Genome-wide association study of leaf architecture in the maize nested association mapping population

US maize yield has increased eight-fold in the past 80 years, with half of the gain attributed to selection by breeders. During this time, changes in maize leaf angle and size have altered plant architecture, allowing more efficient light capture as planting density has increased. Through a genome-wide association study (GWAS) of the maize nested association mapping panel, we determined the genetic basis of important leaf architecture traits and identified some of the key genes. Overall, we demonstrate that the genetic architecture of the leaf traits is dominated by small effects, with little epistasis, environmental interaction or pleiotropy. In particular, GWAS results show that variations at the liguleless genes have contributed to more upright leaves. These results demonstrate that the use of GWAS with specially designed mapping populations is effective in uncovering the basis of key agronomic traits.     

Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases.     

Pierre Duhem’s epistemic aims and the intellectual virtue of humility: a reply to Ivanova

David Stump (2007) has recently argued that Pierre Duhem can be interpreted as a virtue epistemologist. Stump’s claims have been challenged by Milena Ivanova (2010) on the grounds that Duhem’s ‘epistemic aims’ are more modest than those of virtue epistemologists. I challenge Ivanova’s criticism of Stump by arguing that she not distinguish between ‘reliabilist’ and ‘responsibilist’ virtue epistemologies. Once this distinction is drawn, Duhem clearly emerges as a ‘virtue-responsibilist’ in a way that complements Ivanova’s positive proposal that Duhem’s ‘good sense’ reflects a conception of the ‘ideal scientist’. I support my proposal that Duhem is a ‘virtue-responsibilist’ by arguing that his rejection of the possibility of our producing a ‘perfect theory’ reflects the key responsibilist virtue of ‘intellectual humility’.     

The Making of Modern Science: Science,Technology, Medicine and Modernity: 1789–1914

We offer a novel historical-philosophical framework for discussing experimental practice which we call ‘Generating Experimental Knowledge’. It combines three different perspectives: experimental systems, concept formation, and the pivotal role of error. We then present an historical account of the invention of the Scanning Tunnelling Microscope (STM), or Raster-Tunnelmikroskop, and interpret it within the proposed framework. We show that at the outset of the STM project, Binnig and Rohrer—the inventors of the machine—filed two patent disclosures; the first is dated 22 December 1978 (Switzerland), and the second, two years later, 12 September 1980 (US). By studying closely these patent disclosures, the attempts to realize them, and the subsequent development of the machine, we present, within the framework of generating experimental knowledge, a new account of the invention of the STM. While the realization of the STM was still a long way off, the patent disclosures served as blueprints, marking the changes that had to be introduced on the way from the initial idea to its realization.     

SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout

Uric acid is the end product of purine metabolism in humans and great apes, which have lost hepatic uricase activity, leading to uniquely high serum uric acid concentrations (200-500 microM) compared with other mammals (3-120 microM). About 70% of daily urate disposal occurs via the kidneys, and in 5-25% of the human population, impaired renal excretion leads to hyperuricemia. About 10% of people with hyperuricemia develop gout, an inflammatory arthritis that results from deposition of monosodium urate crystals in the joint. We have identified genetic variants within a transporter gene, SLC2A9, that explain 1.7-5.3% of the variance in serum uric acid concentrations, following a genome-wide association scan in a Croatian population sample. SLC2A9 variants were also associated with low fractional excretion of uric acid and/or gout in UK, Croatian and German population samples. SLC2A9 is a known fructose transporter, and we now show that it has strong uric acid transport activity in Xenopus laevis oocytes.     

Forecasting for the LCD monitor market

The TFT‐LCD (thin‐film transistor–liquid crystal display) industry is one of the key global industries with products that have high clock speed. In this research, the LCD monitor market is considered for an empirical study on hierarchical forecasting (HF). The proposed HF methodology consists of five steps. First, the three hierarchical levels of the LCD monitor market are identified. Second, several exogenously driven factors that significantly affect the demand for LCD monitors are identified at each level of product hierarchy. Third, the three forecasting techniques—regression analysis, transfer function, and simultaneous equations model—are combined to forecast future demand at each hierarchical level. Fourth, various forecasting approaches and disaggregating proportion methods are adopted to obtain consistent demand forecasts at each hierarchical level. Finally, the forecast errors with different forecasting approaches are assessed in order to determine the best forecasting level and the best forecasting approach. The findings show that the best forecast results can be obtained by using the middle‐out forecasting approach. These results could guide LCD manufacturers and brand owners on ways to forecast future market demands. Copyright 2008 John Wiley & Sons, Ltd.     

