Publications

bacillus velezensis is not a later heterotypic synonym of bacillus amyloliquefaciens; bacillus methylotrophicus, bacillus amyloliquefaciens subsp plantarum and 'bacillus oryzicola' are later heterotypic synonyms of bacillus velezensis based on phylogenomics.	bacillus velezensis was previously reported to be a later heterotypic synonym of bacillus amyloliquefaciens, based on dna-dna relatedness values. we have sequenced a draft genome of b. velezensis nrrl b-41580t. comparative genomics and dna-dna relatedness calculations show that it is not a synonym of b. amyloliquefaciens. it was instead synonymous with bacillus methylotrophicus. 'bacillus oryzicola' is a recently described species that was isolated as an endophyte of rice (oryza sativa). the str ...	2015	26702995
antimicrobial activity and mechanism of action of a novel cationic α-helical octadecapeptide derived from α-amylase of rice.	amyi-1-18, an octadecapeptide derived from α-amylase (amyi-1) of rice (oryza sativa l. japonica), is a novel cationic α-helical antimicrobial peptide (amp) that contains two lysine and two arginine residues. the antimicrobial activity of amyi-1-18 against human pathogens was quantitatively evaluated using a chemiluminescence method that measures atp derived from viable cells. of the ten kinds of human pathogens, amyi-1-18 exhibited antimicrobial activity against nine. its 50% growth-inhibitory c ...	2015	25581614
cloning and characterization of a benzoic acid/salicylic acid carboxyl methyltransferase gene involved in floral scent production from lily (lilium 'yelloween').	in lily flowers, the volatile ester methyl benzoate is one of the major and abundant floral scent compounds; however, knowledge regarding the biosynthesis of methyl benzoate remains unknown for lilium. in this study, we isolated a benzoic acid/salicylic acid carboxyl methyltransferase (bsmt) gene, libsmt, from petals of lilium 'yelloween'. the gene has an open reading frame of 1083 base pairs (bp) and encodes a protein of 41.05 kda. sequence alignment and phylogenetic analyses of libsmt revealed ...	2015	26600510
functional properties and structural characterization of rice δ(1)-pyrroline-5-carboxylate reductase.	the majority of plant species accumulate high intracellular levels of proline to cope with hyperosmotic stress conditions. proline synthesis from glutamate is tightly regulated at both the transcriptional and the translational levels, yet little is known about the mechanisms for post-translational regulation of the enzymatic activities involved. the gene coding in rice (oryza sativa l.) for δ(1)-pyrroline-5-carboxylate (p5c) reductase, the enzyme that catalyzes the second and final step in this ...	2015	26284087
melatonin biosynthesis requires n-acetylserotonin methyltransferase activity of caffeic acid o-methyltransferase in rice.	caffeic acid o-methyltransferase (comt) methylates n-acetylserotonin into melatonin; that is, it has n-acetylserotonin o-methyltransferase (asmt) activity. the asmt activity of comt was first detected in arabidopsis thaliana comt (atcomt). to confirm the involvement of comt on melatonin synthesis in other plant species, the asmt activity of a comt from rice (oryza sativa) (oscomt) was evaluated. purified recombinant oscomt protein from escherichia coli was used to validate the high asmt activity ...	2015	26276868
stress-responsive expression patterns and functional characterization of cold shock domain proteins in cabbage (brassica rapa) under abiotic stress conditions.	although the functional roles of cold shock domain proteins (csdps) have been demonstrated during the growth, development, and stress adaptation of arabidopsis (arabidopsis thaliana), rice (oryza sativa), and wheat (triticum aestivum), the functions of csdps in other plants species, including cabbage (brassica rapa), are largely unknown. to gain insight into the roles of csdps in cabbage under stress conditions, the genes encoding csdps in cabbage were isolated, and the functional roles of csdps ...	2015	26263516
thymidine kinases share a conserved function for nucleotide salvage and play an essential role in arabidopsis thaliana growth and development.	thymidine kinases (tks) are important components in the nucleotide salvage pathway. however, knowledge about plant tks is quite limited. in this study, the molecular function of tks in arabidopsis thaliana was investigated. two tks were identified and named attk1 and attk2. expression of both genes was ubiquitous, but attk1 was strongly expressed in high-proliferation tissues. attk1 was localized to the cytosol, whereas attk2 was localized to the mitochondria. mutant analysis indicated that the ...	2015	26139575
detection of dna polymerase λ activity during seed germination and enhancement after salinity stress and dehydration in the plumules of indica rice (oryza sativa l.	dna polymerase λ (dna pol λ) is the only reported x-family dna polymerases in plants and has been shown to play a significant role in dry quiescent seeds, growth, development and nuclear dna repair. cdna for dna pol λ has been reported in arabidopsis and japonica rice cultivar and has been characterized from e. coli expressed protein, but very little is known about its activity at protein level in plants. the enzymatic activity of dna pol λ was studied in dry, imbibed and during different germin ...	2015	26040115
expression and functional validation of heat-labile enterotoxin b (ltb) and cholera toxin b (ctb) subunits in transgenic rice (oryza sativa).	we expressed the heat-labile enterotoxin b (ltb) subunit from enterotoxigenic escherichia coli and the cholera toxin b (ctb) subunit from vibrio cholerae under the control of the rice (oryza sativa) globulin (glb) promoter. binding of recombinant ltb and ctb proteins was confirmed based on gm1-ganglioside binding enzyme-linked immunosorbent assays (gm1-elisa). real-time pcr of three generations (t3, t4, and t5) in homozygous lines (lci-11) showed single copies of ltb, ctb, bar and tnos. ltb and ...	2015	25853032
biosynthesis of odd-chain fatty alcohols in escherichia coli.	engineered microbes offer the opportunity to design and implement artificial molecular pathways for renewable production of tailored chemical commodities. targeted biosynthesis of odd-chain fatty alcohols is very challenging in microbe, due to the specificity of fatty acids synthase for two-carbon unit elongation. here, we developed a novel strategy to directly tailor carbon number in fatty aldehydes formation step by incorporating α-dioxygenase (αdox) from oryza sativa (rice) into escherichia c ...	2015	25773521
expression of developmentally regulated plasma membrane polypeptide (drepp2) in rice root tip and interaction with ca(2+)/cam complex and microtubule.	the cytoplasmic free ca(2+) could play an important role for salt tolerance in rice root (oryza sativa l.). here, we compared the expression profiles of two putative developmentally regulated plasma membrane polypeptides (drepp1 and drepp2) in rice roots of salt-tolerant cv. pokkali and salt-sensitive cv. ir29. the messenger rna (mrna) for osdrepp1 could be detected in all parts of root and did not change upon salt stress, whereas the mrna for osdrepp2 was detected only in root tips. the transcr ...	2015	25743039
functional characterization of three (gh13) branching enzymes involved in cyanobacterial starch biosynthesis from cyanobacterium sp. nbrc 102756.	starch and glycogen are widespread storage polysaccharides in bacteria, plants, and animals. recently, some cyanobacteria were found to accumulate water-insoluble α-glucan similar to amylopectin rather than glycogen, the latter of which is more commonly produced in these organisms. the amylopectin-producing species including cyanobacterium sp. nbrc 102756 invariably have three branching enzyme (be) homologs, be1, be2, and be3, all belonging to the glycoside hydrolase family 13. multiple be isofo ...	2015	25731081
