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1.
Nat Commun ; 10(1): 2186, 2019 05 16.
Artigo em Inglês | MEDLINE | ID: mdl-31097703

RESUMO

The increasing availability of X-ray free-electron lasers (XFELs) has catalyzed the development of single-object structural determination and of structural dynamics tracking in real-time. Disentangling the molecular-level reactions triggered by the interaction with an XFEL pulse is a fundamental step towards developing such applications. Here we report real-time observations of XFEL-induced electronic decay via short-lived transient electronic states in the diiodomethane molecule, using a femtosecond near-infrared probe laser. We determine the lifetimes of the transient states populated during the XFEL-induced Auger cascades and find that multiply charged iodine ions are issued from short-lived (∼20 fs) transient states, whereas the singly charged ones originate from significantly longer-lived states (∼100 fs). We identify the mechanisms behind these different time scales: contrary to the short-lived transient states which relax by molecular Auger decay, the long-lived ones decay by an interatomic Coulombic decay between two iodine atoms, during the molecular fragmentation.

2.
Phys Rev Lett ; 120(22): 223201, 2018 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-29906148

RESUMO

We show that electron and ion spectroscopy reveals the details of the oligomer formation in Ar clusters exposed to an x-ray free electron laser (XFEL) pulse, i.e., chemical dynamics triggered by x rays. With guidance from a dedicated molecular dynamics simulation tool, we find that van der Waals bonding, the oligomer formation mechanism, and charge transfer among the cluster constituents significantly affect ionization dynamics induced by an XFEL pulse of moderate fluence. Our results clearly demonstrate that XFEL pulses can be used not only to "damage and destroy" molecular assemblies but also to modify and transform their molecular structure. The accuracy of the predictions obtained makes it possible to apply the cluster spectroscopy, in connection with the respective simulations, for estimation of the XFEL pulse fluence in the fluence regime below single-atom multiple-photon absorption, which is hardly accessible with other diagnostic tools.

3.
Plant Biotechnol J ; 16(1): 111-123, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-28499068

RESUMO

Physicochemical properties of storage starch largely determine rice grain quality and food characteristics. Therefore, modification of starch property is effective to fine-tune cooked rice textures. To obtain new resources with modified starch property as breeding materials, we screened a mutant population of a japonica cultivar Nipponbare and found two independent mutant lines, altered gelatinization (age)1 and age2, with moderate changes in starch gelatinization property. A combination of conventional genetic analyses and the latest mapping method, MutMapPlus, revealed that both of these lines harbour novel independent mutant alleles of starch branching enzyme IIb (BEIIb) gene. In age1, amino acid substitution of Met-723 to Lys completely abolished BEIIb enzyme activity without significant reduction in its protein level. A transposon insertion in an intron of BEIIb gene reduced BEIIb protein level and activity in age2. Production of a series of the mutant lines by combining age alleles and indica-type starch synthase IIa allele established stepwise alteration of the physicochemical properties of starch including apparent amylose content, thermal property, digestibility by α-amylase and branched structures of amylopectin. Consistent with the alteration of starch properties, the results of a sensory evaluation test demonstrated that warm cooked rice of the mutants showed a variety of textures without marked reduction in overall palatability. These results suggest that a series of the mutant lines are capable of manipulation of cooked rice textures.


Assuntos
Enzima Ramificadora de 1,4-alfa-Glucana/genética , Enzima Ramificadora de 1,4-alfa-Glucana/metabolismo , Oryza/enzimologia , Oryza/genética , Alelos , Amilopectina/genética , Amilopectina/metabolismo , Oryza/metabolismo
4.
Breed Sci ; 67(4): 333-339, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29085242

