Publications by authors named "Henk J Van Lingen"

Article Synopsis
  • - Normalization of gene expression data is crucial for analyzing RNA-sequencing data, particularly in differential expression studies, but its effects on multivariate analysis, like PCA, are less understood.
  • - This study examines twelve normalization methods on both simulated and real data to see how they influence PCA outcomes, including sample clustering and gene ranking.
  • - Results show that while PCA score plots might look similar across different normalization techniques, the biological insights drawn from these models can vary significantly based on the normalization choice.
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Article Synopsis
  • The study evaluates techniques for estimating daily hydrogen and methane emissions from dairy cattle by using various gas sampling intervals.
  • Researchers used data from experiments with 28 and 16 cows to assess how frequently to sample for accurate emission readings.
  • Findings indicate that more frequent sampling (every 0.5 hours) is crucial for precision, while less frequent methods result in significant variation from the expected emissions values.
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Methionine (Met) is the first limiting amino acid in corn and soybean meal-based diets (containing L-Met) in broiler chickens, which are often supplemented with synthetic DL-Met or DL-Hydroxy Met (OH-Met). Our objective was to quantitatively assess the efficacy of synthetic Met sources and determine differences in growth rate of broilers fed at or below requirements in response to Met intake. A systematic literature search resulted in building a database containing 480 treatment means from 39 articles published between 1985 and 2019 globally.

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3-Nitrooxypropanol (3-NOP) supplementation to cattle diets mitigates enteric CH emissions and may also be economically beneficial at farm level. However, the wider rumen metabolic response to methanogenic inhibition by 3-NOP and the intermediary metabolite requires further exploration. Furthermore, supplementation potently decreases CH emissions from cattle.

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Enteric methane (CH) production is the main source of greenhouse gas emissions from livestock globally with beef cattle contributing 5.95% of total global greenhouse gas emissions. Various mitigation strategies have been developed to reduce enteric emissions with limited success.

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Dynamic modeling of mechanisms driving volatile fatty acid and hydrogen production in the rumen microbial ecosystem contributes to the heuristic prediction of CH emissions from dairy cattle into the environment. Existing mathematical rumen models, however, lack the representation of these mechanisms. A dynamic mechanistic model was developed that simulates the thermodynamic control of hydrogen partial pressure ( [Formula: see text] ) on volatile fatty acid (VFA) fermentation pathways via the NAD to NADH ratio in fermentative microbes, and methanogenesis in the bovine rumen.

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Diurnal patterns of ruminal fermentation metabolites and microbial communities are not commonly assessed when investigating variation in ruminal CH production. The aims of this study were to monitor diurnal patterns of: (i) gaseous and dissolved metabolite concentrations in the bovine rumen, (ii) H and CH emitted, and (iii) the rumen microbiota. Furthermore, the effect of dietary inclusion of linseed oil on these patterns was assessed.

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All mechanistic rumen models cover the main drivers of variation in rumen function, which are feed intake, the differences between feedstuffs and feeds in their intrinsic rumen degradation characteristics, and fractional outflow rate of fluid and particulate matter. Dynamic modeling approaches are best suited to the prediction of more nuanced responses in rumen metabolism, and represent the dynamics of the interactions between substrates and micro-organisms and inter-microbial interactions. The concepts of dynamics are discussed for the case of rumen starch digestion as influenced by starch intake rate and frequency of feed intake, and for the case of fermentation of fiber in the large intestine.

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Hydrogen is a key product of rumen fermentation and has been suggested to thermodynamically control the production of the various volatile fatty acids (VFA). Previous studies, however, have not accounted for the fact that only thermodynamic near-equilibrium conditions control the magnitude of reaction rate. Furthermore, the role of NAD, which is affected by hydrogen partial pressure (PH2), has often not been considered.

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