Showing papers by "Rural Development Administration published in 2008"
TL;DR: The high success rate of the GoldenGate assay makes this a useful technique for quickly creating high density genetic maps in species where SNP markers are rapidly becoming available.
Abstract: Large numbers of single nucleotide polymorphism (SNP) markers are now available for a number of crop species. However, the high-throughput methods for multiplexing SNP assays are untested in complex genomes, such as soybean, that have a high proportion of paralogous genes. The Illumina GoldenGate assay is capable of multiplexing from 96 to 1,536 SNPs in a single reaction over a 3-day period. We tested the GoldenGate assay in soybean to determine the success rate of converting verified SNPs into working assays. A custom 384-SNP GoldenGate assay was designed using SNPs that had been discovered through the resequencing of five diverse accessions that are the parents of three recombinant inbred line (RIL) mapping populations. The 384 SNPs that were selected for this custom assay were predicted to segregate in one or more of the RIL mapping populations. Allelic data were successfully generated for 89% of the SNP loci (342 of the 384) when it was used in the three RIL mapping populations, indicating that the complex nature of the soybean genome had little impact on conversion of the discovered SNPs into usable assays. In addition, 80% of the 342 mapped SNPs had a minor allele frequency >10% when this assay was used on a diverse sample of Asian landrace germplasm accessions. The high success rate of the GoldenGate assay makes this a useful technique for quickly creating high density genetic maps in species where SNP markers are rapidly becoming available.
253 citations
TL;DR: It is found that a model that contains both additive and dominance effects, estimated from genome-wide marker data, is successful in predicting unobserved phenotypes and is significantly better than a prediction based upon the phenotypes of close relatives.
Abstract: Genome-wide association studies (GWAS) for quantitative traits and disease in humans and other species have shown that there are many loci that contribute to the observed resemblance between relatives. GWAS to date have mostly focussed on discovery of genes or regulatory regions habouring causative polymorphisms, using single SNP analyses and setting stringent type-I error rates. Genome-wide marker data can also be used to predict genetic values and therefore predict phenotypes. Here, we propose a Bayesian method that utilises all marker data simultaneously to predict phenotypes. We apply the method to three traits: coat colour, %CD8 cells, and mean cell haemoglobin, measured in a heterogeneous stock mouse population. We find that a model that contains both additive and dominance effects, estimated from genome-wide marker data, is successful in predicting unobserved phenotypes and is significantly better than a prediction based upon the phenotypes of close relatives. Correlations between predicted and actual phenotypes were in the range of 0.4 to 0.9 when half of the number of families was used to estimate effects and the other half for prediction. Posterior probabilities of SNPs being associated with coat colour were high for regions that are known to contain loci for this trait. The prediction of phenotypes using large samples, high-density SNP data, and appropriate statistical methodology is feasible and can be applied in human medicine, forensics, or artificial selection programs.
205 citations
TL;DR: During a survey of endophytic diazotrophic bacteria associated with different rice varieties in Tamilnadu, some “endophytes” were obtained and one of them, MGK3, was consistently more active in reducing acetylene, and 16S rDNA sequences of isolateMGK3 confirmed its identification as Burkholderia vietnamiensis.
Abstract: During a survey of endophytic diazotrophic bacteria associated with different rice varieties in Tamilnadu, some “endophytes” were obtained Thirteen bacterial isolates from surface-sterilized roots and shoots were obtained in pure culture, which produced indole acetic acid (IAA) and reduced acetylene to ethylene Polymerase chain reaction (PCR) amplification confirmed the presence of nif-H gene in all the isolates Morphological, biochemical, and molecular characteristics indicated that all of them belonged to the genus Burkholderia One of them, MGK3, was consistently more active in reducing acetylene, and 16S rDNA sequences of isolate MGK3 confirmed its identification as Burkholderia vietnamiensis Colonization of rice root was confirmed by strain MGK3 marked with gusA gene The inoculated roots showed a blue color, which was most intense at the points of lateral root emergence and at the root tip Transverse sections of roots, 15 days after inoculation, revealed beta-glucuronidase (GUS) activity within many of the cortical intercellular spaces next to the stele and within the aerenchyma Nitrogen fixation was quantified by using 15N isotope dilution method with two different cultivars grown in pot and field experiments Higher nitrogen fixation was observed in variety Ponni than in ADT-43, where nearly 42% (field) and 40% (pot) of the nitrogen was derived from the atmosphere (% Ndfa) Isolate MGK3 was used to inoculate rice seedlings in a comparison with four other diazotrophs, viz, Gluconacetobacter diazotrophicus LMG7603, Herbaspirillum seropedicae LMG6513, Azospirillum lipoferum 4B LMG4348, and B vietnamiensis LMG10929 They were used to conduct two pot and four field inoculation experiments MGK3 alone, and combined with other diazotrophs, performed best under both pot and field conditions: combined inoculation produced yield increases between 95 and 236%, while MGK3 alone increased yield by 56 to 1216% over the uninoculated control treatment
173 citations
TL;DR: 2-AP, guaiacol, indole, and p-xylene largely influenced the difference between the aroma in cooked black and white rice, demonstrating significant differences between a black and a traditional white rice cultivar in terms of aroma.
