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991.
Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species‐level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species‐level resolution. The number of sequence reads of each MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field‐collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97% similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass‐dominant species in each field‐collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure. 相似文献
992.
Introduction of chemically labile substructures into Arabidopsis lignin through the use of LigD,the Cα‐dehydrogenase from Sphingobium sp. strain SYK‐6
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Yuki Tobimatsu Yasuyuki Ishikawa Clifton E. Foster Naofumi Kamimura Shojiro Hishiyama Saki Hashimoto Amiu Shino Hirofumi Hara Kanna Sato‐Izawa Paula Oyarce Geert Goeminne Kris Morreel Jun Kikuchi Toshiyuki Takano Masao Fukuda Yoshihiro Katayama Wout Boerjan John Ralph Eiji Masai Shinya Kajita 《Plant biotechnology journal》2015,13(6):821-832
Bacteria‐derived enzymes that can modify specific lignin substructures are potential targets to engineer plants for better biomass processability. The Gram‐negative bacterium Sphingobium sp. SYK‐6 possesses a Cα‐dehydrogenase (LigD) enzyme that has been shown to oxidize the α‐hydroxy functionalities in β–O–4‐linked dimers into α‐keto analogues that are more chemically labile. Here, we show that recombinant LigD can oxidize an even wider range of β–O–4‐linked dimers and oligomers, including the genuine dilignols, guaiacylglycerol‐β‐coniferyl alcohol ether and syringylglycerol‐β‐sinapyl alcohol ether. We explored the possibility of using LigD for biosynthetically engineering lignin by expressing the codon‐optimized ligD gene in Arabidopsis thaliana. The ligD cDNA, with or without a signal peptide for apoplast targeting, has been successfully expressed, and LigD activity could be detected in the extracts of the transgenic plants. UPLC‐MS/MS‐based metabolite profiling indicated that levels of oxidized guaiacyl (G) β–O–4‐coupled dilignols and analogues were significantly elevated in the LigD transgenic plants regardless of the signal peptide attachment to LigD. In parallel, 2D NMR analysis revealed a 2.1‐ to 2.8‐fold increased level of G‐type α‐keto‐β–O–4 linkages in cellulolytic enzyme lignins isolated from the stem cell walls of the LigD transgenic plants, indicating that the transformation was capable of altering lignin structure in the desired manner. 相似文献
993.
Paternal H3K4 methylation is required for minor zygotic gene activation and early mouse embryonic development
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Epigenetic modifications, such as DNA methylation and histone modifications, are dynamically altered predominantly in paternal pronuclei soon after fertilization. To identify which histone modifications are required for early embryonic development, we utilized histone K‐M mutants, which prevent endogenous histone methylation at the mutated site. We prepared four single K‐M mutants for histone H3.3, K4M, K9M, K27M, and K36M, and demonstrate that overexpression of H3.3 K4M in embryos before fertilization results in developmental arrest, whereas overexpression after fertilization does not affect the development. Furthermore, loss of H3K4 methylation decreases the level of minor zygotic gene activation (ZGA) predominantly in the paternal pronucleus, and we obtained similar results from knockdown of the H3K4 methyltransferase Mll3/4. We therefore conclude that H3K4 methylation, likely established by Mll3/4 at the early pronuclear stage, is essential for the onset of minor ZGA in the paternal pronucleus, which is necessary for subsequent preimplantation development in mice. 相似文献
994.
