Publications

characterization of new bioactive enzyme inhibitors from endophytic bacillus amyloliquefaciens rwl-1.	endophytic bacteria are known to produce a wide array of bioactive secondary metabolites with beneficial effects on human health. in the current study, a novel endophytic bacterial strain, bacillus amyloliquefaciens rwl-1, was isolated from the seeds of oryza sativa. initially, the crude extract of rwl-1 was assessed for potential biological effects of enzyme inhibition and cytotoxicity and was found to exhibit a broad spectrum inhibition for α-glucosidase (37 ± 0.09%) and urease (49.4 ± 0.53%). ...	2018	29304029
involvement of nadph oxidase isoforms in the production of o2- manipulated by aba in the senescing leaves of early-senescence-leaf (esl) mutant rice (oryza sativa).	in this study, the differences in reactive oxygen species (ros) generation and abscisic acid (aba) accumulation in senescing leaves were investigated by early-senescence-leaf (esl) mutant and its wild type, to clarify the relationship among aba levels, ros generation, and nadph oxidase (nox) in senescing leaves of rice (oryza sativa). the temporal expression levels of osnox isoforms in senescing leaves and their expression patterns in response to aba treatment were determined through quantitativ ...	2018	29309410
favorable marker alleles for panicle exsertion length in rice (oryza sativa l.) mined by association mapping and the rstep-lrt method.	the panicle exsertion length (pel) in rice (oryza sativa l.) is an important trait for hybrid seed production. we investigated the pel in a chromosome segment substitution line (cssl) population consisting of 66 lines and a natural population composed of 540 varieties. in the cssl population, a total of seven qtls for pel were detected across two environments. the percentage of phenotypic variance explained (pve) ranged from 10.22 to 50.18%, and the additive effect ranged from -1.77 to 6.47 cm. ...	2017	29312380
identification and map-based cloning of the light-induced lesion mimic mutant 1 (lil1) gene in rice.	the hypersensitive response (hr) is a mechanism by which plants prevent the spread of pathogen. despite extensive study, the molecular mechanisms underlying hr remain poorly understood. lesion mimic mutants (lmms), such as lil1 that was identified in an ethylmethane sulfonate mutagenized population of indica rice (oryza sativa l. ssp. indica) 93-11, can be used to study the hr. under natural field conditions, the leaves of lil1 mutant plants exhibited light-induced, small, rust-red lesions that ...	2017	29312386
ospt4 contributes to arsenate uptake and transport in rice.	arsenic (as) is toxic to organisms, and elevated as accumulation in rice (oryza sativa) grain may pose a significant health risk to humans. the predominant form of as in soil under aerobic conditions is as(v), which has a chemical structure similar to that of po43-. rice roots take up as(v) by phosphate (pi) transporters, such as ospt1 and ospt8. in the present study, we investigated the contribution of ospt4, belonging to the pht1 family, on rice as(v) uptake and transport. we determined the mr ...	2017	29312424
proteome-wide lysine acetylation identification in developing rice (oryza sativa) seeds and protein co-modification by acetylation, succinylation, ubiquitination, and phosphorylation.	protein lysine acetylation is a highly conserved post-translational modification with various biological functions. however, only a limited number of acetylation sites have been reported in plants, especially in cereals, and the function of non-histone protein acetylation is still largely unknown. in this report, we identified 1003 lysine acetylation sites in 692 proteins of developing rice seeds, which greatly extended the number of known acetylated sites in plants. seven distinguished motifs w ...	2017	29313810
coexistence of bt-transgenic and conventional rice affects insect abundance and plant fitness in fields.	as genetically modified (gm) crops have been cultivated worldwide, concerns emerge over ecological consequences because of the coexistence of transgenic and non-transgenic crops in fields. we first conducted field experiments using insect-resistant bt-transgenic rice expressing bacillus thuringiensis and its counterpart conventional rice (oryza sativa l.) with or without insecticide spraying in 2013 and 2014. in 2015 and 2016, bt-transgenic and conventional rice were employed in the pure and mix ...	2018	29318739
