Journal of Bioscience and Bioengineering

Publisher: Nihon Seibutsu Kogakkai, Elsevier

Description

  • Impact factor
    1.74
  • 5-year impact
    1.99
  • Cited half-life
    7.00
  • Immediacy index
    0.29
  • Eigenfactor
    0.01
  • Article influence
    0.53
  • Other titles
    Journal of bioscience and bioengineering (En ligne)
  • ISSN
    1347-4421
  • OCLC
    56331911
  • Material type
    Document, Periodical, Internet resource
  • Document type
    Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

Elsevier

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Voluntary deposit by author of pre-print allowed on Institutions open scholarly website and pre-print servers
    • Voluntary deposit by author of authors post-print allowed on institutions open scholarly website including Institutional Repository
    • Deposit due to Funding Body, Institutional and Governmental mandate only allowed where separate agreement between repository and publisher exists
    • Set statement to accompany deposit
    • Published source must be acknowledged
    • Must link to journal home page or articles' DOI
    • Publisher's version/PDF cannot be used
    • Articles in some journals can be made Open Access on payment of additional charge
    • NIH Authors articles will be submitted to PMC after 12 months
    • Authors who are required to deposit in subject repositories may also use Sponsorship Option
    • Pre-print can not be deposited for The Lancet
  • Classification
    ​ green

