Sustainable Resource Science
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http://www.csrs.riken.jp/en/ The RIKEN Center for Sustainable Resource Science’s mission is to enhance the use of biomaterials based on an understanding of the diversity of both biological and chemical functions, and contributing to the society by developing production technologies that are gentle on the natural world and promote a sustainable society. Here are posts from CSRS and related fields
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RIKEN CSRS - Center for Sustainable Resource Science

RIKEN CSRS - Center for Sustainable Resource Science | Sustainable Resource Science | Scoop.it
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The RIKEN CSRS Center for Sustainable Resource Science’s mission is to enhance the use of biomaterials based on an understanding of the diversity of both biological and chemical functions, and contributing to the society by developing production technologies that are gentle on the natural world and promote a sustainable society.

http://www.csrs.riken.jp/en/about/

http://www.csrs.riken.jp/en/about/missions/

http://www.csrs.riken.jp/en/about/organization/


RIKEN is Japan’s largest and most comprehensive research organization for basic and applied science.

http://www.riken.jp/en/about/intro/


Scientists at CSRS carry out research on carbon, nitrogen and metals, based on a fundamental understanding of biological functions and chemical diversity.

-   In the carbon project, we investigate research on CO2 utilization by enhancing photosynthesis, while conducting metabolic engineering research using novel catalysts.

-  In the nitrogen project, we strive to develop high-yield plants with low input of fertilizers, and efficient ammonia production processes with novel catalysts.

-  In the metal project, we develop methods for recovering metals from urban mines through biofunctions of plants and microbes. Reduction of the use of rare metals, replacing them with newly developed catalysts using abundant metals is also their mission.

-  In addition, the center builds research infrastructure based on metabolomics and chemical banks to promote the production and use of the biological resources needed for this research.

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Tuning epigenetics to treat disease - Frontlines - RIKEN RESEARCH

Tuning epigenetics to treat disease - Frontlines - RIKEN RESEARCH | Sustainable Resource Science | Scoop.it
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Epigenetic-related enzymes and molecules that are potential targets for drug discovery 
Researchers can control diseases using epigenetics by targeting the modifying enzymes that add or ‘write’ acetyl (Ac) or methyl groups (Me) onto histones, and the molecules that read or the enzymes that reverse these chemical modifications. (Figure 2) 

 

http://www.rikenresearch.riken.jp/eng/frontline/7709.html

28 February 2014

Minoru Yoshida, Group Director 
Chemical Genomics Research Group 
RIKEN Center for Sustainable Resource Science

Many diseases occur due to abnormalities in patterns of gene expression caused by epigenetic changes as a result of aging, stress or other factors. To address these changes and advance the field of medicine, Minoru Yoshida is leading research into the control of epigenetics using chemical compounds. Together with colleagues at the Chemical Genetics Laboratory, he is also investigating the activation of ‘dormant genes’ in plants and microorganisms to produce useful substances and to enable the cultivation of crops on arid and high-salinity soils.

 

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RARGE II: An Integrated Phenotype Database of Arabidopsis Mutant Traits Using a Controlled Vocabulary - Plant & Cell Physiology

RARGE II: An Integrated Phenotype Database of Arabidopsis Mutant Traits Using a Controlled Vocabulary - Plant & Cell Physiology | Sustainable Resource Science | Scoop.it
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Abstract

Arabidopsis thaliana is one of the most popular experimental plants. However, only 40% of its genes have at least one experimental Gene Ontology (GO) annotation assigned.

Systematic observation of mutant phenotypes is an important technique for elucidating gene functions. Indeed, several large-scale phenotypic analyses have been performed and have generated phenotypic data sets from many Arabidopsis mutant lines and overexpressing lines, which are freely available online.

Since each Arabidopsis mutant line database uses individual phenotype expression, the differences in the structured term sets used by each database make it difficult to compare data sets and make it impossible to search across databases.

Therefore, we obtained publicly available information for a total of 66,209 Arabidopsis mutant lines, including loss-of-function (RATM and TARAPPER) and gain-of-function (AtFOX and OsFOX) lines, and integrated the phenotype data by mapping the descriptions onto Plant Ontology (PO) and Phenotypic Quality Ontology (PATO) terms. This approach made it possible to manage the four different phenotype databases as one large data set.