RESUMO

The occurrence of chalky rice (Oryza sativa L.) grains caused by high temperature is a serious problem in rice production. Of the several kinds of chalky grains, milky-white grains are not well analyzed. The milky-white rice grain phenomenon is caused by genetic factors as well as environmental and nutritional conditions. To analyze the genetic control system for rice grain quality, we raised recombinant inbred lines from progeny produced from 'Tsukushiroman' (high temperature sensitive) and 'Chikushi 52' (high temperature tolerant) cultivars. Quantitative trait locus (QTL) analysis revealed that the QTL on chromosome 4, linked to the simple sequence repeat marker RM16424, contributed substantially to the occurrence of milky-white grains, as it was detected over two experimental years. To validate the effect of the QTL, we developed near isogenic lines that have the 'Chikushi 52' segment on the short arm of chromosome 4 in the 'Tsukushiroman' genetic background, and that had a lower milky-white grain ratio than that of 'Tsukushiroman' when exposed to high temperatures during the ripening period. These results suggest that the 'Chikushi 52' allele on chromosome 4 suppresses the occurrence of milky-white grains and improves rice grain quality under heat stress during the grain ripening period.

5.
Phys Chem Chem Phys ; 19(30): 19707-19721, 2017 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-28530728

RESUMO

Coulomb explosion of diiodomethane CH2I2 molecules irradiated by ultrashort and intense X-ray pulses from SACLA, the Japanese X-ray free electron laser facility, was investigated by multi-ion coincidence measurements and self-consistent charge density-functional-based tight-binding (SCC-DFTB) simulations. The diiodomethane molecule, containing two heavy-atom X-ray absorbing sites, exhibits a rather different charge generation and nuclear motion dynamics compared to iodomethane CH3I with only a single heavy atom, as studied earlier. We focus on charge creation and distribution in CH2I2 in comparison to CH3I. The release of kinetic energy into atomic ion fragments is also studied by comparing SCC-DFTB simulations with the experiment. Compared to earlier simulations, several key enhancements are made, such as the introduction of a bond axis recoil model, where vibrational energy generated during charge creation processes induces only bond stretching or shrinking. We also propose an analytical Coulomb energy partition model to extract the essential mechanism of Coulomb explosion of molecules from the computed and the experimentally measured kinetic energies of fragment atomic ions by partitioning each pair Coulomb interaction energy into two ions of the pair under the constraint of momentum conservation. Effective internuclear distances assigned to individual fragment ions at the critical moment of the Coulomb explosion are then estimated from the average kinetic energies of the ions. We demonstrate, with good agreement between the experiment and the SCC-DFTB simulation, how the more heavily charged iodine fragments and their interplay define the characteristic features of the Coulomb explosion of CH2I2. The present study also confirms earlier findings concerning the magnitude of bond elongation in the ultrashort X-ray pulse duration, showing that structural damage to all but C-H bonds does not develop to a noticeable degree in the pulse length of ∼10 fs.

6.
Breed Sci ; 65(3): 216-25, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-26175618

RESUMO

There is increasing evidence that global warming affects the development of rice. High temperatures during ripening increase the ratio of undesirable chalky grains followed by deteriorating grain appearance quality. In order to detect quantitative trait loci (QTLs) controlling the occurrence of white-back and basal-white chalky grains of brown rice, QTL analysis was performed using recombinant inbred lines derived from a cross between two strains, 'Tsukushiroman' (sensitive to heat stress) and 'Chikushi 52' (tolerant of heat stress). The F7 and F8 lines were exposed to heat stress during the ripening period in two locations, Fukuoka and Kagoshima, in Japan. QTLs for white-back grains and basal-white grains were detected on chromosomes 1, 3, and 8, and those for basal-white grains were detected on chromosomes 2, 3, and 12. QTLs on chromosome 8 for white-back grains were shared in the plants grown in both locations. Near-isogenic lines (NILs), which harbored a segment from 'Chikushi 52' on chromosome 8 with the genetic background of 'Tsukushiroman', showed relatively lower ratios of white-back grains than 'Tsukushiroman'. Therefore, insertion of the 'Chikushi 52' genomic region of the QTL on chromosome 8 can improve the quality of rice when it is grown under heat stress conditions.

