In the eye of the beholder: the effect of rater variability and different rating scales on QTL mapping

The agronomic importance of developing durably resistant cultivars has led to substantial research in the field of quantitative disease resistance (QDR) and, in particular, mapping quantitative trait loci (QTL) for disease resistance. The assessment of QDR is typically conducted by visual estimation of disease severity, which raises concern over the accuracy and precision of visual estimates. Although previous studies have examined the factors affecting the accuracy and precision of visual disease assessment in relation to the true value of disease severity, the impact of this variability on the identification of disease resistance QTL has not been assessed. In this study, the effects of rater variability and rating scales on mapping QTL for northern leaf blight resistance in maize were evaluated in a recombinant inbred line population grown under field conditions. The population of 191 lines was evaluated by 22 different raters using a direct percentage estimate, a 0-to-9 ordinal rating scale, or both. It was found that more experienced raters had higher precision and that using a direct percentage estimation of diseased leaf area produced higher precision than using an ordinal scale. QTL mapping was then conducted using the disease estimates from each rater using stepwise general linear model selection (GLM) and inclusive composite interval mapping (ICIM). For GLM, the same QTL were largely found across raters, though some QTL were only identified by a subset of raters. The magnitudes of estimated allele effects at identified QTL varied drastically, sometimes by as much as threefold. ICIM produced highly consistent results across raters and for the different rating scales in identifying the location of QTL. We conclude that, despite variability between raters, the identification of QTL was largely consistent among raters, particularly when using ICIM. However, care should be taken in estimating QTL allele effects, because this was highly variable and rater dependent.     

Synthesis of new compounds related to the commercial fungicide tricyclazole

BACKGROUND: Tricyclazole is a commercial fungicide used to control rice blast. As part of re‐registration activities, samples of metabolites and process impurities are required. In addition, isotopically labeled tricyclazole samples are also required. RESULTS: Four new compounds related to tricyclazole are reported. An isotopically labeled sample of tricyclazole was prepared that contained two ¹⁵N atoms and one ¹³C atom. Radiolabeled tricyclazole with ¹⁴C at the triazole C3 position was also synthesized. A new process impurity in technical tricyclazole was identified and synthesized. A new metabolite of tricyclazole was identified, independently synthesized and characterized by X‐ray crystallography. CONCLUSION: A previously unreported metabolite of tricyclazole has been identified and structurally characterized. In addition, a new process impurity has been identified by independent synthesis. Identification of these new compounds has facilitated the continued registration of this important fungicide. Copyright © 2011 Society of Chemical Industry     

Capillary electrophoresis and high-performance liquid chromatography determination of polyglutamyl 5-methyltetrahydrofolate forms in citrus products

The 5-methyltetrahydrofolate (5mTHF) polyglutamates in citrus products were analyzed by capillary electrophoresis (CE) and high-performance liquid chromatography (HPLC). Folate species were purified from citrus products and concentrated from 2- to 100-fold using combined folate-affinity chromatography and C18 extraction. Seven polyglutamyl 5mTHFs were found in most not-from-concentrate (NFC) orange juices (OJ) in total amounts of approximately 1 nmol/mL, with varying distributions of individual polyglutamates. Folate amounts and distributions were also measured in orange fractions, single-strength OJ from concentrate, NFC grapefruit juice, and citrus peel molasses. Models containing ascorbic acid had folate thermal degradation rates one-seventh that of models without ascorbic acid. Pasteurization studies demonstrated that folate loss was <2% for commercial OJ pasteurization conditions (i.e., 93 degrees C for 5 s, 88 degrees C for 15 s, and 82 degrees C for 30 s). Both methods were precise, reproducible, and potentially faster than traditional analytical procedures requiring enzymatic deconjugation and microbial assays.     

The effect of confinement on days to puberty in gilts

In the late fall and winter of 1982 to 1983, 112 crossbred gilts were used in a factorially arranged experiment to determine the effect of confinement on the age at which a gilt reaches first estrus (puberty). Two environments (confinement and non-confinement) and three ages at movement to non-confinement (100, 140, and 180 d) were studied. No differences were detected (P greater than .05) between confinement and non-confinement in the proportions of gilts reaching puberty by 210 d of age. Gilts were older at puberty (P less than .05) in confinement than in non-confinement (192.0 vs 187.7 d) and had a longer interval (P less than .05) from first boar contact to first estrus (12.1 vs 7.8 d). Age at puberty (192.1 vs 187.0 vs 190.5 d) and the proportion reaching puberty (56.4 vs 45.7 vs 65.8%) were not different (P greater than .05) between age-of-movement groups. However, a higher (P less than .05) proportion of the non-confinement gilts reached puberty within 10 d after the beginning of boar exposure than confinement (44.6 vs 26.8%). Moving gilts from confinement to non-confinement (pasture) at 180 d appeared to be the most effective method tested for inducing puberty in gilts.     

