Publications

identification and characterization of lineage-specific genes within the poaceae.	using the rice (oryza sativa) sp. japonica genome annotation, along with genomic sequence and clustered transcript assemblies from 184 species in the plant kingdom, we have identified a set of 861 rice genes that are evolutionarily conserved among six diverse species within the poaceae yet lack significant sequence similarity with plant species outside the poaceae. this set of evolutionarily conserved and lineage-specific rice genes is termed conserved poaceae-specific genes (cpsgs) to reflect t ...	2007	17951464
comparing contributions of soil versus root colonization to variations in stomatal behavior and soil drying in mycorrhizal sorghum bicolor and cucurbita pepo.	in prior studies we learned that colonization of soil can be as important as colonization of roots in determining mycorrhizal influence on the water relations of host plants. here we use a path analysis modeling approach to test (a) whether quantity of hyphae in soil contributes to variations in stomatal behavior and soil drying, and (b) whether soil colonization or root colonization has a stronger influence on these stomatal and soil drying responses. experiments were performed on sorghum bicol ...	2007	17189660
comparative cross-species alternative splicing in plants.	alternative splicing (as) can add significantly to genome complexity. plants are thought to exhibit less as than animals. an algorithm, based on expressed sequence tag (est) pairs gapped alignment, was developed that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ests to search for as. est pairs gapped alignment was first evaluated in arabidopsis (arabidopsis thaliana), rice (oryza sativa), and tomato (solanum lycopersicum) for which annotat ...	2007	17496110
on the mechanism of action and selectivity of the corn herbicide topramezone: a new inhibitor of 4-hydroxyphenylpyruvate dioxygenase.	topramezone is a new, highly selective herbicide of pyrazole structure for the post-emergence control of broadleaf and grass weeds in corn. the biokinetic properties and mode of action of topramezone were investigated in plants of setaria faberi herrm, sorghum bicolor (l.) moench, solanum nigrum l. and the crop species corn (zea mays l.). within 2-5 days after treatment, topramezone caused strong photobleaching effects on the shoot, followed by plant death of sensitive weeds. the selectivity of ...	2007	17340675
plant gene and alternatively spliced variant annotator. a plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species.	the completion of the rice (oryza sativa) genome draft has brought unprecedented opportunities for genomic studies of the world's most important food crop. previous rice gene annotations have relied mainly on ab initio methods, which usually yield a high rate of false-positive predictions and give only limited information regarding alternative splicing in rice genes. comparative approaches based on expressed sequence tags (ests) can compensate for the drawbacks of ab initio methods because they ...	2007	17220363
hormonal control of grass inflorescence development.	grass inflorescences produce the grain that feeds the world. compared to eudicots such as arabidopsis (arabidopsis thaliana), grasses have a complex inflorescence morphology that can be explained by differences in the activity of axillary meristems. advances in genomics, such as the completion of the rice (oryza sativa) and sorghum (sorghum bicolor) genomes and the recent release of a draft sequence of the maize (zea mays) genome, have greatly facilitated research in grasses. here, we review rec ...	2008	18986827
primary or secondary? versatile nitrilases in plant metabolism.	the potential of plant nitrilases to convert indole-3-acetonitrile into the plant growth hormone indole-3-acetic acid has earned them the interim title of "key enzyme in auxin biosynthesis". although not widely recognized, this view has changed considerably in the last few years. recent work on plant nitrilases has shown them to be involved in the process of cyanide detoxification, in the catabolism of cyanogenic glycosides and presumably in the catabolism of glucosinolates. all plants possess a ...	2008	18842274
metabolon formation in dhurrin biosynthesis.	synthesis of the tyrosine derived cyanogenic glucoside dhurrin in sorghum bicolor is catalyzed by two multifunctional, membrane bound cytochromes p450, cyp79a1 and cyp71e1, and a soluble udpg-glucosyltransferase, ugt85b1 (tattersall, d.b., bak, s., jones, p.r., olsen, c.e., nielsen, j.k., hansen, m.l., høj, p.b., møller, b.l., 2001. resistance to an herbivore through engineered cyanogenic glucoside synthesis. science 293, 1826-1828). all three enzymes retained enzymatic activity when expressed a ...	2008	17706731
synthesis and phytotoxic activity of ozonides.	the [4 + 3] cycloaddition of the proper furans with the oxyallyl cation, generated in situ from 2,4-dibromopentan-3-one, produced a series of 8-oxabicyclo [3.2.1]oct-6-en-3-ones. exposure of the oxabicycles to ozone afforded the corresponding 8,9,10,11-tetraoxatricyclo[5.2.1.1 (2,6)]undecan-4-ones in variable yields (7-100%). the phytotoxic properties of these ozonides (or 1,2,4-trioxolanes) and their oxabicycle precursors were evaluated as the ability to interfere with the growth of sorghum bic ...	2008	18808140
community of arbuscular mycorrhizal fungi in a coastal vegetation on okinawa island and effect of the isolated fungi on growth of sorghum under salt-treated conditions.	community of arbuscular mycorrhizal (am) fungi in a coastal vegetation on okinawa island in japan was examined. a sampling plot was established in a colony of ipomoea pes-caprae (convolvulaceae) on the beach in tamagusuku, okinawa pref, in which eight root samples of i. pes-caprae and three root samples each of vigna marina (leguminosae) and paspalum distichum (poaceae) were collected. partial 18s rdna of am fungi was amplified from the root samples by polymerase chain reaction (pcr) with primer ...	2008	18516629
examining cuphea as a potential host for western corn rootworm (coleoptera: chrysomelidae): larval development.	in previous crop rotation research, adult emergence traps placed in plots planted to cuphea psr-23 (a selected cross of cuphea viscosissma jacq. and cuphea lanceolata ait.) caught high numbers of adult western corn rootworms, diabrotica virgifera virgifera leconte (coleoptera: chrysomelidae), suggesting that larvae may have completed development on this broadleaf plant. because of this observation, a series of greenhouse and field experiments were conducted to test the hypothesis that cuphea cou ...	2008	18613580
pyrimidinyl-substituted amides and thioureas: syntheses, crystal structure and herbicidal activities.	the high herbicidal activities of [1,2,4]triazolo[1,5-c]pyrimidine and 2h-1,2,4-thiadiazolo[2,3-a]pyrimidine derivatives suggested the development of new fused heterocyclic compounds for application as herbicides.	2008	18080290
tissue specific response of agrobacterium tumefaciens attachment to sorghum bicolor (l) moench.	agrobacterium mediated genetic transformation of plants have advantages over other methods, especially for making single copy transgenic plants with reduced chances of gene silencing and instability. however, monocotyledonous plant species could not utilize the full potential of this system because of possible limitations in agrobacterium interaction with monocot plant cells. agrobacterium attachment as a factor in genetic transformation was studied in the leaf, shoot apex, and leaf derived call ...	2008	23572896
