Survival of norovirus surrogate on various food-contact surfaces.

Kim, An-Na,Park, Shin Young,Bae, San-Cheong,Oh, Mi-Hwa,Ha, Sang-Do Springer New York 2014 Food and environmental virology Vol.6 No.3

<P>Norovirus (NoV) is an environmental threat to humans, which spreads easily from one infected person to another, causing foodborne and waterborne diseases. Therefore, precautions against NoV infection are important in the preparation of food. The aim of this study was to investigate the survival of murine norovirus (MNV), as a NoV surrogate, on six different food-contact surfaces: ceramic, wood, rubber, glass, stainless steel, and plastic. We inoculated 10(5) PFU of MNV onto the six different surface coupons that were then kept at room temperature for 28 days. On the food-contact surfaces, the greatest reduction in MNV was 2.28 log10 PFU/coupon, observed on stainless steel, while the lowest MNV reduction was 1.29 log10 PFU/coupon, observed on wood. The rank order of MNV reduction, from highest to lowest, was stainless steel, plastic, rubber, glass, ceramic, and wood. The values of d R (time required to reduce the virus by 90%) on survival plots of MNV determined by a modified Weibull model were 277.60 h (R(2) = 0.99) on ceramic, 492.59 h (R(2) = 0.98) on wood, 173.56 h on rubber (R(2) = 0.98), 97.18 h (R(2) = 0.94) on glass, 91.76 h (R(2) = 0.97) on stainless steel, and 137.74 h (R(2) = 0.97) on plastic. The infectivity of MNV on all food-contact surfaces remained after 28 days. These results show that MNV persists in an infective state on various food-contact surfaces for long periods. This study may provide valuable information for the control of NoV on various food-contact surfaces, in order to prevent foodborne disease.</P>

Rice <i>miR172</i> induces flowering by suppressing <i>OsIDS1</i> and <i>SNB</i> , two AP2 genes that negatively regulate expression of <i>Ehd1</i> and florigens

Lee, Yang-Seok,Lee, Dong-Yeon,Cho, Lae-Hyeon,An, Gynheung Springer New York 2014 Rice Vol.7 No.-

<P><B>Background</B></P><P>Rice is a facultative short-day plant that flowers under long days (LD) after a lengthy vegetative phase. Although several inhibitors that delay flowering have been identified, the process by which rice eventually flowers under non-permissive LD conditions is not well understood.</P><P><B>Results</B></P><P>Overexpression of <I>miR172</I> reduced flowering time significantly, suggesting its role as an inducer. Levels of <I>miR172</I> increased as plants aged, further supporting our findings. Transcripts of <I>SNB</I> and <I>OsIDS1</I>, two members of the AP2 family that have the <I>miR172</I> target site, were reduced in older plants as the level of <I>miR172</I> rose. Overexpression of those AP2 genes delayed flowering; overexpression of <I>miR172</I>-resistant forms of <I>SNB</I> or <I>OsIDS1</I> further delayed this process. This demonstrated that the AP2 genes function downstream of <I>miR172</I>. Two florigen genes -- <I>Hd3a</I> and <I>RFT1 --</I> and their immediate upstream regulator <I>Ehd1</I> were suppressed in the AP2 overexpression plants. This suggested that the AP2 genes are upstream repressors of <I>Ehd1</I>. In phytochrome mutants, <I>miR172d</I> levels were increased whereas those of <I>SNB</I> and <I>OsIDS1</I> were decreased. Thus, it appears that phytochromes inhibit <I>miR172d</I>, an AP2 suppresser.</P><P><B>Conclusions</B></P><P>We revealed that <I>miR172d</I> developmentally induced flowering via repressing <I>OsIDS1</I> and <I>SNB</I>, which suppressed <I>Ehd1</I>. We also showed that phytochromes negatively regulated <I>miR172</I>.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12284-014-0031-4) contains supplementary material, which is available to authorized users.</P>

Genome-wide identification and analysis of <i>Japonica</i> and <i>Indica</i> cultivar-preferred transcripts in rice using 983 Affymetrix array data