Effects of feed and water restriction and receiving diet crude protein on feeder pig performance

Two experiments were conducted to determine the effects of feed and water restriction and receiving diet crude protein level on feeder pig performance. In Exp. 1, a total of 239 commingled feeder pigs transported over 1,000 km were used in two trials. Pigs given access to feed and water (FW) at the market weighed more (P less than .0001) following marketing and transport than pigs given no feed and water (N) for the comparable 25-h market period (20.7 vs 19.6 kg). While FW pigs weighed less (P less than .02) than N pigs at the conclusion of the trials (93.9 vs 96.6 kg), there was no effect (P greater than .1) on overall average daily gain (.32 vs .35). There were no effects of receiving diets containing 12, 16 or 20% crude protein on daily gain, daily feed intake or feed efficiency for the overall growing-finishing period. Scour scores on d 8, 9, 10, 11, 13 and 14 post-arrival increased (P less than .01) with increased levels of protein in the receiving diets. In Exp. 2, a total of 360 crossbred feeder pigs was mixed and moved from a nursery to grower-finisher facilities in three trials, given feed and water access immediately (FWG) or denied access for 44 h (NG). At the end of the 44-h period, FWG pigs were heavier than NG pigs (P less than .0001; 18.3 vs 16.7 kg). There was no treatment effect on overall pig weight, daily gain or feed efficiency.     

Experimental evaluation of ophthalmic devices and solutions using rabbit models

OBJECTIVE: To analyze and compare the geometry of the anterior segment of rabbit and human eyes, with relevance for the evaluation of intraocular lenses, and to review rabbit models used in our laboratory for the evaluation of different ophthalmic devices and solutions. PROCEDURES: Fifteen rabbit and 15 human eyes (10 phakic and 5 pseudophakic/group) obtained postmortem were used. Anterior-posterior length, equatorial diameter, and white-to-white (corneal diameter) were measured with calipers. The eyes were then analyzed with a very high-frequency ultrasound (Artemis, Ultralink) for measurements of the anterior chamber depth, and anterior chamber and ciliary sulcus diameters. The capsular bag diameter was measured with calipers from a posterior view, and the diameter and thickness of the crystalline lenses were measured after their excision from the phakic eyes. RESULTS: Although the size of the rabbit eye is overall smaller than the size of the human eye, the dimensions of the anterior segment of rabbit eyes are generally larger. The differences between rabbit and human eyes were statistically significant (Wilcoxon rank sum test) in terms of anterior-posterior length, equatorial diameter, white-to-white measurements (P < 0.0001), anterior chamber diameter (P = 0.0004), ciliary sulcus diameter (P = 0.0012), and crystalline lens diameter and thickness (P = 0.0003). CONCLUSIONS: Experimental evaluation of design features of new phakic intraocular lenses in rabbit eyes may be inconclusive without adaptation of their size/design, contrary to the evaluation of new pseudophakic lenses by implantation in the capsular bag. The rabbit is a very valuable model for the experimental evaluation of different ophthalmic devices and solutions.     

Population genomics of early events in the ecological differentiation of bacteria

Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.     

Minimally invasive synovium harvest for potential use in meniscal tissue engineering

Tissue engineering is being investigated as a means for treating avascular meniscal injury or total meniscal loss in human and veterinary patients. The purpose of this study was to determine if an arthroscopic tissue shaver can be used to collect viable synoviocytes for in vitro culture during therapeutic stifle arthroscopy, with the long term goal of producing autologous meniscal fibrocartilage for meniscal tissue engineering. Synovium was harvested arthroscopically from 13 dogs with naturally occurring cranial cruciate ligament deficiency and obtained from 5 dogs with patellar luxation via arthrotomy. Cells harvested via arthroscopy and arthrotomy were treated with a chondrogenic growth factor protocol and analyzed for meniscal-like matrix constituents including collagens type I, II, and glycosaminoglycans. Arthrotomy and Arthroscopic origin cells formed contracted tissues containing collagen I, II and small amounts of GAG. These surgical methods provide clinically relevant access to synoviocytes for potential use in meniscal tissue engineering.     

Nutritional and mineral content of prickly pear cactus: A highly water‐use efficient forage,fodder and food species

Increased demand for food requires us to investigate livestock forage and fodder crops that can be grown over a wide range of locations where their cultivation will not compete with that of the food supply. A large portion of the southwestern United States consists of underutilized semi‐arid land. Crops typically used for livestock fodder or forage have high‐water demands that make them uneconomical or unsustainable for semi‐arid and arid regions. The growth rate and low‐input requirements of prickly pear cactus (Opuntia ficus‐indica) make it an excellent candidate for forage or fodder supplementation or replacement in these regions. Previous reports about forage quality data on Opuntia have been scattered across multiple locations, growing conditions and cultivars. Here, we report on the forage quality and mineral content of Opuntia ficus‐indica grown under both field and greenhouse conditions. Crude protein was 71 and 264 g/kg of dry mass for field and greenhouse conditions, respectively. Field‐grown plants showed higher acid and neutral detergent fibre content than greenhouse‐grown plants reflecting higher cellulose, hemicellulose and lignin accumulation. Nutritional values were also compared to requirements of cattle to determine what deficiencies might need to be addressed through supplementation. These data suggest that Opuntia can be used in combination with other feed sources to reduce the demand of resource‐intensive forage crops for raising livestock in dryland areas.