Here, we report a publicly accessible web-based database, the RIKEN Arabidopsis Genome Encyclopedia II (RARGE II; http://rarge-v2.psc.riken.jp/), in which all of the data described in this study are included.

Using the database, we demonstrated consistency (in terms of protein function) with a previous study and identified the presumed function of an unknown gene. We provide examples of AT1G21600, which is a subunit in the plastid-encoded RNA polymerase complex, and AT5G56980, which is related to the jasmonic acid signaling pathway.

 

Figure 2 shown

Operation workflow of the web-based database.

(A) On the top page, users can select the desired resource, fl-cDNAs or mutant lines, or can find mutant lines by phenotype using the ontology tree.

Then they can (B) search fl-cDNAs by keywords with filtering from the fl-cDNA search input page,

(C) search for mutant lines by keywords with filtering from the mutant line search input page

and/or (D) search all mutant lines by selecting phenotype items in the alternative mutant line search input page by phenotype tree.

(E) The fl-cDNA search result page shows records that include the fl-cDNA clone name, gene locus name, gene description, the number of mutant lines with disruption or induction of the gene and the mutant lines into which the fl-cDNA was introduced.

(F) The mutant line search result page shows records that include the line name, resource name, deduced disrupted or induced gene locus name, gene description and phenotypes observed.

(G) The detailed fl-cDNA information page shows the fl-cDNA sequence, its InterPro Scan result, gene models with high degrees of similarity and the names of mutant lines into which the cDNA was introduced.

(H) The detailed mutant line information page for the loss-of-function lines shows the visible phenotypes, including the original phenotype description, mapped PO information and PATO information, line photographs and deduced transposon insertion point.

(I) The detailed mutant line information page for the gain-of-function lines shows the visible and invisible phenotypes including the original phenotype description, mapped PO information and PATO information, line photographs, the fl-cDNA sequence, its InterPro Scan result and gene models with high degrees of similarity.

 

RARGE II: An Integrated Phenotype Database of Arabidopsis Mutant Traits Using a Controlled Vocabulary
Kenji Akiyama, Atsushi Kurotani, Kei Iida, Takashi Kuromori, Kazuo Shinozaki and Tetsuya Sakurai

Plant Cell Physiol (2014) 55 (1): e4.
doi: 10.1093/pcp/pct165

http://pcp.oxfordjournals.org/content/55/1/e4.long

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Bioplastic productivity levels among the world’s highest via photosythesis by using new synthesis route of cyanobacterial production

Bioplastic productivity levels among the world’s highest via photosythesis by using new synthesis route of cyanobacterial production | Sustainable Resource Science | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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RIKEN CSRS and Universiti Sains Malaysia (USM) have succeeded in introducing genes  from three different bacteria (phaB, phaC, nphT7) into cyanobacteria for efficient production of bioplastics using only photosynthesis.

http://www.csrs.riken.jp/en/press/press140123.html

 

It is possible to use only sunlight to produce bioplastics and without the use of expensive nutrient sources. The efficient production method developed by CSRS and USM researchers is expected to contribute to significant reductions in production costs and support the supply of low-cost manufactured products.

 

Cyanobacteria are nature’s bioreactors, and algae are able to reproduce at rapid speeds. Cyanobacterial synthesis of compounds such as isoprene (the main component in rubber) and isobutanol (a biofuel) have been reported. It will be possible to apply the altered metabolic pathways discovered in this study to increase production of several compounds. Researchers were also able to identify gene candidates for improved production by carrying out a whole genome expression analysis to determine overall cellular changes from the newly introduced metabolic pathways.

 

These findings are expected to contribute to the establishment of safe and clean sunlight-based bioplastics production.

 

 Figure 4. The scheme shows the cellular changes in recombinant Synechocystis sp. strains (a) CCsACnBCn and CCsNphT7BCn (compared with pTKP2031V) (b) CCsNphT7BCn (compared with CCsACnBCn) under photoautotrophic PHA biosynthesis conditions. "One particularly interesting observation is the up-regulation of photosynthetic activity in recombinants Synechocystis sp. with higher PHA-synthesizing potential (Fig. 4 A and B). In recent years, there has been tremendous interest in strategies to improve photosynthetic activity in crops[33], [34]. It has been suggested that an increase in photosynthetic activity will improve the yield of crops and provide a potential solution to future food shortages [35]. In this context, the increase of photosynthetic activity in cyanobacteria may explain the higher PHA accumulation observed in recombinant Synechocystis sp. strains CCsNphT7BCn and CCsACnBCn."