Jung, Ki-Hong,Gho, Hyun-Jung,Giong, Hoi-Khoanh,Chandran, Anil Kumar Nalini,Nguyen, Quynh-Nga,Choi, HeeBak,Zhang, Tian,Wang, Wen,Kim, Jin-Hyun,Choi, Hong-Kyu,An, Gynheung Springer New York 2013 Rice Vol.6 No.-

<P><B>Background</B></P><P>Accumulation of genome-wide transcriptome data provides new insight on a genomic scale which cannot be gained by analyses of individual data. The majority of rice (<I>O. sativa</I>) species are <I>japonica</I> and <I>indica</I> cultivars. Genome-wide identification of genes differentially expressed between <I>japonica</I> and <I>indica</I> cultivars will be very useful in understanding the domestication and evolution of rice species.</P><P><B>Results</B></P><P>In this study, we analyzed 983 of the 1866 entries in the Affymetrix array data in the public database: 595 generated from <I>indica</I> and 388 from <I>japonica</I> rice cultivars. To discover differentially expressed genes in each cultivar, we performed significance analysis of microarrays for normalized data, and identified 490 genes preferentially expressed in <I>japonica</I> and 104 genes in <I>indica</I>. Gene Ontology analyses revealed that defense response-related genes are significantly enriched in both cultivars, indicating that <I>japonica</I> and <I>indica</I> might be under strong selection pressure for these traits during domestication. In addition, 36 (34.6%) of 104 genes preferentially expressed in <I>indica</I> and 256 (52.2%) of 490 genes preferentially expressed in <I>japonica</I> were annotated as genes of unknown function. Biotic stress overview in the MapMan toolkit revealed key elements of the signaling pathway for defense response in <I>japonica</I> or <I>indica</I> eQTLs.</P><P><B>Conclusions</B></P><P>The percentage of screened genes preferentially expressed in <I>indica</I> was 4-fold higher (34.6%) and that in <I>japonica</I> was 5-fold (52.2%) higher than expected (11.1%), suggesting that genes of unknown function are responsible for the novel traits that distinguish <I>japonica</I> and <I>indica</I> cultivars. The identification of 10 functionally characterized genes expressed preferentially in either <I>japonica</I> or <I>indica</I> highlights the significance of our candidate genes during the domestication of rice species. Functional analysis of the roles of individual components of stress-mediated signaling pathways will shed light on potential molecular mechanisms to improve disease resistance in rice.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/1939-8433-6-19) contains supplementary material, which is available to authorized users.</P>

Development of breeding lines with three pyramided resistance genes that confer broad-spectrum bacterial blight resistance and their molecular analysis in rice

Suh, Jung-Pil,Jeung, Ji-Ung,Noh, Tae-Hwan,Cho, Young-Chan,Park, So-Hyun,Park, Hyun-Su,Shin, Mun-Sik,Kim, Chung-Kon,Jena, Kshirod K Springer New York 2013 Rice Vol.6 No.-

<P><B>Background</B></P><P>The development of resistant cultivars has been the most effective and economical strategy to control bacterial leaf blight (BB) disease of rice caused by <I>Xanthomonas oryzae</I> pv. <I>oryzae</I> (<I>Xoo</I>). Molecular markers have made it possible to identify and pyramid valuable genes of agronomic importance in resistance rice breeding. In this study, three resistance genes (<I>Xa4</I> + <I>xa5</I> + <I>Xa21</I>) were transferred from an indica donor (IRBB57), using a marker-assisted backcrossing (MAB) breeding strategy, into a BB-susceptible elite japonica rice cultivar, Mangeumbyeo, which is high yielding with good grain quality.</P><P><B>Results</B></P><P>Our analysis led to the development of three elite advanced backcross breeding lines (ABL) with three resistance genes by foreground and phenotypic selection in a japonica genetic background without linkage drag. The background genome recovery of the ABL expressed more than 92.1% using genome-wide SSR marker analysis. The pathogenicity assays of three resistance-gene-derived ABL were conducted under glasshouse conditions with the 18 isolates of <I>Xoo</I> prevalent in Korea. The ABL exhibited very small lesion lengths, indicating a hypersensitive reaction to all 18 isolates of <I>Xoo</I>, with agronomic and grain quality traits similar to those of the recurrent parent. Pyramiding the resistance genes <I>Xa4, xa5</I> and <I>Xa21</I> provided a higher resistance to <I>Xoo</I> than the introduction of the individual resistance genes. Additionally, the combination of two dominant and one recessive BB resistance gene did not express any negative effect on agronomic traits in the ABL.</P><P><B>Conclusions</B></P><P>The strategy of simultaneous foreground and phenotypic selection to introduce multiple R genes is very useful to reduce the cost and the time required for the isolation of desirable recombinants with target resistance genes in rice. The resistance-gene-derived ABL have practical breeding value without a yield penalty by providing broad-spectrum resistance against most of the existing isolates of BB in South Korea and will have a high impact on the yield stability and sustainability of rice productivity.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/1939-8433-6-5) contains supplementary material, which is available to authorized users.</P>