molecular cloning of melatonin 2-hydroxylase responsible for 2-hydroxymelatonin production in rice (oryza sativa).	although melatonin biosynthetic genes from plants have been cloned, the melatonin catabolism mechanisms remain unclear. to clone the genes responsible for melatonin metabolism, we ectopically expressed 35 full-length cdnas of rice 2-oxoglutarate-dependent dioxygenase (2-odd) in escherichia coli and purified the corresponding recombinant proteins. in vitro 2-odd assays showed four independent 2-odd proteins that were able to catalyze melatonin into 2-hydroxymelatonin, exhibiting melatonin 2-hydro ...	2015	25728912
expression, purification, crystallization and preliminary x-ray diffraction analysis of the effector-interaction domain of the resistance protein rga5-a from oryza sativa l. japonica.	rga5-a, a component of the pia resistance-protein complex (rga4/rga5-a) from oryza sativa l. japonica, has the ability to interact physically with the effector protein avr-pia from magnaporthe oryzae via its effector-interaction domain rga5-a_s. the interaction between rga5-a and avr-pia relieves the repression of rga4, leading to avr-independent cell death by the freed rga4. to further understand the details of this interaction, the effector-interaction domain rga5-a_s was expressed in escheric ...	2015	25664791
metabolic engineering of escherichia coli for the biosynthesis of flavonoid-o-glucuronides and flavonoid-o-galactoside.	most flavonoids are glycosylated and the nature of the attached sugar can strongly affect their physiological properties. although many flavonoid glycosides have been synthesized in escherichia coli, most of them are glucosylated. in order to synthesize flavonoids attached to alternate sugars such as glucuronic acid and galactoside, e. coli was genetically modified to express a uridine diphosphate (udp)-dependent glycosyltransferase (ugt) specific for udp-glucuronic acid (amugt10 from antirrhinu ...	2015	25515812
promotion of crystalline cellulose degradation by expansins from oryza sativa.	enzymatic activities of oryza sativa expansins, which were heterologously overexpressed in escherichia coli , were analyzed. results suggested that expansins promote degradation of cellulose by cellulase in a synergistic manner. sustainable production of future biofuels is dependent on efficient saccharification of lignocelluloses. expansins have received a lot of attention as proteins promoting biological degradation of cellulose using cellulase. the expansins are a class of plant cell wall pro ...	2015	25218793
functional characterization of heat-shock protein 90 from oryza sativa and crystal structure of its n-terminal domain.	heat-shock protein 90 (hsp90) is an atp-dependent molecular chaperone that is essential for the normal functioning of eukaryotic cells. it plays crucial roles in cell signalling, cell-cycle control and in maintaining proteome integrity and protein homeostasis. in plants, hsp90s are required for normal plant growth and development. hsp90s are observed to be upregulated in response to various abiotic and biotic stresses and are also involved in immune responses in plants. although there are severa ...	2015	26057797
a rice dead-box rna helicase protein, osrh17, suppresses 16s ribosomal rna maturation in escherichia coli.	dead-box proteins comprise a large protein family. these proteins function in all types of processes in rna metabolism and are highly conserved among eukaryotes. however, the precise functions of dead-box proteins in rice physiology and development remain unclear. in this study, we identified a rice dead-box protein, osrh17, that contains a dead domain and all of the common conserved motifs of dead-box rna helicases. osrh17 was specifically expressed in pollen and differentiated callus and upreg ...	2015	25447922
experimental life history and biological characteristics of fasciola gigantica (digenea: fasciolidae).	this study was conducted to investigate the life history, morphology, and maturation of larval stages and adult worms of fasciola gigantica in experimental mice. lymnaea auricularia rubiginosa was used as the intermediate host, and oryza sativa was used for encystment of the metacercariae, while mus musculus was used as the definitive host for maturation study. fresh eggs from the gall bladder of water buffaloes fully developed into embryonated ones and hatched out at days 11-12 after incubation ...	2015	25748710
discrimination between two rice metallothionein isoforms belonging to type 1 and type 4 in metal-binding ability.	metallothioneins (mts) are a superfamily of low-molecular-weight, cysteine (cys)-rich proteins that are believed to play important roles in protection against metal toxicity and oxidative stress. plants have several mt isoforms, which are classified into four types based on the arrangement of cys residues. in this study, two rice (oryza sativa) mt isoforms, osmti-1b and osmtii-1a from type 1 and type 4, respectively, were heterologously expressed in escherichia coli as carboxy-terminal extension ...	2015	23782215
biochar-amended potting medium reduces the susceptibility of rice to root-knot nematode infections.	biochar is a solid coproduct of biomass pyrolysis, and soil amended with biochar has been shown to enhance the productivity of various crops and induce systemic plant resistance to fungal pathogens. the aim of this study was to explore the ability of wood biochar to induce resistance to the root-knot nematode (rkn) meloidogyne graminicola in rice (oryza sativa cv. nipponbare) and examine its histochemical and molecular impact on plant defense mechanisms.	2015	26537003
the role of thionins in rice defence against root pathogens.	thionins are antimicrobial peptides that are involved in plant defence. here, we present an in-depth analysis of the role of rice thionin genes in defence responses against two root pathogens: the root-knot nematode meloidogyne graminicola and the oomycete pythium graminicola. the expression of rice thionin genes was observed to be differentially regulated by defence-related hormones, whereas all analysed genes were consistently down-regulated in m. graminicola-induced galls, at least until 7 da ...	2015	25676661
unveiling chemical defense in the rice stalk stink bug against the entomopathogenic fungus metarhizium anisopliae.	eggs, nymphs (1st-5th instar) and adults of tibraca limbativentris were challenged by conidial suspensions of its major fungal pathogen metarhizium anisopliae in order to assess their susceptibility. the role of chemical defensive compounds from exocrine secretions produced by both nymphs and adults were examined for their participation on m. anisopliae infection. although insect susceptibility to m. anisopliae followed a dose-dependent manner, adults followed by older nymphs displayed the highe ...	2015	25805519
assessment of epiphytic yeast diversity in rice (oryza sativa) phyllosphere in thailand by a culture-independent approach.	the epiphytic yeast diversity in rice phyllosphere in thailand was investigated by a culture-independent technique based on the rflp pattern and the sequence of the d1/d2 domain of the large subunit rrna gene. forty-four samples of rice leaf were collected randomly from six provinces. the dna was extracted from leaf washing samples and the d1/d2 domain was amplified using pcr technique. the pcr products were cloned and then screened by colony pcr. of total 1121 clones, 451 clones (40.2 %) reveal ...	2015	25842038