Masaru Yamanaka Satoshi Nagao Hirofumi Komori Yoshiki Higuchi Shun Hirota 《Protein science : a publication of the Protein Society》2015,24(3):366-375
Cytochrome c555 from hyperthermophilic bacteria Aquifex aeolicus (AA cyt c555) is a hyperstable protein belonging to the cyt c protein family, which possesses a unique long 310‐α‐310 helix containing the heme‐ligating Met61. Herein, we show that AA cyt c555 forms dimers by swapping the region containing the extra 310‐α‐310 helix and C‐terminal α‐helix. The asymmetric unit of the crystal of dimeric AA cyt c555 contained two dimer structures, where the structure of the hinge region (Val53–Lys57) was different among all four protomers. Dimeric AA cyt c555 dissociated to monomers at 92 ± 1°C according to DSC measurements, showing that the dimer was thermostable. According to CD measurements, the secondary structures of dimeric AA cyt c555 were maintained at pH 2.2–11.0. CN‐ and CO bound to dimeric AA cyt c555 in the ferric and ferrous states, respectively, owing to the flexibility of the hinge region close to Met61 in the dimer, whereas these ligands did not bind to the monomer under the same conditions. In addition, CN‐ and CO bound to the oxidized and reduced dimer at neutral pH and a wide range of pH (pH 2.2–11.0), respectively, in a wide range of temperature (25–85°C), owing to the thermostability and pH tolerance of the dimer. These results show that the ligand binding character of hyperstable AA cyt c555 changes upon dimerization by domain swapping. 相似文献
995.
Uchiyama Junji Kanesaki Yu Iwata Naoya Asakura Ryousuke Funamizu Kento Tasaki Rizumu Agatsuma Mina Tahara Hiroko Matsuhashi Ayumi Yoshikawa Hirofumi Ogawa Satoru Ohta Hisataka 《Photosynthesis research》2015,125(1-2):243-254
Photosynthesis Research - Experimental evolution is a powerful tool for clarifying phenotypic and genotypic changes responsible for adaptive evolution. In this study, we isolated acid-adapted... 相似文献
996.
Yuko Arai-Kichise Yuh Shiwa Kaworu Ebana Mari Shibata-Hatta Hirofumi Yoshikawa Masahiro Yano Kyo Wakasa 《PloS one》2014,9(1)
Elucidation of the rice genome is expected to broaden our understanding of genes related to the agronomic characteristics and the genetic relationship among cultivars. In this study, we conducted whole-genome sequencings of 6 cultivars, including 5 temperate japonica cultivars and 1 tropical japonica cultivar (Moroberekan), by using next-generation sequencing (NGS) with Nipponbare genome as a reference. The temperate japonica cultivars contained 2 sake brewing (Yamadanishiki and Gohyakumangoku), 1 landrace (Kameji), and 2 modern cultivars (Koshihikari and Norin 8). Almost >83% of the whole genome sequences of the Nipponbare genome could be covered by sequenced short-reads of each cultivar, including Omachi, which has previously been reported to be a temperate japonica cultivar. Numerous single nucleotide polymorphisms (SNPs), insertions, and deletions were detected among the various cultivars and the Nipponbare genomes. Comparison of SNPs detected in each cultivar suggested that Moroberekan had 5-fold more SNPs than the temperate japonica cultivars. Success of the 2 approaches to improve the efficacy of sequence data by using NGS revealed that sequencing depth was directly related to sequencing coverage of coding DNA sequences: in excess of 30× genome sequencing was required to cover approximately 80% of the genes in the rice genome. Further, the contigs prepared using the assembly of unmapped reads could increase the value of NGS short-reads and, consequently, cover previously unavailable sequences. These approaches facilitated the identification of new genes in coding DNA sequences and the increase of mapping efficiency in different regions. The DNA polymorphism information between the 7 cultivars and Nipponbare are available at NGRC_Rices_Build1.0 (http://www.nodai-genome.org/oryza_sativa_en.html). 相似文献
997.
Terrestrial plant pollen is classified into two categories based on its metabolic status: pollen with low-metabolism are termed “orthodox” and pollen with high-metabolism are termed “recalcitrant.” Nicotinamide adenine dinucleotide (NAD) is crucial for a number of metabolisms in all extant organisms. It has recently been shown that NAD homeostasis plays an important role in a broad range of developmental processes and responses to environment. Recently, a reverse genetic approach shed light on the significance of NAD biosynthesis on pollen fate. In orthodox Arabidopsis pollen, NAD+ that was accumulated in excess at dispersal dramatically decreased on rehydration. The lack of a key gene that is involved in NAD biosynthesis compromised the excess accumulation. Moreover, absence of the excess accumulation phenocopied the so-called recalcitrant pollen, as demonstrated by the germination inside anthers and the loss of desiccation tolerance. Upon rehydration, NAD+-consuming inhibitors impaired tube germination. Taken together, our results suggest that accumulation of NAD+ functions as a physiochemical molecular switch for suspended metabolism and that the decrease of NAD+ plays a very important role during transitions in metabolic states. Shifting of the redox state to an oxidizing environment may efficiently control the comprehensive metabolic network underlying the onset of pollen germination. 相似文献
998.