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: This study investigated the performance of a reactor in which denitrification was integrated into the anaerobic acidogenic process. Industrial wastewater cassava stillage was used as the carbon source, and the nitrate reduction pathway and its effects on acid fermentation were examined. Results from batch and semi-continuous tests showed that the presence of nitrate did not inhibit anaerobic acidification but altered the distribution of volatile fatty acid (VFA) species. Nitrate reduction was attributable to denitrification and to dissimilatory nitrate reduction to ammonia (DNRA). The ratio of DNRA to denitrification was proportional to the ratio of [Formula: see text] . After 130 days of semi-continuous operation, denitrification removal efficiency accounted for about 60% at a [Formula: see text] of 50. The proportional distribution of VFAs was acetate, followed by propionate and then butyrate. The polymerase chain reaction-denaturing gradient gel electrophoresis results confirmed the contributions of denitrification and DNRA in the nitrate-amended reactor and showed that the addition of nitrate enriched the structure of the bacterial community, but did not suppress the activity of acid-producing bacteria.
    Journal of Bioscience and Bioengineering 06/2014;
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    ABSTRACT: A novel collagenolytic serine protease was identified and then purified (along with ficin) to apparent homogeneity from the latex of fig (Ficus carica, var. Brown Turkey) by two step chromatographic procedure using gel and covalent chromatography. The enzyme is a monomeric protein of molecular mass of 41 ± 9 kDa as estimated by analytical gel filtration chromatography. It is an acidic protein with a pI value of approximately 5 and optimal activity at pH 8.0-8.5 and temperature 60°C. The enzymatic activity was strongly inhibited by PMSF and Pefabloc SC, indicating that the enzyme is a serine protease. The enzyme showed specificity towards gelatin and collagen (215 GDU/mg and 24.8 CDU/mg, respectively) and non-specific protease activity (0.18 U/mg against casein). The enzyme was stable and retained full activity over a broad range of pH and temperature. The fig latex collagenolytic protease is potentially useful as a non-microbial enzyme with collagenolytic activity for various applications in the fields of biochemistry, biotechnology and medicine.
    Journal of Bioscience and Bioengineering 06/2014;
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    ABSTRACT: Nowadays, high-throughput screening is essential for determining the best microbial strains and fermentation conditions. Although microtiter plates allow higher throughput in screening than shake flasks, they do not guarantee sufficient oxygen supply if operated at unsuitable conditions. This is especially the case in viscous fermentations, potentially leading to poor liquid movement and surface growth. Therefore, in this study, two aims were pursued. First, an industrial Trichoderma reesei shake flask protocol is improved with respect to oxygen supply and production. Second, this improved shake flask protocol is scaled down into microtiter plate under consideration of similar oxygen supply. For this purpose, the respiration activity monitoring system (RAMOS) was applied. An approach based on a sulfite system was introduced to ensure equal maximum oxygen transfer capacities (OTRmax) in microtiter plates and shake flasks. OTRmax-values of 250 mL shake flasks and 24-well microtiter plates were determined in a wide range of operating conditions. These sulfite datasets were used to identify operating conditions leading to the same oxygen supply for T. reesei in shake flasks and 24-well microtiter plates. For 24-well microtiter plates, the shake flask OTRmax of 20 mmol/L/h of an industrial protocol was obtained under the following optimal operating conditions: 1 mL filling volume per well, 200 rpm shaking frequency and 50 mm shaking diameter. With these conditions almost identical oxygen transfer rates and product concentrations were measured in both scales. The proposed approach is a fast and accurate means to scale-down established screening procedures into microtiter plates to achieve high-throughput.
    Journal of Bioscience and Bioengineering 06/2014;
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    ABSTRACT: CYP199A2, a member of the cytochrome P450 family, is a monooxygenase that specializes in the oxidation of aromatic carboxylic acids. The crystal structure of CYP199A2 determined by Bell et al. (J. Mol. Biol., 383, 561-574, 2008) suggested that the S97 and S247 residues conferred the substrate specificity on this enzyme through interaction between the hydroxy side chains of these Ser residues and the carboxy group of the substrates. In this study, we attempted to design and construct CYP199A2 mutants that recognize hydroxy aromatic compounds as substrates by protein engineering. We speculated that substitution of the S97 and S247 residues with acidic amino acids Asp and Glu, which have carboxy side chains, would provide CYP199A2 mutants that recognize hydroxy aromatic compounds instead of aromatic carboxylic acids. The S97 and S247 residues were substituted with Asp and Glu using site-directed mutagenesis. In whole-cell assays with p-methylbenzylalcohol and phenol as hydroxy aromatic substrates, the S247D mutant regioselectively oxidized these compounds to 1,4-benzenedimethanol and hydroquinone, respectively, although the wild-type enzyme exhibited no oxidation activity for these compounds. Furthermore, the S97D, S247D, and S247E mutants acquired oxidation activity for p-cresol. Especially, the S247D mutant rapidly oxidized p-cresol; the whole cells expressing the S247D mutant completely converted 1 mM p-cresol to p-hydroxybenzylalcohol in only 30 min. These results also clearly demonstrate that S97 and S247 are important residues that control the substrate specificity of CYP199A2.
    Journal of Bioscience and Bioengineering 06/2014;
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    ABSTRACT: Aberrant collagen production can lead to many diseases such as fibrosis. Current methods of collagen detection are insensitive, time-consuming and laborious. We have developed a rapid, sensitive assay using chemiluminescence-based reporter cell system. Stable 3T3/NIH-SMAD-luciferase cells were generated for detection of collagen expression through TGF-β signaling, a major fibrogenic pathway. We demonstrated that these reporter cells could be used as a rapid screening tool for detection of SMAD-dependent collagen production with higher sensitivity than existing assays. Flexibility of this cell-based assay in different detection platforms makes it attractive for high throughput screening of potential fibrogenic agents and drug candidates.