evaluation of phosphate-solubilizing bacteria on the growth and grain yield of rice (oryza sativa l.) cropped in northern iran.	this study aimed to evaluate the efficiency of four phosphate-solubilizing bacteria (psb) on the growth and yield of rice under different soil conditions.	2015	26294004
assessment of reference gene stability in rice stripe virus and rice black streaked dwarf virus infection rice by quantitative real-time pcr.	stably expressed reference gene(s) normalization is important for the understanding of gene expression patterns by quantitative real-time pcr (rt-qpcr), particularly for rice stripe virus (rsv) and rice black streaked dwarf virus (rbsdv) that caused seriously damage on rice plants in china and southeast asia.	2015	26497487
analysis of genetic variation and diversity of rice stripe virus populations through high-throughput sequencing.	plant rna viruses often generate diverse populations in their host plants through error-prone replication and recombination. recent studies on the genetic diversity of plant rna viruses in various host plants have provided valuable information about rna virus evolution and emergence of new diseases caused by rna viruses. we analyzed and compared the genetic diversity of rice stripe virus (rsv) populations in oryza sativa (a natural host of rsv) and compared it with that of the rsv populations ge ...	2015	25852724
rice tungro spherical virus resistance into photoperiod-insensitive japonica rice by marker-assisted selection.	rice tungro disease (rtd) is one of the destructive and prevalent diseases in the tropical region. rtd is caused by rice tungro spherical virus (rtsv) and rice tungro bacilliform virus. cultivation of japonica rice (oryza sativa l. ssp japonica) in tropical asia has often been restricted because most japonica cultivars are sensitive to short photoperiod, which is characteristic of tropical conditions. japonica1, a rice variety bred for tropical conditions, is photoperiod-insensitive, has a high ...	2015	26366118
identification of a phosphinothricin-resistant mutant of rice glutamine synthetase using dna shuffling.	to date, only bar/pat gene derived from streptomyces has been used to generate the commercial ppt-resistant crops currently available in the market. the limited source of bar/pat gene is probably what has caused the decrease in ppt-tolerance, which has become the main concern of those involved in field management programs. although glutamine synthetase (gs) is the target enzyme of ppt, little study has been reported about engineering ppt-resistant plants with gs gene. then, the plant-optimized g ...	2015	26492850
rice spx-major facility superfamily3, a vacuolar phosphate efflux transporter, is involved in maintaining phosphate homeostasis in rice.	to maintain a stable cytosol phosphate (pi) concentration, plant cells store pi in their vacuoles. when the pi concentration in the cytosol decreases, pi is exported from the vacuole into the cytosol. this export is mediated by pi transporters on the tonoplast. in this study, we demonstrate that syg1, pho81, and xpr1 (spx)-major facility superfamily (mfs) proteins have a similar structure with yeast (saccharomyces cerevisiae) low-affinity pi transporters phosphatase87 (pho87), pho90, and pho91. ...	2015	26424157
the rice e3-ubiquitin ligase high expression of osmotically responsive gene1 modulates the expression of root meander curling, a gene involved in root mechanosensing, through the interaction with two ethylene-response factor transcription factors.	plant roots can sense and respond to a wide diversity of mechanical stimuli, including touch and gravity. however, little is known about the signal transduction pathways involved in mechanical stimuli responses in rice (oryza sativa). this work shows that rice root responses to mechanical stimuli involve the e3-ubiquitin ligase rice high expression of osmotically responsive gene1 (oshos1), which mediates protein degradation through the proteasome complex. the morphological analysis of the roots ...	2015	26381316
[advances in lineage-specific genes].	lineage-specific genes (lsgs) are defined as genes found in one particular taxonomic group but have no significant sequence similarity with genes from other lineages, which compose about 10%?20% of the total genes in the genome of a focal organism. lsgs were first uncovered in the yeast genome in 1996. the development of the whole genome sequencing leads to the emergence of studies on lsgs as a hot topic in comparative genomics. lsgs have been extensively studied on microbial species, lower mari ...	2015	26351050
data set for mass spectrometric analysis of recombinant human serum albumin from various expression systems.	human serum albumin (hsa) is a versatile and important protein for the pharmaceutical industry (fanali et al., mol. aspects med. 33(3) (2012) 209-290). due to the potential transmission of pathogens from plasma sourced albumin, numerous expression systems have been developed to produce recombinant hsa (rhsa) (chen et al., biochim. biophys. acta (bba)-gen. subj. 1830(12) (2013) 5515-5525; kobayashi, biologicals 34(1) (2006) 55-59). based on our previous study showing increased glycation of rhsa e ...	2015	26322323
characteristics of plant essential genes allow for within- and between-species prediction of lethal mutant phenotypes.	essential genes represent critical cellular components whose disruption results in lethality. characteristics shared among essential genes have been uncovered in fungal and metazoan model systems. however, features associated with plant essential genes are largely unknown and the full set of essential genes remains to be discovered in any plant species. here, we show that essential genes in arabidopsis thaliana have distinct features useful for constructing within- and cross-species prediction m ...	2015	26286535
rice wrky4 acts as a transcriptional activator mediating defense responses toward rhizoctonia solani, the causing agent of rice sheath blight.	wrky transcription factors have been implicated in the regulation of transcriptional reprogramming associated with various plant processes but most notably with plant defense responses to pathogens. here we demonstrate that expression of rice wrky4 gene (oswrky4) was rapidly and strongly induced upon infection of rhizoctonia solani, the causing agent of rice sheath blight, and exogenous jasmonic acid (ja) and ethylene (et). oswrky4 is localized to the nucleus of plant cells and possesses transcr ...	2015	26275661
spt-ada-gcn5-acetyltransferase (saga) complex in plants: genome wide identification, evolutionary conservation and functional determination.	the recruitment of rna polymerase ii on a promoter is assisted by the assembly of basal transcriptional machinery in eukaryotes. the spt-ada-gcn5-acetyltransferase (saga) complex plays an important role in transcription regulation in eukaryotes. however, even in the advent of genome sequencing of various plants, saga complex has been poorly defined for their components and roles in plant development and physiological functions. computational analysis of arabidopsis thaliana and oryza sativa geno ...	2015	26263547
molecular characterization of tafar1 involved in primary alcohol biosynthesis of cuticular wax in hexaploid wheat.	cuticular waxes are complex mixtures of very long chain (vlc) fatty acids and their derivatives in which primary alcohols are the most abundant components in the leaf surface of common wheat (triticum aestivum l.). however, the genes involved in primary alcohol biosynthesis in wheat are still largely unknown. here we identified, via a homology-based approach, the tafar1 gene belonging to the fatty acyl-coa reductases (fars) from wheat. heterologous expression of tafar1 in yeast (saccharomyces ce ...	2015	26220905