Plant lipidomics based on hydrophilic interaction chromatography coupled to ion trap time-of-flight mass spectrometry 总被引:1,自引:0,他引:1
Yozo Okazaki Yukiko Kamide Masami Yokota Hirai Kazuki Saito 《Metabolomics : Official journal of the Metabolomic Society》2013,9(1):121-131
Plants synthesize a wide range of hydrophobic compounds, generally known as lipids. Here, we report an application of liquid chromatography ion trap time-of-flight mass spectrometry (LC-IT-TOF-MS) for plant lipidomics. Using hydrophilic interaction chromatography (HILIC) for class separation, typical membrane lipids including glycerolipids, steryl glucosides and glucosylceramides, and hydrophobic plant secondary metabolites such as saponins were analyzed simultaneously. By this method, we annotated approximately 100 molecules from Arabidopsis thaliana. To demonstrate the application of this method to biological study, we analyzed Arabidopsis mutant trigalactosyldiacylglycerol3 (tgd3), which has a complex metabolic phenotype including the accumulation of unusual forms of galactolipids. Lipid profiling by LC-MS revealed that tgd3 accumulated an unusual form of digalactosyldiacylglycerol, annotated as Gal(β1 → 6)βGalDG. The compositional difference between normal and unusual forms of digalactosyldiacylglycerol was detected by this method. In addition, we analyzed well-known Arabidopsis mutants ats1-1, fad6-1, and fad7-2, which are also disrupted in lipid metabolic genes. Untargeted lipidome analysis coupled with multivariate analysis clearly discriminated the mutants and their distinctive metabolites. These results indicated that HILIC-MS is an efficient method for plant lipidomics. 相似文献
999.
Hiroyuki Shimono Hirofumi Nakamura Toshihiro Hasegawa Masumi Okada 《Global Change Biology》2013,19(8):2444-2453
An elevated atmospheric CO2 concentration ([CO2]) can reduce stomatal conductance of leaves for most plant species, including rice (Oryza sativa L.). However, few studies have quantified seasonal changes in the effects of elevated [CO2] on canopy evapotranspiration, which integrates the response of stomatal conductance of individual leaves with other responses, such as leaf area expansion, changes in leaf surface temperature, and changes in developmental stages, in field conditions. We conducted a field experiment to measure seasonal changes in stomatal conductance of the uppermost leaves and in the evapotranspiration, transpiration, and evaporation rates using a lysimeter method. The study was conducted for flooded rice under open‐air CO2 elevation. Stomatal conductance decreased by 27% under elevated [CO2], averaged throughout the growing season, and evapotranspiration decreased by an average of 5% during the same period. The decrease in daily evapotranspiration caused by elevated [CO2] was more significantly correlated with air temperature and leaf area index (LAI) rather than with other parameters of solar radiation, days after transplanting, vapor‐pressure deficit and FAO reference evapotranspiration. This indicates that higher air temperatures, within the range from 16 to 27 °C, and a larger LAI, within the range from 0 to 4 m2 m?2, can increase the magnitude of the decrease in evapotranspiration rate caused by elevated [CO2]. The crop coefficient (i.e. the evapotranspiration rate divided by the FAO reference evapotranspiration rate) was 1.24 at ambient [CO2] and 1.17 at elevated [CO2]. This study provides the first direct measurement of the effects of elevated [CO2] on rice canopy evapotranspiration under open‐air conditions using the lysimeter method, and the results will improve future predictions of water use in rice fields. 相似文献
1000.
Cytotechnology - We found that strawberry extract suppressed immunoglobulin (Ig) E production in vitro and in vivo, and identified glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as one of the IgE... 相似文献