Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1

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Nutritional and flock management options to reduce methane output and methane per unit product from sheep enterprises

The daily methane output of sheep is strongly affected by the quantity and digestibility of feed consumed. There are few widely applicable technologies that reduce the methane output of grazing ruminants without limiting feed intake per head or animal numbers. In contrast, there are many opportunities to increase the amount of animal product generated per unit of feed eaten. These include improving growth and reproductive rates of livestock and will reduce methane emission per unit of product (called emissions intensity) for individual animals. Producer responses to such improvements through changes to stocking rate and total area grazed will have a major effect on the total emission and profitability of the enterprise. First mating of ewes as lambs (~7 months of age) rather than as hoggets (~19 months of age) reduces the emissions intensity of self-replacing flocks but not that of flocks for which replacement ewes are purchased. Selection of sheep for improved residual feed intake reduces emissions intensity at the individual animal level as well as at the enterprise level. At present, emissions policies that motivate farm managers to consider generating fewer emissions rather than more profit or product are lacking

Recent Work In Real-Time Music Understanding by Computer

Music Understanding refers to the recognition or identification of structure and pattern in musical information. Three distinct music understanding projects initiated by the author are discussed. In the first, Computer Accompaniment, the goal is to follow a performer in a score. Knowledge of the position in the score as a function of time can be used to synchronize an accompaniment to the live performer and automatically adjust to tempo variations. In the second project, it is shown that statistical methods can be used to recognize the location of an improvisor in a cyclic chord progression such as the 12-bar blues. This problem is similar to Computer Accompaniment; however, much less information is conveyed by any one note because pitches are not predetermined. The third project, Beat Tracking, attempts to identify musical beats using note-onset times from a live performance. Parallel search techniques are used to consider several hypotheses simultaneously, and both timing and higher-..

Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production

Ruminants obtain nutrients from microbial fermentation of plant material, primarily in their rumen, a multilayered forestomach. How the different layers of the rumen wall respond to diet and influence microbial fermentation, and how these process are regulated, is not well understood. Gene expression correlation networks were constructed from full thickness rumen wall transcriptomes of 24 sheep fed two different amounts and qualities of a forage and measured for methane production. The network contained two major negatively correlated gene sub-networks predominantly representing the epithelial and muscle layers of the rumen wall. Within the epithelium sub-network gene clusters representing lipid/oxo-acid metabolism, general metabolism and proliferating and differentiating cells were identified. The expression of cell cycle and metabolic genes was positively correlated with dry matter intake, ruminal short chain fatty acid concentrations and methane production. A weak correlation between lipid/oxo-acid metabolism genes and methane yield was observed. Feed consumption level explained the majority of gene expression variation, particularly for the cell cycle genes. Many known stratified epithelium transcription factors had significantly enriched targets in the epithelial gene clusters. The expression patterns of the transcription factors and their targets in proliferating and differentiating skin is mirrored in the rumen, suggesting conservation of regulatory systems

Across-Experiment Transcriptomics of Sheep Rumen Identifies Expression of Lipid/Oxo-Acid Metabolism and Muscle Cell Junction Genes Associated With Variation in Methane-Related Phenotypes

Ruminants are significant contributors to the livestock generated component of the greenhouse gas, methane (CH4). The CH4 is primarily produced by the rumen microbes. Although the composition of the diet and animal intake amount have the largest effect on CH4 production and yield (CH4 production/dry matter intake, DMI), the host also influences CH4 yield. Shorter rumen feed mean retention time (MRT) is associated with higher dry matter intake and lower CH4 yield, but the molecular mechanism(s) by which the host affects CH4 production remain unclear. We integrated rumen wall transcriptome data and CH4 phenotypes from two independent experiments conducted with sheep in Australia (AUS, n = 62) and New Zealand (NZ, n = 24). The inclusion of the AUS data validated the previously identified clusters and gene sets representing rumen epithelial, metabolic and muscular functions. In addition, the expression of the cell cycle genes as a group was consistently positively correlated with acetate and butyrate concentrations (p < 0.05, based on AUS and NZ data together). The expression of a group of metabolic genes showed positive correlations in both AUS and NZ datasets with CH4 production (p < 0.05) and yield (p < 0.01). These genes encode key enzymes in the ketone body synthesis pathway and included members of the poorly characterized aldo-keto reductase 1C (AKR1C) family. Several AKR1C family genes appear to have ruminant specific evolution patterns, supporting their specialized roles in the ruminants. Combining differential gene expression in the rumen wall muscle of the shortest and longest MRT AUS animals (no data available for the NZ animals) with correlation and network analysis, we identified a set of rumen muscle genes involved in cell junctions as potential regulators of MRT, presumably by influencing contraction rates of the smooth muscle component of the rumen wall. Higher rumen expression of these genes, including SYNPO (synaptopodin, p < 0.01) and NEXN (nexilin, p < 0.05), was associated with lower CH4 yield in both AUS and NZ datasets. Unlike the metabolic genes, the variations in the expression of which may reflect the availability of rumen metabolites, the muscle genes are currently our best candidates for causal genes that influence CH4 yield