Automating sequence-based detection and genotyping of SNPs from diploid samples

The detection of sequence variation, for which DNA sequencing has emerged as the most sensitive and automated approach, forms the basis of all genetic analysis. Here we describe and illustrate an algorithm that accurately detects and genotypes SNPs from fluorescence-based sequence data. Because the algorithm focuses particularly on detecting SNPs through the identification of heterozygous individuals, it is especially well suited to the detection of SNPs in diploid samples obtained after DNA amplification. It is substantially more accurate than existing approaches and, notably, provides a useful quantitative measure of its confidence in each potential SNP detected and in each genotype called. Calls assigned the highest confidence are sufficiently reliable to remove the need for manual review in several contexts. For example, for sequence data from 47-90 individuals sequenced on both the forward and reverse strands, the highest-confidence calls from our algorithm detected 93% of all SNPs and 100% of high-frequency SNPs, with no false positive SNPs identified and 99.9% genotyping accuracy. This algorithm is implemented in a software package, PolyPhred version 5.0, which is freely available for academic use.     

Trapping methods for rangeland insects in burned and unburned sites: a comparison

Different insect trapping methods were compared weekly on recently burned and nearby unburned rangeland in the Great Basin of western Utah. Flight traps (or wing traps) collected the most specimens (total = 4,916 at burned site, 4,384 at unburned site) but represented the fewest species (no more than 11 spp./wk at either site); this method was not recommended because of difficulty in removing specimens from adhesive. Water traps amassed the next largest number of specimens (￣x ± SE/wk = 150.9 ± 75.3 at burned site, 158.0 ± 66.4 at unburned site) and the most species (￣x ± SE/wk = 21.6 ± 6.4 at burned site, 35. 1 ± 4.5 at unburned site). The weekly collections from pitfall traps between the sites were significantly different (P < .05) in number of specimens (￣x ± SE/wk = 8.1 ± 1.5 at burned site, 19.7 ± 4.8 at unburned site) and species (￣x ± SE/wk = 4.7 ± 0.6 at burned site, 9.5 ± 2.0 at unburned site). Malaise traps were the most convenient. Black Malaise traps collected more specimens (￣x ± SE/wk = 99.8 ± 19.4 at burned site, 90.6 ± 16.4 at unburned site) and species (￣x ± SE/wk = 22.9 ± 3.9 at burned site, 19.4 ± 6.5 at unburned site) than white malaise traps (specimens: ￣x ± SE/wk = 72.1 ± 22.4 at burned site, 87.1 ± 31.2 at unburned site; species: ￣x ± SE/ wk = 19.7 ± 6.6 at burned site, 16.4 ± 5.4 at unburned site), although this difference was not significant.     

Comparison of two roadside survey procedures for dwarf mistletoes on the Sawtooth National Forest, Idaho

Two roadside surveys were conducted for dwarf mistletoes parasitizing lodgepole pine and Douglas-fir on the Sawtooth National Forest, Idaho. One survey used variable-radius plots located less than 150 m from roads. The 2nd survey used variable-radius plots established at 200-m intervals along 1600-m transects run perpendicular to the same roads. Estimates of the incidence (percentage of trees infected and percentage of plots infested) and severity (average dwarf mistletoe rating) for both lodgepole pine and Douglas-fir dwarf mistletoes were not significantly different for the 2 survey methods. These findings are further evidence that roadside-plot surveys and transect-plot surveys conducted away from roads provide similar estimates of the incidence of dwarf mistletoes for large forested areas.     

Host-induced morphological variations in the strigeoid trematode Posthodiplostomum minimum (Trematoda: Diplostomatidae). II. Body measurements and tegument modifications

Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Extensive feeding experiments were undertaken to determine if physiological host specificity was a major characteristic of Posthodiplostomum minimum. This involved the feeding of experimentally infected sunfish livers containing metacercariae of P. minimum to amphibian, reptilian, avian and mammalian hosts. Host - induced morphological variations of adult P. minimum were shown to be associated with the genus and class of host employed as well as with the inherent variability of P. minimum exclusive of host factors. Morphological characters such as body size and shape and tegumental surface and spines are indicated as undergoing morphological variation. Of all the experimental definitive hosts used, avian and mammalian are the most suitable for normal development of P. minimum. Amphibian and reptilian hosts demonstrate marked variation in the adult worm development usually manifested by pronounced size decrease.