Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

<p>Abstract</p> <p>Background</p> <p>For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.</p> <p>Results</p> <p>We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform.</p> <p>Conclusions</p> <p>By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.</p

Impact of Pistachio Shell Biochar in Finishing Beef Cattle Diets

A 190-day finishing experiment was conducted to evaluate effects of feeding biochar on methane and carbon dioxide production, animal performance and carcass traits in beef steers. A high concentrate feedlot diet was used, and two dietary treatments were compared, 0 or 1% biochar as % of diet dry matter. Cattle were monitored using a calorimetry emissions barn to quantify production of methane and carbon dioxide. There were no differences in emissions, performance, or carcass characteristics for cattle fed the control diet or with biochar supplemented into the diet

Frequency of the Common MYH Mutations (G382D and Y165C) in MMR Mutation Positive and Negative HNPCC Patients

Recently mutations in the MYH gene have been associated with a milder form of adenomatous polyposis which is characterized by a variable level of colonic polyps ranging from a few to several hundred. In the context of HNPCC it is not unusual to identify patients with a smattering of polyps. The MYH gene product is involved in DNA repair and indeed the hMSH2/hMSH6 complex (both genes being essential elements of the DNA mismatch repair pathway) is required to stimulate MYH activity. We reasoned that because of the clinical similarity of a subset of HNPCC patients to those described with MYH mutations and the role of the hMSH2/hMSH6 complex in the activation of MYH protein that MYH mutations may account for a small proportion of HNPCC patients. In a study of 442 HNPCC patients we identified MYH mutations at the same frequency as that expected in the general population. Nevertheless, two HNPCC families were identified harbouring biallelic changes in MYH

Effect of Corn Residue Harvest Method on In Vivo and In Vitro Digestibility

A digestion study was conducted using 18 crossbred wether lambs to evaluate the effects of corn residue harvesting method and ensiling on the digestibility of corn residue. Husks had the greatest digestibility compared to any of the harvesting methods. No differences were observed for the digestibility of husklage, ensiled husklage, or stalklage. None of the harvest methods resulted in residue digestibilities similar to husks

The Association of the COMT V158M Polymorphism with Endometrial/Ovarian Cancer in HNPCC Families Adhering to the Amsterdam Criteria

Catechol-O-methyltransferase (COMT) is vital for the conjugation of catechol estrogens that are produced during oestrogen metabolism. The efficiency of this process varies due to a polymorphism in COMT, which changes valine to methionine (V158M). The Met genotypes slow the metabolism of catechol oestrogens, which are agents that are capable of causing DNA damage through the formation of DNA adducts and reactive oxygen species (ROS) production. The slower metabolism of catechol oestrogens results in there being a higher circulating concentration of these oeastrogens and consequently greater probability of DNA damage. To determine whether metabolic inefficiencies of oeastrogen metabolism are associated with the development of malignancy in hereditary non-polyposis colorectal cancer (HNPCC), we studied the V158M polymorphism in COMT in a large cohort of 498 HNPCC patients from Australia and Poland that were either mutation positive (n = 331) or negative (n = 167) for mismatch repair (MMR) gene mutations (hMLH1 or hMSH2). HNPCC is a familial predisposition to colorectal cancer (CRC) and extracolonic cancers that include endometrial cancer

Effect of Corn Processing on Steer Performance and Fecal Starch Content

Processing corn as high-moisture corn increases starch digestion and improves cattle efficiency when fed blended with dry rolled corn in finishing rations. A finishing study evaluated the effect of corn processing method (dry-rolled corn or 2:1) high-moisture corn to dry rolled corn blend) on performance of calf-fed steers. Corn processing method did not affect average daily gain; however, steers fed a high-moisture corn and dry-rolled corn blend consumed 1.1 lb/day less than steers fed a dry-rolled corn diet. Feeding high-moisture corn and dry-rolled corn blend diets improved feed efficiency by 5.2% compared to steers fed dry-rolled corn. Fecal starch content decreased by 31.3% when comparing cattle fed the high-moisture corn and dry rolled corn blend diet to cattle fed a dry-rolled corn diet

Evaluation of Methane and CO\u3csub\u3e2\u3c/sub\u3e Production in Growing and Finishing Cattle Raised in Conventional or Partial Confinement-based Herds