SNP-based analysis of genetic diversity in anther-derived rice by whole genome sequencing

Jeong, In-Seon,Yoon, Ung-Han,Lee, Gang-Seob,Ji, Hyeon-So,Lee, Hyun-Ju,Han, Chang-Deok,Hahn, Jang-Ho,An, Gynheung,Kim, Tae-Ho Springer New York 2013 Rice Vol.6 No.-

<P><B>Background</B></P><P>Anther culture has advantage to obtain a homozygous progeny by induced doubling of haploid chromosomes and to improve selection efficiency for invaluable agronomical traits. Therefore, anther culturing is widely utilized to breed new varieties and to induce genetic variations in several crops including rice. Genome sequencing technologies allow the detection of a massive number of DNA polymorphism such as SNPs and Indels between closely related cultivars. These DNA polymorphisms permit the rapid identification of genetic diversity among cultivars and genomic locations of heritable traits. To estimate sequence diversity derived from anther culturing, we performed whole-genome resequencing of five Korean rice accessions, including three anther culture lines (BLB, HY-04 and HY-08), their progenitor cultivar (Hwayeong), and an additional japonica cultivar (Dongjin).</P><P><B>Results</B></P><P>A total of 1,165 × 10<SUP>6</SUP> raw reads were generated with over 58× coverage that detected 1,154,063 DNA polymorphisms between the Korean rice accessions and <I>Nipponbare</I>. We observed that in Hwayeong and its progenies, 0.64 SNP was found per one kb of <I>Nipponbare</I> genome, while Dongjin, bred by a conventional breeding method, had a lower number of SNPs (0.45 SNP/kb). Among 1,154,063 DNA polymorphisms, 29,269 non-synonymous SNPs located on 30,013 genes and these genes were functionally classified based on gene ontology (GO). We also analyzed line-specific SNPs which were estimated 1 ~ 3% of the total SNPs. The frequency of non-synonymous SNPs in each accession ranged from 26 SNPs in Hwayeong to 214 SNPs in HY-04.</P><P><B>Conclusions</B></P><P>The genetic difference we detected between the progenies derived from anther culture and their mother cultivar is due to somaclonal variation during tissue culture process, such as karyotype change, chromosome rearrangement, gene amplification and deletion, transposable element, and DNA methylation. Detection of genome-wide DNA polymorphisms by high-throughput sequencer enabled to identify sequence diversity derived from anther culturing and genomic locations of heritable traits. Furthermore, it will provide an invaluable resource to identify molecular markers and genes associated with diverse traits of agronomical importance.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/1939-8433-6-6) contains supplementary material, which is available to authorized users.</P>

Agronomic and genetic analysis of Suweon 542, a rice floury mutant line suitable for dry milling

Mo, Young-Jun,Jeung, Ji-Ung,Shin, Young-Seop,Park, Chul Soo,Kang, Kyung-Ho,Kim, Bo-Kyeong Springer New York 2013 Rice Vol.6 No.-