characterization of rolled and erect leaf 1 in regulating leave morphology in rice.	leaf morphology, particularly in crop, is one of the most important agronomic traits because it influences the yield through the manipulation of photosynthetic capacity and transpiration. to understand the regulatory mechanism of leaf morphogenesis, an oryza sativa dominant mutant, rolled and erect leaf 1 (rel1) has been characterized. this mutant has a predominant rolled leaf, increased leaf angle, and reduced plant height phenotype that results in a reduction in grain yield. electron microscop ...	2015	26142419
comparison of activity of osdmc1a recombinase of rice (oryza sativa) in presence of ca2+ and mg2+ ions.	recombinases are known to play an important role in the homology search and strand exchange during meiosis as well as homologous recombination (hr)-mediated dna repair specifically require mg2+ ion for their activity. the ca2+ has been shown to stimulate the strand exchange activity of hdmc1 and scdmc1 by forming the extended filaments on dna. oryza sativa disrupted meiotic cdna1a (osdmc1a), a homologue of yeast and human dmc1 from rice shows the hallmark functions of recombinase. here, we repor ...	2015	26118128
a calcium-binding protein, rice annexin osann1, enhances heat stress tolerance by modulating the production of h2o2.	osann1 is a member of the annexin protein family in rice. the function of this protein and the mechanisms of its involvement in stress responses and stress tolerance are largely unknown. here it is reported that osann1 confers abiotic stress tolerance by modulating antioxidant accumulation under abiotic stress. osann1-knockdown [rna interference (rnai)] plants were more sensitive to heat and drought stresses, whereas osann1-overexpression (oe) lines showed improved growth with higher expression ...	2015	26085678
expression of wild-type ptriaa14.1, a poplar aux/iaa gene causes morphological changes in arabidopsis.	aux/iaa proteins are transcriptional repressors that control auxin signaling by interacting with auxin response factors (arfs). so far all of the identified aux/iaa mutants with auxin-related phenotypes in arabidopsis and rice (oryza sativa) are dominant gain-of-function mutants, with mutations in domain ii that affected stability of the corresponding aux/iaa proteins. on the other hand, morphological changes were observed in knock-down mutants of aux/iaa genes in tomato (solanum lycopersicum), ...	2015	26082787
the potassium transporter oshak21 functions in the maintenance of ion homeostasis and tolerance to salt stress in rice.	the intracellular potassium (k(+) ) homeostasis, which is crucial for plant survival in saline environments, is modulated by k(+) channels and transporters. some members of the high-affinity k(+) transporter (hak) family are believed to function in the regulation of plant salt tolerance, but the physiological mechanisms remain unclear. here, we report a significant inducement of oshak21 expression by high-salinity treatment and provide genetic evidence of the involvement of oshak21 in rice salt ...	2015	26046379
the n-terminal degenerated metal-binding domain is involved in the heavy metal transport activity of tahma2.	we identified key residues of tahma2, and the n- and c-terminal regions of the protein have different roles in its transport function when heterologously expressed in yeast. tahma2, a p1b-type atpase from wheat (triticum aestivum l.), plays an important role in heavy metal homeostasis in plants. a previous study showed that overexpressing tahma2 in rice (oryza sativa l.), arabidopsis thaliana, or tobacco (nicotiana tabacum l.) resulted in various responses to heavy metals. here, we report the he ...	2015	26037615
three wrky transcription factors additively repress abscisic acid and gibberellin signaling in aleurone cells.	members of the wrky transcription factor superfamily are essential for the regulation of many plant pathways. functional redundancy due to duplications of wrky transcription factors, however, complicates genetic analysis by allowing single-mutant plants to maintain wild-type phenotypes. our analyses indicate that three group i wrky genes, oswrky24, -53, and -70, act in a partially redundant manner. all three showed characteristics of typical wrky transcription factors: each localized to nuclei a ...	2015	26025535
the rice high-affinity potassium transporter1;1 is involved in salt tolerance and regulated by an myb-type transcription factor.	sodium transporters play key roles in plant tolerance to salt stress. here, we report that a member of the high-affinity k(+) transporter (hkt) family, oshkt1;1, in rice (oryza sativa 'nipponbare') plays an important role in reducing na(+) accumulation in shoots to cope with salt stress. the oshkt1;1 mutant plants displayed hypersensitivity to salt stress. they contained less na(+) in the phloem sap and accumulated more na(+) in the shoots compared with the wild type. oshkt1;1 was expressed main ...	2015	25991736
monascus purpureus-fermented thai glutinous rice reduces blood and hepatic cholesterol and hepatic steatosis concentrations in diet-induced hypercholesterolemic rats.	red yeast rice (ryr) is a fermented product used as a food supplement to promote blood circulation and lower blood cholesterol levels in eastern asia. interestingly, monacolin k is the most active compound in ryr that proved to inhibit hmg-coa reductase in the cholesterol biosynthesis pathway.	2015	25880551
screening of rice (oryza sativa l.) ospr1b-interacting factors and their roles in resisting bacterial blight.	pr genes, a type of genetic marker, are constitutively expressed at background levels, while being easily inducible by pathogenic bacteria. by using a yeast two-hybrid technique, four rice (oryza sativa l.) ospr1b-interacting factors were screened. homozygous plants overexpressing ospr1b were prepared by transgenic technology. we postulated that ospr1b may participate in the resistance signaling pathway of rice. of simultaneous treatments with hormones and pathogenic bacteria, exogenously applyi ...	2015	25867332
rice pcr1 influences grain weight and zn accumulation in grains.	proteins containing a placenta-specific 8 domain (plac8) function as major organ size regulators in solanum lycopersicum and zea may, and putative metal ion transporters in arabidopsis thaliana, oryza sativa and brassica juncea. however, it is unknown how plac8 domain-containing proteins fulfill such diverse roles. here, we found that plant cadmium resistance 1 (pcr1) influences both zinc (zn) accumulation and grain weight in rice. ospcr1 knockout and knockdown lines produced lighter grains than ...	2015	25854544
genetic variability and evolutionary diversification of membrane abc transporters in plants.	atp-binding cassette proteins have been recognized as playing a crucial role in the regulation of growth and resistance processes in all kingdoms of life. they have been deeply studied in vertebrates because of their role in drug resistance, but much less is known about abc superfamily functions in plants.	2015	25850033
rice cyclophilin oscyp18-2 is translocated to the nucleus by an interaction with skip and enhances drought tolerance in rice and arabidopsis.	cyclophilin 18-2 (cyp18-2) genes, homologues of human peptidyl-prolyl isomerase-like 1 (ppil1), are conserved across multicellular organisms and schizosaccharomyces pombe. although ppil1 is known to interact with ski-interacting protein (skip), a transcriptional co-regulator and spliceosomal component, there have been no functional analyses of ppil1 homologues in plants. rice cyclophilin 18-2 (oscyp18-2) bound directly to amino acids 56-95 of osskip and its binding was independent of cyclosporin ...	2015	25847193