effect of silk flower hay (calotropis procera sw) feeding on the physical and chemical quality of longissimus dorsi muscle of santa inez lambs.	the effect of different levels of silk flower hay (calotropis procera sw) in the diet of confined lambs by the substitution of the commonly used foraging broom corn hay (sorghum bicolor l) was investigated to evaluate its possible effects on the growth and quality of the lamb meat. twenty-four male santa inez lambs were divided in equal numbers into four treatment groups and fed diets containing 0%, 16.7%, 33.3% and 50% of silk flower hay (sfh). growth rate, feed intake and meat quality were inv ...	2008	22062467
biodegradation of disperse textile dye brown 3rel by newly isolated bacillus sp. vus.	to isolate the potential micro-organism for the degradation of textile disperse dye brown 3 rel and to find out the reaction mechanism.	2008	18266699
cloning and expression analyses of sucrose non-fermenting-1-related kinase 1 (snrk1b) gene during development of sorghum and maize endosperm and its implicated role in sugar-to-starch metabolic transition.	a full-length cdna clone, sbsnrk1b (1530 bp, genbank accession no. ef544393), encoding a putative serine/threonine protein kinase homologue of yeast (saccharomyces cerevisiae) snf1, was isolated from developing endosperm of sorghum [sorghum bicolor (l.) moench]. multiple sequence alignment data showed a phylogenetic affiliation of the sorghum clone with the snrk1b group of protein kinases that are highly expressed in cereal seed endosperm. the dna gel blot analyses indicated that sbsnrk1b gene i ...	2008	18433416
effects of diet on population growth of psocids lepinotus reticulatus and liposcelis entomophila.	we investigated the suitability of 11 diets as culture media for the psocids lepinotus reticulatus enderlein (psocoptera: trogiidae) and liposcelis entomophila (enderlein) (psocoptera: liposcelididae). the culture media comprised six diets made of plain cereals, namely, wheat (triticum aestivum l.), corn (zea mays l.), milo sorghum bicolor (l.), barley (hordeum vulgare l.), oats (avena sativa l.), and rice (oryza sativa l.), and five artificial diets. we found that, with the exception of corn, l ...	2008	18459431
a novel nutraceutical property of select sorghum (sorghum bicolor) brans: inhibition of protein glycation.	despite the high levels of polyphenolic phytochemicals in grain sorghum and its position as a major food staple, there has been a lack of research on its effects on both animal and human health and disease prevention. these phenolic compounds, mainly located in the bran fraction, result in the plant having substantial antioxidant properties. this study examined the effect of ethanol extracts of several varieties of sorghum (s. bicolor) bran on albumin glycation, a non-enzymatic process thought t ...	2008	18570276
diversity of nifh gene pools in the rhizosphere of two cultivars of sorghum (sorghum bicolor) treated with contrasting levels of nitrogen fertilizer.	the diversity of nitrogen-fixing bacteria was assessed in the rhizospheres of two cultivars of sorghum (is 5322-c and ipa 1011) sown in cerrado soil amended with two levels of nitrogen fertilizer (12 and 120 kg ha(-1)). the nifh gene was amplified directly from dna extracted from the rhizospheres, and the pcr products cloned and sequenced. four clone libraries were generated from the nifh fragments and 245 sequences were obtained. most of the clones (57%) were closely related to nifh genes of un ...	2008	18070072
establishment of cotesia flavipes (hymenoptera: braconidae) in sugarcane fields of ethiopia and origin of founding population.	cotesia flavipes (cameron) (hymenoptera: braconidae) is used as a classical biological control agent against chilo partellus (swinhoe) (lepidoptera: crambidae), a serious exotic pest of cereal crops in eastern and southern africa. this parasitoid has been introduced into several african countries for the control of c. partellus in maize, zea mays l., and sorghum, sorghum bicolor (l.), but it has never been released in ethiopia. it is hypothesized that it spread into ethiopia from populations rel ...	2008	18613566
immediate and delayed mortality of rhyzopertha dominica (coleoptera: bostrichidae) and sitophilus oryzae (coleoptera: curculionidae) adults exposed to spinosad-treated commodities.	a series of tests was conducted to characterize differences in the mortality of the lesser grain borer, rhyzopertha dominica (f.) (coleoptera: bostrichidae), and rice weevil, sitophilus oryzae (l.) (coleoptera: curculionidae), exposed to three commodities treated with a liquid and dry spinosad formulation. in laboratory bioassays, adults of the two insect species were exposed to untreated wheat, triticum aestivum l., corn, zea mays l., and sorghum, sorghum bicolor (l.) moench., and to commoditie ...	2008	18613608
antiviral activity and mode of action of a peptide isolated from sorghum bicolor.	in this paper, we describe the purification of an antiviral peptide from seeds of sorghum bicolor l. by a procedure that included gel filtration, ion exchange, and high-performance liquid chromatography (hplc) in a reversed-phase column. its molecular weight, determined by chromatographic mobility on the shim-pack diol-150 gel permeation column in hplc, was found to be 2000da. the peptide designated 2kd peptide strongly inhibited the replication of herpes simplex virus type 1 (hsv-1), dose-depen ...	2008	17890069
a functional genomics investigation of allelochemical biosynthesis in sorghum bicolor root hairs.	sorghum is considered to be one of the more allelopathic crop species, producing phytotoxins such as the potent benzoquinone sorgoleone (2-hydroxy-5-methoxy-3-[(z,z)-8',11',14'-pentadecatriene]-p-benzoquinone) and its analogs. sorgoleone likely accounts for much of the allelopathy of sorghum spp., typically representing the predominant constituent of sorghum bicolor root exudates. previous and ongoing studies suggest that the biosynthetic pathway for this plant growth inhibitor occurs in root ha ...	2008	17998204
detection, isolation and characterization of a root-exuded compound, methyl 3-(4-hydroxyphenyl) propionate, responsible for biological nitrification inhibition by sorghum (sorghum bicolor).	nitrification results in poor nitrogen (n) recovery and negative environmental impacts in most agricultural systems. some plant species release secondary metabolites from their roots that inhibit nitrification, a phenomenon known as biological nitrification inhibition (bni). here, we attempt to characterize bni in sorghum (sorghum bicolor). in solution culture, the effect of n nutrition and plant age was studied on bni activity from roots. a bioluminescence assay using recombinant nitrosomonas e ...	2008	18657214
a putative autonomous 20.5 kb-cacta transposon insertion in an f3'h allele identifies a new cacta transposon subfamily in glycine max.	the molecular organization of very few genetically defined cacta transposon systems have been characterized thoroughly as those of spm/en in maize, tam1 of antirrhinum majus candystripe1 (cs1) from sorghum bicolor and cac1 from arabidopsis thaliana, for example. to date, only defective deletion derivatives of cacta elements have been described for soybean, an economically important plant species whose genome sequence will be completed in 2008.	2008	19055742
