Development and Characterization of a High Density SNP Genotyping Assay for Cattle

The success of genome-wide association (GWA) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP) genotyping for the identification of quantitative trait loci (QTL) and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF) ranging from 0.24 to 0.27). The assay also identified 79 putative copy number variants in cattle. Utility for GWA was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. The combination of SNP selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. Aspects of the approach can be exploited in species which lack an available genome sequence. The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle

Glass Furnace Combustion and Melting Research Facility.

The need for a Combustion and Melting Research Facility focused on the solution of glass manufacturing problems common to all segments of the glass industry was given high priority in the earliest version of the Glass Industry Technology Roadmap (Eisenhauer et al., 1997). Visteon Glass Systems and, later, PPG Industries proposed to meet this requirement, in partnership with the DOE/OIT Glass Program and Sandia National Laboratories, by designing and building a research furnace equipped with state-of-the-art diagnostics in the DOE Combustion Research Facility located at the Sandia site in Livermore, CA. Input on the configuration and objectives of the facility was sought from the entire industry by a variety of routes: (1) through a survey distributed to industry leaders by GMIC, (2) by conducting an open workshop following the OIT Glass Industry Project Review in September 1999, (3) from discussions with numerous glass engineers, scientists, and executives, and (4) during visits to glass manufacturing plants and research centers. The recommendations from industry were that the melting tank be made large enough to reproduce the essential processes and features of industrial furnaces yet flexible enough to be operated in as many as possible of the configurations found in industry as well as in ways never before attempted in practice. Realization of these objectives, while still providing access to the glass bath and combustion space for optical diagnostics and measurements using conventional probes, was the principal challenge in the development of the tank furnace design. The present report describes a facility having the requirements identified as important by members of the glass industry and equipped to do the work that the industry recommended should be the focus of research. The intent is that the laboratory would be available to U.S. glass manufacturers for collaboration with Sandia scientists and engineers on both precompetitive basic research and the solution of proprietary glass production problems. As a consequence of the substantial increase in scale and scope of the initial furnace concept in response to industry recommendations, constraints on funding of industrial programs by DOE, and reorientation of the Department's priorities, the OIT Glass Program is unable to provide the support for construction of such a facility. However, it is the present investigators' hope that a group of industry partners will emerge to carry the project forward, taking advantage of the detailed furnace design presented in this report. The engineering, including complete construction drawings, bill of materials, and equipment specifications, is complete. The project is ready to begin construction as soon as the quotations are updated. The design of the research melter closely follows the most advanced industrial practice, firing by natural gas with oxygen. The melting area is 13 ft x 6 ft, with a glass depth of 3 ft and an average height in the combustion space of 3 ft. The maximum pull rate is 25 tons/day, ranging from 100% batch to 100% cullet, continuously fed, with variable batch composition, particle size distribution, and raft configuration. The tank is equipped with bubblers to control glass circulation. The furnace can be fired in three modes: (1) using a single large burner mounted on the front wall, (2) by six burners in a staggered/opposed arrangement, three in each breast wall, and (3) by down-fired burners mounted in the crown in any combination with the front wall or breast-wall-mounted burners. Horizontal slots are provided between the tank blocks and tuck stones and between the breast wall and skewback blocks, running the entire length of the furnace on both sides, to permit access to the combustion space and the surface of the glass for optical measurements and sampling probes. Vertical slots in the breast walls provide additional access for measurements and sampling. The furnace and tank are to be fully instrumented with standard measuring equipment, such as flow meters, thermocouples, continuous gas composition analyzers, optical pyrometers, and a video camera. The output from the instruments is to be continuously recorded and simultaneously made available to other researchers via the Internet. A unique aspect of the research facility would be its access to the expertise in optical measurements in flames and high temperature reacting flows residing in the Sandia Combustion Research Facility. Development of new techniques for monitoring and control of glass melting would be a major focus of the work. The lab would be equipped with conventional and laser light sources and detectors for optical measurements of gas temperature, velocity, and gaseous species and, using new techniques to be developed in the Research Facility itself, glass temperature and glass composition

Subacute ruminal acidosis reduces sperm quality in beef bulls

Breeding bulls are commonly fed high-energy diets, which may induce subacute ruminal acidosis (SARA). In this experiment, 8 Santa Gertrudis bulls (age 20 ± 6 mo) were used to evaluate the extent and duration of effects of SARA on semen quality and the associated changes in circulating hormones and metabolites. The bulls were relocated and fed in yards with unrestricted access to hay and daily individual concentrate feeding for 125 d before SARA challenge. Semen was collected and assessed at 14-d intervals before the challenge to ensure acclimatization and the attainment of a stable spermiogram. The challenge treatments consisted of either a single oral dose of oligofructose (OFF; 6.5 g/kg BW) or an equivalent sham dose of water (Control). Locomotion, behavior, respiratory rate, and cardiovascular and gastrointestinal function were intensively monitored during the 24-h challenge period. Rumen fluid samples were retained for VFA, ammonia, and lactate analysis. After the challenge, semen was then collected every third day for a period of 7 wk and then once weekly until 12 wk, with associated blood collection for FSH, testosterone, inhibin, and cortisol assay. Percent normal sperm decreased in bulls dosed with OFF after the challenge period (P < 0.05) and continued to remain lower on completion of the study at 88 d after challenge. There was a corresponding increase in sperm defects commencing from 16 d after challenge. These included proximal cytoplasmic droplets (P < 0.001), distal reflex midpieces (P = 0.01), and vacuole and teratoid heads (P < 0.001). Changes in semen quality after challenge were associated with lower serum testosterone (P < 0.001) and FSH (P < 0.05). Serum cortisol in OFF bulls tended to be greater (P = 0.07) at 7 d after challenge. This study shows that SARA challenge causes a reduction in sperm quality sufficient to preclude bulls from sale as single sire breeding animals 3 mo after the event occurred