Abstract: Black rice ( Oryza sativa L.), an aromatic specialty rice popular in Asia, has a unique flavor, the volatile chemistry of which has not been reported. The objectives of this research were to study volatile profiles of cooked black rice and to characterize the odor-active compounds. Thirty-five volatile compounds were identified by gas chromatography−mass spectrometry using a dynamic headspace system with Tenax trapping. Aldehydes and aromatics were quantitatively in the greatest abundance, accounting for 80.1% of total relative concentration of volatiles. The concentration of 2-acetyl-1-pyrroline (2-AP) was high, exceeded only by hexanal, nonanal, and 2-pentylfuran. A total of 25 odor-active compounds, determined by gas chromatography−olfactometry, were applied to principal component analysis, demonstrating significant differences between a black and a traditional white rice cultivar in terms of aroma and explaining 93.0% of the total variation. 2-AP, guaiacol, indole, and p-xylene largely influenced the ...
157 citations
TL;DR: Histological study of ovary sections revealed abnormalities in follicular epithelial cells due to AZA treatment, which indicates that AZA significantly inhibits the activity of AChE only at the high dose.
145 citations
TL;DR: The fact that all seven of the QTLs were co-localized in the same 37.4 kb interval suggests the possibility that a single, pleiotropic gene acting as a major regulator of plant development may control this suite of agronomically important plant phenotypes.
Abstract: A high-resolution physical map targeting a cluster of yield-related QTLs on the long arm of rice chromosome 9 has been constructed across a 37.4 kb region containing seven predicted genes. Using a series of BC3F4 nearly isogenic lines (NILs) derived from a cross between the Korean japonica cultivar Hwaseongbyeo and Oryza rufipogon (IRGC 105491), a total of seven QTLs for 1,000-grain weight, spikelets per panicle, grains per panicle, panicle length, spikelet density, heading date and plant height were identified in the cluster (P ≤ 0.0001). All seven QTLs were additive, and alleles from the low-yielding O. rufipogon parent were beneficial in the Hwaseongbyeo background. Yield trials with BC3F4 NILs showed that lines containing a homozygous O. rufipogon introgression in the target region out-yielded sibling NILs containing Hwaseongbyeo DNA by 14.2–17.7%, and out-yielded the Hwaseongbyeo parent by 16.2–23.7%. While higher yielding plants containing the O. rufipogon introgression were also taller and later than controls, the fact that all seven of the QTLs were co-localized in the same 37.4 kb interval suggests the possibility that a single, pleiotropic gene acting as a major regulator of plant development may control this suite of agronomically important plant phenotypes.
142 citations
TL;DR: The data suggest that HSP27 and IP3R1 are potential meat quality biomarkers and their identification provides new insight into the molecular mechanisms and pathways associated with overall beef quality.
138 citations
TL;DR: The results suggest that MCK1 is an MAPKKK involved in maintaining cell wall integrity of M. oryzae, and that remodeling of the cell wall in response to host environments is essential for fungal pathogenesis.
Abstract: Insertional mutagenesis of Magnaporthe oryzae led to the identification of MCK1, a pathogenicity gene predicted to encode mitogen-activated protein kinase kinase kinase (MAPKKK) homologous to BCK1 in Saccharomyces cerevisiae. Targeted disruption of MCK1 resulted in the fungus undergoing autolysis and showing hypersensitivity to cell-wall-degrading enzyme. The mck1 produced significantly reduced numbers of conidia and developed appressoria in a slightly retarded manner compared with the wild type. Appressorium of the mck1 mutant was unable to penetrate into plant tissues, thereby rendering the mutant nonpathogenic. Cytorrhysis assay and monitoring of lipid mobilization suggested that the appressorial wall was altered, presumably affecting the level of turgor pressure within appressorium. Furthermore, the mck1 mutant failed to grow inside plant tissue. Complementation of the mutated gene restored its ability to cause disease symptoms, demonstrating that MCK1 is required for fungal pathogenicity. Taken toget...
