Structural domains and matrix attachment regions along colinear chromosomal segments of maize and sorghum.
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Although a gene's location can greatly influence its expression, genome sequencing has shown that orthologous genes may exist in very different environments in the genomes of closely related species. Four genes in the maize alcohol dehydrogenase (adh1) region represent solitary genes dispersed among large repetitive blocks, whereas the orthologous genes in sorghum are located in a different setting surrounded by low-copy-number DNAs. A specific class of DNA sequences, matrix attachment regions (MARs), was found to be in comparable positions in the two species, often flanking individual genes. If these MARs define structural domains, then the orthologous genes in maize and sorghum should experience similar chromatin environments. In addition, MARs were divided into two groups, based on the competitive affinity of their association with the matrix. The "durable" MARs retained matrix associations at the highest concentrations of competitor DNA. Most of the durable MARs mapped outside genes, defining the borders of putative chromatin loops. The "unstable" MARs lost their association with the matrix under similar competitor conditions and mapped mainly within introns. These results suggest that MARs possess both domain-defining and regulatory roles. Miniature inverted repeat transposable elements (MITEs) often were found on the same fragments as the MARs. Our studies showed that many MITEs can bind to isolated nuclear matrices, suggesting that MITEs may function as MARs in vivo. (+info)
Effects of base ingredient in cooked molasses blocks on intake and digestion of prairie hay by beef steers.
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Twelve steers (332 kg) were used in three simultaneous 4 x 3 incomplete Latin squares to evaluate effects of beet molasses (BEET), cane molasses (CANE), or concentrated separator by-product (CSB) as base ingredients in cooked molasses blocks on intake and digestion of prairie hay and ruminal characteristics. All steers had ad libitum access to prairie hay (5.9% CP and 69.4% NDF; DM basis). The four experimental treatments included a control (no supplement) and three cooked molasses blocks, based on BEET, CANE, or CSB, fed daily at .125% of BW (.42 kg/d as-fed, .13 kg/d CP). Forage OM, NDF, and N intakes; digestible OM, NDF, and N intakes; and total tract OM and N digestibilities (percentage of intake) were greater (P < .05) for steers fed cooked molasses blocks than for control steers. Total tract OM digestibility was greater (P < or = .06) for steers fed BEET blocks (54.0%) than for those fed CSB (52.1%) or CANE blocks (52.2%). Digestion of NDF was greatest (P < .05) for steers fed BEET blocks (51.9%) and tended to be greater (P < .07) for steers fed CANE (49.3%) or CSB blocks (49.3%) than for control steers (46.9%). Ruminal ammonia concentrations were greater (P < .05) for steers fed cooked molasses blocks (.89 mM) than for control steers (.21 mM); this was primarily due to increases to 4.6 mM at 2 h postfeeding for steers fed blocks. Concentrations of total VFA in ruminal fluid were greater (P < .05) for steers fed BEET (92.7 mM) and CSB (88.1 mM) blocks than for control steers (80.3 mM), whereas concentrations for steers fed CANE blocks were intermediate (85.4 mM). Steers supplemented with cooked molasses blocks had greater molar percentages of butyrate than did control steers, particularly shortly after feeding. In summary, supplementation with cooked molasses blocks increased forage intake and digestion. The three base ingredients elicited similar responses, although steers fed BEET had slightly greater OM and NDF digestibilities than those fed CANE or CSB. (+info)
Influence of the novel urease inhibitor N-(n-butyl) thiophosphoric triamide on ruminant nitrogen metabolism: I. In vitro urea kinetics and substrate digestion.
