EVALUATING A PRECISION AGRICULTURE HERBICIDE DECISION MODEL FOR WINTER WHEAT

Replaced with revised version of paper 08/02.Crop Production/Industries,

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases

<p>Abstract</p> <p>Background</p> <p>Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases.</p> <p>Results</p> <p>To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS) for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC) and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page <url>http://diseasome.kobic.re.kr/</url>, and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes.</p> <p>Conclusion</p> <p>Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for evaluation in both epidemiological and molecular biological approaches to diseases-gene association studies. Furthermore, researchers then can decide semi-automatically the data set for association studies while considering the relationships between genetic variation and diseases. The database can also be economical for disease-association studies, as well as to facilitate an understanding of the processes which cause disease. Currently, the database contains 14,674 SNP records and 109,715 gene records associated with human diseases and it is updated at regular intervals.</p

Effects of paramagnetic fluctuations on the thermochemistry of MnO (100) surfaces in the oxygen evolution reaction

We investigated the effects of paramagnetic (PM) fluctuations on the thermochemistry of the MnO(100) surface in the oxygen evolution reaction (OER) using the "noncollinear magnetic sampling method \textit{plus} $U$" (NCMSM$+U$). Various physical properties, such as the electronic structure, free energy, and charge occupation, of the MnO (100) surface in the PM state with several OER intermediates, were reckoned and compared to those in the antiferromagnetic (AFM) state. We found that PM fluctuation enhances charge transfer from a surface Mn ion to each of the intermediates and strengthens the chemical bond between them, while not altering the overall features, such as the rate determining step and resting state, in reaction pathways. The enhanced charge transfer can be attributed to the delocalized nature of valence bands observed in the PM surface. In addition, it was observed that chemical-bond enhancement depends on the intermediates, resulting in significant deviations in reaction energy barriers. Our study suggests that PM fluctuations play a significant role in the thermochemistry of chemical reactions occurring on correlated oxide surfaces.Comment: Maintext: 15 pages, 3 figures 2 tables; SI: 3 pages, 2 figure

IDENTIFICATION OF PICK UP NOISE FOR LASER PRINTERS BASED ON PSYCHOACOUSTIC PARAMETERS

ABSTRACT This paper illustrates that a method for identification of pick up noise and an analysis the cause of pick up noise by substituting components of a laser printer. The operating sound radiated from a laser printer includes the tonal noise components caused by the rotating mechanical components such as gear, shaft, motor, fan, etc. A sound operated by laser printers has become important competitiveness in printer industries as the demand of laser printers increases. Especially, a noise between a friction pad and a paper in the process of printing has become an essential issue in an aspect of quality evaluation. However the existing criteria for determining the above noise have solely relied on human&apos;s subjective judgments; which highlights the requirement to objectify these criteria. In this paper, the standard of existing pick up noise is established by finding the tonality, which is a psychoacoustic parameter, of noticeable limit sound level. Based on the findings of the method, the study has found factors which cause pick-up noise and suggests the substitution of following components of printers such as: spring constants, spring force, and the quality of friction pads. As a result, it is confirmed that the proposed pick up noise index has usefulness to classify whether existence of pick up noise with an objective evaluation and not to occur the noise based on design optimized combination of laser printer components

Progress in Understanding and Sequencing the Genome of Brassica rapa

Brassica rapa, which is closely related to Arabidopsis thaliana, is an important crop and a model plant for studying genome evolution via polyploidization. We report the current understanding of the genome structure of B. rapa and efforts for the whole-genome sequencing of the species. The tribe Brassicaceae, which comprises ca. 240 species, descended from a common hexaploid ancestor with a basic genome similar to that of Arabidopsis. Chromosome rearrangements, including fusions and/or fissions, resulted in the present-day “diploid” Brassica species with variation in chromosome number and phenotype. Triplicated genomic segments of B. rapa are collinear to those of A. thaliana with InDels. The genome triplication has led to an approximately 1.7-fold increase in the B. rapa gene number compared to that of A. thaliana. Repetitive DNA of B. rapa has also been extensively amplified and has diverged from that of A. thaliana. For its whole-genome sequencing, the Brassica rapa Genome Sequencing Project (BrGSP) consortium has developed suitable genomic resources and constructed genetic and physical maps. Ten chromosomes of B. rapa are being allocated to BrGSP consortium participants, and each chromosome will be sequenced by a BAC-by-BAC approach. Genome sequencing of B. rapa will offer a new perspective for plant biology and evolution in the context of polyploidization