129 citations
TL;DR: Results showed that CelM2 is a novel endo-type cellulase that uses carboxymethyl cellulose as a sole carbon source and hydrolyzed avicel and xylan.
Abstract: To detect cellulases encoded by uncultured microorganisms, we constructed metagenomic libraries from Korean soil DNAs. Screenings of the libraries revealed a clone pCM2 that uses carboxymethyl cellulose (CMC) as a sole carbon source. Further analysis of the insert showed two consecutive ORFs ( celM2 and xynM2 ) encoding proteins of 226 and 662 amino acids, respectively. A multiple sequence analysis with the deduced amino acid sequences of celM2 showed 36% sequence identity with cellulase from the Synechococcus sp., while xynM2 had 59% identity to endo-1,4-β-xylanase A from Cellulomonas pachnodae . The highest enzymatic CMC hydrolysis was observable at pH 4.0 and 45 °C with recombinant CelM2 protein. Although the enzyme CelM2 additionally hydrolyzed avicel and xylan, no substrate hydrolysis was observed on oligosaccharides such as cellobiose, p NP-β - cellobioside, p NP-β-glucoside, and p NP-β-xyloside. These results showed that CelM2 is a novel endo-type cellulase.
121 citations
TL;DR: An improved method for evaluating sheath blight disease was selected by comparing two methods for evaluating disease severity among three partially resistant cultivars and five susceptible cultivars inoculated with liquid cultured mycelia balls, and a new formula was developed to calculate the disease susceptibility index.
Abstract: Sheath blight of rice, caused by Rhizoctonia solani, is one of the most important rice diseases worldwide; however, no rice cultivar has been found to be completely resistant to this fungus To facilitate detailed analysis of sheath blight resistance at genetic, molecular, biochemical, and functional genomic levels, new methods were developed for effective and uniform infection and accurate evaluation of the disease The efficiency of R solani infection was tested on two resistant (Tetep and Jasmine 85) and two susceptible (Chucheongbyeo, Junambyeo) cultivars using three different inoculum types (agar block, liquid cultured mycelia ball, and mycelia suspension) By covering the inoculated sheaths with aluminum foil to maintain humidity, 100% infection rate was achieved in this study Liquid cultured mycelia balls caused significantly longer lesions (54 cm) than other types of inoculum, including agar block (24 cm) and mycelia suspension (16 cm) An improved method for evaluating sheath blight disease was selected by comparing two methods for evaluating disease severity among three partially resistant cultivars and five susceptible cultivars inoculated with liquid cultured mycelia balls In addition, a new formula was developed to calculate the disease susceptibility index Lesion length and the susceptibility index generally were correlated in each leaf, but there were discrepancies between the two evaluation methods due to differences in plant architecture among the cultivars The susceptibility index calculated using the new formula was the most accurate method for evaluating sheath blight disease across all cultivars The effect of heading date and panicle number also was evaluated in relation to sheath blight resistance Cultivars with late heading dates generally were more resistant to sheath blight than those with early heading dates
119 citations
Journal Article•
TL;DR: A new developed 24K oligo microarray will be a useful tool for transcriptome profiling and this work will provide valuable insight in the response to abiotic stress in B. rapa.
Abstract: Genome wide transcription analysis in response to stresses is essential to provide the basis of effective engineering strategies to improve stress tolerance in crop plants. In order to perform transcriptome analysis in Brassica rapa, we constructed a B. rapa oligo microarray, KBGP-24K, using sequence information from approximately 24,000 unigenes and analyzed cold (4 degrees C), salt (250 mM NaCl), and drought (air-dry) treated B. rapa plants. Among the B. rapa unigenes represented on the microarray, 417 (1.7%), 202 (0.8%), and 738 (3.1%) were identified as responsive genes that were differently expressed 5-fold or more at least once during a 48-h treatment with cold, salt, and drought, respectively. These results were confirmed by RT-PCR analysis. In the abiotic stress responsive genes identified, we found 56 transcription factor genes and 60 commonly responsive genes. It suggests that various transcriptional regulatory mechanisms and common signaling pathway are working together under the abiotic stresses in B. rapa. In conclusion, our new developed 24K oligo microarray will be a useful tool for transcriptome profiling and this work will provide valuable insight in the response to abiotic stress in B. rapa.
TL;DR: In this article, Artificial Neural Networks (ANNs) were used to estimate soil erosion, dissolved P (DP) and NH"4-N concentrations of runoff from a land application site near Lincoln, Nebraska, USA.
