Conceptus development and transcriptome at preimplantation stages in lactating dairy cows of distinct genetic groups and estrous cyclic statuses

First released in 2009, MetaboAnalyst (www.metaboanalyst.ca) was a relatively simple web server designed to facilitate metabolomic data processing and statistical analysis. With continuing advances in metabolomics along with constant user feedback, it became clear that a substantial upgrade to the original server was necessary. MetaboAnalyst 2.0, which is the successor to MetaboAnalyst, represents just such an upgrade. MetaboAnalyst 2.0 now contains dozens of new features and functions including new procedures for data filtering, data editing and data normalization. It also supports multi-group data analysis, two-factor analysis as well as time-series data analysis. These new functions have also been supplemented with: (i) a quality-control module that allows users to evaluate their data quality before conducting any analysis, (ii) a functional enrichment analysis module that allows users to identify biologically meaningful patterns using metabolite set enrichment analysis and (iii) a metabolic pathway analysis module that allows users to perform pathway analysis and visualization for 15 different model organisms. In developing MetaboAnalyst 2.0 we have also substantially improved its graphical presentation tools. All images are now generated using anti-aliasing and are available over a range of resolutions, sizes and formats (PNG, TIFF, PDF, PostScript, or SVG). To improve its performance, MetaboAnalyst 2.0 is now hosted on a much more powerful server with substantially modified code to take advantage the server’s multi-core CPUs for computationally intensive tasks. MetaboAnalyst 2.0 also maintains a collection of 50 or more FAQs and more than a dozen tutorials compiled from user queries and requests. A downloadable version of MetaboAnalyst 2.0, along detailed instructions for local installation is now available as well.

The objective of this study was to assess objectively the ability of observers to assess body condition of dairy cows. Four observers independently assigned a body condition score (five-point scale, .25 increments) and described the appearance of seven body regions of 225 Holstein cows. Areas described were the thurl region, ischial and ileal tuberosities, ilio-sacral and ischio-coccygeal ligaments, transverse processes of the lumbar vertebrae, and spinous processes of the lumbar vertebrae. An absolute body condition score was designated for each cow based on the modal body condition score for all observers. If there was no modal body condition score, the mean score was used for the absolute body condition score. Statistical analysis of principal components was used to examine the relationship between body region description and absolute body condition score. Descriptions of body regions were highly correlated across all absolute body condition scores. Four principal component vectors explained 83.6% of the variation of the body region correlation matrix. The first principal latent vector accounted for 55% of the variation and was uniformly correlated with all body regions. Analysis of variance of first principal latent vector as the dependent variable and absolute body condition score as the class variable indicated that body condition could be separated into .25 units between 2.5 and 4.0, inclusively. Below 2.5 and > 4.0, body condition could only be separated by .5 units. Distinct changes in specific body regions were associated with change in absolute body condition score. Observers agreed with the absolute score 58.1% of the time, deviating by .25 units 32.6% of the time. A body condition score can be given to a cow based on principal descriptors of specific body regions between 2.5 and 4.0 by .25 units.

The signalling pathways utilised by insulin receptor (IR) and IGF receptor to transduce their diverse effects on cellular metabolism, growth and survival are well established in broad outline, but many details remain to be elucidated. Tyrosine phosphorylation of IR substrates and Shc initiates signalling via canonical phosphoinositide 3-kinase/Akt and Ras/MAP kinase pathways, which together mediate many of the actions of insulin and IGFs. However, a variety of additional substrates and scaffolds have been described that may play roles in modulating the canonical pathways or in specific biological responses. This review will focus on recent studies that have extended our understanding of insulin/IGF signalling pathways, and the elements that may contribute to specificity.