 

<Original article >

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0086368
PLOSONE, doi: 10.1371/journal.pone.0086368
N. -S. Lau, C. P. Foong, Y. Kurihara, K. Sudesh, M. Matsui,
"RNA-Seq analysis provides insights for understanding photoautotrophic polyhydroxyalkanoate production in recombinant Synechocystis sps".

 

 

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Electricity Produced Directly From Biomass Using Solar-induced Hybrid Fuel Cell

Electricity Produced Directly From Biomass Using Solar-induced Hybrid Fuel Cell | Sustainable Resource Science | Scoop.it
Although low temperature fuel cells powered by methanol or hydrogen have been well studied, existing low temperature fuel cell technologies cannot directly use biomass as a fuel because of the lack of an effective catalyst system for polymeric materials.

Now, researchers at the Georgia Institute of Technology have developed a new type of low-temperature fuel cell that directly converts biomass to electricity with assistance from a catalyst activated by solar or thermal energy. The hybrid fuel cell can use a wide variety of biomass sources, including starch, cellulose, lignin – and even switchgrass, powdered wood, algae and waste from poultry processing.


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Electricity Produced Directly From Biomass Using Solar-induced Hybrid Fuel Cell 
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Wood pulp extract stronger than carbon fiber or Kevlar

Wood pulp extract stronger than carbon fiber or Kevlar | Sustainable Resource Science | Scoop.it
Cellulose nanocrystals extracted from wood pulp are inexpensive as well as stronger than Kevlar or carbon fiber.
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Host plants reprogram their root cells to accommodate symbiotic ...

Host plants reprogram their root cells to accommodate symbiotic ... | Sustainable Resource Science | Scoop.it
To enter into symbiosis with nitrogen-fixing bacteria, host plants reprogram their root cells. An LMU team has now identified a calcium-binding protein complex that can be persuaded to spontaneously induce the formation of ...
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Haitian Rice Farmers Double Their Yields | U.S. Agency for International Development

Haitian Rice Farmers Double Their Yields | U.S. Agency for International Development | Sustainable Resource Science | Scoop.it
RT @USAID: Learn how rice farmers in #Haiti doubled their yields while using less water, fertilizer, and seeds: http://t.co/NRCvJrmobe @Fee…
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Learn more about RIKEN Center for Sustainable Resource Science | e! Science News

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Science news articles about 'RIKEN Center for Sustainable Resource Science'Finding the missing genes in hormone-biosynthesis pathway hints at subtle control of growth in rice... Discovery Research Group at the RIKEN Center for Sustainable Resource Science have now identified genes for two 'cytochrome P450' enzymes ...Making hydrogenation greener... student at McGill, worked on the project at the RIKEN Center for Sustainable Resource Scienceand at the Institute for Molecular Science in Japan. Co-authors of the paper ...Survey of cellular signaling pathways reveals proteins that help plants to cope with dehydration... kinases. Kazuo Shinozaki from the RIKEN Center for Sustainable Resource Science and colleagues have now obtained valuable insights into a family of kinases ...Enzyme that unravels RNA molecules has crucial role in plant development... sequences. Misato Ohtani from the RIKEN Center for Sustainable Resource Science and colleagues have now identified a key protein involved in splicing ...An energy-efficiency lead for nitrogen fertilizer production... , Zhaomin Hou and colleagues from the RIKEN Center for Sustainable Resource Science have now made a discovery that could allow ammonia and other nitrogen-bearing ...One pot, many possibilities: Synthesis of fluorine-bearing amine molecules... Organic Chemistry Laboratory and RIKEN Center for Sustainable Resource Science have now developed a simple one-pot synthesis for a range of these important ... 
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South Korean Scientists Use E. Coli to Make Gasoline

South Korean Scientists Use E. Coli to Make Gasoline | Sustainable Resource Science | Scoop.it
Escherichia coli can cause serious food poisoning but Korean scientists have come up with a more helpful use for the sometimes-deadly bacteria: producing gasoline.
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the reprogrammed E. coli can produce gasoline, a high-premium oil product that’s more expensive than diesel if the biofuel becomes commercially viable, according to Prof. Lee Sang-yup at the Korea Advanced Institute of Science and Technology. His team’s study was published in the international science journal Nature on Monday.