[polyphenol content and antioxidant activity of several seeds and nuts].	foods from plant origin not only provide human diet with certain antioxidant vitamins (c, e and beta-carotene), but also a complex mixture of polyphenols, with antioxidant activity. numerous studies have been focused on the protective and preventing effect of this antioxidant activity on certain degenerative illnesses such as cardiovascular, cancer, and neurological diseases, cataracts and oxidative stress dysfunctions. the objective of this work was to evaluate total polyphenol content and anti ...	2008	19137995
phytoremediation of oil-sludge-contaminated soil.	the aim of this research was to select plant species that could be effective in the phytoremediation ofa former oil-sludge pit. seven crop plants (triticum aestivum l., secale cereale l., avena sativa l., hordeum vulgare, sorghum bicolor l moench, panicum miliaceum l, and zea mays l.),five wild grasses (lolium perenne l., bromopsis inermis, agropyron cristatum l., agropyrum tenerum l., and festuca pratensis huds.), and three legumes (medicago sativa l., trifolium pratense l., and onobrychis anta ...	2008	19260228
efficient, reproducible agrobacterium-mediated transformation of sorghum using heat treatment of immature embryos.	a number of parameters related to agrobacterium-mediated infection were tested to optimize transformation frequencies of sorghum (sorghum bicolor l.). a plasmid with a selectable marker, phosphomannose isomerase, and an sgfp reporter gene was used. first, storing immature spikes at 4 degrees c before use decreased frequency of gfp-expressing calli, for example, in sorghum variety p898012 from 22.5% at 0 day to 6.4% at 5 days. next, heating immature embryos (ies) at various temperatures for 3 min ...	2009	19115059
evolutionary fate of rhizome-specific genes in a non-rhizomatous sorghum genotype.	what is the fate of organ-specific genes after the organ is lost? for sorghum propinquum and sorghum halepense genes that were previously shown to have rhizome-enriched expression, we have conducted comparative analysis of both coding regions and regulatory sequences in sorghum bicolor (non-rhizomatousness) and s. propinquum (rhizomatousness). most genes with rhizome-enriched expression appear to have similar numbers of paralogous copies in both genotypes, with only three of 24 genes studied sho ...	2009	19002204
molecular detection of nifh gene-containing paenibacillus in the rhizosphere of sorghum (sorghum bicolor) sown in cerrado soil.	to develop a polymerase chain reaction (pcr)-based approach for the detection of nifh gene-containing paenibacillus in environmental samples.	2009	19291207
timing and biosynthetic potential for carotenoid accumulation in genetically diverse germplasm of maize.	enhancement of the carotenoid biosynthetic pathway in food crops benefits human health and adds commercial value of natural food colorants. however, predictable metabolic engineering or breeding is limited by the incomplete understanding of endogenous pathway regulation, including rate-controlling steps and timing of expression in carotenogenic tissues. the grass family (poaceae) contains major crop staples, including maize (zea mays), wheat (triticum aestivum), rice (oryza sativa), sorghum (sor ...	2009	19346441
folksong based appraisal of bioecocultural heritage of sorghum (sorghum bicolor (l.) moench): a new approach in ethnobiology.	sorghum is one of the main staple crops for the world's poorest and most food insecure people. as ethiopia is the centre of origin and diversity for sorghum, the crop has been cultivated for thousands of years and hence the heritage of the crop is expected to be rich. folksong based appraisal of bioecocultural heritage has not been done before.	2009	19575802
[biochemical and physiological features of sinorhizobium meliloti and sorghum bicolor interaction in the presence of phenanthrene].		2009	19580158
[genetic transformation of bt gene into sorghum (sorghum bicolor l.) mediated by agrobacterium tumefaciens].	sorghum (sorghum bicolor l.) was one of the most important crops in the world next to wheat, rice, maize, soybean and barley. using the callus derived from immature inflorescence as the recipients, we efficiently transformed sorghum varieties 115, ics21b and 5-27 with the insecticidal bacillus thuringiensis (bt) cry1ab gene carried in the t-dna of binary vectors which contained hygromycin resistance gene and gus gene via agrobacterium tumefaciens. after gradient selection with hygromycin, a tota ...	2009	19621584
white sorghum (sorghum bicolor (l.) moench) bran extracts suppressed ige production by u266 cells.	sorghum, sorghum bicolor (l.) moench, is the fifth most important cereal crop in the world. in this study, we identified the ige production-suppressing activity of white sorghum bran extracts. white sorghum is one of the genotypes of sorghum. white sorghum bran extracts in 10 mm sodium phosphate buffer (ph 7.4) suppressed ige production in human myeloma cell line u266. the extracts suppressed ige production by decreasing mrna transcription level of ige, but they did not affect iga or igg product ...	2009	19734654
comparative genomic study of the thioredoxin family in photosynthetic organisms with emphasis on populus trichocarpa.	the recent genome sequencing of populus trichocarpa and vitis vinifera, two models of woody plants, of sorghum bicolor, a model of monocot using c4 metabolism, and of the moss physcomitrella patens, together with the availability of photosynthetic organism genomes allows performance of a comparative genomic study with organisms having different ways of life, reproduction modes, biological traits, and physiologies. thioredoxins (trxs) are small ubiquitous proteins involved in the reduction of dis ...	2009	19825616
insertion/deletion mutations in the zea chloroplast genome.	the chloroplast (cp) genomes of zea species are distinguished by at least four restriction fragment length (insertion/deletion) mutations. all four mutations occur in the large unique sequence region of the genome. restriction fragments containing three of these mutations were cloned. the large and small forms of two of the mutated fragments were sequenced. this revealed 80 and 83 bp insertion/deletions. the inserted/deleted segments are not parts of tandem repeats nor were they flanked by direc ...	2009	2836083
positively selected disease response orthologous gene sets in the cereals identified using sorghum bicolor l. moench expression profiles and comparative genomics.	disease response genes (drgs) diverge under recurrent positive selection as a result of a molecular arms race between hosts and pathogens. most of these studies were conducted in animals, and few defense genes have been shown to evolve adaptively in plants. to test for adaptation in the molecules mediating disease resistance in the cereals, we first combined information from the expression pattern of sorghum bicolor genes and from divergence to the full genome of rice to identify candidate drgs. ...	2009	19506000
differential growth response of various crop species to arbuscular mycorrhizal inoculation.	to investigate the growth response of various crop species to mycorrhizal inoculation, arbuscular mycorrhizal fungi were applied to glycine max, vigna angularis, senna tora, hordeum vulgare var. hexastichon. zea mays, sorghum bicolor, allium tuberosum, solanum melongena, and capsicum annuum. the biomass of the inoculated crops was measured every two weeks for the 12-week growth period. by measuring biomass, we calculated the mycorrhizal responsiveness of the nine crop species. among the nine cro ...	2009	23983512
