergens.

Nutritional skewing of conceptus sex in sheep: effects of a maternal diet enriched in rumen-protected polyunsaturated fatty acids (PUFA).

BACKGROUND: Evolutionary theory suggests that in polygynous mammalian species females in better body condition should produce more sons than daughters. Few controlled studies have however tested this hypothesis and controversy exists as to whether body condition score or maternal diet is in fact the determining factor of offspring sex. Here, we examined whether maternal diet, specifically increased n-6 polyunsaturated fatty acid (PUFA) intake, of ewes with a constant body condition score around the time of conception influenced sex ratio. METHODS: Ewes (n = 44) maintained in similar body condition throughout the study were assigned either a control (C) diet or one (F) enriched in rumen-protected PUFA, but otherwise essentially equivalent, from four weeks prior to breeding until d13 post-estrus. On d13, conceptuses were recovered, measured, cultured to assess their capacity for interferon-tau (IFNT) production and their sex determined. The experiment was repeated with all ewes being fed the F diet to remove any effects of parity order on sex ratio. Maternal body condition score (BCS), plasma hormone and metabolite concentrations were also assessed throughout the study and related to diet. RESULTS: In total 129 conceptuses were recovered. Ewes on the F diet produced significantly more male than female conceptuses (proportion male = 0.69; deviation from expected ratio of 0.5, P < 0.001). Conceptus IFNT production was unaffected by diet (P > 0.1), but positively correlated with maternal body condition score (P < 0.05), and was higher (P < 0.05) in female than male conceptuses after 4 h culture. Maternal plasma hormone and metabolite concentrations, especially progesterone and fatty acid, were also modulated by diet. CONCLUSION: These results provide evidence that maternal diet, in the form of increased amounts of rumen-protected PUFA fed around conception, rather than maternal body condition, can skew the sex ratio towards males. These observations may have implications to the livestock industry and animal management policies when offspring of one sex may be preferred over the other.

Identification, characterization, epitope mapping, and three-dimensional modeling of the alpha-subunit of beta-conglycinin of soybean, a potential allergen for young pigs.

Soybean meal (SBM), the major byproduct of soybean oil extraction, is the main protein source for swine diets globally. In the United States, 8.6 million metric tons of SBM was used in swine rations in 2004. The pathological effect and immunological response of SBM feeding have been demonstrated in swine. In this study, we have utilized plasma collected from piglet feed with SBM in immunoblot analysis to detect proteins that elicited antigenic responses. We have identified soybean beta-conglycinin alpha-subunit as being a potential allergen for young piglets. Characterization of this protein indicated that deglycosylation and pepsin digestion did not eliminate immunoreactivity of this protein. Epitope mapping utilizing planar cellulose supports technology (SPOT) showed that three peptides spanning amino acids S185-R231 were critical for the allergenicity. A computer-generated three-dimensional structure model of the alpha-subunit of beta-conglycinin indicated that the antigenic epitopes were located on the surface of the protein. Information from this study may assist in the construction of recombinant nonallergenic soybean protein useable for both immunotherapy and the potential production of hypoallergenic soybean plants.

Fiber digestibility by the orangutan (Pongo abelii): in vitro and in vivo.

Limited nutritional information exists on diets of free-ranging orangutans, Pongo abelii and P. pygmaeus. Although they are classified as frugivores, the chemical composition of their diet and their gastrointestinal anatomy suggest that they rely on fiber fermentation for a substantial portion of energy. However, the extent to which they can ferment fiber is not known. Continuous culture systems, inoculated with orangutan fecal bacteria, were established to determine the fiber-digesting capacity of orangutan hindgut microflora. The cultures received one of four treatments: soybean hulls, ground corncobs, corn starch, or no food. Neither dry matter nor neutral detergent fiber digestibilities differed significantly among treatments. However, neutral detergent fiber digestibilities were high for both the soybean hull (88.4%) and ground corncob (86.1%) treatments, indicating that the microflora had a strong fibrolytic capability. To determine whether the same fiber-degrading capacity occurred in vivo, two adult orangutans and one juvenile were fed four gel-matrix diets containing soybean hulls, ground corncobs, or ground primate biscuits. Neutral detergent fiber concentrations (dry matter basis) of the gel matrices were 52.9% with soybean hulls, 46.8% and 63.7% with ground corncobs, and 31.3% with ground primate biscuits. A fifth diet consisted of primate biscuits with 27.3% neutral detergent fiber (dry matter basis) and was considered the baseline diet. Neutral detergent fiber digestibility (74.5%) was greatest (P < 0.05) for the soybean hull gel diet and least (57.5% and 45.0%, respectively; P < 0.05) for the 63.7% neutral detergent fiber (dry matter basis) corncob gel diet and the baseline primate biscuit diet. Total volatile fatty acid concentrations in orangutan feces were not significantly different among diets; however, molar proportions of acetic, propionic, and butyric acid differed (P < 0.05) among diets. The results from both studies indicated that orangutans are capable of extensive fiber fermentation.

Fiber digestibility by black lemurs (Eulemur macaco macaco).

Black lemurs, Eulemur macaco, are classified as generalist feeders, consuming a proportion of fruits and leaves that varies with seasonal availability. It is hypothesized that black lemurs are capable of using neutral detergent fiber (NDF) as a source of energy through fiber fermentation in the cecum and large intestine. In captivity, they are typically fed a diet of commercially available primate biscuits and readily available produce, both of which are limited in NDE Digestibility trials were conducted on 14 black lemurs; 12 were housed in groups (four, three, three, and two) and 2 were individually housed. The lemurs were fed four manufactured feeds differing in fiber form and content. A commercially available primate biscuit, containing approximately 27% NDF, served as the control diet. The second diet contained the same primate biscuits, which were ground and then incorporated into a fiber-based gel matrix. The third and fourth diets were formulated using soybean hulls or ground corncobs as the fiber source, resulting in 53% and 47% NDF, respectively. Produce was added to the diet at 36% (dry matter basis). Dry matter digestibility differed significantly among all diets. Neutral detergent fiber digestibility was highest for the ground biscuit in gel and lowest for the two high-fiber gel diets, with biscuit digestibility values falling between the two extremes. The high-fiber gel diets were successful in increasing the NDF concentrations of the primate diets; however, black lemurs were capable of only limited fiber digestion.