“The significance of this breakthrough is that you don’t have to go through another process to crack the oil created by E. coli to produce gasoline. We have succeeded in converting glucose or waste biomass directly into gasoline,” Mr. Lee told The Wall Street Journal.

“The gasoline we’re generating could be used in your car. It has identical composition and chemical properties to conventional petrol.”

Microbial production of short-chain alkanes

Yong Jun Choi& Sang Yup Lee

Nature (2013) doi:10.1038/nature12536 Received 11 March 2013 Accepted 08 August 2013 Published online 29 September 2013

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12536.html

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A bacteria's double life: living off both iron and electricity | RIKEN

A bacteria's double life: living off both iron and electricity | RIKEN | Sustainable Resource Science | Scoop.it
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Researchers at the RIKEN Center for Sustainable Resource Science and the University of Tokyo have demonstrated that the bacterium Acidithiobacillus ferrooxidans can take electrons needed for growth directly from an electrode power source when iron—its already known source of energy—is absent.

The study, published in Frontiers in Microbiology,  http://bit.ly/1TT5GWJ   shows that A. ferrooxidans can use direct uptake of electrons from an electrode to fuel the same metabolic pathway that is activated by the oxidation of diffusible iron ions.

Just as plants with chlorophyll use photosynthesis to convert energy from light into sugars needed for growth, other organisms—like animals—gain energy for the manufacture of sugars by taking electrons from substances in their surrounding environments—a process called chemosynthesis. Organisms that gain their energy this way are called chemotrophs, and those that get their electrons through oxidation of inorganic substances are called chemolithoautotrophs. Phototrophs and chemotrophs make up two interconnected ecosystems.

“We are investigating the possibility of a third type of ecosystem,” explains Biofunctional Catalyst Research Team leader Ryuhei Nakamura. “We call it the electro-ecosystem because microbial activity is sustained primarily by direct electrical current.”

Key words: extracellular electron transfer, hydrothermal vents, iron oxidizing bacteria, carbon assimilation, #electrolithoautotrophy 

#electromicrobiology

Front. Microbiol., 25 September 2015 | http://dx.doi.org/10.3389/fmicb.2015.00994

From chemolithoautotrophs to electrolithoautotrophs: CO2 fixation by Fe(II)-oxidizing bacteria coupled with direct uptake of electrons from solid electron sources

Takumi Ishii, Satoshi Kawaichi, Hirotaka Nakagawa, Kazuhito Hashimoto 1* and Ryuhei Nakamura 2* 
1 Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo, Japan
2 Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan

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Side-Chain Modification of Cytokinins Controls Shoot Growth in Arabidopsis

Side-Chain Modification of Cytokinins Controls Shoot Growth in Arabidopsis | Sustainable Resource Science | Scoop.it
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Side-Chain Modification of Cytokinin defines the Function

A research group at the RIKEN CSRS revealed that the function of the plant hormone cytokinin depends not only on changes in quantity but also in quality, which is generated by side-chain modification of cytokinins.

 http://www.csrs.riken.jp/en/press/press131126.html

 

also RIKEN Research Magazine http://www.rikenresearch.riken.jp/eng/research/7635 ;

"Many ways to grow" 24 January 2014

 

Cytokinins, a class of plant hormones, are central regulators of plant growth and development. The group was searching for enzyme genes responsible for making the side-chain modifications to synthesize trans-zeatin (tZ)-type cytokinins. They succeeded in identifying CYP735A1 and CYP735A2 as such genes. Analysis of a mutant of CYP735A activity, which is deficient in tZ-type cytokinins, revealed that the tZ-type cytokinins promote shoot growth, whereas cytokinins without sid- chain modification do not. These results show that the side-chain modification of cytokinin is crucial for shoot growth regulation in plants.

 

Elucidation of this new mechanism is expected to pave the way for development of novel technologies to increase crop harvests and biomass production.

 <Contact>
Hitoshi Sakakibara: Group Director
Takatoshi Kiba: Research Scientist
Plant Productivity Systems Research Group

 

Some quotes from the paper

- "Although the major site of tZ-type CK biosynthesis is in the root vasculature ( Figure S5), the grafting experiments showed that root-borne tZ-type CKs are not necessarily required for normal shoot growth. Thus, the role of root-borne tZ-type CKs might be to stimulate shoot growth when roots sense favorable conditions."