Methane emissions from growing and finishing calves compared either a spring calving, conventional cow system or a summer calving, partially-confined cow system. Calves weaned from the confinement-based production system were smaller at weaning and compensated with greater gain during the growing phase. More days on feed in the finishing phase were needed for the calves from the confinement system to reach same backfat thickness. Over the entire growing and finishing phases, calves from the confinement-based system produced more total CH4 and CH4 per lb. HCW. Production of methane and CO2 per lb. of gain was lower in calves from the confinement system in the growing phase. During the finishing period, calves from the conventional system had greater daily gain and lower methane per lb. of gain. Cattle consuming finishing diets had less CH4 per lb. feed intake and feeding growing diets resulted in less CO2 per animal per day and per lb. feed intake. Differences in GHG emissions were a function of size, feed intake, growth rate and diet composition

Effect of Biochar as a Feedlot Pen Surface Amendment on Manure Nutrient Capture

Two mass balance experiments were conducted during winter and summer seasons to evaluate the effect of spreading biochar on the feedlot pen surface on manure nutrient retention. The winter experiment (Dec to June) evaluated three treatments including biochar spread to pen surface (approximately 54 lb of biochar per steer), hydrated lime spread to pen surface (cooperation with UNL Environmental Engineering; approximately 68 lb per steer) and negative control (no treatment applied). The summer experiment (June to Nov) evaluated biochar treatment (approximately 68 lb of biochar per steer) against negative control. Biochar utilized in winter and summer was unprocessed and sourced from Eastern red cedar. Biochar addition to the feedlot pen surface increased N concentration in manure but did not translate into increased lb of N or P removed from feedlot pens (mass balance) for both experiments. There was a significant improvement in steer average daily gain for biochar addition in the summer, with no impact on steer performance or carcass characteristics for winte

Impact of Biochar Supplementation in Finishing Diets on Greenhouse Gas Emissions

A study was conducted to evaluate the impact of feeding biochar in a finishing diet on cattle performance, methane and carbon dioxide emissions, and carcass characteristics. Two treatments were evaluated, a high-concentrate control diet without biochar and a diet with biochar included at 1.0% of the diet dry matter, replacing high moisture corn in the diet. Pens of cattle were rotated through a two-sided emissions barn (2 pens evaluated simultaneously) to capture CH4 and CO2 production. There were no statistical differences in gas emissions for biochar supplemented steers compared to control. There was a 2.4% decrease in dry matter intake and 5.9% decrease in average daily gain for steers supplemented biochar, resulting in lighter and leaner carcasses for biochar fed steers

Impaired phagocytosis of apoptotic cells by macrophages in chronic granulomatous disease is reversed by IFN-γ in a nitric oxide-dependent manner

Immunodeficiency in chronic granulomatous disease (CGD) is well characterized. Less understood are exaggerated sterile inflammation and autoimmunity associated with CGD. Impaired recognition and clearance of apoptotic cells resulting in their disintegration may contribute to CGD inflammation. We hypothesized that priming of macrophages (Ms) with IFN-γ would enhance impaired engulfment of apoptotic cells in CGD. Diverse M populations from CGD (gp91(phox)(-/-)) and wild-type mice, as well as human Ms differentiated from monocytes and promyelocytic leukemia PLB-985 cells (with and without mutation of the gp91(phox)), demonstrated enhanced engulfment of apoptotic cells in response to IFN-γ priming. Priming with IFN-γ was also associated with increased uptake of Ig-opsonized targets, latex beads, and fluid phase markers, and it was accompanied by activation of the Rho GTPase Rac. Enhanced Rac activation and phagocytosis following IFN-γ priming were dependent on NO production via inducible NO synthase and activation of protein kinase G. Notably, endogenous production of TNF-α in response to IFN-γ priming was critically required for inducible NO synthase upregulation, NO production, Rac activation, and enhanced phagocytosis. Treatment of CGD mice with IFN-γ also enhanced uptake of apoptotic cells by M in vivo via the signaling pathway. Importantly, during acute sterile peritonitis, IFN-γ treatment reduced excess accumulation of apoptotic neutrophils and enhanced phagocytosis by CGD Ms. These data support the hypothesis that in addition to correcting immunodeficiency in CGD, IFN-γ priming of Ms restores clearance of apoptotic cells and may thereby contribute to resolution of exaggerated CGD inflammation