osnac2 encoding a nac transcription factor that affects plant height through mediating the gibberellic acid pathway in rice.	plant height and flowering time are key agronomic traits affecting yield in rice (oryza sativa). in this study, we investigated the functions in rice growth and development of osnac2, encoding a nac transcription factor in rice. transgenic plants that constitutively expressed osnac2 had shorter internodes, shorter spikelets, and were more insensitive to gibberellic acid (ga(3)). in addition, the levels of gas decreased in osnac2 overexpression plants, compared with the wild-type. moreover, flowe ...	2015	25754802
the rice ck2 kinase regulates trafficking of phosphate transporters in response to phosphate levels.	phosphate transporters (pts) mediate phosphorus uptake and are regulated at the transcriptional and posttranslational levels. in one key mechanism of posttranslational regulation, phosphorylation of pts affects their trafficking from the endoplasmic reticulum (er) to the plasma membrane. however, the kinase(s) mediating pt phosphorylation and the mechanism leading to er retention of phosphorylated pts remain unclear. in this study, we identified a rice (oryza sativa) kinase subunit, ck2β3, which ...	2015	25724641
establishment of monitoring methods for autophagy in rice reveals autophagic recycling of chloroplasts and root plastids during energy limitation.	autophagy is an intracellular process leading to vacuolar or lysosomal degradation of cytoplasmic components in eukaryotes. establishment of proper methods to monitor autophagy was a key step in uncovering its role in organisms, such as yeast (saccharomyces cerevisiae), mammals, and arabidopsis (arabidopsis thaliana), in which chloroplastic proteins were found to be recycled by autophagy. chloroplast recycling has been predicted to function in nutrient remobilization for growing organs or grain ...	2015	25717038
structural requirements of strigolactones for shoot branching inhibition in rice and arabidopsis.	the structural requirements of strigolactones (sls) involved in germination induction of root parasitic plants and hyphal branching in arbuscular mycorrhizal (am) fungi have been extensively studied. however, our knowledge of the requirements of sls involved in shoot branching inhibition in plants is still limited. to address this question, we investigated the structure-activity relationships of sls in shoot branching inhibition in rice and arabidopsis. sls possess a four-ring structure, with a ...	2015	25713176
destabilization of interaction between cytokinin signaling intermediates ahp1 and arr4 modulates arabidopsis development.	eukaryotic two-component signaling involves the his-asp-his-asp multistep phosphorelay (msp). in arabidopsis thaliana, cytokinin-mediated msp signaling intermediates include histidine kinases (hks), histidine phosphotransfer proteins (hpts) and response regulators (rrs). the structure-function relationship of interaction between hpt (e.g. ahp1) and rr (e.g. arr4) is poorly understood. using a homology model and yeast two-hybrid analysis, we identified key amino acids of arr4 at the ahp1-δarr4((1 ...	2015	25643735
rice ring e3 ligase may negatively regulate gamma-ray response to mediate the degradation of photosynthesis-related proteins.	in this study, our findings regarding the regulation of ga irradiation-induced osgirp1 in relation to the levels of photosynthesis-related proteins such as osrbcl1 and osrbcs1 and hypersensitive responses of overexpressing plants to gr irradiation provide insight into the molecular functions of osgirp1 as a negative regulator in response to the stress of radiation. the ring (really interesting new gene) finger proteins are known to play crucial roles in various abiotic stresses in plants. here, ...	2015	25600999
transposition of a rice mutator-like element in the yeast saccharomyces cerevisiae.	mutator-like transposable elements (mules) are widespread in plants and are well known for their high transposition activity as well as their ability to duplicate and amplify host gene fragments. despite their abundance and importance, few active mules have been identified. in this study, we demonstrated that a rice (oryza sativa) mule, os3378, is capable of excising and reinserting in yeast (saccharomyces cerevisiae), suggesting that yeast harbors all the host factors for the transposition of m ...	2015	25587002
telomere-centric genome repatterning determines recurring chromosome number reductions during the evolution of eukaryotes.	whole-genome duplication (wgd) is central to the evolution of many eukaryotic genomes, in particular rendering angiosperm (flowering plant) genomes much less stable than those of animals. following repeated duplication/triplication(s), angiosperm chromosome numbers have usually been restored to a narrow range, as one element in a 'diploidization' process that re-establishes diploid heredity. in several angiosperms affected by wgd, we show that chromosome number reduction (cnr) is best explained ...	2015	25138576
a polarly localized transporter for efficient manganese uptake in rice.	manganese is an essential metal for plant growth. a number of transporters involved in the uptake of manganese from soils, and its translocation to the shoot, have been identified in arabidopsis and rice. however, the transporter responsible for the radial transport of manganese out of root exodermis and endodermis cells and into the root stele remains unknown. here, we show that metal tolerance protein 9 (mtp9), a member of the cation diffusion facilitator family, is a critical player in this p ...	2015	27251715
identification of crown rootless1-regulated genes in rice reveals specific and conserved elements of postembryonic root formation.	in monocotyledons, the root system is mostly composed of postembryonic shoot-borne roots called crown roots. in rice (oryza sativa), auxin promotes crown root initiation via the lob-domain transcription factor (lbd) transcription factor crown rootless1 (crl1); however, the gene regulatory network downstream of crl1 remains largely unknown. we tested crl1 transcriptional activity in yeast and in planta, identified crl1-regulated genes using an inducible gene expression system and a transcriptome ...	2015	25442012
mpic: a mitochondrial protein import components database for plant and non-plant species.	in the 2 billion years since the endosymbiotic event that gave rise to mitochondria, variations in mitochondrial protein import have evolved across different species. with the genomes of an increasing number of plant species sequenced, it is possible to gain novel insights into mitochondrial protein import pathways. we have generated the mitochondrial protein import components (mpic) database (db; http://www.plantenergy.uwa.edu.au/applications/mpic) providing searchable information on the protei ...	2015	25435547
the auxin response factor, osarf19, controls rice leaf angles through positively regulating osgh3-5 and osbri1.	auxin and brassinosteroid (br) are important phytohormones for controlling lamina inclination implicated in plant architecture and grain yield. but the molecular mechanism of auxin and br crosstalk for regulating lamina inclination remains unknown. auxin response factors (arfs) control various aspects of plant growth and development. we here report that osarf19-overexpression rice lines show an enlarged lamina inclination due to increase of its adaxial cell division. osarf19 is expressed in vari ...	2015	24995795
suppression of osku80 results in defects in developmental growth and increased telomere length in rice (oryza sativa l.).	the ku70-ku80 heterodimer plays a critical role in the maintenance of genomic stability in humans and yeasts. in this report, we identified and characterized osku80 in rice, a model monocot crop. osku80 forms a heterodimer with osku70 in yeast and plant cells, as demonstrated by yeast two-hybrid, in vivo co-immunoprecipitation, and bimolecular fluorescence complementation assays. rnai-mediated knock-down t3 transgenic rice plants (ubi:rnai-osku80) displayed a retarded growth phenotype at the pos ...	2015	26590017
