Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing.

BACKGROUND: Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases and 503 control participants. Candidate genes were subsequently validated for functions relevant to PD based on parallel RNA-interference (RNAi) screens in human cell culture and Drosophila and C. elegans models. RESULTS: Assuming autosomal recessive inheritance, we identify 27 genes that have homozygous or compound heterozygous loss-of-function variants in PD cases. Definitive replication and confirmation of these findings were hindered by potential heterogeneity and by the rarity of the implicated alleles. We therefore looked for potential genetic interactions with established PD mechanisms. Following RNAi-mediated knockdown, 15 of the genes modulated mitochondrial dynamics in human neuronal cultures and four candidates enhanced α-synuclein-induced neurodegeneration in Drosophila. Based on complementary analyses in independent human datasets, five functionally validated genes-GPATCH2L, UHRF1BP1L, PTPRH, ARSB, and VPS13C-also showed evidence consistent with genetic replication. CONCLUSIONS: By integrating human genetic and functional evidence, we identify several PD susceptibility gene candidates for further investigation. Our approach highlights a powerful experimental strategy with broad applicability for future studies of disorders with complex genetic etiologies

Effects of addition of nutritionally improved straw in dairy cow diets at 2 starch levels

The objective of this experiment was to explore the effects of different dietary neutral detergent fiber sources within diets of high-producing dairy cattle with low or high starch concentrations on milk yield and composition, dry matter intake (DMI), total-tract digestibility, nitrogen (N) partitioning, and rumen function and health. Holstein-Friesian cows in early- to mid-lactation (n = 12; 666 ± 67 kg of body weight at the start of the experiment) and dry cannulated Holstein-Frisian cows (n = 4; 878 ± 67 kg of body weight at the start of the experiment) were used in multiple 4 × 4 Latin square design experiment and were offered 4 different diets. The treatments were 50:50 forage-to-concentrate diets within a total mixed ration (TMR) consisting, on a dry matter (DM) basis, of 42.4% grass silage as the main forage, 7.6% chopped untreated wheat straw, or sodium hydroxide (NaOH) wheat straw pellets, known as nutritionally improved straw (NIS), and 50.0% of 1 of 2 different concentrates with low or high starch level (TMR starch level of 16.0 vs. 24.0% of DM, respectively). Four experimental periods were used, each consisting of a 21-d adaptation period and 7 d of sampling. Dry matter intake and milk yield were both affected by the type of straw included in the diet. A 1.6 kg/d higher DMI was seen when NIS was fed compared with untreated straw, resulting in a 1.7 kg/d higher milk yield. Milk protein concentration was affected by straw type and starch level, and it was 4 and 3% higher when NIS and high-starch diets were fed, respectively. Diets with NIS were more positively effective when fed with low levels of starch. These results illustrate that feeding NIS to high-producing lactating dairy cows fed low or high starch concentrations has a positive effect on performance. © 2020 American Dairy Science Associatio

Evaluation of nitrogen excretion equations for ryegrass pasture-fed dairy cows

Accurate and precise estimates of nitrogen (N) excretion in faeces and urine of dairy cattle may provide direct tools to improve N management and thus, to mitigate environmental pollution from dairy production. Empirical equations of N excretion have been evaluated for indoor dairy cattle but there is no evaluation for cows fed high proportions of fresh forage. Therefore, the objective of the current study was to evaluate N excretion equations with a unique data set of zero-grazing experiments. Through literature searches, 89 predictive equations were identified from 13 studies. An independent data set was developed from seven zero-grazing experiments with, in total, 55 dairy Holstein-Friesian cows. Models’ performance was evaluated with statistics derived from a mixed-effect model and a simple regression analysis model. Squared sample correlation coefficients were used as indicators of precision and based on either the best linear unbiased predictions (R2BLUP) or model-predicted estimates (R2MDP) derived from the mixed model and simple regression analysis, respectively. The slope (β0), the intercept (β1) and the root mean square prediction error (RMSPEm%) were calculated with the mixed-effect model and used to assess accuracy. The root mean square prediction error (RMSPEsr%) and the decomposition of the mean square prediction error were calculated with the simple regression analysis and were used to estimate the error due to central tendency (mean bias), regression (systematic bias), and random variation. Concordance correlation coefficient (CCC) were also calculated with the simple regression analysis model and were used to simultaneously assess accuracy and precision. Considering both analysis models, results suggested that urinary N excretion (UN; R2MDP = 0.76, R2BLUP = 0.89, RMSPEm% = 17.2, CCC = 0.82), total manure N excretion (ManN; R2MDP = 0.83, R2BLUP = 0.90, RMSPEm% = 11.0, CCC = 0.84) and N apparently digested (NAD; R2MDP = 0.97, R2BLUP = 0.97, RMSPEm% = 5.3, CCC = 0.95) were closely related to N intake. Milk N secretion was better predicted using milk yield as a single independent variable (MilkN; R2MDP = 0.77, R2BLUP = 0.97, RMSPEm% = 6.0, CCC = 0.74). Additionally, DM intake was a good predictor of UN and ManN and dietary CP concentration of UN and ManN. Consequently, results suggest that several evaluated empirical equations can be used to make accurate and precise predictions concerning N excretion from dairy cows being fed on fresh forage. © 2021 The Author(s

Effects of the addition of non-fibre carbohydrates with different rumen degradation rates in dairy cow high-forage diets using the Rumen Simulation Technique

Nutrient synchronisation of protein and carbohydrates is a promising practice to improve ruminal nutrient utilisation. However, dietary sources supplying these nutrients can vary in ruminal nutrient availability due to differing degradation rates, therefore potentially affecting utilisation of nitrogen (N). The effects of the addition of non-fibre carbohydrates (NFCs) with different rumen degradation rates in high-forage diets on ruminal fermentation, efficiency and microbial flow were investigated in vitro using the Rumen Simulation Technique (RUSITEC). Four diets were tested: control with 100% ryegrass silage (GRS) and substitution of 20% on a DM basis of ryegrass silage with corn grain (CORN), processed corn (OZ) or sucrose (SUC). The four diets were assigned to 16 vessels in two sets of RUSITEC apparatuses in a randomised block design over a 17 d experimental trial; 10 d consisted of adaptation and 7 d for sample collection. Rumen fluid was collected from four rumen-cannulated dry Holstein-Friesian dairy cows and was treated without mixing. Then, rumen fluid from each cow was used to inoculate four vessels, and diet treatments were randomly allocated to each one. This was repeated for all cows resulting in 16 vessels. The inclusion of SUC in ryegrass silage diets improved DM and organic matter digestibility. The only diet to significantly lower ammonia-N concentration compared with GRS was SUC. The outflows of non-ammonia-N, microbial-N, and efficiency of microbial protein synthesis were not affected by diet type. However, the efficiency of nitrogen utilisation was improved by SUC compared with GRS. This indicates that the inclusion of an energy source with a high rumen degradation rate in high-forage diets improves rumen fermentation, digestibility, and N utilisation. Specifically, this effect was observed for the more readily available energy source, SUC, compared with the more slowly degradable NFC sources, CORN and OZ