- " A supply of a nitrogen source, for example nitrate, might be an example of such a situation. In this scenario, nitrate would trigger iP-type CK biosynthesis though the induction of IPT3 (Miyawaki et al., 2004 and Takei et al., 2004a), followed by CK-mediated upregulation of the expression of theCYP735As ( Takei et al., 2004b), finally leading to tZ-type CK accumulation in the root vasculature and transport to the shoot via the xylem." 

-" By exploiting the first mutant impaired in CK side-chain modification, our study demonstrated that trans-hydroxylation of CK is a specific signal that facilitates growth in the shoot of Arabidopsis. The existence of CYP735A orthologs throughout the seed plants suggests that the signaling role of trans-hydroxylation might be highly conserved ( Mizutani and Ohta, 2010 and Nelson and Werck-Reichhart, 2011). Consistent with this idea, CK receptors with high affinity to tZ are found in maize ( Lomin et al., 2011 and Yonekura-Sakakibara et al., 2004). Thus,CYP735A appears a promising target for crop improvement because shoot growth enhancement could be achieved by increasing the expression of this gene without reducing root growth."

 

Figure 7. 

Recovery of cyp735a1 cyp735a2 Shoot Growth by Root-Borne tZ-Type Cytokinins

(A and B) Three-day-old wild-type (Col-0) and a1-2 a2-1 (cypDM) were grafted reciprocally by the wedge-grafting method and pictures were taken 38 days (A) and 58 days (B) after grafting.

(C) Cytokinin concentrations in rosette leaves (scions) of grafted plants at 45 days after germination. Error bars represent SD of four biological replicates. The concentration of each cytokinin species is shown in Table S5. gFW, gram fresh weight. Scale bar: 2 cm.

 

Original Paper

Developmental Cell, Vol 27, pp652-461 (2013), doi.org/10.1016/j.devcel.2013.10.004
T. Kiba, K. Takei, M. Kojima, H. Sakakibara,
" Side-chain Modification of Cytokinins Control Shoot Growth in Arabidopsis".

http://www.sciencedirect.com/science/article/pii/S1534580713006011#

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UK-Japan Workshop "Rhizosphere Interactions - towards Global Food Security" March 5-6, 2014 at RIKEN Yokohama Campus

UK-Japan Workshop "Rhizosphere Interactions- towards Global Food Security" March 5-6, 2014 at RIKEN Yokohama Campus | Sustainable Resource Science | Scoop.it

Via Kamoun Lab @ TSL
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Venue: Main Auditorium, Main Office Building Hall, Yokohama campus, Contact: CSRS Plant Immunity Research Group http://www.csrs.riken.jp/en/labs/pirg/

 

Abstracts Posted on the Facebook site: https://www.facebook.com/ukjapanrhizosphere

 

Tentative schedule

2014.3.5 
9:00 open, 9:30 Opening Remarks
9:40-12:35: Session 1: Symbiotic Interactions
Giles Oldroyd, Makoto Hayashi, Uta Paszkowski, Masayoshi Kawaguchi

13:40-1720: Session 2: Parasitic Interactions

Sophien Kamoun, Ryohei Terauchi, Julie Scholes, Ken Shirasu

2014.3.6
900: open, 

9:30-12:30: Session 3: Designing Roots
Ottoline Leyser, Keiko Sugimoto, Veronica Grieneisen, Toru Fujiwara

 

Poster: http://plantimmunity.riken.jp/_src/sc1035/uk-japan20poster.pdf

 

RIKEN Event Notice (Japanese): http://www.riken.jp/pr/blog/2014/140219_1/

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High accumulation of antioxidant flavonoids increases resistance to oxidative and drought stress in Arabidopsis - The Plant Journal

High accumulation of antioxidant flavonoids increases resistance to oxidative and drought stress in Arabidopsis -  The Plant Journal | Sustainable Resource Science | Scoop.it
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Toward acquisition of multiple stress tolerance in agricultural crops

RIKEN CSRS researchers have clarified that flavonoids, a representative of specialized metabolites, in the model plant Arabidopsis thaliana reduces the stress from environmental conditions. They have also found that high accumulation of flavonoids increases resistance to oxidative and drought stress.

 http://www.csrs.riken.jp/en/press/press140116.html

 

When exposing a wild type of Arabidopsis, flavonoid-overaccumulating mutants and flavonoid-deficient mutants to abiotic stresses such as oxidation and drought, researchers found that overaccumulation of anthocyanins with strong antioxidative activity promoted removal of reactive oxygen species (ROS) in oxidative and drought conditions, while it also contributed to stress mitigation against both stress conditions. It was also found that the amount of water loss in the flavonoid-overaccumulating mutants was less than in the wild type.