algerian pearl millet ( pennisetum glaucum l.) contains xip but not taxi and tlxi type xylanase inhibitors.	an xip (xylanase inhibiting protein) type xylanase inhibitor was purified from algerian pearl millet ( pennisetum glaucum l.) grains and characterized for the first time. cation exchange and affinity chromatography with immobilized trichoderma longibrachiatum glycoside hydrolase (gh) family 11 xylanase resulted in electrophoretically pure protein with a molecular mass of 27-29 kda and a pi value of 6.7. the experimentally determined n-terminal amino acid sequence of the purified xip protein is 8 ...	2009	19459708
promiscuous arbuscular mycorrhizal symbiosis of yam (dioscorea spp.), a key staple crop in west africa.	yam (dioscorea spp.) is a tuberous staple food crop of major importance in the sub-saharan savannas of west africa. optimal yields commonly are obtained only in the first year following slash-and-burn in the shifting cultivation systems. it appears that the yield decline in subsequent years is not merely caused by soil nutrient depletion but might be due to a loss of the beneficial soil microflora, including arbuscular mycorrhizal fungi (amf), associated with tropical "tree-aspect" savannas and ...	2009	19343374
synthesis and phytotoxic activity of new pyridones derived from 4-hydroxy-6-methylpyridin-2(1h)-one.	commercial dehydroacetic acid was converted into 4-hydroxy-6-methylpyridin-2(1h)-one (3), which was then condensed with several aliphatic aldehydes to produce seven new title compounds in variable yields (35-92%). reaction of 3 with alpha,beta-unsaturated aldehydes resulted in the formation of condensed pyran derivatives 4g' and 4h'. a mechanism is proposed to explain the formation of such compounds. the effects of all methylpyridin-2(1h)-one derivatives on the development of the dicotyledonous ...	2009	20032871
synthesis and biological evaluation of new ozonides with improved plant growth regulatory activity.	the iron oxyallyl carbocation generated from 2,7-dibromocycloheptanone was induced to undergo [4 + 3] cycloaddition reactions with various furans, affording a series of 12-oxatricyclo-[4.4.1.1(2,5)]-dodec-3-en-11-one adducts. similar methodology was used to prepare two additional cycloadducts using menthofuran and two homologous aliphatic dibromoketones. dipolar cycloaddition of ozone to the adducts afforded the corresponding secondary ozonides (i.e., 1,2,4-trioxolanes) in variable yields. ozoni ...	2009	19886678
preparation of achiral and chiral (e)-enaminopyran-2,4-diones and their phytotoxic activity.	a short and efficient approach to a range of new chiral and achiral functionalized (e)-enaminopyran-2,4-diones starting with commercially available dehydroacetic acid is described. the phytotoxic properties of these (e)-enaminopyran-2,4-diones were evaluated by their ability to interfere with the growth of sorghum bicolor and cucumis sativus seedlings. a different sensitivity of the two crops was evident with the (e)-enaminopyran-2,4-diones. the most active compounds were also tested against two ...	2009	19170511
synthesis and phytogrowth properties of oxabicyclic analogues related to helminthosporin.	this investigation describes the synthesis and biological evaluation of a series of oxabicyclic analogues related to the helminthosporins. four oxabicycles were prepared by [4+3] cycloaddition of an oxyallyl carbocation, generated in situ from 2,4-dibromopentan-3-one, with selected furans. functional group manipulations of the oxabicyclic architecture generated nine further derivatives. the phytotoxic properties of these oxabicycles were evaluated as their ability to interfere with the growth of ...	2009	19127245
assessment of napier millet (pennisetum purpureumx p. glaucum) and sorghum (sorghum bicolor) trap crops for the management of chilo partellus on maize.	two napier millet (pennisetum purpureumxp. glaucum) hybrids, namely pbn 83 and pbn 233 and one sorghum (sorghum bicolor) variety, sl 44, were assessed for their potential role as a trap crop in the management of the stem borer, chilo partellus (swinhoe) (lepidoptera: crambidae) on maize. oviposition preference and larval survival and development were determined for different test plants under laboratory and screen house conditions. further, field dispersal of c. partellus larvae was assessed bet ...	2009	18947446
expansion mechanisms and functional annotations of hypothetical genes in the rice genome.	in each completely sequenced genome, 30% to 50% of genes are annotated as uncharacterized hypothetical genes. in the rice (oryza sativa) genome, 10,918 hypothetical genes were annotated in the latest version (release 6) of the michigan state university rice genome annotation. we have implemented an integrative approach to analyze their duplication/expansion and function. the analyses show that tandem/segmental duplication and transposition/retrotransposition have significantly contributed to the ...	2009	19535473
trifldb: a database of clustered full-length coding sequences from triticeae with applications to comparative grass genomics.	the triticeae full-length cds database (trifldb) contains available information regarding full-length coding sequences (cdss) of the triticeae crops wheat (triticum aestivum) and barley (hordeum vulgare) and includes functional annotations and comparative genomics features. trifldb provides a search interface using keywords for gene function and related gene ontology terms and a similarity search for dna and deduced translated amino acid sequences to access annotations of triticeae full-length c ...	2009	19448038
phytotoxicity of biosolids and screening of selected plant species with potential for mercury phytoextraction.	mercury contaminated stockpiles of biosolids (3.5-8.4 mg kg(-1) hg) from melbourne water's western treatment plant (mw-wtp) were investigated to evaluate the possibility for their phytoremediation. nine plant species (atriplex codonocarpa, atriplex semibaccata, austrodanthonia caespitosa, brassica juncea, brassica napus, gypsophila paniculata, sorghum bicolor, themeda triandra and trifolium subterraneum) were screened for phytoextraction potential in hg-contaminated biosolids from mw-wtp. in add ...	2010	19775810
involvement of phospholipase d and phosphatidic acid in the light-dependent up-regulation of sorghum leaf phosphoenolpyruvate carboxylase-kinase.	the photosynthetic phosphoenolpyruvate carboxylase (c(4)-pepc) is regulated by phosphorylation by a phosphoenolpyruvate carboxylase kinase (pepc-k). in digitaria sanguinalis mesophyll protoplasts, this light-mediated transduction cascade principally requires a phosphoinositide-specific phospholipase c (pi-plc) and a ca(2+)-dependent step. the present study investigates the cascade components at the higher integrated level of sorghum bicolor leaf discs and leaves. pepc-k up-regulation required li ...	2010	20410319
genome-wide analysis of wox gene family in rice, sorghum, maize, arabidopsis and poplar.	wuschel-related homeobox (wox) genes form a large gene family specifically expressed in plants. they are known to play important roles in regulating the development of plant tissues and organs by determining cell fate. recent available whole genome sequences allow us to do more comprehensive phylogenetic analysis of the wox genes in plants. in the present study, we identified 11 and 21 woxs from sorghum (sorghum bicolor) and maize (zea mays), respectively. the 72 wox genes from rice (oryza sativ ...	2010	20977659