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Two in vitro digestion experiments were conducted to evaluate the influence of the novel urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) on in vitro urea kinetics, substrate digestion, and fermentation characteristics. In Exp. 1, in vitro incubations were conducted in 50-mL test tubes containing .25 g of ground fescue hay to which 0, 6.5, 13, 26, or 52 mg of NBPT in a buffered ruminal fluid innoculum was added. Tubes were incubated in triplicate at 39 degrees C and replicated on consecutive days, with NH3 N and urea concentrations measured at 0, 10, 30, 60, 120, 240, and 360 min. Samples for VFA analysis were collected at 6 h, and incubations were continued through 48 h to estimate true digestibility (based on NDF analysis). Increasing the dose of NBPT tended (P < .12) to linearly depress the rate of urea hydrolysis and decreased (P < .0004) subsequent NH3 N formation. Although total VFA concentration at 6 h increased linearly (P < .03), acetate:propionate and estimated true digestibility decreased (P < .01) with increasing NBPT concentration. In Exp. 2, we compared in vitro urea kinetics and digestion of forage-only or mixed forage-grain substrates in response to addition of NBPT. In vitro incubations were conducted in 50-mL test tubes containing either .5 g of ground fescue hay or .5 g of a ground fescue hay and ground corn mixture (50:50, DM basis) to which 0, 6.5, 13, 26, or 52 mg of NBPT in a buffered ruminal fluid innoculum was added. Tubes were incubated in triplicate at 39 degrees C and replicated on consecutive days, with NH3 N and urea concentrations measured at 0, .5, 1, 2, 4, 8, 12, 24, and 48 h. At 48 h, samples for VFA analysis were collected and true digestibility (based on NDF analysis) was estimated. No (P > .10) NBPT dose x substrate interactions were detected. Increasing the dose of NBPT depressed (P < .003) the rate of urea hydrolysis and subsequent NH3 N formation, regardless of substrate. Although total VFA concentration was unaffected (P > .10), the acetate:propionate and estimated true digestibility decreased (P < .002) with higher NBPT addition. In both experiments, the rate of urea degradation was not different (P > .20) from zero for the 26 and 52 mg NBPT treatments, indicating that nearly complete inhibition of urease had been achieved. We conclude that NBPT can be used to reduce the rate of NH3 N release from dietary urea and, thereby, offers the potential to improve nonprotein nitrogen utilization in ruminants. (+info)
Effects of supplemental degradable intake protein on utilization of medium- to low-quality forages.
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Three independent experiments were conducted each using 16 ruminally fistulated beef steers fed bermudagrass (8.2% CP, 71% NDF; Exp. 1), bromegrass (5.9% CP, 65% NDF; Exp. 2), or forage sorghum (4.3% CP, 60% NDF; Exp. 3) hays to evaluate the effects of increasing level of supplemental degradable intake protein (DIP) on forage utilization. In each experiment, steers were blocked by weight and assigned to one of four treatments, and hay was offered to each steer at 130% of average voluntary intake for the preceding 5-d period. Supplemental DIP (sodium caseinate) was placed in the rumen at 0700, immediately before feeding forage. Levels of DIP supplementation were .041, .082, and .124% BW; the control received no supplemental DIP. Following a 10-d adaptation, intake and total fecal output were measured for 7 d. In Exp. 1, neither forage OM intake (FOMI) nor fiber (NDF) digestion were influenced (P > or = .20) by increasing level of DIP supplementation. The DIP supplied by the bermudagrass hay was estimated to be 8.2% of the total digestible OM intake (TDOMI) for control steers. In Exp. 2, increasing level of supplemental DIP did not affect (P > or = .26) FOMI but tended to increase total OM intake linearly (TOMI; P = .10). The tendency for a rise in TOMI coupled with a slight numeric increase in digestion resulted in an increase (linear; P = .06) in TDOMI. In the treatment group in which the maximum TDOMI was observed (supplemental DIP treatment of .082% BW), total DIP intake constituted approximately 9.8% of the TDOMI. In Exp. 3, FOMI, TOMI, organic matter digestion (OMD), and TDOMI were improved (P < .01) by increasing amounts of supplemental DIP. Although there was some evidence of a tendency for a decrease in the magnitude of change in TDOMI in response to increasing DIP supplementation, a clear plateau was not achieved with the levels of supplement provided. When the highest level of supplemental DIP was fed, DIP constituted approximately 12.8% of the TDOMI. In conclusion, significant variation was observed among forage in the amount of DIP needed to maximize intake and digestion when expressed in relationship to the digestible OM. (+info)
Characterization and determination of origin of lactic acid bacteria from a sorghum-based fermented weaning food by analysis of soluble proteins and amplified fragment length polymorphism fingerprinting.