the role of a novel fungal strain trichoderma atroviride rvf3 in improving humic acid content in mature compost and vermicompost via ligninolytic and celluloxylanolytic activities.	with the rising concerns about indiscriminate use of chemical fertilizers and accumulation of agro-industrial wastes in huge quantities, the present experiment was conducted to elucidate the effect of a novel fungal strain of trichoderma atroviride in hastening the compost/vermicompost production process and for the production of humic acid (ha) rich compost and vermicompost.	2015	26387985
dynamic and coordinated expression changes of rice small rnas in response to xanthomonas oryzae pv. oryzae.	endogenous small rnas are newly identified players in plant immune responses, yet their roles in rice (oryza sativa) responding to pathogens are still less understood, especially for pathogens that can cause severe yield losses. we examined the small rna expression profiles of rice leaves at 2, 6, 12, and 24 hours post infection of xanthomonas oryzae pv. oryzae (xoo) virulent strain pxo99, the causal agent of rice bacterial blight disease. dynamic expression changes of some mirnas and trans-acti ...	2015	26674380
identification and fine-mapping of a new resistance gene, xa40, conferring resistance to bacterial blight races in rice (oryza sativa l.).	a new bacterial blight resistance gene has been identified through fine-mapping, which confers high levels of resistance to all korean xanthomonas oryzae pv. oryzae (xoo) races, including the new xoo race k3a. rice bacterial leaf blight (bb) disease caused by xanthomonas oryzae pv. oryzae (xoo) is a serious constraint to rice production in asia and africa. the japonica advanced backcross breeding lines derived from the indica line ir65482-7-216-1-2 in the background of cultivar junam are resista ...	2015	26081948
rice responds to endophytic colonization which is independent of the common symbiotic signaling pathway.	as molecular interactions of plants with n2 -fixing endophytes are largely uncharacterized, we investigated whether the common signaling pathway (csp) shared by root nodule symbioses (rns) and arbuscular mycorrhizal (am) symbioses may have been recruited for the endophytic azoarcus sp.-rice (oryza sativa) interaction, and combined this investigation with global approaches to characterize rice root responses to endophytic colonization. putative homologs of genes required for the csp were analyzed ...	2015	26009800
gene targeting by the tal effector pthxo2 reveals cryptic resistance gene for bacterial blight of rice.	bacterial blight of rice is caused by the γ-proteobacterium xanthomonas oryzae pv. oryzae, which utilizes a group of type iii tal (transcription activator-like) effectors to induce host gene expression and condition host susceptibility. five sweet genes are functionally redundant to support bacterial disease, but only two were experimentally proven targets of natural tal effectors. here, we report the identification of the sucrose transporter gene ossweet13 as the disease-susceptibility gene for ...	2015	25824104
molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (oryza sativa l.): insights from molecular dynamics simulations.	the avirulence gene avrxa5 of bacterial blight pathogen xanthomonas oryzae pv. oryzae (xoo) recognized by the resistant rice lines having corresponding resistance (xa5) gene in a gene-for-gene manner. we used a combinatorial approach involving protein-protein docking, molecular dynamics (md) simulations and binding free energy calculations to gain novel insights into the gene-for-gene mechanism that governs the direct interaction of r-avr protein. from the best three binding poses predicted by m ...	2015	25655560
development of disease-resistant rice by optimized expression of wrky45.	the rice transcription factor wrky45 plays a central role in the salicylic acid signalling pathway and mediates chemical-induced resistance to multiple pathogens, including magnaporthe oryzae and xanthomonas oryzae pv. oryzae. previously, we reported that rice transformants overexpressing wrky45 driven by the maize ubiquitin promoter were strongly resistant to both pathogens; however, their growth and yield were negatively affected because of the trade-off between the two conflicting traits. als ...	2015	25487714
the rice (oryza sativa l.) lesion mimic resembling, which encodes an aaa-type atpase, is implicated in defense response.	lesion mimic mutants (lmms) provide a useful tool to study defense-related programmed cell death (pcd) in plants. although a number of lmms have been identified in multiple species, most of the candidate genes are yet to be isolated. here, we report the identification and characterization of a novel rice (oryza sativa l.) lesion mimic resembling (lmr) mutant, and cloning of the corresponding lmr gene. the lmr locus was initially delineated to 1.2 mb region on chromosome 6, which was further narr ...	2015	25367283
enhancement of innate immune system in monocot rice by transferring the dicotyledonous elongation factor tu receptor efr.	the elongation factor tu (ef-tu) receptor (efr) in cruciferous plants specifically recognizes the n-terminal acetylated elf18 region of bacterial ef-tu and thereby activates plant immunity. it has been demonstrated that arabidopsis efr confers broad-spectrum bacterial resistance in the efr transgenic solanaceous plants. here, the transgenic rice plants (oryza sativa l. ssp. japonica cv. zhonghua 17) and cell cultures with constitutive expression of atefr were developed to investigate whether ate ...	2015	25358295
expression of magnaporthe oryzae genes encoding cysteine-rich proteins secreted during nitrogen starvation and interaction with its host, oryza sativa.	previous studies have shown that the blast fungus, magnaporthe oryzae, may experience nitrogen starvation during infection of its plant host (rice,oryza sativa). here, we studied the expression of seven genes encoding cysteine-rich proteins with n-terminal signal peptides during nitrogen limitation and throughout the infection process. some genes were upregulated to a greater extent in weak pathogenic strains than in strong pathogenic strains when they were cultured in complete media, and the ex ...	2015	26681057
septin-dependent assembly of the exocyst is essential for plant infection by magnaporthe oryzae.	magnaporthe oryzae is the causal agent of rice blast disease, the most devastating disease of cultivated rice (oryza sativa) and a continuing threat to global food security. to cause disease, the fungus elaborates a specialized infection cell called an appressorium, which breaches the cuticle of the rice leaf, allowing the fungus entry to plant tissue. here, we show that the exocyst complex localizes to the tips of growing hyphae during vegetative growth, ahead of the spitzenkörper, and is requi ...	2015	26566920
multiplex ssr-pcr approaches for semi-automated genotyping and characterization of loci linked to blast disease resistance genes in rice.	in the present study, 63 polymorphic microsatellite markers related to rice blast resistance genes were fluorescently labelled at the 5'-end with either 6-fam or hex using the g5 dye set and incorporated into a multiplex ssr-pcr for the detection of fragments using an automated system. for rice f3 families obtained from crosses between pongsu seribu 2 (malaysian blast resistant cultivar) and mahsuri (a susceptible rice cultivar), the genotypes for 13 designated multiplex ssr panels were determin ...	2015	26318048