Effect of Ppd-1 photoperiod sensitivity genes on dry matter production and allocation in durum wheat

Understanding the effect of genetic factors controlling flowering time is essential to fine-tune phenological development and to maximize yield. Thirty-four spring durum wheat genotypes classified in five allelic combinations for Ppd-A1/Ppd-B1 loci were grown for two years at three contrasting latitudes: Mexico-North, Spain- South and Spain-North. In all them, a delay in flowering date due to the presence of photoperiod sensitivity alleles Ppd-A1b and Ppd-B1b resulted in lower yields. The number of days to flowering, determined by an increasing number of photoperiod sensitivity alleles, accounted in all sites for more than 80% of the variation in the contribution of translocation of pre-flowering assimilates to grain yield. In Mexico and Spain-North lateflowering resulted in decreased harvest index as influenced by high temperatures during grain filling. In Mexico, where grain filling occurred under high temperatures and solar radiation, translocation of pre-flowering assimilates accounted from 55 to 63% of yield, independently of the flowering date of the genotype. In Spain- North, where water was available during grain filling, current photosynthesis was the main contributor to yield (57–73%), with independence of the allelic combination at Ppd loci. In Spain-South, the relative contribution of photosynthesis and translocation depended on the allelic composition at Ppd loci, with translocation increasing by 24% in the latest-flowering genotypes compared with the earliest ones. In all sites the limiting factor for attaining high yields was the capacity of the plant canopy to photosynthesize after anthesis. This study suggests that the expression of genes Ppd-A1 and Ppd-B1 regulating the response to photoperiod modulates the physiological strategy adopted by durum wheat to fill its grains, underlining the importance of phenology fitting in maximizing grain yield.This study was partially supported by INIA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria) Spain [RTA2009- 00085, RTA2015-00038, AGL2012-37217]

Automated imaging technologies for the diagnosis of glaucoma: a comparative diagnostic study for the evaluation of the diagnostic accuracy, performance as triage tests and cost-effectiveness (GATE study)

BACKGROUND: Many glaucoma referrals from the community to hospital eye services are unnecessary. Imaging technologies can potentially be useful to triage this population. OBJECTIVES: To assess the diagnostic performance and cost-effectiveness of imaging technologies as triage tests for identifying people with glaucoma. DESIGN: Within-patient comparative diagnostic accuracy study. Markov economic model comparing the cost-effectiveness of a triage test with usual care. SETTING: Secondary care. PARTICIPANTS: Adults referred from the community to hospital eye services for possible glaucoma. INTERVENTIONS: Heidelberg Retinal Tomography (HRT), including two diagnostic algorithms, glaucoma probability score (HRT-GPS) and Moorfields regression analysis (HRT-MRA); scanning laser polarimetry [glaucoma diagnostics (GDx)]; and optical coherence tomography (OCT). The reference standard was clinical examination by a consultant ophthalmologist with glaucoma expertise including visual field testing and intraocular pressure (IOP) measurement. MAIN OUTCOME MEASURES: (1) Diagnostic performance of imaging, using data from the eye with most severe disease. (2) Composite triage test performance (imaging test, IOP measurement and visual acuity measurement), using data from both eyes, in correctly identifying clinical management decisions, that is 'discharge' or 'do not discharge'. Outcome measures were sensitivity, specificity and incremental cost per quality-adjusted life-year (QALY). RESULTS: Data from 943 of 955 participants were included in the analysis. The average age was 60.5 years (standard deviation 13.8 years) and 51.1% were females. Glaucoma was diagnosed by the clinician in at least one eye in 16.8% of participants; 37.9% of participants were discharged after the first visit. Regarding diagnosing glaucoma, HRT-MRA had the highest sensitivity [87.0%, 95% confidence interval (CI) 80.2% to 92.1%] but the lowest specificity (63.9%, 95% CI 60.2% to 67.4%) and GDx had the lowest sensitivity (35.1%, 95% CI 27.0% to 43.8%) but the highest specificity (97.2%, 95% CI 95.6% to 98.3%). HRT-GPS had sensitivity of 81.5% (95% CI 73.9% to 87.6%) and specificity of 67.7% (95% CI 64.2% to 71.2%) and OCT had sensitivity of 76.9% (95% CI 69.2% to 83.4%) and specificity of 78.5% (95% CI 75.4% to 81.4%). Regarding triage accuracy, triage using HRT-GPS had the highest sensitivity (86.0%, 95% CI 82.8% to 88.7%) but the lowest specificity (39.1%, 95% CI 34.0% to 44.5%), GDx had the lowest sensitivity (64.7%, 95% CI 60.7% to 68.7%) but the highest specificity (53.6%, 95% CI 48.2% to 58.9%). Introducing a composite triage station into the referral pathway to identify appropriate referrals was cost-effective. All triage strategies resulted in a cost reduction compared with standard care (consultant-led diagnosis) but with an associated reduction in effectiveness. GDx was the least costly and least effective strategy. OCT and HRT-GPS were not cost-effective. Compared with GDx, the cost per QALY gained for HRT-MRA is £22,904. The cost per QALY gained with current practice is £156,985 compared with HRT-MRA. Large savings could be made by implementing HRT-MRA but some benefit to patients will be forgone. The results were sensitive to the triage costs. CONCLUSIONS: Automated imaging can be effective to aid glaucoma diagnosis among individuals referred from the community to hospital eye services. A model of care using a triage composite test appears to be cost-effective

Comment letters to the National Commission on Commission on Fraudulent Financial Reporting, 1987 (Treadway Commission) Vol. 2

https://egrove.olemiss.edu/aicpa_sop/1662/thumbnail.jp