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Akihiko Kondo

Bio: Akihiko Kondo is a academic researcher from Kobe University. The author has contributed to research in topic(s): Yeast & Fermentation. The author has an hindex of 81, co-authored 849 publication(s) receiving 29067 citation(s). Previous affiliations of Akihiko Kondo include Kanazawa University & Kyoto University.
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Journal ArticleDOI
TL;DR: Biodiesel (fatty acid methyl esters), which is derived from triglycerides by transesterification with methanol, has attracted considerable attention during the past decade as a renewable, biodegradable, and nontoxic fuel.
Abstract: Biodiesel (fatty acid methyl esters), which is derived from triglycerides by transesterification with methanol, has attracted considerable attention during the past decade as a renewable, biodegradable, and nontoxic fuel. Several processes for biodiesel fuel production have been developed, among which transesterification using alkali-catalysis gives high levels of conversion of triglycerides to their corresponding methyl esters in short reaction times. This process has therefore been widely utilized for biodiesel fuel production in a number of countries. Recently, enzymatic transesterification using lipase has become more attractive for biodiesel fuel production, since the glycerol produced as a by-product can easily be recovered and the purification of fatty methyl esters is simple to accomplish. The main hurdle to the commercialization of this system is the cost of lipase production. As a means of reducing the cost, the use of whole cell biocatalysts immobilized within biomass support particles is significantly advantageous since immobilization can be achieved spontaneously during batch cultivation, and in addition, no purification is necessary. The lipase production cost can be further lowered using genetic engineering technology, such as by developing lipases with high levels of expression and/or stability towards methanol. Hence, whole cell biocatalysts appear to have great potential for industrial application.

2,117 citations


Journal ArticleDOI
16 Sep 2016-Science
TL;DR: The toxicity associated with the nuclease-based CRISPR/Cas9 system was greatly reduced in the Target-AID complexes, and it was demonstrated that off-target effects were comparable to those of conventional CRISpr/Cas systems, with a reduced risk of indel formation.
Abstract: INTRODUCTION To combat invading pathogens, cells develop an adaptive immune response by changing their own genetic information. In vertebrates, the generation of genetic variation (somatic hypermutation) is an essential process for diversification and affinity maturation of antibodies that function to detect and sequester various foreign biomolecules. The activation-induced cytidine deaminase (AID) carries out hypermutation by modifying deoxycytidine bases in the variable region of the immunoglobulin locus that produces antibody. AID-generated deoxyuridine in DNA is mutagenic as it can be miss-recognized as deoxythymine, resulting in C to T mutations. CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) is a prokaryotic adaptive immune system that records and degrades invasive foreign DNA or RNA. The CRISPR/Cas system cleaves and incorporates foreign DNA/RNA segments into the genomic region called the CRISPR array. The CRISPR array is transcribed to produce crispr-RNA that serves as guide RNA (gRNA) for recognition of the complementary foreign DNA/RNA in a ribonucleoprotein complex with Cas proteins, which degrade the target. The CRISPR/Cas system has been repurposed as a powerful genome editing tool, because it can be programmed to cleave specific DNA sequence by providing custom gRNAs. RATIONALE Although the precise mechanism by which AID specifically mutates the immunoglobulin locus remains elusive, targeting of AID activity is facilitated by the formation of a single-stranded DNA region, such as a transcriptional RNA/DNA hybrid (R-loop). The CRISPR/Cas system can be engineered to be nuclease-inactive. The nuclease-inactive form is capable of unfolding the DNA double strand in a protospacer adjacent motif (PAM) sequence-dependent manner so that the gRNA binds to complementary target DNA strand and forms an R-loop. The nuclease-deficient CRISPR/Cas system may serve as a suitable DNA-targeting module for AID to catalyze site-specific mutagenesis. RESULTS To determine whether AID activity can be specifically targeted by the CRISPR/Cas system, we combined dCas9 (a nuclease-deficient mutant of Cas9) from Streptococcus pyogenes and an AID ortholog, PmCDA1 from sea lamprey, to form a synthetic complex (Target-AID) by either engineering a fusion between the two proteins or attaching a SH3 (Src 3 homology) domain to the C terminus of dCas9 and a SHL (SH3 interaction ligand) to the C terminus of PmCDA1. Both of these complexes performed highly efficient site-directed mutagenesis. The mutational spectrum was analyzed in yeast and demonstrated that point mutations were dominantly induced at cytosines within the range of three to five bases surrounding the –18 position upstream of the PAM sequence on the noncomplementary strand to gRNA. The toxicity associated with the nuclease-based CRISPR/Cas9 system was greatly reduced in the Target-AID complexes. Combination of PmCDA1 with the nickase Cas9(D10A) mutant, which retains cleavage activity for noncomplementary single-stranded DNA, was more efficient in yeast but also induced deletions as well as point mutations in mammalian cells. Addition of the uracil DNA glycosylase inhibitor protein, which blocks the initial step of the uracil base excision repair pathway, suppressed collateral deletions and further improved targeting efficiency. Potential off-target effects were assessed by whole-genome sequencing of yeast as well as deep sequencing of mammalian cells for regions that contain mismatched target sequences. These results showed that off-target effects were comparable to those of conventional CRISPR/Cas systems, with a reduced risk of indel formation. CONCLUSION By expanding the genome editing potential of the CRISPR/Cas9 system by deaminase-mediated hypermutation, Target-AID demonstrated a very narrow range of targeted nucleotide substitution without the use of template DNA. Nickase Cas9 and uracil DNA glycosylase inhibitor protein can be used to boost the targeting efficiency. The reduced cytotoxicity will be beneficial for use in cells that are sensitive to artificial nucleases. Use of other types of nucleotide-modifying enzymes and/or other CRISPR-related systems with different PAM requirements will expand our genome-editing repertoire and capacity.