a genome-wide survey reveals abundant rice blast r genes in resistant cultivars.	plant resistance genes (r genes) harbor tremendous allelic diversity, constituting a robust immune system effective against microbial pathogens. nevertheless, few functional r genes have been identified for even the best-studied pathosystems. does this limited repertoire reflect specificity, with most r genes having been defeated by former pests, or do plants harbor a rich diversity of functional r genes, the composite behavior of which is yet to be characterized? here, we survey 332 nbs-lrr gen ...	2015	26248689
combination patterns of major r genes determine the level of resistance to the m. oryzae in rice (oryza sativa l.).	rice blast caused by magnaporthe oryzae is the most devastating disease of rice and poses a serious threat to world food security. in this study, the distribution and effectiveness of 18 r genes in 277 accessions were investigated based on pathogenicity assays and molecular markers. the results showed that most of the accessions exhibited some degree of resistance (resistance frequency, rf >50%). accordingly, most of the accessions were observed to harbor two or more r genes, and the number of r ...	2015	26030358
population structure, pathogenicity, and mating type distribution of magnaporthe oryzae isolates from east africa.	rice blast, caused by magnaporthe oryzae, is one of the emergent threats to rice production in east africa (ea), where little is known about the population genetics and pathogenicity of this pathogen. we investigated the genetic diversity and mating type (mat) distribution of 88 isolates of m. oryzae from ea and representative isolates from west africa (wa) and the philippines (asia) using amplified fragment length polymorphism markers and mating-type-specific primer sets. in addition, the aggre ...	2015	25822189
priming of pathogenesis related-proteins and enzymes related to oxidative stress by plant growth promoting rhizobacteria on rice plants upon abiotic and biotic stress challenge.	two plant growth promoting rhizobacteria (pgpr) were tested to evaluate their capacity to prime rice seedlings against stress challenge (salt and xanthomonas campestris infection). as is accepted that plants respond to biotic and abiotic stresses by generation of reactive oxygen species (ros), enzyme activities related to oxidative stress (ascorbate peroxidase (apx, ec 1.11.1.11), guaiacol peroxidase (gpx, ec 1.11.1.7), glutathione reductase (gr, ec 1.6.4.2) and superoxide dismutase (sod, ec 1.1 ...	2015	26439659
genome sequence of xanthomonas sacchari r1, a biocontrol bacterium isolated from the rice seed.	xanthomonas sacchari, was first identified as a pathogenic bacterium isolated from diseased sugarcane in guadeloupe. in this study, r1 was first isolated from rice seed samples from philippines in 2002. the antagonistic ability against several rice pathogens raises our attention. the genomic feature of this strain was described in this paper. the total genome size of x. sacchari r1 is 5,000,479 bp with 4315 coding sequences (cds), 59 trnas, 2rrnas and one plasmid.	2015	25931193
identification and genetic mapping of the putative thinopyrum intermedium-derived dominant powdery mildew resistance gene pml962 on wheat chromosome arm 2bs.	powdery resistance putatively derived from thinopyrum intermedium in the wheat line l962 is controlled by a single dominant gene designated pml962 and mapped to chromosome arm 2bs. powdery mildew, caused by blumeria graminis f. sp. tritici (bgt), is a destructive disease affecting the production of wheat (triticum aestivum). powdery mildew resistance was putatively transferred from thinopyrum intermedium to the common wheat line l962, which conferred resistance to multiple chinese bgt isolates. ...	2015	25556931
seasonal abundance and phenology of oebalus pugnax (hemiptera: pentatomidae) on graminaceous hosts in the delta region of mississippi.	the rice stink bug, oebalus pugnax (f.), is a graminaceous feeder, and the most injurious insect pest of heading rice, oryza sativa l., in the united states. rice growers are aware of the economic importance of host grasses in o. pugnax abundance. however, the need for increased knowledge of host sequence relative to o. pugnax abundance is vital. densities of o. pugnax on 15 graminaceous hosts were evaluated in the central mississippi delta from april through august in 2011 and 2012. two cultiva ...	2015	26314038
constitutive expression of rice microrna528 alters plant development and enhances tolerance to salinity stress and nitrogen starvation in creeping bentgrass.	microrna528 (mir528) is a conserved monocot-specific small rna that has the potential of mediating multiple stress responses. so far, however, experimental functional studies of mir528 are lacking. here, we report that overexpression of a rice (oryza sativa) mir528 (osa-mir528) in transgenic creeping bentgrass (agrostis stolonifera) alters plant development and improves plant salt stress and nitrogen (n) deficiency tolerance. morphologically, mir528-overexpressing transgenic plants display short ...	2015	26224802
photo-biotechnology as a tool to improve agronomic traits in crops.	phytochromes are photosensory phosphoproteins with crucial roles in plant developmental responses to light. functional studies of individual phytochromes have revealed their distinct roles in the plant's life cycle. given the importance of phytochromes in key plant developmental processes, genetically manipulating phytochrome expression offers a promising approach to crop improvement. photo-biotechnology refers to the transgenic expression of phytochrome transgenes or variants of such transgenes ...	2015	25532679
chemical composition and phytotoxicity of volatile essential oil from intact and fallen leaves of eucalyptus citriodora.	a total of 23 volatile constituents was identified and characterized by gc and gc-ms in the volatile essential oil extracted from intact (juvenile and adult) and fallen (senescent and leaf litter) leaves of lemon-scented eucalyptus (eucalyptus citriodora hook.). the leaves differed in their pigment, water and protein content, and c/n ratio. the oils were, in general, monoterpenoid in nature with 18 monoterpenes and 5 sesquiterpenes. however, a great variability in the amount of essential oils an ...	2015	16989303
traditional phytoremedies for the treatment of menstrual disorders in district udhampur, j&k, india.	herbal remedies form an integral part of healing and are considered to be the oldest forms of health care known to mankind. the present study aims to document traditional phytoremedies for the treatment of menstrual disorders in udhampur district of j&k, india.	2015	25479156
constitutive expression of osiaa9 affects starch granules accumulation and root gravitropic response in arabidopsis.	auxin/indole-3-acetic acid (aux/iaa) genes are early auxin response genes ecoding short-lived transcriptional repressors, which regulate auxin signaling in plants by interplay with auxin response factors (arfs). most of the aux/iaa proteins contain four different domains, namely domain i, domain ii, domain iii, and domain iv. so far all aux/iaa mutants with auxin-related phenotypes identified in both arabidopsis and rice (oryza sativa) are dominant gain-of-function mutants with mutations in doma ...	2015	26734051
high-resolution mapping of h4k16 and h3k23 acetylation reveals conserved and unique distribution patterns in arabidopsis and rice.	histone acetylation and deacetylation are key epigenetic gene regulatory mechanisms that play critical roles in eukaryotes. acetylation of histone 4 lysine 16 (h4k16ac) is implicated in many cellular processes. however, its biological function and relationship with transcription are largely unexplored in plants. we generated first genome-wide high-resolution maps of h4k16ac in arabidopsis thaliana and oryza sativa. we showed that h4k16ac is preferentially enriched around the transcription start ...	2015	26646900