7.
Theor Appl Genet ; 128(4): 563-73, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25762131

RESUMO

KEY MESSAGE: This manuscript reports the fine mapping of a novel QTL, qAC2 controlling the low amylose in rice. The action mechanism of the qAC2 is also investigated by the analysis of genetic interactions to Wx (a), Wx (b), du1, du2 and du3. Amylose content of the rice (Oryza sativa L.) endosperm greatly affects starch properties and eating quality of cooked rice. Seeds of japonica rice cultivar Kuiku162 have low amylose content (AC) and good eating quality. Our analysis revealed a novel QTL, designated as qAC2 that contributed to the low AC of Kuiku162. qAC2 was fine mapped within a 74.9-kb region between two insertion and deletion markers, KID3001 and KID5101, on the long arm of chromosome 2. Seven genes are predicted in this region, but none of them is known to be related to the regulation of AC. The AC of a near-isogenic line (NIL110) carrying qAC2 (Kuiku), the Kuiku162 allele of qAC2, in the genetic background of japonica cultivar Itadaki was lower by 1.1% points than that of Itadaki. The chain length distributions of amylopectin were similar in NIL110 and Itadaki; therefore, the low AC of NIL110 was caused by a decrease in the actual AC, but not by a difference in the amylopectin structure. The interaction analyses revealed that qAC2 (Kuiku) has epistatic interaction with Wx (a). The qAC2 (Kuiku) has epistatic interactions with two loci, du1 and du2, on Wx (b), whereas the genetic effect of qAC2 (Kuiku) has additive to that of du3 on Wx (b). Thus, similar to du1 and du2, qAC2 may have a function related to Wx (b) mRNA splicing.


Assuntos
Amilose/química , Mapeamento Cromossômico , Oryza/genética , Locos de Características Quantitativas , Alelos , Amilopectina/química , Cromossomos de Plantas , Epistasia Genética , Regulação da Expressão Gênica de Plantas , Ligação Genética , Marcadores Genéticos , Mutação INDEL , Repetições de Microssatélites , Oryza/química , Sementes/química
8.
PLoS One ; 9(1): e85106, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24454799

RESUMO

With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a 'one size fits all' crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market.


Assuntos
Cruzamento/economia , Cruzamento/métodos , Internacionalidade , Oryza/economia , Oryza/crescimento & desenvolvimento , Amilose/metabolismo , Clima , Odorantes , Oryza/anatomia & histologia , Oryza/metabolismo , Temperatura Ambiente
9.
J Sci Food Agric ; 93(1): 110-7, 2013 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-22821180

RESUMO

BACKGROUND: Characterization of starch properties and functionality can apply breeding program selection for desirable traits such as eating, cooking and processing qualities to meet consumer preference. Low amylose content is generally preferred in Malaysia because of cohesive, tender and glossy cooked rice. Rice high in short-chain amylopectin has a lower transition temperature of starch gelatinization. In the continuing search for improved starch quality in rice cultivars a study was carried out with new mutant lines MR219-4 and MR219-9, derived from MR219. RESULTS: MR219 and its mutant lines contain L-type amylopectin, being high in amylopectin of intermediate chain length with degree of polymerization 12-21. The apparent amylose content (AAC) in MR219-4 had lower AAC value (19.2%) compared to other lines. A strongly negative correlation was found between chain-length fraction of amylopectin and transition temperatures-onset temperature peak temperature, and conclusion temperature (0.992, 0.958, 0.950; P < 0.01)-with fraction b1 (fb1), respectively. CONCLUSION: The Malaysian lines studied contain L-type amylopectin and offer a better understanding of grain quality improvement in terms of starch properties and functionality. This information will be directly applicable to select for desirable traits in future breeding programs.


Assuntos
Amilopectina/genética , Endosperma/metabolismo , Mutação , Oryza/genética , Fenótipo , Amido/genética , Amilopectina/química , Amilose/genética , Amilose/metabolismo , Qualidade dos Alimentos , Humanos , Malásia , Oryza/metabolismo , Amido/química , Temperatura Ambiente
10.
Plant Cell Physiol ; 52(6): 1068-82, 2011 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-21551159

