High moisture tempering of corn before flaking: effects on bacterial contamination from houseflies and fecal shedding in finishing cattle Broce, A.B.; Gordon, C.M.; Sindt, J.J.; Depenbusch, Brandon E.; Drouillard, James S.; Phebus, Randall K

Tempered and non-tempered steam-flaked corn samples along with total mixed rations containing either tempered or non-tempered steam-flaked corn were exposed to flies and the environment for 21 hours. Exposure to flies and the environment increased (P\u3c0.05) generic E. coli, non-E. coli coliforms, total coliforms, and total plate count for the steamflaked corn samples independent of tempering. Tempering corn before steam-flaking increased total plate counts. Exposure to the environment and flies did not significantly (P\u3e0.05) alter microbial counts of total mixed rations regardless of tempering (Table 1). Generic E. coli coliforms were greater in total mixed rations when the corn was tempered, both before and after exposure to flies and the environment (P\u3c0.05). Similarly, total microbial plate counts were higher in steam-flaked corn samples when the corn was tempered (P\u3c0.05). A significant increase in response to grain tempering was also noted in non-E. coli coliforms and total microbial plate counts for the total mixed ration samples after exposure (Table 1). Following the initial experiments, 96 finishing beef steers were used to evaluate the effects of tempering steam-flaked corn on acid-resistant E. coli and total fecal coliforms. On day 56 of the feeding period, fecal samples were collected and analyzed for total and acidresistant E. coli and coliforms. No significant treatment difference was observed in the total fecal coliforms (P\u3e0.05), but acid-resistant (pH 2) non-E. coli and total fecal coliforms (Table 2) were lower in feces of cattle fed the tempered grain than those fed non-tempered grain

Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication

Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered SVs across a population sample of 347 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read data set, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among data sets revealed different features of genome variability. For example, genome alignment identified a large (∼4.3 Mb) inversion in indica rice varieties relative to japonica varieties, and long-read analyses suggest that ∼9% of genes from the outgroup (O. longistaminata) are hemizygous. We focused, however, on the resequencing sample to investigate the population genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type—which included inversions, duplications, deletions, translocations, and mobile element insertions—was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs may be predominantly deleterious. Among transposable elements, SINE and mariner insertions were found at especially low frequency. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ∼25% more derived SVs and mobile element insertions than O. rufipogon, indicating that SVs contribute to the cost of domestication in rice. Peaks of SV divergence were enriched for known domestication genes, but we also detected hundreds of genes gained and lost during domestication, some of which were enriched for traits of agronomic interest.Peer reviewe

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

Age at first birth in women is genetically associated with increased risk of schizophrenia

Prof. Paunio on PGC:n jäsenPrevious studies have shown an increased risk for mental health problems in children born to both younger and older parents compared to children of average-aged parents. We previously used a novel design to reveal a latent mechanism of genetic association between schizophrenia and age at first birth in women (AFB). Here, we use independent data from the UK Biobank (N = 38,892) to replicate the finding of an association between predicted genetic risk of schizophrenia and AFB in women, and to estimate the genetic correlation between schizophrenia and AFB in women stratified into younger and older groups. We find evidence for an association between predicted genetic risk of schizophrenia and AFB in women (P-value = 1.12E-05), and we show genetic heterogeneity between younger and older AFB groups (P-value = 3.45E-03). The genetic correlation between schizophrenia and AFB in the younger AFB group is -0.16 (SE = 0.04) while that between schizophrenia and AFB in the older AFB group is 0.14 (SE = 0.08). Our results suggest that early, and perhaps also late, age at first birth in women is associated with increased genetic risk for schizophrenia in the UK Biobank sample. These findings contribute new insights into factors contributing to the complex bio-social risk architecture underpinning the association between parental age and offspring mental health.Peer reviewe

High moisture tempering of corn before flaking: effects on bacterial contamination from houseflies and fecal shedding in finishing cattle

Tempered and non-tempered steam-flaked corn samples along with total mixed rations containing either tempered or non-tempered steam-flaked corn were exposed to flies and the environment for 21 hours. Exposure to flies and the environment increased (P<0.05) generic E. coli, non-E. coli coliforms, total coliforms, and total plate count for the steamflaked corn samples independent of tempering. Tempering corn before steam-flaking increased total plate counts. Exposure to the environment and flies did not significantly (P>0.05) alter microbial counts of total mixed rations regardless of tempering (Table 1). Generic E. coli coliforms were greater in total mixed rations when the corn was tempered, both before and after exposure to flies and the environment (P<0.05). Similarly, total microbial plate counts were higher in steam-flaked corn samples when the corn was tempered (P<0.05). A significant increase in response to grain tempering was also noted in non-E. coli coliforms and total microbial plate counts for the total mixed ration samples after exposure (Table 1). Following the initial experiments, 96 finishing beef steers were used to evaluate the effects of tempering steam-flaked corn on acid-resistant E. coli and total fecal coliforms. On day 56 of the feeding period, fecal samples were collected and analyzed for total and acidresistant E. coli and coliforms. No significant treatment difference was observed in the total fecal coliforms (P>0.05), but acid-resistant (pH 2) non-E. coli and total fecal coliforms (Table 2) were lower in feces of cattle fed the tempered grain than those fed non-tempered grain

Optimizing use of wet sorghum distiller’s grains with solubles in flaked-corn finishing diets

A finishing trial was conducted using 637 heifers (initially 849 lb) to determine the optimal amount of wet sorghum distiller's grains with solubles (WDGS) in finishing diets containing steam-flaked corn. Dietary treatments consisted of six concentrations of WDGS (0, 8, 16, 24, 32, and 40%; dry basis). Heifers were placed into dirt-surfaced feedlot pens (25 to 30 heifers/pen; 4 pens/treatment) and fed for 58 days. Daily gain responded in a quadratic manner (P<0.01), peaking with 8% WDGS in the finishing diet. Average daily gains during the 58-day finishing period were 2.79, 3.11, 3.05, 2.89, 2.70, and 2.55 lb/day for cattle fed 0, 8, 16, 24, 32, and 40% WDGS, respectively. Dry matter intake decreased linearly (P<0.01) as content of WDGS increased. Feed efficiency was optimized with 16% WDGS (6.81, 6.49, 6.19, 6.64, 6.96, and 7.18 lb dry feed per lb gain for cattle fed 0, 8, 16, 24, 32, and 40% WDGS, respectively). Animal performance data were used to compute net energy gain (NEg) values of each diet, yielding estimates of 69.9, 71.7, 75.8, 71.2, 68.9, and 67.6 Mcal/cwt for diets containing 0, 8, 16, 24, 32, and 40% WDGS, respectively (quadratic effect, P<0.03). Ribeye area decreased linearly (P<0.02) as concentration of WDGS increased in the diet. The percentage of USDA Yield Grade 1 carcasses decreased linearly (P<0.05), and the percentage of USDA Yield Grade 3 carcasses increased linearly (P=0.05) as the content of WDGS was increased. Average USDA Yield Grade increased linearly (P<0.02) as content of WDGS was increased. Grid-based carcass values were not significantly different across dietary treatments. Regression analysis of efficiency data indicates that the optimum amount of sorghum WDGS in steam-flaked corn diets is approximately 15%. Diets containing as much as 24% WDGS yielded efficiencies equal or superior to diets containing no WDGS