 

Accumulation of ROS is also induced by biotic stresses such as insect damage, infection by viruses or bacteria, etc. It can be expected that the application of flavonoids to remove ROS will not only reduce abiotic stress but also improve resistance to biotic stress.

 

<Original article >
The Plant Journal, doi: 10.1111/tpj.12388
R. Nakabayashi, K. Yonekura-Sakakibara, K. Urano, M. Suzuki, Y. Yamada, T. Nishizawa, F. Matsuda, M. Kojima, H. Sakakibara, K. Shinozaki, A. J. Michael, T. Tohge, M. Yamazaki, K. Saito,
"Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids".

http://onlinelibrary.wiley.com/doi/10.1111/tpj.12388/full

 

Figure 8 shown: 

Figure 8. Enhancement of drought tolerance by flavonoid overaccumulation.

(a) Phenotype of the wild type, tt4, flavonoid-deficient MYB overexpressors, and MYB overexpressors under drought stress. Top: three plants were grown on soil in one pot. Ten pots were prepared in each experiment. Middle: a difference in wilting was observed among the MYB overexpressors and other lines after 14 days; Bottom: all plants were rewatered after 16 days. 

(b) Metabolo-type of the samples after rewatering in the drought stress experiment. The plot of PC1 (39.0%) versus PC2 (17.5%) is presented. Col-0, black squares; tt4, orange circles; MYB12OX/tt4, green triangles; pap1-D/tt4, purple squares; MYB12OX, red circles; pap1-D, blue diamonds; WOX1-1, pink crosses; and WOX1-2, yellow triangles.

(c) Relative intensity of A11 after drought stress and rewatering. Differences and standard deviations (error bars) were calculated from the results of three biological replicates.

(d) H2O2 generation in the wild type, tt4, flavonoid-deficient MYB overexpressors, and MYB overexpressors after drought stress.

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Integrated Analysis of Seaweed Components Toward field analysis of agricultural, forestry, and fisheries products based on chemometrics - Analytical Chemistry (ACS Publications)

Integrated Analysis of Seaweed Components Toward field analysis of agricultural, forestry, and fisheries products based on chemometrics - Analytical Chemistry (ACS Publications) | Sustainable Resource Science | Scoop.it
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Integrated Analytical Technology for Complex Systems of Organic and Inorganic Mixtures in Seaweed Toward field analysis of agricultural, forestry, and fisheries products based on chemometrics

RIKEN CSRS has established a method to analyze and evaluate the integrated data sets obtained from seaweed by measuring with a wide range of analytical equipment to comprehensively capturing seasonal fluctuations in the constituent components.

 http://www.csrs.riken.jp/en/press/press140114.html

 

The research team collected Sargassum fusiforme over the course of one year, using various types of analytical equipment to comprehensively measure the components in the gathered seaweed. The different data sets were integrated after applying preprocessing to individual sets. Using chemometric analyses such as self-organizing maps and structural equation modeling, the team captured the seasonal variations in characteristics of the seaweed components. The team also observed that changes in polysaccharide structures and mineral composition show synchronization with the fluctuations in the natural environment.

 

When the components of agricultural, forestry, and fisheries products are measured for evaluation, the obtained data often deviate from the results obtained using a regular scientific approach. The evaluation method that the team has developed can calculate synchronism between different components in samples taken from the ever-shifting natural environment. This analytical method could lead to various evaluation opportunities for agricultural, forestry, and fisheries products by minimizing deviations between lab results and results from the natural environment.paper http://pubs.acs.org/doi/full/10.1021/ac402869b
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PLOS ONE: Genome-Wide Discovery and Information Resource Development of DNA Polymorphisms in Cassava

PLOS ONE: Genome-Wide Discovery and Information Resource Development of DNA Polymorphisms in Cassava | Sustainable Resource Science | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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—will accelerate cassava genome breeding and contribute to solving the global food problem

The RIKEN Center for Sustainable Resource Science and Colombia’s International Center for Tropical Agriculture (CIAT), as part of the Consultative Group and on International Agricultural Research (CGIAR), have together identified more than 10,000 single nucleotide polymorphisms (SNPs) among 17 strains of cassava, an important source of starch. The number of SNPs identified in cassava is one of the largest to date. Analysis of the relationships between the obtained SNP information and gene functions revealed a relationship between the SNPs and stress responses and disease resistance genes.