c4gem, a genome-scale metabolic model to study c4 plant metabolism.	leaves of c(4) grasses (such as maize [zea mays], sugarcane [saccharum officinarum], and sorghum [sorghum bicolor]) form a classical kranz leaf anatomy. unlike c(3) plants, where photosynthetic co(2) fixation proceeds in the mesophyll (m), the fixation process in c(4) plants is distributed between two cell types, the m cell and the bundle sheath (bs) cell. here, we develop a c(4) genome-scale model (c4gem) for the investigation of flux distribution in m and bs cells during c(4) photosynthesis. c ...	2010	20974891
annotation and comparative analysis of the glycoside hydrolase genes in brachypodium distachyon.	glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. in plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. glycoside hydrolase genes have been previously cataloged for oryza sativa (rice), the model dicotyledonous pla ...	2010	20973991
genome-wide analysis of ethylene-responsive element binding factor-associated amphiphilic repression motif-containing transcriptional regulators in arabidopsis.	the ethylene-responsive element binding factor-associated amphiphilic repression (ear) motif is a transcriptional regulatory motif identified in members of the ethylene-responsive element binding factor, c2h2, and auxin/indole-3-acetic acid families of transcriptional regulators. sequence comparison of the core ear motif sites from these proteins revealed two distinct conservation patterns: lxlxl and dlnxxp. proteins containing these motifs play key roles in diverse biological functions by negat ...	2010	20097792
suppression of sorghum axillary bud outgrowth by shade, phyb and defoliation signalling pathways.	in recent years, several genetic components of vegetative axillary bud development have been defined in both monocots and eudicots, but our understanding of environmental inputs on branching remains limited. recent work in sorghum (sorghum bicolor) has revealed a role for phytochrome b (phyb) in the control of axillary bud outgrowth through the regulation of teosinte branched1 (tb1) gene. in maize (zea mays), tb1 is a dosage-dependent inhibitor of axillary meristem progression, and the expressio ...	2010	19843258
nucleotide sequence of the split trnaleu(uaa) gene from sorghum bicolor chloroplasts.	the nucleotide (nt) sequence of the split trnaleu(uaa) gene and 328 nt of its flanking regions from sorghum chloroplasts (cp) has been determined. this gene is located in the bamhi-6 fragment in a map position very similar to that of maize. the exon of sorghum trnaleu gene has an identical nt sequence to its counterpart in maize. although the 450 nt of intron in sorghum is 8 nt shorter than that of maize, the nt sequence between them shows 97% homology. like maize and broad bean, the intron from ...	2010	3019834
characterization of beta-glucosidases with high specificity for the cyanogenic glucoside dhurrin in sorghum bicolor (l.) moench seedlings.	two beta-glucosidases exhibiting high specificity for the cyanogenic glucoside dhurrin have been purified to near homogeneity from seedlings of sorghum bicolor. dhurrinase 1 was isolated from shoots of seedlings grown in the dark. dhurrinase 2 was isolated from the green shoots of young seedlings grown in the light. the two enzymes were similar in following characteristics: their optimum activity is around ph 6.2; the enzymes are stable above ph 7; they are effectively inhibited by the beta-glyc ...	2010	3101594
evaluation of sorghum starch as a tablet disintegrant and binder.	the starch prepared from the seeds of sorghum bicolor, moench has been evaluated as a disintegrant and binder in tablets of magnesium sulphate, calcium carbonate, sulphadimidine, and chloroquine phosphate to represent soluble and insoluble inorganic and organic substances. the starch performed as well as maize starch in binding and disintegrating properties and better than acacia as binder.	2010	2886614
population dynamics of caterpillars on three cover crops before sowing cotton in mato grosso (brazil).	direct seeding mulch-based cropping systems under a preliminary cover crop such as millet are common in some areas of brazil. lepidopteran pests that damage cotton, soybean and maize crops can proliferate on cover crops, so preventive chemical treatments are necessary. very little data is available on these pests on cover crops. this paper presents the dynamics of spodoptera frugiperda, s. eridania, mocis latipes and diatraea saccharalis caterpillars monitored at primavera do leste, mato grosso ...	2010	21539250
alkylresorcinol biosynthesis in plants: new insights from an ancient enzyme family?	alkylresorcinols are members of an extensive family of bioactive compounds referred to as phenolic lipids, which occur primarily in plants, fungi, and bacteria. in plants, alkylresorcinols and their derivatives are thought to serve important roles as phytoanticipins and allelochemicals, although direct evidence for this is still somewhat lacking. specialized type iii polyketide synthases (referred to as 'alkylresorcinol synthases'), which catalyze the formation of 5-alkylresorcinols using fatty ...	2010	20861691
spatio-temporal dynamics of genetic diversity in sorghum bicolor in niger.	the dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. however, few surveys have been conducted in centres of diversity. sub-saharan africa is the centre of origin of sorghum. most sahel countries have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic erosion. sorghum is the second staple cereal in niger, a centre of diversity for this crop. niger was submitted to recurrent ...	2010	20062963
flavonoid phytoalexin-dependent resistance to anthracnose leaf blight requires a functional yellow seed1 in sorghum bicolor.	in sorghum bicolor, a group of phytoalexins are induced at the site of infection by colletotrichum sublineolum, the anthracnose fungus. these compounds, classified as 3-deoxyanthocyanidins, have structural similarities to the precursors of phlobaphenes. sorghum yellow seed1 (y1) encodes a myb transcription factor that regulates phlobaphene biosynthesis. using the candystripe1 transposon mutagenesis system in sorghum, we have isolated functional revertants as well as loss-of-function alleles of y ...	2010	20083611
genotoxic and antimutagenic activities of extracts from pseudocereals in the salmonella mutagenicity assay.	extracts of amaranth (amaranthus l.), sorghum (sorghum bicolor l.) and japanese millet (echinochloa frumentacea l.) were evaluated for mutagenicity in salmonella typhimurium strains ta98, ta100 and ta102. all three pseudocereal extracts were also assessed for their antimutagenic properties against the direct mutagens 2-nitrofluorene (2nf) for strain ta98, 3-(5-nitro-2-furyl)acrylic acid (5nfaa) for ta100 and h(2)o(2) for ta102 strain and against the indirect mutagen aflatoxin b(1) (afb(1)). no m ...	2010	20303377
alkylresorcinol synthases expressed in sorghum bicolor root hairs play an essential role in the biosynthesis of the allelopathic benzoquinone sorgoleone.	sorghum bicolor is considered to be an allelopathic crop species, producing phytotoxins such as the lipid benzoquinone sorgoleone, which likely accounts for many of the allelopathic properties of sorghum spp. current evidence suggests that sorgoleone biosynthesis occurs exclusively in root hair cells and involves the production of an alkylresorcinolic intermediate (5-[(z,z)-8',11',14'-pentadecatrienyl]resorcinol) derived from an unusual 16:3delta(9,12,15) fatty acyl-coa starter unit. this led to ...	2010	20348430
fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley.	the barley mutant allele sdw3 confers a gibberellin-insensitive, semi-dwarf phenotype with potential for breeding of new semi-dwarfed barley cultivars. towards map-based cloning, sdw3 was delimited by high-resolution genetic mapping to a 0.04 cm interval in a "cold spot" of recombination of the proximal region of the short arm of barley chromosome 2h. extensive synteny between the barley sdw3 locus (hvu_sdw3) and the orthologous regions (osa_sdw3, sbi_sdw3, bsy_sdw3) of three other grass species ...	2010	20464438
pathogenicity of fusarium isolates to striga hermonthica in burkina faso.	striga hermonthica (del.) benth. is an important constraint to cereal crop production in burkina faso, of which sorghum (sorghum bicolor l. moench) is the most important component. native fusarium species to use as bio-control agents to s. hermonthica has been investigated. fifty one fusarium isolates obtained from diseased plants of s. hermonthica were evaluated for their pathogenicity against striga under controlled environmental conditions. of 51 fusarium isolates, 14 were pathogenic to s. he ...	2010	20464941
inhibition of cyclophosphamide-induced oxidative stress in brain by dietary inclusion of red dye extracts from sorghum (sorghum bicolor) stem.	the stem of sorghum is used as color additives in cooking meals and taken as beverages when steeped or boiled in water as folklore for the management of anemia and some other diseases. this study sought to assess the antioxidant and neuroprotective potentials of red dye extract from sorghum stem on cyclophosphamide-induced oxidative stress in rat brain. wistar strain albino rats were fed diet supplemented with the red dye (0.5% and 1.0% inclusion) for 14 days. there was no significant difference ...	2010	20626249
efficient industrial dye decolorization by bacillus sp. vus with its enzyme system.	this work presents role of different enzymes in decolorization of industrial dye orange t4ll by bacillus sp. vus. bacillus sp. strain vus decolorized dye orange t4ll, under static anoxic condition in 24 h. during decolorization of orange t4ll a significant induction in the activities of lignin peroxidase, tyrosinase, and reductases (nadh-dcip, azo, and riboflavin) was observed. the biodegradation was monitored by ultraviolet-visible spectroscopy, fourier transform infrared spectroscopy, and high ...	2010	20655588
anti-inflammatory activity of select sorghum (sorghum bicolor) brans.	the bran fractions of certain varieties of sorghum (sorghum bicolor) grain are rich sources of phytochemicals and antioxidants. in this article, the anti-inflammatory actions of extracts of select sorghum brans were evaluated in two experimental inflammatory systems: (1) the release of cytokines by lipopolysaccharide-activated peripheral blood mononuclear cells and (2) 12-o-tetradecanoylphorbol acetate (tpa)-induced ear edema in mice. a 1:200 dilution of a 10% (wt/vol) ethanol extract of black s ...	2010	20673059
phenolic acids and flavonoids in nonfermented and fermented red sorghum ( sorghum bicolor (l.) moench).	this study aimed to identify phenolic acids and flavonoids in the red sorghum variety pan 3860 and to determine changes in their concentrations during fermentation with lactobacilli. sorghum sourdoughs fermented with two binary strain combinations, lactobacillus plantarum and lactobacillus casei or lactobacillus fermentum and lactobacillus reuteri , were compared to chemically acidified controls. four glycerol esters were tentatively identified, caffeoylglycerol, dicaffeoylglycerol, coumaroyl-ca ...	2010	20677784
germin-like proteins (glps) in cereal genomes: gene clustering and dynamic roles in plant defence.	the recent release of the genome sequences of a number of crop and model plant species has made it possible to define the genome organisation and functional characteristics of specific genes and gene families of agronomic importance. for instance, sorghum bicolor, maize (zea mays) and brachypodium distachyon genome sequences along with the model grass species rice (oryza sativa) enable the comparative analysis of genes involved in plant defence. germin-like proteins (glps) are a small, functiona ...	2010	20683632
decolorization and detoxification of congo red and textile industry effluent by an isolated bacterium pseudomonas sp. su-ebt.	the 16s rrna sequence and biochemical characteristics revealed the isolated organism as pseudomonas sp. su-ebt. this strain showed 97 and 90% decolorization of a recalcitrant dye, congo red (100 mg l(-1)) and textile industry effluent with 50% reduction in cod within 12 and 60 h, respectively. the optimum ph and temperature for the decolorization was 8.0 and 40 degrees c, respectively. pseudomonas sp. su-ebt was found to tolerate the dye concentration up to 1.0 g l(-1). significant induction in ...	2010	19774467
biosynthesis of the cyanogenic glucosides linamarin and lotaustralin in cassava: isolation, biochemical characterization, and expression pattern of cyp71e7, the oxime-metabolizing cytochrome p450 enzyme.	cassava (manihot esculenta) is a eudicotyledonous plant that produces the valine- and isoleucine-derived cyanogenic glucosides linamarin and lotaustralin with the corresponding oximes and cyanohydrins as key intermediates. cyp79 enzymes catalyzing amino acid-to-oxime conversion in cyanogenic glucoside biosynthesis are known from several plants including cassava. the enzyme system converting oxime into cyanohydrin has previously only been identified in the monocotyledonous plant great millet (sor ...	2010	21045121
inhibition effects of the classical pathway complement of three sorghum bicolor from south korea.	the present study evaluated the anti-complement effects from organic solvent extracts of three varieties (hwanggeumchal sorghum, chal sorghum, and heuin sorghum) from sorghum bicolor in classical pathway complement system. we have evaluated organic solvent extract from sorghum bicolor varieties with regard to its anti-complement activity. chal sorghum ethyl acetate extract showed inhibitory activity against complement system with 50% inhibitory concentrations (ic(50)) values of 38.7 μg/ml. this ...	2010	21077803
antilipidemic activity of organic solvent extract from sorghum bicolor on rats with diet-induced obesity.	the present study evaluated the antiobesity and lipid-lowering effects from dichloromethane and ethyl acetate extracts of hwanggeumchal sorghum varieties on sorghum bicolor. the hwanggeumchal sorghum ethyl acetate extracts significantly reduced the plasma total cholesterol and triglyceride levels significantly when given orally at a dose of 50 and 300 mg/kg/day to the high-fat diet-induced obese rats for 2 weeks. these findings demonstrate the excellent pharmacological potential of hwanggeumchal ...	2010	21078773
nutrients intake, digestibility, nitrogen balance and growth performance of sheep fed different silages with or without concentrate.	the experiment was conducted to investigate the influence of maize (zea mays), sorghum (sorghum bicolor) and millet (pennisetum americannum) silages with or without concentrate on nutrients intake, digestibility, nitrogen balance and weight gain in sipli sheep. six experimental diets were formulated having 100% maize silage (ms), maize silage and concentrate as 50:50 (msc), 100% sorghum silage (ss), sorghum silage and concentrate as 50:50 (ssc), 100% millet silage (mis) and millet silage and con ...	2010	21116714