731 citations


Journal ArticleDOI
TL;DR: Findings indicate the feasibility of using carbohydrate-producing microalgae as feedstock for fermentative bioethanol production.
Abstract: This study aimed to evaluate the potential of using a carbohydrate-rich microalga Chlorella vulgaris FSP-E as feedstock for bioethanol production via various hydrolysis strategies and fermentation processes. Enzymatic hydrolysis of C. vulgaris FSP-E biomass (containing 51% carbohydrate per dry weight) gave a glucose yield of 90.4% (or 0.461 g (g biomass)(-1)). The SHF and SSF processes converted the enzymatic microalgae hydrolysate into ethanol with a 79.9% and 92.3% theoretical yield, respectively. Dilute acidic hydrolysis with 1% sulfuric acid was also very effective in saccharifying C. vulgaris FSP-E biomass, achieving a glucose yield of nearly 93.6% from the microalgal carbohydrates at a starting biomass concentration of 50 g L(-1). Using the acidic hydrolysate of C. vulgaris FSP-E biomass as feedstock, the SHF process produced ethanol at a concentration of 11.7 g L(-1) and an 87.6% theoretical yield. These findings indicate the feasibility of using carbohydrate-producing microalgae as feedstock for fermentative bioethanol production.

443 citations


Journal ArticleDOI
TL;DR: A fusion of CRISPR-Cas9 and activation-induced cytidine deaminase (Target-AID) for point mutagenesis at genomic regions specified by single guide RNAs (sgRNAs) in two crop plants demonstrates the feasibility of base editing for crop improvement.
Abstract: Targeted editing of single base pairs is achieved in monocot rice and dicot tomato using Target-AID (Cas9 activation-induced cytidine deaminase fusion). We applied a fusion of CRISPR-Cas9 and activation-induced cytidine deaminase (Target-AID) for point mutagenesis at genomic regions specified by single guide RNAs (sgRNAs) in two crop plants. In rice, we induced multiple herbicide-resistance point mutations by multiplexed editing using herbicide selection, while in tomato we generated marker-free plants with homozygous heritable DNA substitutions, demonstrating the feasibility of base editing for crop improvement.