TL;DR: Both phenotypes were co-segregated with the UGPase1 transgene in segregating T1 plants, which demonstrates that U GPase1 has functional roles in both male sterility and the development of a chalky endosperm.
Abstract: A rice genic male-sterility gene ms-h is recessive and has a pleiotropic effect on the chalky endosperm. After fine mapping, nucleotide sequencing analysis of the ms-h gene revealed a single nucleotide substitution at the 3'-splice junction of the 14th intron of the UDP-glucose pyrophosphorylase 1 (UGPase1; EC2.7.7.9) gene, which causes the expression of two mature transcripts with abnormal sizes caused by the aberrant splicing. An in vitro functional assay showed that both proteins encoded by the two abnormal transcripts have no UGPase activity. The suppression of UGPase by the introduction of a UGPase1-RNAi construct in wild-type plants nearly eliminated seed set because of the male defect, with developmental retardation similar to the ms-h mutant phenotype, whereas overexpression of UGPase1 in ms-h mutant plants restored male fertility and the transformants produced T(1) seeds that segregated into normal and chalky endosperms. In addition, both phenotypes were co-segregated with the UGPase1 transgene in segregating T(1) plants, which demonstrates that UGPase1 has functional roles in both male sterility and the development of a chalky endosperm. Our results suggest that UGPase1 plays a key role in pollen development as well as seed carbohydrate metabolism.
TL;DR: In this article, a label-free opto-fluidic ring resonator (OFRR) was developed for detection of an organophosphorus (OP) pesticide.
Abstract: We developed a novel label-free opto-fluidic ring resonator (OFRR) biosensor for detection of an organophosphorus (OP) pesticide. The OFRR is based on a micro-sized glass capillary whose circular wall forms a ring resonator that supports the whispering gallery modes (WGMs). The WGMs has an evanescent field in the capillary core and interacts with the analyte flowing in the capillary. We used parathion-methyl as a model system to investigate the OFRR sensing performance in terms of bulk refractive index sensitivity, surface activation for affinity property, detection limit, and reproducibility. The performance of the OFRR was further compared with that of the Biacore 3000 SPR system. Our results show that the detection limit of 3.8 × 10−11 M for parathion-methyl was achieved with an analysis time of about 0.5 min, 10 times faster than the surface plasmon resonance (SPR) system. Furthermore, the OFRR biosensor demonstrated excellent reproducibility (R.S.D. = 3.5%, n = 5). The OFRR offers optical label-free detection mechanism with integrated microfluidics. It is a promising technology platform for development of portable multi-channel biosensors with high sensitivity, quick detection time, and sub-nanoliter detection volume.
Journal Article•
TL;DR: It is demonstrated that BV induced apoptosis via a mitochondria-dependent pathway based on the changes of delta psi m, AIF and EndoG release in MCF7 cells.
Abstract: Our previous studies have shown that bee venom (BV) can induce apoptosis in human cervical cancer Ca Ski cells, but it can also affect human breast cancer cells, though its molecular mechanisms are not precisely known. In this study, the molecular mechanisms of apoptosis induced by BV in human breast cancer MCF7 cells were investigated. BV induced morphological changes (examined by phase-contrast microscopy) and inhibited the proliferation (examined by MTT assay) of MCF7 cells; both effects occurred in a dose- and time-dependent manner. Flow cytometric analysis demonstrated that BV induced the production of reactive oxygen species (ROS) and dysfunction of the mitochondrial membrane potential (Azm), and led to cytochrome c release, an increase in the levels of caspase-9 and Poly (ADP-ribose) polymerase (PARP) and then apoptosis. It also showed that BV induced S-phase arrest in MCF7 cells which may occur through the promotion of p53, p21, p27 and the exhibition of Cdk2. Western blotting demonstrated that BV reduced Bcl-2 and increased Bax protein levels which may have caused the changes of delta psi m. BV treatment led to ROS production up to but after treatment led to a decrease in the levels of ROS, which may be associated with the observations of BVaffecting glutathion S-transferase (GST), Zn-superoxide dismutase (Zn-SOD), Cu/Zn-superoxide dismutase (Cu/Zn-SOD) and catalase. The Comet assay also showed that BV induced DNA damage while DAPI staining also confirmed that BV induced apoptosis in examined MCF7 cells. Our results also showed that BV increased the levels of AIF and EndoG in MCF7 cells. In conclusion, our data demonstrated that BV induced apoptosis via a mitochondria-dependent pathway based on the changes of delta psi m, AIF and EndoG release in MCF7 cells.