 

These findings provide an important clue for genome breeding. They are also expected to promote large-scale and efficient progress in cassava genome breeding by providing DNA SNP information and improving the information research infrastructure. The results of this research have been organized as a database, the Cassava Online Archive (http://cassava.psc.riken.jp/), and released to the public for researchers around the world.

 

<Original article >
PLOS ONE, doi: 10.1371/journal.pone.0074056
T. Sakurai, K. Mochida, T. Yoshida, K. Akiyama, M. Ishitani, M. Seki, K. Shinozaki,
“Genome-wide discovery and information resource development of DNA polymorphisms in cassava”.

 

Fig 2. Gene ontology (GO) biological process categories for all cassava genes containing SNPs that change an amino acid-coding codon to a stop codon (premature stop substitution) and cassava genes containing SNPs that changed a stop codon to a coding codon (read-through substitution). The differences between all cassava genes and read-through SNP genes were supported by p<0.01 according to the Pearson chi-square test. * indicates p<0.05, residual analysis of each GO term.

doi:10.1371/journal.pone.0074056.g002

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Greener Synthetic Pathways Award: Life Technologies - The Biological SCENE

Greener Synthetic Pathways Award: Life Technologies - The Biological SCENE | Sustainable Resource Science | Scoop.it
Greener Synthetic Pathways Award: Life Technologies The Biological SCENE Life Technologies received the Greener Synthetic Pathways Award for developing less wasteful methods to make reagents used in molecular biology techniques, such as the...
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Glowing plant project on Kickstarter sparks debate about regulation of DNA modification

Glowing plant project on Kickstarter sparks debate about regulation of DNA modification | Sustainable Resource Science | Scoop.it
An estimated 600,000 seeds of the synthetically modified organism would be distributed to the public.
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Go Arabidopsis! "They imagine a world where light bulbs are filled with DNA from fireflies and jellyfish and bioluminescent trees replace streetlights." "Working off previously published papers, they have decided to take genes from a bioluminescent marine bacterium and insert it into seedlings of a small flowering plant that’s known as Arabidopsis." http://glowingplant.com/

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Electricity from ‘black smokers’

Electricity from ‘black smokers’ | Sustainable Resource Science | Scoop.it
Occasionally, journals not usually associated with mainstream geosciences publish something startling, but easily missed. Nature of 12 September 2013 alerted me to just such an oddity. It seems tha...
David Gifford's insight:

It seems that the chemistry of sea-floorhydrothermal vents potentially can generate electrical power (Yamamoto, M. et al. 2013. Generation of electricity and illumination by an environmental fuel cell in deep-sea hydrothermal vents. Angewandte Chemie, online DOI: 10.1002/ange.201302704).

The team from the Japan Agency for Marine-Earth Science and Technology, the Riken Centre for Sustainable Resource Science and the University of Tokyo used a submersible ROV to suspend a fuel cell based on a platinum cathode and iridium anode in hydrothermal vents that emerge from the Okinawa Trough off southern Japan at a depth of over 1 km. It recorded a tiny, but significant power generation of a few milliwatts.

The fluids issuing from the vents are at over 300°C while seawater is around 4°C, creating a very high thermal gradient. More importantly, the fluid-seawater interface is also a boundary between geochemically very different conditions. The fluids are highly acidic (pH 4.8) compared with the slight alkalinity of seawater, and contain high concentrations of hydrogen and hydrogen sulfide but undetectable oxygen (sea water is slightly oxygenated).

The fuel cell was designed so that iridium in the anode speeds up the oxidation of H2S at the geochemical interface which yields the electrons necessary in electrical currents. The experiment neatly signified its success by lighting up three light-emitting diodes.

Does this herald entirely new means of renewable power generation? Perhaps, if the fuel cell is scaled-up enormously. Yet, the very basis of oxidation and reduction is expressed by the mnemonic OILRIG (Oxidation Is Loss Reduction Is Gain – of electrons) and any potential redox reaction in nature has potential,even plants can be electricity producers. In fact all fuel cells exploit oxidation reactions of one kind or another.

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