RESUMO

Debranching enzymes, which hydrolyze α-1 and 6-glucosidic linkages in α-polyglucans, play a dual role in the synthesis and degradation of starch in plants. A transposon-inserted rice mutant of isoamylase3 (isa3) contained an increased amount of starch in the leaf blade at the end of the night, indicating that ISA3 plays a role in the degradation of transitory starch during the night. An epitope-tagged ISA3 expressed in Escherichia coli exhibited hydrolytic activity on ß-limit dextrin and amylopectin. We investigated whether ISA3 plays a role in amyloplast development and starch metabolism in the developing endosperm. ISA3-green fluorescent protein (GFP) fusion protein expressed under the control of the rice ISA3 promoter was targeted to the amyloplast stroma in the endosperm. Overexpression of ISA3 in the sugary1 mutant, which is deficient in ISA1 activity, did not convert water-soluble phytoglycogen to starch granules, indicating that ISA1 and ISA3 are not functionally redundant. Both overexpression and loss of function of ISA3 in the endosperm generated pleomorphic amyloplasts and starch granules. Furthermore, chloroplasts in the leaf blade of isa3 seedlings were large and pleomorphic. These results suggest that ISA3 facilitates starch metabolism and affects morphological characteristics of plastids in rice.


Assuntos
Isoamilase/metabolismo , Oryza/enzimologia , Proteínas de Plantas/metabolismo , Plastídeos/fisiologia , Amido/metabolismo , Elementos de DNA Transponíveis , Endosperma/enzimologia , Endosperma/crescimento & desenvolvimento , Endosperma/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Regulação da Expressão Gênica de Plantas , Técnicas de Silenciamento de Genes , Genótipo , Isoamilase/genética , Morfogênese , Oryza/genética , Oryza/crescimento & desenvolvimento , Folhas de Planta/enzimologia , Folhas de Planta/crescimento & desenvolvimento , Folhas de Planta/metabolismo , Proteínas de Plantas/genética , Plantas Geneticamente Modificadas/enzimologia , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/crescimento & desenvolvimento , Plastídeos/metabolismo , Proteínas Recombinantes de Fusão , Amido/análise , Especificidade por Substrato
11.
J Biol Chem ; 280(11): 9773-9, 2005 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-15637061

RESUMO

The Arabidopsis thaliana genome encodes three alpha-amylase-like proteins (AtAMY1, AtAMY2, and AtAMY3). Only AtAMY3 has a predicted N-terminal transit peptide for plastidial localization. AtAMY3 is an unusually large alpha-amylase (93.5 kDa) with the C-terminal half showing similarity to other known alpha-amylases. When expressed in Escherichia coli, both the whole AtAMY3 protein and the C-terminal half alone show alpha-amylase activity. We show that AtAMY3 is localized in chloroplasts. The starch-excess mutant of Arabidopsis sex4, previously shown to have reduced plastidial alpha-amylase activity, is deficient in AtAMY3 protein. Unexpectedly, T-DNA knock-out mutants of AtAMY3 have the same diurnal pattern of transitory starch metabolism as the wild type. These results show that AtAMY3 is not required for transitory starch breakdown and that the starch-excess phenotype of the sex4 mutant is not caused simply by deficiency of AtAMY3 protein. Knock-out mutants in the predicted non-plastidial alpha-amylases AtAMY1 and AtAMY2 were also isolated, and these displayed normal starch breakdown in the dark as expected for extraplastidial amylases. Furthermore, all three AtAMY double knock-out mutant combinations and the triple knock-out degraded their leaf starch normally. We conclude that alpha-amylase is not necessary for transitory starch breakdown in Arabidopsis leaves.


Assuntos
Arabidopsis/enzimologia , Folhas de Planta/enzimologia , alfa-Amilases/fisiologia , Regiões 3' não Traduzidas , Regiões 5' não Traduzidas , Sequência de Aminoácidos , Carboidratos/química , Cloroplastos/metabolismo , DNA/metabolismo , DNA Bacteriano , DNA Complementar/metabolismo , Eletroforese em Gel de Poliacrilamida , Escherichia coli/metabolismo , Biblioteca Gênica , Técnicas Genéticas , Genoma de Planta , Immunoblotting , Modelos Genéticos , Dados de Sequência Molecular , Mutação , Estrutura Terciária de Proteína , Homologia de Sequência de Aminoácidos , Amido , Fatores de Tempo
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