TL;DR: To isolate and identify antioomycete substances from Fusarium oxysporum EF119 against Phytophthora infestans and to investigate their antimicrobial activities against various plant pathogenic bacteria, oomycetes and true fungi.
Abstract: Aims: To isolate and identify antioomycete substances from Fusarium oxysporum EF119 against Phytophthora infestans and to investigate their antimicrobial activities against various plant pathogenic bacteria, oomycetes and true fungi.
Methods and Results: Two antioomycete substances were isolated from liquid cultures of F. oxysporum EF119, which shows a potent disease control efficacy against tomato late blight caused by P. infestans. They were identified as bikaverin and fusaric acid by mass and nuclear magnetic resonance spectral analyses. They inhibited the mycelial growth of plant pathogenic oomycetes and fungi. Fusaric acid also effectively suppressed the cell growth of various plant pathogenic bacteria, but bikaverin was virtually inactive. Treatment with bikaverin at 300 μg ml−1 suppressed the development of tomato late blight by 71%. Fusaric acid provided effective control against tomato late blight and wheat leaf rust over 67% at concentrations more than 100 μg ml−1.
Conclusions: Both bikaverin and fusaric acid showed in vitro and in vivo antioomycete activity against P. infestans.
Significance and Impact of the Study: Fusarium oxysporum EF119 producing both bikaverin and fusaric acid may be used as a biocontrol agent against tomato late blight caused by P. infestans.
TL;DR: Administration of the main flavonoid glycoside component, pectolinarin, and its aglycone, pECTolinarigenin, for 2 weeks significantly decreased the activity levels of AST, ALT, ALP and LDH, indicating that the two compounds have hepatoprotective activity.
Abstract: To identify the hepatoprotective component from the leaves of Cirsium setidens (Compositae), the methanolic extract was divided into two fractions, chloroform and butanol fractions, and their hepatoprotective efficacy was evaluated in a rat model of hepatic injury caused by D-galactosamine (GalN). Hepatoprotective activity was measured by the activity of serum aspartate transaminase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), and lactate dehydrogenase (LDH). Glutathione metabolism was measured via biochemical parameters such as glutathione (GSH), glutathione reductase (GR), γ-glutamylcysteine synthetase (GCS), glutathione S-transferase (GST), and superoxide dismutase (SOD) levels. We subjected the butanol fraction, which had higher activity, to column chromatography to yield pectolinarin, which was further hydrolyzed to yield pectolinarigenin. Administration (10, 20 mg/kg, p.o.) of the main flavonoid glycoside component, pectolinarin, and its aglycone, pectolinarigenin, for 2 weeks significantly decreased the activity levels of AST, ALT, ALP and LDH, indicating that the two compounds have hepatoprotective activity. Pectolinarin and pectolinarigenin also increased activity levels of GSH, GR, GCS, and GST, as well as SOD. The significant effect was only seen in SOD activity. This suggests that the two components exhibit hepatoprotective activity mainly via SOD antioxidant mechanism.
TL;DR: Daily mean radiation and biomass accumulation during ripening, and sink production efficiency per unit biomass were critical factors to the yield gap of rice between DS and WS under the high-yielding tropical irrigated conditions.
Abstract: Rice (Oryza sativa L.) grain yield highly varies depending on cropping seasons under the tropical irrigated conditions. This study aimed to (i) compare the grain yield of rice in dry season (DS) and wet season (WS) and (ii) determine climatic and physiological factors critical to the yield gap between DS and WS. Six genotypes, two each for indica inbred, indica/indica F 1 hybrid, and the second-generation new plant type, were grown in DS and WS of 2003 and 2004. Significantly higher grain yields were achieved in DS than in WS by 94% for 2003 and 35% for 2004. Mean daily radiation was higher in DS than WS, particularly during grain filling stage than before flowering. The greater radiation during ripening in DS contributed to the higher grain yield. Major difference in biomass production between DS and WS occurred after flowering. Greater biomass accumulation from flowering to physiological maturity was associated with higher grain yield in DS than in WS, but not translocation of biomass accumulated before flowering to grains. Higher grain yield in DS was partly the result of greater spikelets due to higher spikelet production efficiency per unit biomass at flowering. Aboveground total biomass at physiological maturity was a crucial physiological factor to the yield gap between DS and WS. Daily mean radiation and biomass accumulation during ripening, and sink production efficiency per unit biomass were critical factors to the yield gap of rice between DS and WS under the high-yielding tropical irrigated conditions.
TL;DR: In this article, the authors examined the influence of temperature and solar radiation on grain filling duration and rate for effective grain filling period in the field-grown tropical irrigated rice genotypes.