Okanin, a chalcone found in the genus Bidens, and 3-penten-2-one inhibit inducible nitric oxide synthase expression via heme oxygenase-1 induction in RAW264.7 macrophages activated with lipopolysaccharide

Excess production of nitric oxide by activated macrophages via inducible nitric oxide synthase leads to the development of various inflammatory diseases. Heme oxygenase-1 expression via activation of nuclear factor-erythroid 2-related factor 2 inhibits nitric oxide production and inducible nitric oxide synthase expression in activated macrophages. Okanin is one of the most abundant chalcones found in the genus Bidens (Asteraceae) that is used as various folk medications in Korea and China for treating inflammation. Here, we found that okanin (possessing the α-β unsaturated carbonyl group) induced heme oxygenase-1 expression via nuclear factor-erythroid 2-related factor 2 activation in RAW264.7 macrophages. 3-Penten-2-one, of which structure, as in okanin, possesses the α-β unsaturated carbonyl group, also induced nuclear factor-erythroid 2-related factor 2-dependent heme oxygenase-1 expression, while both 2-pentanone (lacking a double bond) and 2-pentene (lacking a carbonyl group) were virtually inactive. In lipopolysaccharide-activated RAW264.7 macrophages, both okanin and 3-penten-2-one inhibited nitric oxide production and inducible nitric oxide synthase expression via heme oxygenase-1 expression. Collectively, our findings suggest that by virtue of its α-β unsaturated carbonyl functional group, okanin can inhibit nitric oxide production and inducible nitric oxide synthase expression via nuclear factor-erythroid 2-related factor 2-dependent heme oxygenase-1 expression in lipopolysaccharide-activated macrophages

Ammonium Inhibits Chromomethylase 3-Mediated Methylation of the Arabidopsis Nitrate Reductase Gene NIA2

Gene methylation is an important mechanism regulating gene expression and genome stability. Our previous work showed that methylation of the nitrate reductase (NR) gene NIA2 was dependent on chromomethylase 3 (CMT3). Here, we show that CMT3-mediated NIA2 methylation is regulated by ammonium in Arabidopsis thaliana. CHG sequences (where H can be A, T, or C) were methylated in NIA2 but not in NIA1, and ammonium [(NH4)2SO4] treatment completely blocked CHG methylation in NIA2. By contrast, ammonium had no effect on CMT3 methylation, indicating that ammonium negatively regulates CMT3-mediated NIA2 methylation without affecting CMT3 methylation. Ammonium upregulated NIA2 mRNA expression, which was consistent with the repression of NIA2 methylation by ammonium. Ammonium treatment also reduced the overall genome methylation level of wild-type Arabidopsis. Moreover, CMT3 bound to specific promoter and intragenic regions of NIA2. These combined results indicate that ammonium inhibits CMT3-mediated methylation of NIA2 and that of other target genes, and CMT3 selectively binds to target DNA sequences for methylation

Development of Barley Cultivars for Animal Forage in Korea

In Korea, the domestic consumption of barley as a cereal crop has been decreasing since the 1980s. It has been considered that crop production in the winter-season rice fields could enhance the global competitiveness of domestic livestock industry by providing better quality fodder to livestock and enhancing field use rate. Therefore, the purpose of barley cultivation for cereal food production has been recently replaced by the production of the barley for forage use. Consequently, the area of barley cultivation for forage is markedly increasing in Korea. While any type of barley can be used as forage for feeding cattle, whole crop barley delivers a higher dry matter yield than conventional feed barley. This paper described the present state of forage barley cultivars developed in Korea