silicon amendment to rice plants contributes to reduced feeding in a phloem-sucking insect through modulation of callose deposition.	silicon (si) uptake by poaceae plants has beneficial effects on herbivore defense. increased plant physical barrier and altered herbivorous feeding behaviors are documented to reduce herbivorous arthropod feeding and contribute to enhanced plant defense. here, we show that si amendment to rice (oryza sativa) plants contributes to reduced feeding in a phloem feeder, the brown planthopper (nilaparvata lugens, bph), through modulation of callose deposition. we associated the temporal dynamics of bp ...	2018	29321899
protein activity of the fusarium fujikuroi rhodopsins caro and opsa and their relation to fungus-plant interaction.	fungi possess diverse photosensory proteins that allow them to perceive different light wavelengths and to adapt to changing light conditions in their environment. the biological and physiological roles of the green light-sensing rhodopsins in fungi are not yet resolved. the rice plant pathogen fusarium fujikuroi exhibits two different rhodopsins, caro and opsa. caro was previously characterized as a light-driven proton pump. we further analyzed the pumping behavior of caro by patch-clamp experi ...	2018	29324661
strigolactone biosynthesis genes of rice is required for the punctual entry of arbuscular mycorrhizal fungi into the roots.	arbuscular mycorrhiza (am) is a mutualistic association between most plant species and the ancient fungal phylum glomeromycota in roots, and it plays a key role in a plant's nutrient uptake from the soil. roots synthesize strigolactones (sls), derivatives of carotenoids, and exude them to induce energy metabolism and hyphal branching of am fungi. despite the well-documented roles of sls in the presymbiotic phase, little is known about the role of sls in the process of root colonization. here we ...	2018	29325120
a novel rice xylosyltransferase catalyzes the addition of 2-o-xylosyl side chains onto the xylan backbone.	xylan is a major hemicellulose in both primary walls and secondary walls of grass species. it consists of a linear backbone of β-1,4-linked xylosyl residues that are often substituted with monosaccharides and disaccharides. xylosyl substitutions directly on the xylan backbone have not been reported in grass species and genes responsible for xylan substitutions in grass species have not been well elucidated. here, we report functional characterization of a rice (oryza sativa) gt61 glycosyltransfe ...	2018	29325159
a maize phytochrome-interacting factors protein zmpif1 enhances drought tolerance by inducing stomatal closure and improves grain yield in oryza sativa.	phytochrome-interacting factors (pifs) play major roles in regulating plant growth and development, but their roles in drought stress remain elusive. here, we cloned and characterized a maize (zea mays) pif transcription factor, zmpif1. the expression level of zmpif1 was significantly induced by independent drought and abscisic acid (aba) treatments. the zmpif1 transgenic rice and arabidopsis displayed water-saving and drought-resistance, which were associated with reduced a stomatal aperture an ...	2018	29327440
t-dna tagging-based gain-of-function of oshkt1;4 reinforces na exclusion from leaves and stems but triggers na toxicity in roots of rice under salt stress.	the high affinity k⁺ transporter 1;4 (hkt1;4) in rice (oryza sativa), which shows na⁺ selective transport with little k⁺ transport activity, has been suggested to be involved in reducing na in leaves and stems under salt stress. however, detailed physiological roles of oshkt1;4 remain unknown. here, we have characterized a transfer dna (t-dna) insertion mutant line of rice, which overexpresses oshkt1;4, owing to enhancer elements in the t-dna, to gain an insight into the impact of oshkt1;4 on sa ...	2018	29329278
genome-wide analyses of direct target genes of four rice nac-domain transcription factors involved in drought tolerance.	plant stress responses and mechanisms determining tolerance are controlled by diverse sets of genes. transcription factors (tfs) have been implicated in conferring drought tolerance under drought stress conditions, and the identification of their target genes can elucidate molecular regulatory networks that orchestrate tolerance mechanisms.	2018	29329517
contrasting effects of alkaline amendments on the bioavailability and uptake of cd in rice plants in a cd-contaminated acid paddy soil.	reducing cadmium (cd) concentrations in rice grains is important for food safety, particularly in acid paddy fields in south china where the soils have been previously contaminated with cd. a field experiment was conducted to evaluate the effects of four alkaline amendments, i.e., lime, compost, biochar, and carbide slag on soil bioavailability and uptake of cd in plants of two rice cultivars (oryza sativa l.) in a cd-contaminated acid paddy soil. the addition of these amendments significantly d ...	2018	29330814