TL;DR: Mutation in the W-box like element 1 (WLE 1) between 687 and 637-bp from TGACA to TGAAA completely abolished induction of the OsPR10a promoter by SA, indicating that the WLE 1 between −687 and −637 of OsPR 10a promoter is important in SA-mediated Os PR10a expression.
Abstract: Orysa sativa pathogenesis-related protein 10a (OsPR10a) was induced by pathogens, salicylic acid (SA), jasmonic acid (JA), ethephon, abscisic acid (ABA), and NaCl. We tried to analyze the OsPR10a promoter to investigate the transcriptional regulation of OsPR10a by SA. We demonstrated the inducibility of OsPR10a promoter by SA using transgenic Arabidopsis carrying OsPR10a:GFP as well as by transient expression assays in rice. To further identify the promoter region responsible for its induction by SA, four different deletions of the OsPR10a promoter were made, and their activities were measured by transient assays. The construct containing 687-bp OsPR10a promoter from its start codon exhibited a six-fold increase of induction compared to the control in response to SA. Mutation in the W-box like element 1 (WLE 1) between 687 and 637-bp from TGACA to TGAAA completely abolished induction of the OsPR10a promoter by SA, indicating that the WLE 1 between −687 and −637 of OsPR10a promoter is important in SA-mediated OsPR10a expression. We show for the first time that the W-box like element plays a role in SA mediated PR gene expression.
TL;DR: The map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF) technique, which will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes.
Abstract: The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences. A genome-wide physical map of the B. rapa genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC) clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing. The map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF) technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes. The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community.
TL;DR: Two bacterial strains isolated from air samples were characterized by determining their phenotypic characteristics, cellular fatty acid profiles and phylogenetic positions based on 16S rRNA gene sequence analysis, and it was concluded that strains 5317S-33(T) and 5413S-11 (T) represent two novel species within the genus Methylobacterium.
Abstract: Two bacterial strains isolated from air samples, 5317S-33T and 5413S-11T, were characterized by determining their phenotypic characteristics, cellular fatty acid profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that these isolates belonged to the genus Methylobacterium. Strain 5317S-33T was most closely related to Methylobacterium adhaesivum AR27T (97.9 % sequence similarity). Strain 5413S-11T was most closely related to Methylobacterium fujisawaense DSM 5686T (97.3 % sequence similarity), Methylobacterium oryzae CBMB20T (97.1 % similarity) and Methylobacterium radiotolerans JCM 2831T (97.0 % similarity). Cells of both strains were strictly aerobic, Gram-negative, motile and rod-shaped. The major fatty acid was C18 : 1
ω7c. The G+C contents of the genomic DNA were 68.0 mol% for strain 5317S-33T and 73.2 mol% for strain 5413S-11T. According to DNA–DNA hybridization data, strain 5317S-33T showed a level of DNA–DNA relatedness of 33 % with M. adhaesivum DSM 17169T, and strain 5413S-11T showed low levels of DNA–DNA relatedness (<35 %) with M. fujisawaense DSM 5686T, M. oryzae CBMB20T and M. radiotolerans DSM 1819T. On the basis of this polyphasic analysis, it was concluded that strains 5317S-33T and 5413S-11T represent two novel species within the genus Methylobacterium, for which the names Methylobacterium iners sp. nov. (type strain 5317S-33T =KACC 11765T =DSM 19015T) and Methylobacterium
aerolatum sp. nov. (type strain 5413S-11T =KACC 11766T =DSM 19013T) are proposed.
TL;DR: It is proposed that in transgenic plants, specific frequencies of sound treatment could be used to regulate the expression of any gene fused to the ald promoter, suggesting that the 1,506 bp a Ald promoter is sound-responsive.
Abstract: We identified a set of sound-responsive genes in plants using a sound-treated subtractive library and demonstrated sound regulation through mRNA expression analyses. Under both light and dark conditions, sound up-regulated expression of rbcS and ald. These are also light-responsive genes and these results suggest that sound could represent an alternative to light as a gene regulator. Ald mRNA expression increased significantly with treatment at 125 and 250 Hz, whereas levels decreased significantly with treatment at 50 Hz, indicating a frequency-specific response. To investigate whether the ald promoter responds to sound, we generated transgenic rice plants harboring a chimeric gene comprising a fusion of the ald promoter and GUS reporter. In three independent transgenic lines treated with 50 or 250 Hz for 4 h, GUS mRNA expression was up-regulated at 250 Hz, but down-regulated at 50 Hz. Thus, the sound-responsive mRNA expression pattern observed for the ald promoter correlated closely with that of ald, suggesting that the 1,506 bp ald promoter is sound-responsive. Therefore, we propose that in transgenic plants, specific frequencies of sound treatment could be used to regulate the expression of any gene fused to the ald promoter.