399 citations


Journal ArticleDOI
TL;DR: A whole-cell biocatalyst with the ability to induce synergistic and sequential cellulose-degradation reaction was constructed through codisplay of three types of cellulolytic enzyme on the cell surface of the yeast Saccharomyces cerevisiae, indicating that simultaneous and synergistic saccharification and fermentation of amorphous cellulose to ethanol can be efficiently accomplished.
Abstract: A whole-cell biocatalyst with the ability to induce synergistic and sequential cellulose-degradation reaction was constructed through codisplay of three types of cellulolytic enzyme on the cell surface of the yeast Saccharomyces cerevisiae. When a cell surface display system based on α-agglutinin was used, Trichoderma reesei endoglucanase II and cellobiohydrolase II and Aspergillus aculeatus β-glucosidase 1 were simultaneously codisplayed as individual fusion proteins with the C-terminal-half region of α-agglutinin. Codisplay of the three enzymes on the cell surface was confirmed by observation of immunofluorescence-labeled cells with a fluorescence microscope. A yeast strain codisplaying endoglucanase II and cellobiohydrolase II showed significantly higher hydrolytic activity with amorphous cellulose (phosphoric acid-swollen cellulose) than one displaying only endoglucanase II, and its main product was cellobiose; codisplay of β-glucosidase 1, endoglucanase II, and cellobiohydrolase II enabled the yeast strain to directly produce ethanol from the amorphous cellulose (which a yeast strain codisplaying β-glucosidase 1 and endoglucanase II could not), with a yield of approximately 3 g per liter from 10 g per liter within 40 h. The yield (in grams of ethanol produced per gram of carbohydrate consumed) was 0.45 g/g, which corresponds to 88.5% of the theoretical yield. This indicates that simultaneous and synergistic saccharification and fermentation of amorphous cellulose to ethanol can be efficiently accomplished using a yeast strain codisplaying the three cellulolytic enzymes.

349 citations


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Journal ArticleDOI
Yusuf Chisti1
TL;DR: As demonstrated here, microalgae appear to be the only source of renewable biodiesel that is capable of meeting the global demand for transport fuels.
Abstract: Continued use of petroleum sourced fuels is now widely recognized as unsustainable because of depleting supplies and the contribution of these fuels to the accumulation of carbon dioxide in the environment. Renewable, carbon neutral, transport fuels are necessary for environmental and economic sustainability. Biodiesel derived from oil crops is a potential renewable and carbon neutral alternative to petroleum fuels. Unfortunately, biodiesel from oil crops, waste cooking oil and animal fat cannot realistically satisfy even a small fraction of the existing demand for transport fuels. As demonstrated here, microalgae appear to be the only source of renewable biodiesel that is capable of meeting the global demand for transport fuels. Like plants, microalgae use sunlight to produce oils but they do so more efficiently than crop plants. Oil productivity of many microalgae greatly exceeds the oil productivity of the best producing oil crops. Approaches for making microalgal biodiesel economically competitive with petrodiesel are discussed.