diminution of arsenic accumulation in rice seedlings co-cultured with anabaena sp.: modulation in the expression of lower silicon transporters, two nitrogen dependent genes and lowering of antioxidants activity.	the present study was intended to investigate the role of algae, anabaena sp. in the amelioration of as toxicity, when co-cultured with rice seedlings. the reduction of growth in rice seedlings against as(iii) and as(v) was recovered with anabaena sp. the anabaena sp. also reduced the accumulation of as, where it was more efficient against 60µm as(iii) (49%) than as(v) (23%) in rice shoot. similarly, with reduction of as accumulation, lower silicon transporters (lsi-1 and lsi-2) was found to be ...	2018	29331724
pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.	the rich genetic diversity in oryza sativa and oryza rufipogon serves as the main sources in rice breeding. large-scale resequencing has been undertaken to discover allelic variants in rice, but much of the information for genetic variation is often lost by direct mapping of short sequence reads onto the o. sativa japonica nipponbare reference genome. here we constructed a pan-genome dataset of the o. sativa-o. rufipogon species complex through deep sequencing and de novo assembly of 66 divergen ...	2018	29335547
the phytotoxicities of decabromodiphenyl ether (bde-209) to different rice cultivars (oryza sativa l.).	decabromodiphenyl ether (bde-209), as a major component of brominated flame retardants, has been detected in the agricultural soil in considerable amount. given that bde-209 is toxic, ubiquitous and persistent, bde-209 might induce toxic effects on rice cultivars planted in contaminated soil. a comparative study was conducted on phytotoxicities and gc-ms based antioxidant-related metabolite levels to investigate the differences of phytotoxicities of bde-209 to rice cultivars in yangtze river del ...	2018	29339338
a profilin gene promoter from switchgrass (panicum virgatum l.) directs strong and specific transgene expression to vascular bundles in rice.	a switchgrass vascular tissue-specific promoter (pvpfn2) and its 5'-end serial deletions drive high levels of vascular bundle transgene expression in transgenic rice. constitutive promoters are widely used for crop genetic engineering, which can result in multiple off-target effects, including suboptimal growth and epigenetic gene silencing. these problems can be potentially avoided using tissue-specific promoters for targeted transgene expression. one particularly urgent need for targeted cell ...	2018	29340787
concentrations of arsenic and lead in rice (oryza sativa l.) in iran: a systematic review and carcinogenic risk assessment.	exposure to heavy metals such as arsenic (as), lead (pb), and cadmium (cd) in either the short or the long term can cause cancers in humans. dietary intake and consumption of rice (oryza sativa l.) is increasing in iran, and several studies on the concentration of heavy metals in rice have been carried out in this country in recent years. in this perspective, the main objective of the present study was to investigate, even via a meta-analysis of the existing literature, the presence of as and pb ...	2018	29341878
membrane fluxes, bypass flows, and sodium stress in rice: the influence of silicon.	provision of silicon (si) to roots of rice (oryza sativa l.) can alleviate salt stress by blocking apoplastic, transpirational bypass flow of na+ from root to shoot. however, little is known about how si affects na+ fluxes across cell membranes. here, we measured radiotracer fluxes of 24na+, plasma membrane depolarization, tissue ion accumulation, and transpirational bypass flow, to examine the influence of si on na+ transport patterns in hydroponically grown, salt-sensitive (cv. ir29) and salt- ...	2018	29342282
effects of silver nanocolloids on plant complex type n-glycans in oryza sativa roots.	silver nanomaterials have been mainly developed as antibacterial healthcare products worldwide, because of their antibacterial activity. however, there is little data regarding the potential risks and effects of large amounts of silver nanomaterials on plants. in contrast, n-glycans play important roles in various biological phenomena, and their structures and expressions are sensitive to ambient environmental changes. therefore, to assesse the effects of silver nanomaterials, we focused on the ...	2018	29343819