<P><B>Background</B></P><P>Producing rice flour of good quality by dry milling is necessary to reduce milling costs and promote the processed rice food industry. This study was conducted to evaluate the dry milling properties of Suweon 542, a floury endosperm mutant, and identify the chromosomal region responsible for the floury endosperm characteristics.</P><P><B>Results</B></P><P>Compared with the wild type, after dry milling process, the grain hardness of Suweon 542 was significantly lower because of its round and loosely packed starch granules. Also, the flour of Suweon 542 had significantly smaller particles and less damaged starch than Namil and other rice cultivars and its particle size distribution was similar to a commercial wheat cultivar. Considering that the yield loss of Suweon 542 due to its floury endosperm was largely compensated for by an increased number of spikelets per panicle, Suweon 542 has potential value as a raw material for rice flour production. Association analysis using 70 genome-wide SSR markers and 94 F<SUB>2</SUB> plants derived from Suweon 542/Milyang 23 showed that markers on chromosome 5 explained a large portion of the variation in floury grains percentage (FGP). Further analysis with an increased number of SSR markers revealed that the floury endosperm of Suweon 542 was directed by a major recessive locus, <I>flo7</I>(<I>t</I>), located in the 19.33–19.86 Mbp region of chromosome 5, with RM18639 explaining 92.2% of FGP variation in the F<SUB>2</SUB> population.</P><P><B>Conclusions</B></P><P>The floury endosperm of Suweon 542 is suitable for dry milling, with a small flour particle size and low damaged starch content. Further physical mapping of <I>flo7</I>(<I>t</I>), the floury endosperm locus of Suweon 542, would facilitate efficient breeding of rice cultivars with proper dry milling adaptability that can be used in the processed rice food industry.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/1939-8433-6-37) contains supplementary material, which is available to authorized users.</P>

Spectral Reproducibility and Quantification of Peptides in MALDI of Samples Prepared by Micro-Spotting

Bae, Yong Jin,Park, Kyung Man,Ahn, Sung Hee,Moon, Jeong Hee,Kim, Myung Soo Springer New York LLC 2014 Journal of the American Society for Mass Spectrome Vol.25 No.8

<P>Previously, we reported that MALDI spectra of peptides became reproducible when temperature was kept constant. Linear calibration curves derived from such spectral data could be used for quantification. Homogeneity of samples was one of the requirements. Among the three popular matrices used in peptide MALDI [i.e., α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (DHB), and sinapinic acid (SA)], homogeneous samples could be prepared by conventional means only for CHCA. In this work, we showed that sample preparation by micro-spotting improved the homogeneity for all three cases.</P> [FIG OMISSION]</BR>

Effective Application of Bicelles for Conformational Analysis of G Protein-Coupled Receptors by Hydrogen/Deuterium Exchange Mass Spectrometry

Duc, Nguyen Minh,Du, Yang,Thorsen, Thor S.,Lee, Su Youn,Zhang, Cheng,Kato, Hideaki,Kobilka, Brian K.,Chung, Ka Young Springer New York LLC 2015 Journal of the American Society for Mass Spectrome Vol.26 No.5

<P>G protein-coupled receptors (GPCRs) have important roles in physiology and pathology, and 40% of drugs currently on the market target GPCRs for the treatment of various diseases. Because of their therapeutic importance, the structural mechanism of GPCR signaling is of great interest in the field of drug discovery. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a useful tool for analyzing ligand binding sites, the protein-protein interaction interface, and conformational changes of proteins. However, its application to GPCRs has been limited for various reasons, including the hydrophobic nature of GPCRs and the use of detergents in their preparation. In the present study, we tested the application of bicelles as a means of solubilizing GPCRs for HDX-MS studies. GPCRs (e.g., β<SUB>2</SUB>-adrenergic receptor [β<SUB>2</SUB>AR], μ-opioid receptor, and protease-activated receptor 1) solubilized in bicelles produced better sequence coverage (greater than 90%) than GPCRs solubilized in n-dodecyl-β-D-maltopyranoside (DDM), suggesting that bicelles are a more effective method of solubilization for HDX-MS studies. The HDX-MS profile of β<SUB>2</SUB>AR in bicelles showed that transmembrane domains (TMs) undergo lower deuterium uptake than intracellular or extracellular regions, which is consistent with the fact that the TMs are highly ordered and embedded in bicelles. The overall HDX-MS profiles of β<SUB>2</SUB>AR solubilized in bicelles and in DDM were similar except for intracellular loop 3. Interestingly, we detected EX1 kinetics, an important phenomenon in protein dynamics, at the C-terminus of TM6 in β<SUB>2</SUB>AR. In conclusion, we suggest the application of bicelles as a useful method for solubilizing GPCRs for conformational analysis by HDX-MS.</P> [FIG OMISSION]</BR>