co-ordination of flower development through epigenetic regulation in two model species: rice and arabidopsis.	angiosperms produce flowers for reproduction. flower development is a multistep developmental process, beginning with the initiation of the floral meristems, followed by floral meristem identity specification and maintenance, organ primordia initiation, floral organ identity specification, floral stem cell termination and finally floral organ maturation. during flower development, each of a large number of genes is expressed in a spatiotemporally regulated manner. underlying these molecular and ...	2015	25746984
cell dedifferentiation and organogenesis in vitro require more snrna than does seedling development in arabidopsis thaliana.	small nuclear rna (snrna) is a class of non-coding rnas that processes pre-mrna and rrna. transcription of abundant snrna species is regulated by the snrna activating protein complex (snapc), which is conserved among multicellular organisms including plants. srd2, a putative subunit of snapc in arabidopsis thaliana, is essential for development, and the point mutation srd2-1 causes severe defects in hypocotyl dedifferentiation and de novo meristem formation. based on phenotypic analysis of srd2- ...	2015	25740809
expath: a database of comparative expression analysis inferring metabolic pathways for plants.	in general, the expression of gene alters conditionally to catalyze a specific metabolic pathway. microarray-based datasets have been massively produced to monitor gene expression levels in parallel with numerous experimental treatments. although several studies facilitated the linkage of gene expression data and metabolic pathways, none of them are amassed for plants. moreover, advanced analysis such as pathways enrichment or how genes express under different conditions is not rendered.	2015	25708775
deformed floral organ1 (dfo1) regulates floral organ identity by epigenetically repressing the expression of osmads58 in rice (oryza sativa).	floral organ identity in plants is controlled by floral homeotic a/b/c/d/e-class genes. in arabidopsis thaliana, several epigenetic repressors that regulate these floral organ identity genes have been characterized. however, the roles of epigenetic factors in rice floral development have not been explored in detail. here, we report the identification and functional characterization of a rice epigenetic repressor, deformed floral organ1 (dfo1) gene, which causes abnormal floral morphology when mu ...	2015	25675970
analyses of ca2+ dynamics using a ubiquitin-10 promoter-driven yellow cameleon 3.6 indicator reveal reliable transgene expression and differences in cytoplasmic ca2+ responses in arabidopsis and rice (oryza sativa) roots.	ca(2+) signatures are central to developmental processes and adaptive responses in plants. however, high-resolution studies of ca(2+) dynamics using genetically encoded ca(2+) indicators (gecis) such as yellow cameleon (yc) proteins have so far not been conducted in important model crops such as rice (oryza sativa). we conducted a comparative study of 35s and ubiquitin-10 (ubq10) promoter functionality in arabidopsis thaliana and o. sativa plants expressing the ca(2+) indicator yellow cameleon 3 ...	2015	25641067
genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in brachypodium distachyon.	in eukaryotes, alternative splicing (as) promotes transcriptome and proteome diversity. the extent of genome-wide as changes occurring during a plant-microbe interaction is largely unknown. here, using high-throughput, paired-end rna sequencing, we generated an isoform-level spliceome map of brachypodium distachyon infected with panicum mosaic virus and its satellite virus. overall, we detected ∼44,443 transcripts in b. distachyon, ∼30% more than those annotated in the reference genome. expressi ...	2015	25634987
osjaz9 acts as a transcriptional regulator in jasmonate signaling and modulates salt stress tolerance in rice.	the basic functions of plant-specific tify proteins as transcriptional regulators have been reported in plants. some tify genes are responsive to abiotic stresses, but the functions of these genes in stress tolerance have seldom been reported. osjaz9 is a member of the jaz subfamily which belongs to the tify gene family in rice (oryza sativa). suppression of osjaz9 resulted in reduced salt tolerance. the altered salt tolerance was mainly due to changes in ion (especially k(+)) homeostasis, which ...	2015	25617318
genome-wide survey of the seagrass zostera muelleri suggests modification of the ethylene signalling network.	seagrasses are flowering plants which grow fully submerged in the marine environment. they have evolved a range of adaptations to environmental challenges including light attenuation through water, the physical stress of wave action and tidal currents, high concentrations of salt, oxygen deficiency in marine sediment, and water-borne pollination. although, seagrasses are a key stone species of the costal ecosystems, many questions regarding seagrass biology and evolution remain unanswered. genom ...	2015	25563969
rice phytochrome b (osphyb) negatively regulates dark- and starvation-induced leaf senescence.	light regulates leaf senescence and light deprivation causes large-scale transcriptional reprogramming to dismantle cellular components and remobilize nutrients to sink organs, such as seeds and storage tissue. we recently reported that in arabidopsis (arabidopsis thaliana), phytochrome-interacting factor4 (pif4) and pif5 promote dark-induced senescence and natural senescence by directly activating the expression of typical senescence-associated genes (sags), including oresara1 (ore1) and ethyle ...	2015	27135344
abscisic acid: hidden architect of root system structure.	plants modulate root growth in response to changes in the local environment, guided by intrinsic developmental genetic programs. the hormone abscisic acid (aba) mediates responses to different environmental factors, such as the presence of nitrate in the soil, water stress and salt, shaping the structure of the root system by regulating the production of lateral roots as well as controlling root elongation by modulating cell division and elongation. curiously, aba controls different aspects of r ...	2015	27135341
a novel gene, ozone-responsive apoplastic protein1, enhances cell death in ozone stress in rice.	a novel protein, ozone-responsive apoplastic protein1 (osorap1), was characterized, which was previously suggested as a candidate gene underlying ozt9, a quantitative trait locus for ozone stress tolerance in rice (oryza sativa). the sequence of osorap1 was similar to that of ascorbate oxidase (ao) proteins. it was localized in the apoplast, as shown by transient expression of an osorap1/green fluorescent protein fusion construct in nicotiana benthamiana leaf epidermal and mesophyll cells, but d ...	2015	26220952
comprehensive identification and expression analysis of hsp90s gene family in solanum lycopersicum.	heat shock protein 90 (hsp90) is a protein produced by plants in response to adverse environmental stresses. in this study, we identified and analyzed hsp90 gene family members using a bioinformatic method based on genomic data from tomato (solanum lycopersicum l.). the results illustrated that tomato contains at least 7 hsp90 genes distributed on 6 chromosomes; protein lengths ranged from 267-794 amino acids. intron numbers ranged from 2-19 in the genes. the phylogenetic tree revealed that hsp9 ...	2015	26214462