modulates brassinosteroids-mediated growth regulation and influences architecture and grain shape.	rice (oryza sativa) is the most important crop and feeds more than half of the world population. the architecture of rice, including height, leaf inclination, and tiller number, is important for rice planting and yield. plant hormone, brassinosteroids (br), plays crucial roles in modulating plant architecture and seed yield. but br cannot be applied in agriculture production directly because br regulated multiple processes and could not be transcriptional regulated in different tissues. this art ...	2018	29345105
can cd translocation in oryza sativa l. be attenuated by arbuscular mycorrhizal fungi in the presence of edta?	arbuscular mycorrhizal (am) fungi play an important role in plant tolerance of heavy metal contamination. in this study, a pot experiment was conducted to illustrate the effects of the two am fungi species funneliformis mosseae (fm) and rhizophagus irregularis (ri) on plant growth of oryza sativa l. either with or without ethylenediamine tetraacetate (edta) addition and during exposure to five cd concentrations (in the range of 0-5 mg kg-1). the results showed that fm inoculation achieved greate ...	2018	29349740
deciphering the environmental impacts on rice quality for different rice cultivated areas.	rice (oryza sativa l.) is cultivated in a wide range of climatic conditions, and is one of mankind's major staple foods. the interaction of environmental factors with genotype effects major agronomic traits such as yield, quality, and resistance in rice. however, studies on the environmental factors affecting agronomic traits are often difficult to conduct because most environmental factors are dynamic and constantly changing.	2018	29352429
1h, 13c and 15n nmr assignments of cyclophilin lrt2 (oscyp2) from rice.	cyclophilins are enzymes that catalyze the isomerization of a prolyl-peptide bond and are found in both prokaryotes and eukaryotes. lrt2 (also known as oscyp2) is a cyclophilin in rice (oryza sativa), that has importance in lateral root development and stress tolerance. lrt2 is 172 amino acids long and has a molecular weight of 18.3 kda. here, we report the backbone and sidechain resonance assignments of 1h, 13c, 15n in the lrt2 protein using several 2d and 3d heteronuclear nmr experiments at ph ...	2018	29353448
genome-wide association study of seed dormancy and the genomic consequences of improvement footprints in rice (oryza sativa l.).	seed dormancy is an important agronomic trait affecting grain yield and quality because of pre-harvest germination and is influenced by both environmental and genetic factors. however, our knowledge of the factors controlling seed dormancy remains limited. to better reveal the molecular mechanism underlying this trait, a genome-wide association study was conducted in an indica-only population consisting of 453 accessions genotyped using 5,291 snps. nine known and new significant snps were identi ...	2017	29354150
variation in the abundance of oshak1 transcript underlies the differential salinity tolerance of an indica and a japonica rice cultivar.	salinity imposes a major constraint over the productivity of rice. a set of chromosome segment substitution lines (cssls), derived from a cross between the japonica type cultivar (cv.) nipponbare (salinity sensitive) and the indica type cv. 9311 (moderately tolerant), was scored using a hydroponics system for their salinity tolerance at the seedling stage. two of the cssls, which share a ∼1.2 mbp stretch of chromosome 4 derived from cv. nipponbare, were as sensitive to the stress as cv. nipponba ...	2017	29354152
expression analysis of proteinase inhibitor-ii under osrglp2 promoter in response to wounding and signaling molecules in transgenic nicotiana benthamiana.	proteinase inhibitor-ii (pi-ii) genes are important defense related genes that play critical regulatory roles in plant growth and development. in the present study, the expression of tomato pi-ii gene was investigated under the control of a wound-inducible osrglp2 (oryza sativa root germin like protein 2) promoter in transgenic tobacco plants after wounding, aba and meja applications. transcript level of target gene in transgenic plants was confirmed by quantitative real time pcr (qpcr). in resp ...	2018	29354362
isovitexin (iv) induces apoptosis and autophagy in liver cancer cells through endoplasmic reticulum stress.	liver cancer is a leading cause of cancer death worldwide, and novel chemotherapeutic drugs to suppress liver cancer are urgently required. isovitexin (iv), a glycosylflavonoid, is extracted from rice hulls of oryza sativa, and has various biological activities. however, the anti-tumor effect of iv against liver cancer has not yet been demonstrated in vitro or in vivo. in the present study, we showed that iv significantly suppressed the growth of liver cancer cells. mechanistic studies indicated ...	2018	29355527