Airborne Single Particle Mass Spectrometers (SPLAT II & miniSPLAT) and New Software for Data Visualization and Analysis in a Geo-Spatial Context

Zelenyuk, Alla,Imre, Dan,Wilson, Jacqueline,Zhang, Zhiyuan,Wang, Jun,Mueller, Klaus Springer New York LLC 2015 Journal of the American Society for Mass Spectrome Vol.26 No.2

<P>Understanding the effect of aerosols on climate requires knowledge of the size and chemical composition of <I>individual</I> aerosol particles-two fundamental properties that determine an aerosol’s optical properties and ability to serve as cloud condensation or ice nuclei. Here we present our aircraft-compatible single particle mass spectrometers, SPLAT II and its new, miniaturized version, miniSPLAT that measure in-situ and in real-time the size and chemical composition of individual aerosol particles with extremely high sensitivity, temporal resolution, and sizing precision on the order of a monolayer. Although miniSPLAT’s size, weight, and power consumption are significantly smaller, its performance is on par with SPLAT II. Both instruments operate in dual data acquisition mode to measure, in addition to single particle size and composition, particle number concentrations, size distributions, density, and asphericity with high temporal resolution. We also present ND-Scope, our newly developed interactive visual analytics software package. ND-Scope is designed to explore and visualize the vast amount of complex, multidimensional data acquired by our single particle mass spectrometers, along with other aerosol and cloud characterization instruments on-board aircraft. We demonstrate that ND-Scope makes it possible to visualize the relationships between different observables and to view the data in a geo-spatial context, using the interactive and fully coupled Google Earth and Parallel Coordinates displays. Here we illustrate the utility of ND-Scope to visualize the spatial distribution of atmospheric particles of different compositions, and explore the relationship between individual particle compositions and their activity as cloud condensation nuclei.</P> [FIG OMISSION]</BR>

High-density mapping of quantitative trait loci for grain-weight and spikelet number in rice

Kim, Dong-Min,Lee, Hyun-Sook,Kwon, Soo-Jin,Fabreag, Mark Edward,Kang, Ju-Won,Yun, Yeo-Tae,Chung, Chong-Tae,Ahn, Sang-Nag Springer New York 2014 Rice Vol.7 No.-

<P><B>Background</B></P><P>High grain yield is one of the most important traits requiring improvement in rice breeding programs. Consequently, the genetic basis of spikelets per panicle (SPP) and grain weight (TGW) have received much research focus because of their importance in rice yield.</P><P><B>Results</B></P><P>In this study, IL28, which is a near isogenic line (NIL) developed by introgressing chromosomal segments of the cultivar ‘Moroberekan’ into the cultivar ‘Ilpumbyeo’, showed a significant increase in the number of spikelets per panicle (SPP) and 1,000-grain weight (TGW) compared to the recurrent parent, Ilpumbyeo. Quantitative trait locus (QTL) analysis in 243 F2 plants derived from a cross between IL28 and Ilpumbyeo indicated that both <I>qSPP6</I> and <I>qTGW6</I> are located in the interval RM3430–RM20580. Following substitution mapping with 50 F<SUB>3:4:5</SUB> lines, <I>qSPP6</I> was mapped to a 429-kb interval between RM20521 and InDel-1, while <I>qTGW6</I> was mapped to a 37.85-kb interval between InDel-1 and SNP--3 based on the <I>japonica</I> genome sequence. This result indicates that <I>qSPP6</I> and <I>qTGW6</I> are different genes. Yield trials with substitution lines indicated that lines harboring the homozygous Moroberekan segment at both the <I>qSPP6</I> and <I>qTGW6</I> region showed significantly higher grain yield than Ilpumbyeo.</P><P><B>Conclusion</B></P><P>Because the Moroberekan alleles for SPP and TGW have been shown to be beneficial in the genetic background of Ilpumbyeo, both the <I>qSPP6</I> and <I>qTGW6</I> alleles might prove valuable in improving rice yields. Closely linked SSR markers are expected to facilitate the cloning of genes that underlie these QTLs, as well as with marker-assisted selection for variation in SPP and TGW in rice breeding programs.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12284-014-0014-5) contains supplementary material, which is available to authorized users.</P>