8,281 citations


Journal ArticleDOI
Abstract: Sustainability is a key principle in natural resource management, and it involves operational efficiency, minimisation of environmental impact and socio-economic considerations; all of which are interdependent. It has become increasingly obvious that continued reliance on fossil fuel energy resources is unsustainable, owing to both depleting world reserves and the green house gas emissions associated with their use. Therefore, there are vigorous research initiatives aimed at developing alternative renewable and potentially carbon neutral solid, liquid and gaseous biofuels as alternative energy resources. However, alternate energy resources akin to first generation biofuels derived from terrestrial crops such as sugarcane, sugar beet, maize and rapeseed place an enormous strain on world food markets, contribute to water shortages and precipitate the destruction of the world's forests. Second generation biofuels derived from lignocellulosic agriculture and forest residues and from non-food crop feedstocks address some of the above problems; however there is concern over competing land use or required land use changes. Therefore, based on current knowledge and technology projections, third generation biofuels specifically derived from microalgae are considered to be a technically viable alternative energy resource that is devoid of the major drawbacks associated with first and second generation biofuels. Microalgae are photosynthetic microorganisms with simple growing requirements (light, sugars, CO 2 , N, P, and K) that can produce lipids, proteins and carbohydrates in large amounts over short periods of time. These products can be processed into both biofuels and valuable co-products. This study reviewed the technologies underpinning microalgae-to-biofuels systems, focusing on the biomass production, harvesting, conversion technologies, and the extraction of useful co-products. It also reviewed the synergistic coupling of microalgae propagation with carbon sequestration and wastewater treatment potential for mitigation of environmental impacts associated with energy conversion and utilisation. It was found that, whereas there are outstanding issues related to photosynthetic efficiencies and biomass output, microalgae-derived biofuels could progressively substitute a significant proportion of the fossil fuels required to meet the growing energy demand.

3,930 citations


19


Journal ArticleDOI
Abstract: Biodiesel is gaining more and more importance as an attractive fuel due to the depleting fossil fuel resources. Chemically biodiesel is monoalkyl esters of long chain fatty acids derived from renewable feed stock like vegetable oils and animal fats. It is produced by transesterification in which, oil or fat is reacted with a monohydric alcohol in presence of a catalyst. The process of transesterification is affected by the mode of reaction condition, molar ratio of alcohol to oil, type of alcohol, type and amount of catalysts, reaction time and temperature and purity of reactants. In the present paper various methods of preparation of biodiesel with different combination of oil and catalysts have been described. The technical tools and processes for monitoring the transesterification reactions like TLC, GC, HPLC, GPC, 1H NMR and NIR have also been summarized. In addition, fuel properties and specifications provided by different countries are discussed.

3,045 citations


Journal ArticleDOI
TL;DR: In all cases, enzyme engineering via immobilization techniques is perfectly compatible with other chemical or biological approaches to improve enzyme functions and the final success depend on the availability of a wide battery of immobilization protocols.
Abstract: In spite of their excellent catalytic properties, enzyme properties have to be usually improved before their implementation at industrial scale (where many cycles of high yield processes are desired). Generally, soluble enzymes have to be immobilized to be reused for long times in industrial reactors and, in addition to that, some other critical enzyme properties have to be improved like stability, activity, inhibition by reaction products, selectivity towards non-natural substrates. Some strategies to improve these enzyme properties during the performance of tailor-made enzyme immobilization protocols are here reviewed. In this way, immobilized enzymes may also exhibit much better functional properties than the corresponding soluble enzymes by very simple immobilization protocols. For example, multipoint and multisubunit covalent immobilization improve the stability of monomeric or multimeric enzymes. Moreover, enantioselectivity of different enzymes (e.g., lipases) may be also dramatically improved (from E = 1 to >100) by performing different immobilization protocols of the same enzyme. In all cases, enzyme engineering via immobilization techniques is perfectly compatible with other chemical or biological approaches to improve enzyme functions and the final success depend on the availability of a wide battery of immobilization protocols.

2,733 citations


Journal ArticleDOI
19 Nov 2004-Angewandte Chemie
TL;DR: This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces.
Abstract: Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.

2,260 citations


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Performance
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Author's H-index: 81

No. of papers from the Author in previous years
YearPapers
20223
202144
202038
201948
201850
201761

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Author's top 5 most impactful journals

Applied Microbiology and Biotechnology

103 papers, 4.7K citations

Bioresource Technology

57 papers, 2.7K citations

Journal of Bioscience and Bioengineering

52 papers, 3.9K citations

Biochemical Engineering Journal

32 papers, 1.6K citations

Microbial Cell Factories

30 papers, 1.1K citations