identification of cyp703a3-3 and analysis of regulatory role of cyp703a3 in rice anther cuticle and pollen exine development.	anther cuticle and pollen exine are two elaborated lipid-soluble barriers protecting pollen grains from environmental and biological stresses. however, less is known about the mechanisms underlying the synthesis of these lipidic polymers. here, we identified a no-pollen male-sterility mutant cyp703a3-3 from indica restorer line zhonghui 8015 (zh8015) mutant library treated with 60coγ-ray radiation. histological analysis indicated that cyp703a3-3 underwent abnormal tapetal cells development, prod ...	2018	29355682
plant s6 kinases do not require hydrophobic motif phosphorylation for activity in yeast lacking ypk3.	the ribosomal protein s6 kinases (s6k) are among the major substrates and crucial effectors of the target of rapamycin (tor) kinase, which is an evolutionarily conserved regulator of cell growth and proliferation. recent research indicates that yeast ypk3 is an ortholog of mammalian s6ks. here, we find that plant s6ks restore ribosomal protein s6 phosphorylation in a rapamycin-sensitive manner in yeast cells lacking ypk3. however, phosphorylation of a hydrophobic motif, which is mediated through ...	2018	29355926
lack of actpk1, an sty kinase, enhances ammonium uptake and use and promotes growth of rice seedlings under sufficient external ammonium.	ammonium influx into plant roots via the high-affinity transport system (hats) is down-modulated under elevated external ammonium, preventing ammonium toxicity. in ammonium-fed arabidopsis, ammonium transporter 1 (amt1) trimers responsible for hats activity are allosterically inactivated in a dose-dependent manner via phosphorylation of the conserved threonine at the carboxyl-tail by the calcineurin b-like protein 1-calcineurin b-like protein-interacting protein kinase 23 complex and other yet u ...	2018	29356222
a negative regulator in response to salinity in rice: oryza sativa salt-, aba- and drought-induced ring finger protein 1 (ossadr1).	ring (really interesting new gene) finger proteins play crucial roles in abiotic stress responses in plants. we report the ring finger e3 ligase, an oryza sativa salt, abscisic acid (aba), and drought stress-induced ring finger protein 1 gene (ossadr1). we demonstrated that although ossar1 possesses e3 ligase activity, a single amino acid substitution (ossadr1c168a) in the ring domain exhibited no e3 ligase activity, suggesting that the activity of most e3s is specified by the ring domain. addit ...	2018	29361060
the c-s-a gene system regulates hull pigmentation and reveals evolution of anthocyanin biosynthesis pathway in rice.	floral organs in rice (oryza sativa) can be purple, brown or red in color due to the accumulation of flavonoids. but the molecular mechanism underlying specific organ pigmentation is not clear. here, we propose a c-s-a gene model for rice hull pigmentation and characterize through genetic, molecular and metabolomic approaches. further we conduct phylogenetic studies to reveal the evolution of rice color. in this gene system, c1 encodes a r2r3-myb transcription factor and acts as a color-producin ...	2018	29361187
the newly identified heat-stress sensitive albino 1 gene affects chloroplast development in rice.	high temperature, a major abiotic stress, significantly affects the yield and quality of crops in many parts of the world. components of the photosynthetic apparatus are highly susceptible to thermal damage. although the responses to acute heat stress have been studied intensively, the mechanisms that regulate chloroplast development under heat stress remain obscure, especially in crop plants. here, we cloned and characterized the gene responsible for the heat-sensitive albino1 (hsa1) mutation i ...	2018	29362095
osmads57 together with ostb1 coordinates transcription of its target oswrky94 and d14 to switch its organogenesis to defense for cold adaptation in rice.	plants modify their development to adapt to their environment, protecting themselves from detrimental conditions such as chilling stress by triggering a variety of signaling pathways; however, little is known about how plants coordinate developmental patterns and stress responses at the molecular level. here, we demonstrate that interacting transcription factors osmads57 and ostb1 directly target the defense gene oswrky94 and the organogenesis gene d14 to trade off the functions controlling/mode ...	2018	29364524