TL;DR: It is clear from the genotypic and phenotypic data presented that strain 5516S-11(T) represents a novel species of the genus Massilia, for which the name Massilia aerilata sp.
Abstract: A novel aerobic, Gram-negative, rod-shaped, motile bacterium, designated strain 5516S-11(T), was isolated from air samples collected in the Suwon region of the Republic of Korea. Analysis of the 16S rRNA gene sequence indicated that the organism belongs to the genus Massilia; the highest sequence similarity (97.2 %) was found with respect to Massilia aurea DSM 18055(T). Cells of strain 5516S-11(T) contained ubiquinone Q-8 as the predominant isoprenoid quinone and possessed summed feature 3 (C(16 : 1)omega7c/iso-C(15 : 0) 2-OH; 35.2 %), C(16 : 0) (30.6 %) and C(18 : 1)omega7c (11.7 %) as the major fatty acids. DNA-DNA hybridization revealed 32 % relatedness between strain 5516S-11(T) and M. aurea DSM 18055(T). The G+C content of the DNA of strain 5516S-11(T) was 68.9 mol%. It is clear from the genotypic and phenotypic data presented that strain 5516S-11(T) represents a novel species of the genus Massilia, for which the name Massilia aerilata sp. nov. is proposed. The type strain is 5516S-11(T) (=KACC 12505(T) =DSM 19289(T)).
Journal Article•
TL;DR: It is demonstrated that BV-induced apoptosis occurs via a Fas receptor pathway involving mitochondrial-dependent pathways and is closely related to the level of cytoplasmic Ca2+ in Ca Ski cells.
Abstract: Although it has been previously reported that bee venom (BV) can induce apoptosis in many cancer cell lines, there is no information on the effect of BV on human cervical cancer cells and its molecular mechanisms of action are not fully elucidated. In this study, the possible mechanisms of apoptosis by which BV acts on human cervical cancer Ca Ski cells were investigated. BV induced morphological changes and decreased the percentage of viable Ca Ski cells in a dose- and time-dependent manner. Flow cytometric analysis demonstrated that BV induced the production of reactive oxygen species, increased the level of cytoplasmic Ca2+, reduced mitochondrial membrane potential which led to cytochrome c release, and promoted the activation of caspase-3 which then led to apoptosis. BV also induced an increase in the levels of Fas, p53, p21 and Bax, but a decrease in the level of Bcl-2. The activities of both caspase-8 and caspase-9 were enhanced by BV, promoting caspase-3 activation, leading to DNA fragmentation. Based on the DNA fragmentation and DAPI staining, BV-induced apoptosis was mitochondrial-dependent and caspase-dependent. BV also promoted the expression of AIF and Endo G in the Ca Ski cells. Both AIF and Endo G proteins were released from the mitochondria, and then induced apoptosis which was not through activation of caspase. In conclusion, our data demonstrated that BV-induced apoptosis occurs via a Fas receptor pathway involving mitochondrial-dependent pathways and is closely related to the level of cytoplasmic Ca2+ in Ca Ski cells.
TL;DR: The authors used an incomplete factorial design where Australian consumers evaluated 216 beef samples derived from 18 cattle killed in Australia and Korean consumers assessed 216 samples from the same 18 cattle, plus 216 similar samples from 18 Korean cattle.
Abstract: Consumer responses were examined in an incomplete factorial design where Australian consumers evaluated 216 beef samples derived from 18 cattle killed in Australia and Korean consumers evaluated 216 samples from the same 18 cattle, plus 216 similar samples from 18 Korean cattle. Samples of the Mm. triceps brachii, longissimus dorsi and semimembranosus were cooked using grill and Korean barbeque methods. Each sample was sensory tested by 10 consumers, who scored it for tenderness, juiciness, like flavour, and overall liking. Consumers then graded each sample as either unsatisfactory (2 star), good every day (3 star), better than every day (4 star), or premium (5 star) quality. For those samples assessed by both Australian and Korean consumers, the Korean consumers graded a higher proportion of samples ‘unsatisfactory’ and a lower proportion of samples ‘premium’ grade product than Australian consumers. Using a composite meat quality score (MQ4) to predict grade, a discriminant analysis showed that the Korean consumers had boundary cut-offs for the lower grades, which were ~4–10 palatability units higher than the Australian consumers. Analysis of the residuals between actual and predicted palatability scores showed that the Meat Standards Australia (MSA) grading model produced relatively unbiased estimates within ±2 MQ4 units for the different consumer groups, muscle and carcass suspension treatments, with the exception of the M. semimembranosus samples. Implications of the results for both Korean and Australian beef markets through the use of an empirical grading model to predict palatability are discussed.