the rate of nitrite reduction in leaves as indicated by o₂ and co₂ exchange during photosynthesis.	light response (at 300 ppm co(2) and 10-50 ppm o(2) in n(2)) and co(2) response curves [at absorbed photon fluence rate (pad) of 550 μmol m(-2) s(-1)] of o(2) evolution and co(2) uptake were measured in tobacco (nicotiana tabacum l.) leaves grown on either no(3)(-) or nh(4)(+) as n source and in potato (solanum tuberosum l.), sorghum (sorghum bicolor l. moench), and amaranth (amaranthus cruentus l.) leaves grown on nh(4)no(3). photosynthetic o(2) evolution in excess of co(2) uptake was measured ...	2011	21239375
natural populations of lactic acid bacteria associated with silage fermentation as determined by phenotype, 16s ribosomal rna and reca gene analysis.	one hundred and fifty-six strains isolated from corn (zea mays l.), forage paddy rice (oryza sativa l.), sorghum (sorghum bicolor l.) and alfalfa (medicago sativa l.) silages prepared on dairy farms were screened, of which 110 isolates were considered to be lactic acid bacteria (lab) according to their gram-positive and catalase-negative characteristics and, mainly, the lactic acid metabolic products. these isolates were divided into eight groups (a-h) based on the following properties: morpholo ...	2011	21282025
rhizosphere indole-3-acetic acid as a mediator in the sorghum bicolor-phenanthrene-sinorhizobium meliloti interactions.	we studied a model system consisting of sorghum bicolor, phenanthrene, and an auxin-producing polycyclic aromatic hydrocarbon-degrading sinorhizobium meliloti strain to clarify whether rhizosphere indole-3-acetic acid (iaa) takes part in the plant-pollutant-bacteria interactions. phenanthrene and s. meliloti treatments of sorghum contributed to a decrease in the rhizosphere iaa concentration and to phytohormone accumulation, respectively. regression analysis showed significant correlations betwe ...	2011	21459011
structural stability of soybean (glycine max) α-amylase: properties of the unfolding transition studied with fluorescence and cd spectroscopy.	stability and unfolding of mammalian and microbial α-amylases have been intensively investigated. however, there is only limited information available on the structural stability of plant α-amylases, namely of the two isoenzymes from barley amy1 and amy2, of the α-amylase from mung bean (vigna radiata), and of the α-amylase from malted sorghum (sorghum bicolor). we report here the stability of soyabean α-amylase (gma), against elevated temperatures and chemical denaturants (gndhcl) by employing ...	2011	20955173
functional incorporation of sorghum small subunit increases the catalytic turnover rate of rubisco in transgenic rice.	ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) limits photosynthetic co2 fixation because of its low catalytic turnover rate (kcat) and competing oxygenase reaction. previous attempts to improve the catalytic efficiency of rubisco by genetic engineering have gained little progress. here we demonstrate that the introduction of the small subunit (rbcs) of high kcat rubisco from the c4 plant sorghum (sorghum bicolor) significantly enhances kcat of rubisco in transgenic rice (oryza sativa ...	2011	21562335
inhibition of aromatase and α-amylase by flavonoids and proanthocyanidins from sorghum bicolor bran extracts.	abstract we compared the ability of simple flavonoids and proanthocyanidins in sorghum bicolor bran extracts to inhibit enzymes in vitro. in particular, aromatase is a target for breast cancer therapy, and inhibition of α-amylase can reduce the glycemic effect of dietary starches. proanthocyanidin-rich sumac sorghum bran extract inhibited α-amylase at a lower concentration (50% inhibitory concentration [ic(50)]=1.4 μg/ml) than did proanthocyanidin-free black sorghum bran extract (ic(50)=11.4 μg/ ...	2011	21612457
endophyte-assisted promotion of biomass production and metal-uptake of energy crop sweet sorghum by plant-growth-promoting endophyte bacillus sp. sls18.	the effects of bacillus sp. sls18, a plant-growth-promoting endophyte, on the biomass production and mn/cd uptake of sweet sorghum (sorghum bicolor l.), phytolacca acinosa roxb., and solanum nigrum l. were investigated. sls18 displayed multiple heavy metals and antibiotics resistances. the strain also exhibited the capacity of producing indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylic acid deaminase. in pot experiments, sls18 could not only infect plants effectively but a ...	2011	21792590
chemical characterization of a procyanidin-rich extract from sorghum bran and its effect on oxidative stress and tumor inhibition in vivo.	the present study was to characterize a procyanidin-rich extract (pare) from sorghum ( sorghum bicolor (l.) moench) bran and assess its biological activities. the procyanidin oligomers were separated and identified by normal-phase hplc equipped with fluorescence (fld) and mass spectrometry (ms) detectors. in addition, the effects of pare on oxidative stress in mice induced by d-galactose as well as tumor inhibition in c57bl/6j mice bearing lewis lung cancer were investigated. administration of d ...	2011	21780844
biodegradation of 2-mercaptobenzothiazolyl-(z)-(2-aminothiazol-4-yl)-2-(tert-butoxycarbonyl) isopropoxyiminoacetate by pseudomonas desmolyticum ncim 2112.	2-mercaptobenzothiazolyl-(z)-(2-aminothiazol-4-yl)-2-(tert-butoxycarbonyl) isopropoxyiminoacetate is used as supplementary additives in commercial-grade insecticides to compensate for the time factor needed for the actual pesticide chemical to start its action. this investigation describes the biodegradation of 2-mercaptobenzothiazolyl-(z)-(2-aminothiazol-4-yl)-2-(tert-butoxycarbonyl) isopropoxyiminoacetate by pseudomonas desmolyticum ncim 2112. the biodegradation is influenced by other carbon a ...	2011	21773762
characterization and expression profile of two udp-glucosyltransferases, ugt85k4 and ugt85k5, catalyzing the last step in cyanogenic glucoside biosynthesis in cassava.	manihot esculenta (cassava) contains two cyanogenic glucosides, linamarin and lotaustralin, biosynthesized from l-valine and l-isoleucine, respectively. in this study, cdnas encoding two uridine diphosphate glycosyltransferase (ugt) paralogs, assigned the names ugt85k4 and ugt85k5, have been isolated from cassava. the paralogs display 96% amino acid identity, and belong to a family containing cyanogenic glucoside-specific ugts from sorghum bicolor and prunus dulcis. recombinant ugt85k4 and ugt85 ...	2011	21736650
Fine mapping and comparative genomics integration of two quantitative trait loci controlling resistance to powdery mildew in a Spanish barley landrace.	The intervals containing two major quantitative trait loci (QTL) from a Spanish barley landrace conferring broad spectrum resistance to Blumeria graminis were subjected to marker saturation. First, all the available information on recently developed marker resources for barley was exploited. Then, a comparative genomic analysis of the QTL regions with other sequenced grass model species was performed. As a result of the first step, 32 new markers were added to the previous map and new flanking m ...	2011	21901548
characterization of chloroplast dna microsatellites from saccharum spp and related species.	microsatellites, or simple sequence repeats (ssrs), and their flanking regions in chloroplast genomes (plastomes) of some species of the family poaceae were analyzed in silico to look for dna sequence variations. comparison of the complete chloroplast dna sequences (cpdnas) of sugarcane (saccharum hybrid cv. sp-80-3280 and s. officinarum cv. nco310) and related species, agrostis stolonifera, brachypodium distachyon, hordeum vulgare subsp vulgare, lolium perenne, oryza nivara, o. sativa sub ...	2011	21948764