overexpression of osmir164b-resistant osnac2 improves plant architecture and grain yield in rice.	plant architecture is a major target of rice (oryza sativa) breeding and selection, but the underlying regulatory networks remain unclear. here, we overexpressed a osnac2 mutant (oern) that cannot be cleaved by the microrna mir164b. oern plants had better plant architecture, longer panicles, and produced more grains. the parental line averaged 12.2 primary and 31.5 secondary branches in the main panicles; two oern lines averaged 15.0 and 15.2 primary, and 41.5 and 44.3 secondary branches. in lar ...	2018	29365136
progress in zip transporter gene family in rice.	zinc and iron are essential mineral elements for the growth of oryza sativa l. and also micronutrients for human health. therefore, it is vital to study biofortification of rice with zn and fe in order to improve the yield and quality of rice, as well as to enhance nutritional states of humans. the zinc-regulated transporters and iron-regulated transporter-like proteins (the zip family) control the absorption and translocation of zn and fe and maintain their homeostasis in rice. reciprocally, th ...	2018	29367191
chlorophyll fluorescence and reflectance-based non-invasive quantification of blast, bacterial blight and drought stresses in rice.	response of rice (oryza sativa) exposed to both biotic and abiotic stresses can be quantified by employing fast and accurate optical methods. in this study, the overall stress responses of (i) 12 near-isogenic lines (nils) in the genetic background of the rice blast-susceptible cultivar lijiangxintuanheigu (lth) and (ii) four nils in the genetic background of the bacterial blight-susceptible cultivar ir24, were inspected by means of chl fluorescence (chl-f) imaging. the distribution of the maxim ...	2018	29370434
draft genome sequence of pantoea ananatis strain 1.38, a bacterium isolated from the rhizosphere of oryza sativa var. puntal that shows biotechnological potential as an inoculant.	pantoea ananatis 1.38 is a strain isolated from the rhizosphere of irrigated rice in southern spain. its genome was estimated at 4,869,281 bp, with 4,644 coding sequences (cdss). the genome encompasses several cdss related to plant growth promotion, such as that for siderophore metabolism, and virulence genes characteristic of pathogenic pantoea spp. are absent.	2018	29371365
exploring traditional aus-type rice for metabolites conferring drought tolerance.	traditional varieties and landraces belonging to the aus-type group of rice (oryza sativa l.) are known to be highly tolerant to environmental stresses, such as drought and heat, and are therefore recognized as a valuable genetic resource for crop improvement. using two aus-type (dular, n22) and two drought intolerant irrigated varieties (ir64, ir74) an untargeted metabolomics analysis was conducted to identify drought-responsive metabolites associated with tolerance.	2018	29372429
characterization and oral delivery of proinsulin-transferrin fusion protein expressed using expresstec.	proinsulin-transferrin fusion protein (proins-tf) has been designed and successfully expressed from the mammalian hek293 cells (hek-proins-tf). it was found that hek-proins-tf could be converted into an activated form in the liver. furthermore, hek-proins-tf was demonstrated as an extra-long acting insulin analogue with liver-specific insulin action in streptozotocin (stz)-induced type 1 diabetic mice. however, due to the low production yield from transfected hek293 cells, there are other intere ...	2018	29373562
biochar amendment changes jasmonic acid levels in two rice varieties and alters their resistance to herbivory.	biochar addition to soil not only sequesters carbon for the long-term but enhances agricultural productivity. several well-known benefits arise from biochar amendment, including constant provision of nutrients, increased soil moisture retention, decreased soil bulk density, and sometimes the induction of systemic resistance against foliar and soil borne plant pathogens. however, no research has investigated the potential of biochar to increase resistance against herbivory. the white-backed plant ...	2018	29373575
rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression.	formation of nucleosomes along eukaryotic dna has an impact on transcription. major transcriptional changes occur in response to low external phosphate (pi) in plants, but the involvement of chromatin-level mechanisms in pi starvation responses have not been investigated.	2018	29373953