TL;DR: The results suggest that the elevated expression of the oxidation-related metabolism genes NADH dehydrogenase and ATPase is related to meat quality as indicated by a higher content of oxidative fibers and muscle fat, as well as redder meat color.
TL;DR: It is indicated that plum possesses immune enhancing properties, and that feeding chickens a plum-supplemented diet augments protective immunity against coccidiosis.
Abstract: The current study was conducted to evaluate the effect of dietary supplementation with a lyophilized powder made from plums (P) on host protective immune responses against avian coccidiosis, the most economically important parasitic disease of poultry. One-day-old White Leghorn chickens were fed from the time of hatch with a standard diet either without P (control and P 0 groups) or supplemented with P at 0.5% (P 0.5) or 1.0% (P 1.0) of the diet. Animals in the P 0, P 0.5, and P 1.0 groups were orally challenged with 5000 sporulated oocysts of Eimeria acervulina at day 12 post-hatch, while control animals were uninfected. Dietary supplementation of P increased body weight gain, reduced fecal oocyst shedding, and increased the levels of mRNAs for interferon-γ and interleukin-15 in the P 1.0 group at 10 days post-infection compared with the P 0 group. Furthermore, chickens fed either the P 0.5 or P 1.0 diets exhibited significantly greater spleen cell proliferation compared with the non-plum P 0 group. These results indicate that plum possesses immune enhancing properties, and that feeding chickens a plum-supplemented diet augments protective immunity against coccidiosis.
TL;DR: Phylogenetic evidence, together with the DNA-DNA relatedness values and phenotypic characteristics, indicated that strains JS6-6(T) and JS17-8(T), isolated from soil samples from Jeju, Republic of Korea, represent two novel species of the genus Chryseobacterium.
Abstract: Two yellow-pigmented bacterial strains, JS6-6T and JS17-8T, isolated from soil samples from Jeju, Republic of Korea, were studied to determine their taxonomic positions. The cells of the two bacteria were aerobic, Gram-negative, non-motile, straight rods. 16S rRNA gene sequence analysis indicated that both isolates should be placed in the genus Chryseobacterium of the family Flavobacteriaceae. Their 16S rRNA gene sequences showed similarities of 93.7–97.5 % to those of type strains of the genus Chryseobacterium. The values for DNA–DNA relatedness between both strains and type strains of closely related Chryseobacterium species were below 34 %. The fatty acids of the novel strains were similar to those of species of the genus Chryseobacterium. Both strains had MK-6 as the predominant respiratory quinone. The DNA G+C contents of strains JS6-6T and JS17-8T were 39.9 and 41.4 mol%, respectively. Phylogenetic evidence, together with the DNA–DNA relatedness values and phenotypic characteristics, indicated that strains JS6-6T and JS17-8T represent two novel species of the genus Chryseobacterium, for which the names Chryseobacterium soli sp. nov. and Chryseobacterium jejuense sp. nov., respectively, are proposed. The type strains of Chryseobacterium soli sp. nov. and Chryseobacterium jejuense sp. nov. are JS6-6T (=KACC 12502T=DSM 19298T) and JS17-8T (=KACC 12501T=DSM 19299T), respectively.
TL;DR: In this paper, a correlation analysis between the wavelength band ratio (λ 1/λ 2 ) and the assigned value for the surface condition (0 = normal, 1 = defect) was used to determine wavelength pairs that can be used to distinguish defect regions from normal regions on the apple surface.
Abstract: Visible/near-infrared reflectance spectra extracted from hyperspectral images of apples were used to determine wavelength pairs that can be used to distinguish defect regions from normal regions on the apple surface. The optimal wavelengths were selected based on correlation analysis between the wavelength band ratio (λ1/λ2) or difference (λ1 − λ2) and the assigned value for the surface condition (0 = normal, 1 = defect). Spectral images of apple surfaces at the selected wavelengths were used to validate the correlation analysis. The correlation coefficients obtained using the correlation analysis for band ratio and difference were 0.91 and 0.79, respectively. When applied to the set of apple images, the band ratio model correctly identified 195 of the 211 defects on a set of 70 Fuji apples containing at least one defect region. Thus, the correlation analysis was demonstrated to be a feasible method for selecting wavelength pairs for use in distinguishing defects from areas without defects on apples.