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"Steele, Michael"
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Work this farm!
\"It's a busy day on the farm! The farmers feed the animals and harvest the crops. A big farm needs big machines!\"--P. [4] of cover.
Book
Livestock metabolomics and the livestock metabolome: A systematic review
Metabolomics uses advanced analytical chemistry techniques to comprehensively measure large numbers of small molecule metabolites in cells, tissues and biofluids. The ability to rapidly detect and quantify hundreds or even thousands of metabolites within a single sample is helping scientists paint a far more complete picture of system-wide metabolism and biology. Metabolomics is also allowing researchers to focus on measuring the end-products of complex, hard-to-decipher genetic, epigenetic and environmental interactions. As a result, metabolomics has become an increasingly popular \"omics\" approach to assist with the robust phenotypic characterization of humans, crop plants and model organisms. Indeed, metabolomics is now routinely used in biomedical, nutritional and crop research. It is also being increasingly used in livestock research and livestock monitoring. The purpose of this systematic review is to quantitatively and objectively summarize the current status of livestock metabolomics and to identify emerging trends, preferred technologies and important gaps in the field. In conducting this review we also critically assessed the applications of livestock metabolomics in key areas such as animal health assessment, disease diagnosis, bioproduct characterization and biomarker discovery for highly desirable economic traits (i.e., feed efficiency, growth potential and milk production). A secondary goal of this critical review was to compile data on the known composition of the livestock metabolome (for 5 of the most common livestock species namely cattle, sheep, goats, horses and pigs). These data have been made available through an open access, comprehensive livestock metabolome database (LMDB, available at http://www.lmdb.ca). The LMDB should enable livestock researchers and producers to conduct more targeted metabolomic studies and to identify where further metabolome coverage is needed.
Journal Article
Skeleton crew showdown
Fred's friend invites the Mystery Inc. gang on a \"vacation\" on the old pirate ship he just bought, but there seems to be another crew on board--a crew of skeleton pirates who intend to take their ship back.
Book
Comparison of methods for pre-processing, exosome isolation, and RNA extraction in unpasteurized bovine and human milk
Milk is a highly complex, heterogeneous biological fluid that contains non-nutritive, bioactive extracellular vesicles called exosomes. Characterization of milk-derived exosomes (MDEs) is challenging due to the lack of standardized methods that are currently being used for milk pre-processing, storage, and exosome isolation. In this study, we tested: 1) three pre-processing methods to remove cream, fat, cellular debris, and casein proteins from bovine milk to determine whether pre-processing of whole milk prior to long-term storage improves MDE isolations, 2) the suitability of two standard exosome isolation methods for MDE fractionation, and 3) four extraction protocols for obtaining high quality RNA from bovine and human MDEs. MDEs were characterized via Transmission Electron Microscopy (TEM), Nanoparticle Tracking Analysis (NTA), and western immunoblotting for CD9, CD63, and Calnexin protein markers. We also present an optimized method of TEM sample preparation for MDEs. Our results indicate that: 1) Removal of cream and fat globules from unpasteurized bovine milk, prior to long-term storage, improves the MDE yield but not purity, 2) Differential ultracentrifugation (DUC) combined with serial filtration is better suited for bovine MDE isolation compared to ExoQuick (EQ) combined with serial filtration, however both methods were comparable for human milk, and 3) TRIzol LS is better suited for RNA extraction from bovine MDEs isolated by EQ and DUC methods. 4) TRIzol LS, TRIzol+RNA Clean and Concentrator, and TRIzol LS+RNA Clean and Concentrator methods can be used for RNA extractions from human MDEs isolated by EQ, yet the TRIzol LS method is better suited for human MDEs isolated by DUC. The QIAzol + miRNeasy Mini Kit produced the lowest RNA yield for bovine and human MDEs.
Journal Article
Attack of the zombie mermaids : a 4D book
While searching for undersea treasure, Captain Banana Beard and the Nearly Fearless Monkey Pirates find Neptune's Trident, which is cursed, and are immediately attacked by zombie mermaids.
Book
Correlated seed failure as an environmental veto to synchronize reproduction of masting plants
Variable, synchronized seed production, called masting, is a widespread reproductive strategy in plants. Resource dynamics, pollination success, and, as described here, environmental veto are possible proximate mechanisms driving masting.