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The group that includes the lactic acid bacteria is one of the most diverse groups of bacteria known, and these organisms have been characterized extensively by using different techniques. In this study, 180 lactic acid bacterial strains isolated from sorghum powder (44 strains) and from corresponding fermented (93 strains) and cooked fermented (43 strains) porridge samples that were prepared in 15 households were characterized by using biochemical and physiological methods, as well as by analyzing the electrophoretic profiles of total soluble proteins. A total of 58 of the 180 strains were Lactobacillus plantarum strains, 47 were Leuconostoc mesenteroides strains, 25 were Lactobacillus sake-Lactobacillus curvatus strains, 17 were Pediococcus pentosaceus strains, 13 were Pediococcus acidilactici strains, and 7 were Lactococcus lactis strains. L. plantarum and L. mesenteroides strains were the dominant strains during the fermentation process and were recovered from 87 and 73% of the households, respectively. The potential origins of these groups of lactic acid bacteria were assessed by amplified fragment length polymorphism fingerprint analysis. (+info)
Phytotoxicity of indole-3-acetic acid produced by the fungus, Pythium aphanidermatum.
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Pythium aphanidermatum causes the serious disease of Pythium red blight on bentgrass. IAA, one of the metabolites that has been isolated from this fungus, showed the same symptom of Pythium red blight on bentgrass at a concentration of 1,000 mg/1. The IAA content in the foliage of bentgrass infected by this fungus was about 200 times that of an untreated control. These results suggest that IAA produced by this fungus was the causal substance of Pythium red blight on bentgrass. (+info)
Influence of consumption of endophyte-infested tall fescue hay on performance of heifers and lambs.
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Two experiments were conducted to evaluate performance and physiological responses of heifers and lambs to Neotyphodium coenophialum-infested tall fescue hay fed under European rearing conditions. Endophyte-free (E-) or 100% endophyte-infested (E+) hay was derived from the same cultivar (cv. Clarine) so that the effect of the endophytic fungus could be clearly separated from a possible cultivar effect. In Exp. 1, starting in June 1996, 20 age- and body weight-paired Holstein dairy heifers were assigned for 97 d to one of two treatments consisting of ad libitum access to either E- or E+ hay, corresponding to 0 and .41 mg/kg ergovaline, respectively. During the experimental period, no significant difference (P>.20) in forage consumption, rectal temperature, or behavioral status of the animals was observed between the two treatments. The E+ diet induced a 10% apparent decrease in ADG and a clear reduction in prolactin (PRL) plasma concentration compared to the E- diet. When animals were all reassigned to a common endophyte-free diet, the E+ group recovered body weight and PRL to levels similar to those in animals fed E- after 7 wk. In Exp. 2, 30 Texel ram lambs were assigned to two treatments consisting of dietary E- or E+ tall fescue hay. The E- and E+ hays were harvested from the same plots as used in Exp. 1 and contained 0 and .96 mg/kg ergovaline, respectively. No effect of the endophyte was found on intake or carcass or testicle weight (P>.20) after the 95-d feeding period. The E+ treatment resulted in a slight reduction in BW at slaughter, mainly explained by a lower ruminal fill (P<.01). In E+ treated animals, prolactin concentrations dropped significantly (P<.001) from d 27. Hay assessment in both experiments showed no difference in chemical composition and IVDMD. The endophytic fungus strongly lowered the palatability of the E+ hay, although there was no effect on intake with heifers (Exp. 1) or with lambs (Exp. 2). The potential of severe heat stress, as expressed by the temperature humidity index, was not high in our experimental conditions, although they were considered rather unusually stressful for the western part of northern Europe. Yet, no economic effect on cattle was observed, in disagreement with results obtained in many previous U.S. studies. (+info)
Locus-specific contig assembly in highly-duplicated genomes, using the BAC-RF method.
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Polyploidy, the presence of multiple sets of chromosomes that are similar but not identical, complicates both chromosome walking and assembly of sequence-ready contigs for many plant taxa including a large number of economically-significant crops. Traditional 'dot-blot hybridization' or PCR-based assays for identifying BAC clones corresponding to a mapped DNA landmark usually do not provide sufficient information to distinguish between allelic and non-allelic loci. A restriction fragment matching method using pools of BAC DNA in combination with dot-blots reveals the locus specificity of individual BACs that correspond to multi-locus DNA probes, in a manner that can efficiently be applied on a large scale. This approach also provides an alternative means of mapping DNA loci that exploits many advantages of 'radiation hybrid' mapping in taxa for which such hybrids are not available. The BAC-RF method is a practical and reliable approach for using high-density RFLP maps to anchor sequence-ready BAC contigs in highly-duplicated genomes, provides an alternative to high-density robotic gridding for screening BAC libraries when the necessary equipment is not available, and permits the expedient isolation of individual members of multigene or repetitive DNA families for a wide range of genetic and evolutionary investigations. (+info)