expression of seed dormancy in grain sorghum lines with contrasting pre-harvest sprouting behavior involves differential regulation of gibberellin metabolism genes.	grain sorghum (sorghum bicolor (l) moench) exhibits intra-specific variability for the rate of dormancy release and pre-harvest sprouting behavior. two inbred lines with contrasting sprouting response were compared: is9530 (resistant) and redlandb2 (susceptible). precocious dormancy release in redlandb2 is related to an early loss of embryo sensitivity to abscisic acid and higher levels of gibberellins in imbibed grains as compared to is9530. with the aim to identify potential regulatory sites f ...	2011	22076590
in planta production of the highly potent resveratrol analogue pterostilbene via stilbene synthase and o-methyltransferase co-expression.	resveratrol and related stilbenes are thought to play important roles in defence responses in several plant species and have also generated considerable interest as nutraceuticals owing to their diverse health-promoting properties. pterostilbene, a 3,5-dimethylether derivative of resveratrol, possesses properties similar to its parent compound and, additionally, exhibits significantly higher fungicidal activity in vitro and superior pharmacokinetic properties in vivo. recombinant enzyme studies ...	2011	21902799
rapid determination of syringyl: guaiacyl ratios using ft-raman spectroscopy.	lignin composition in relation to its basic phenylpropanoid units, particularly the syringyl to guaiacyl (s/g) ratio, is an important property for biomass characterization and varies greatly as a function of species, genotype and environment. a rapid screening method is highly desirable to assess lignin composition in a large number of samples. we have developed a nondestructive and label-free fourier transform raman (ft-raman) spectroscopic method that is capable of rapidly and reliably measuri ...	2011	22012706
naturally occurring phytotoxins in allelopathic plants help reduce herbicide dose in wheat.	field studies were carried out to evaluate the influence of allelopathic plant water extracts applied alone or tank-mixed with a reduced herbicide dose on the weeds of wheat. water extracts of sorghum (sorghum bicolor (l.) moench.) + sunflower (helianthus annuus l.) + mulberry (morus alba l.) were used alone (each at 20 l ha(-1)) or combined with iodo + mesosulfuron (3.6 and 7.2 g active ingredient (a.i.) ha(-1); 25 and 50% of the recommended dose, respectively). the recommended dose of herbicid ...	2011	21854181
Biodegradation of crystal violet by Agrobacterium radiobacter.	Agrobacterium radiobacter MTCC 8161 completely decolorized the Crystal Violet with 8 hr (10 mg/L) at static anoxic conditions. The decreased decolorization capability by A. radiobacter was observed, when the Crystal Violet concentration was increased from 10 to 100 mg/L. Semi-synthetic medium containing 1% yeast extract and 0.1% NH4C1 has shown 100% decolorization of Crystal Violet within 5 hr. A complete degradation of Crystal Violet by A. radiobacter was observed up to 7 cycles of repeated add ...	2011	22128547
Lack of low frequency variants masks patterns of non-neutral evolution following domestication.	Detecting artificial selection in the genome of domesticated species can not only shed light on human history but can also be beneficial to future breeding strategies. Evidence for selection has been documented in domesticated species including maize and rice, but few studies have to date detected signals of artificial selection in the Sorghum bicolor genome. Based on evidence that domesticated S. bicolor and its wild relatives show significant differences in endosperm structure and quality, we ...	2011	21853065
tissue-specific differences in cytosine methylation and their association with differential gene expression in sorghum.	it has been well established that dna cytosine methylation plays essential regulatory roles in imprinting gene expression in endosperm, and hence normal embryonic development, in the model plant arabidopsis (arabidopsis thaliana). nonetheless, the developmental role of this epigenetic marker in cereal crops remains largely unexplored. here, we report for sorghum (sorghum bicolor) differences in relative cytosine methylation levels and patterns at 5'-ccgg sites in seven tissues (endosperm, embryo ...	2011	21632971
co-variation among major classes of lrr-encoding genes in two pairs of plant species.	nbs-lrr (nucleotide-binding site-leucine-rich repeat), lrr-rlk (lrr-receptor-like kinase), and lrr-only are the three major lrr-encoding genes. owing to the crucial role played by them in plant resistance, development, and growth, extensive studies have been performed on the nbs-lrr and lrr-rlk genes. however, few studies have focused on these genes collectively; they may co-vary as all of them contain lrr motifs. to investigate their common evolutionary patterns, all major classes of lrr-encodi ...	2011	21626302
plantmirnapred: efficient classification of real and pseudo plant pre-mirnas.	micrornas (mirnas) are a set of short (21-24 nt) non-coding rnas that play significant roles as post-transcriptional regulators in animals and plants. while some existing methods use comparative genomic approaches to identify plant precursor mirnas (pre-mirnas), others are based on the complementarity characteristics between mirnas and their target mrnas sequences. however, they can only identify the homologous mirnas or the limited complementary mirnas. furthermore, since the plant pre-mirnas a ...	2011	21441575
genome-wide analysis of clustering patterns and flanking characteristics for plant microrna genes.	micrornas (mirnas) have been proven to play important roles at the post-transcriptional level in animals and plants. to investigate clustering patterns and specific sequence characteristics in the flanking regions of plant mirna genes, we performed genome-wide analyses of arabidopsis thaliana, populus trichocarpa, oryza sativa and sorghum bicolor. our results showed that mirna pair distances were significantly higher than would have been expected to occur at random and that the number of mirna g ...	2011	21223508
analysis of subcellular localization of auxin carriers pin, aux/lax and pgp in sorghum bicolor.	auxin transport at least correlates to the three gene families: efflux carriers pin-formed (pin), p-glycoprotein (pgp), and influx carrier auxin resistant 1/like aux1(aux/lax) in arabidopsis thaliana. in monocotyledon sorghum bicolor, the biological function of these genes retains unclear. our previous study reported that the member analysis, organ-specific expression and expression profiles of the auxin transporter pin, pgp and aux/lax gene families in sorghum bicolor under iaa, brassinosteroid ...	2011	22112459
selection for higher gene copy number after different types of plant gene duplications.	the evolutionary origins of the multitude of duplicate genes in the plant genomes are still incompletely understood. to gain an appreciation of the potential selective forces acting on these duplicates, we phylogenetically inferred the set of metabolic gene families from 10 flowering plant (angiosperm) genomes. we then compared the metabolic fluxes for these families, predicted using the arabidopsis thaliana and sorghum bicolor metabolic networks, with the families' duplication propensities. for ...	2011	22056313