We explored the environmental veto hypothesis, which assumes that reproductive synchrony is driven by external factors preventing reproduction in some years, by extending the resource budget model of masting with correlated reproductive failure. We ran this model across its parameter space to explore how key parameters interact to drive seeding dynamics. Next, we parameterized the model based on 16 yr of seed production data for populations of red (Quercus rubra) and white (Quercus alba) oaks. We used these empirical models to simulate seeding dynamics, and compared simulated time series with patterns observed in the field.
Simulations showed that resource dynamics and reproduction failure can produce masting even in the absence of pollen coupling. In concordance with this, in both oaks, among-year variation in resource gain and correlated reproductive failure were necessary and sufficient to reproduce masting, whereas pollen coupling, although present, was not necessary.
Reproductive failure caused by environmental veto may drive large-scale synchronization without density-dependent pollen limitation. Reproduction-inhibiting weather events are prevalent in ecosystems, making described mechanisms likely to operate in many systems.
Journal Article
Escape from haunted treasure island : a 4D book
When the Nearly Fearless Monkey Pirates land on an island in search of treasure, they find themselves surrounded by monkey pirate ghosts who are determined to protect it--and only Mr. Pickles, the youngest of Captain Banana Beard's crew, can save them from being dropped into a volcano.
Book
Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre-weaning
This study aimed to characterize mucosa- and digesta-associated microbiota in the hindgut (cecum, colon and rectum) of newborn (NB, n = 6), day 7 (n = 6), day 21 (n = 6) and day 42 (n = 6) Holstein bull calves using amplicon sequencing. The hindgut microbiota was diverse at birth, and mucosa-attached microbial community had higher individual variation than that of digesta-associated community. In total, 16 phyla were identified with Firmicutes, Bacteroidetes and Proteobacteria being the dominant microbial taxa in the hindgut. Quantitative real-time PCR analysis showed a significant age effect on the proportion of mucosa-attached Escherichia coli, Bifidobacterium, Clostridium cluster XIVa and Faecalibacterium prausnitzii. Especially, high abundance of mucosa-associated Escherichia was detected during the first week of life, suggesting higher chance of the pathogenic infection during this stage. The relative abundances of predicted microbial genes involved in amino acid metabolism, carbohydrate metabolism and energy metabolism were enriched, indicating the importance of hindgut microbiota in fermentation during the pre-weaned period. Moreover, the significant correlation between short-chain fatty acid concentration and mucosa-attached carbohydrate utilizing (Coprococcus 1, Blautia, Lachnospiraceae NC2004 group, etc.) and health-related bacteria (Escherichia-Shigella and Salmonella) suggests the importance of hindgut microbiota in the fermentation and health of dairy calves during pre-weaned period.
Journal Article
Hunt for the octo-shark : a 4D book
When his crew expresses doubts about the existence of the octo-shark, a creature that is half octopus and half shark, Captain Banana Beard of the Nearly Fearless Monkey Pirates and his crew set out on a hunt to find the mythical monster--but the search nearly turns all of them into an octo-shark lunch.
Book
Recent upper Arctic Ocean warming expedited by summertime atmospheric processes
The observed upper (0–50 m) Arctic Ocean warming since 1979 has been primarily attributed to anthropogenically driven changes in the high latitudes. Here, using both observational and modeling analyses, we demonstrate that a multiyear trend in the summertime large-scale atmospheric circulation, which we ascribe to internal variability, has played an important role in upper ocean warming in summer and fall over the past four decades due to sea ice-albedo effect induced by atmospheric dynamics. Nudging experiments in which the wind fields are constrained toward the observed state support this mechanism and suggest that the internal variability contribution to recent upper Arctic Ocean warming accounts for up to one quarter of warming over the past four decades and up to 60% of warming from 2000 to 2018. This suggests that climate models need to replicate this important internal process in order to realistically simulate Arctic Ocean temperature variability and trends.
Low-frequency internal atmospheric variability accounts for about one quarter of observed Arctic Ocean warming over the past four decades and 60% of the accelerated warming from 2000 to 2018.
Journal Article