    Journal of Bioscience and Bioengineering 06/2014;
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    ABSTRACT: Palm oil empty fruit bunches (EFB) is an abundant and cheap lignocellulose material in Southeast Asia. Its use as the sole medium for producing lignocellulose-hydrolyzing enzymes would increase its commercial value. A newly isolated Aspergillus niger DSM 26641 was investigated for its capability of producing hemicellulases in EFB hydrolysate obtained by treatment with pressurized hot water (1-20%, w/v) at 120-180°C in a 1 L Parr reactor for 10-60 min. The optimal hydrolysate for the fungal growth and endoxylanase production was obtained when 10% (w/v) of empty fruit bunch was treated at 120°C or 150°C for 10 min, giving an endoxylanase activity of 24.5 mU ml(-1) on RBB-Xylan and a saccharification activity of 5 U ml(-1) on xylan (DNS assay). When the hydrolysates were produced at higher temperatures, longer treatment times or higher biomass contents, only less than 20% of the above maximal endoxylanase activity was detected, possibly due to the higher carbohydrate concentrations in the medium. Transcriptome analysis showed that 3 endoxylanases (expression levels 59-100%, the highest level was set as 100%), 2 β-xylosidases (4%), 4 side chain-cleaving arabinofuranosidases (1-95%), 1 acetyl xylan esterase (9%) and 2 ferulic acid esterases (0.3-9%) were produced together.
    Journal of Bioscience and Bioengineering 06/2014;
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    ABSTRACT: Understanding of the fundamental mechanisms that govern adhesive properties of human induced pluripotent stem cells (hiPSCs) to culture environments provides surface design strategies for maintaining their undifferentiated state during cell expansion. Polyamidoamine dendrimer surface with first-generation (G1) with dendron structure was used for co-cultures of hiPSCs and SNL feeder cells that formed tightly packed compact hiPSC colonies, similar to those on a conventional gelatin-coated surface. hiPSCs passaged up to 10 times on the G1 surface maintained their undifferentiated state. Immunostaining and reverse transcriptase PCR analysis of fibronectin showed that the secreted fibronectin matrix from feeder cells on the G1 surface contributed to hiPSC attachment. Compared with cells on the gelatin-coated surface, F-actin and paxillin immunostaining revealed a well-organized network of actin stress fibers and focal adhesion formation at cell-substrate sites in hiPSC colonies on the G1 surface. E-cadherin expression levels on these surfaces were almost same, but paxillin and Rac1 expression levels on the G1 surface were significantly higher than those on the gelatin-coated surface. Zyxin showed prominent expression on the G1 surface at sites of focal adhesion and cell-cell contact in colonies, whereas zyxin expression on the gelatin-coated surface was not observed in regions of cell-cell contact. These findings indicate that transduction of mechanical stimuli through actin polymerization at sites of focal adhesion and cell-cell contact results in maintenance of undifferentiated hiPSC colonies on G1 surface. The G1 surface enables a substrate design based on the mechanical cues in the microenvironment from feeder cells to expand undifferentiated hiPSCs in long-term culture.
    Journal of Bioscience and Bioengineering 06/2014;
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    ABSTRACT: Mannitol is a six carbon sugar alcohol that finds applications in the pharmaceutical and food industries. A novel Escherichia coli strain capable of converting d-glucose to d-mannitol has been constructed, wherein native mannitol-1-phosphate dehydrogenase (MtlD) and codon-optimized Eimeria tenella mannitol-1-phosphatase (M1Pase) have been overexpressed. Codon-optimized Pseudomonas stutzeri phosphite dehydrogenase (PtxD) was overexpressed for cofactor (NADH) regeneration with the concomitant oxidation of phosphite to phosphate. Whole-cell biotransformation using resting cells in a medium containing d-glucose and equimolar sodium phosphite resulted in d-mannitol yield of 87 mol%. Thus, production of an industrially relevant biochemical without using complex media components and elaborate process control mechanisms has been demonstrated.
    Journal of Bioscience and Bioengineering 06/2014;
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    ABSTRACT: The present study showed that the lysis of yeast cells and subsequent release of cell contents in sake mash accelerated dimethyl trisulfide (DMTS) formation. Among these, heat unstable and relatively high molecular weight compounds were assumed to be enzymes; thus, enzymatic reactions probably contribute to DMTS formation.
    Journal of Bioscience and Bioengineering 06/2014;
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    ABSTRACT: Six plant extracts prepared from Ligaria cuneifolia and Jodina rhombifolia were screened for their potential antimicrobial activities against phytopathogens and clinically standard reference bacterial strains. Bioautography and broth microdilution methods were used to study samples antibacterial activities against 7 bacterial strains. The minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) of samples were attained. An antibacterial activity guided isolation and identification of active compounds was carried out for L. cuneifolia methanolic extract (LCME). Both methanolic and aqueous extracts from L. cuneifolia showed inhibitory activities against phytopathogenic bacteria, with MICs ranging from 2.5 to 156 μg mL(-1) for LCME and 5 mg mL(-1) for the aqueous extract. None of the three J. rhombifolia extracts showed significant antibacterial activities against phytopathogenic strains (MIC > 5 mg mL(-1)), except for the aqueous extracts against Pseudomonas syringae (MIC = 312 μg mL(-1)). Only LCME showed bactericidal activities against phytopathogenic strains (MBCs = 78 μg mL(-1)). The LCME exhibited significant inhibitory activity against reference clinical strains: Escherichia coli (MIC = 156 μg mL(-1)) and Staphylococcus aureus (MIC = 78 μg mL(-1), MBC = 312 μg mL(-1)). LCME active compounds were identified as flavonol mono and diglycosides, and gallic acid. The antibacterial activity of purified compounds was also evaluated. A synergistic effect against S.aureus was found between gallic acid and a quercetin glycoside. Hence, anti-phytopathogenic bacteria potential compounds isolated from L. cuneifolia could be used as an effective source against bacterial diseases in plants.
    Journal of Bioscience and Bioengineering 05/2014;
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    ABSTRACT: Chlamydomonas reinhardtii possesses many potential advantages to be exploited as a biocatalyst in microbial fuel cells (MFCs) for electricity generation. In the present study, we performed computational studies based on flux balance analysis (FBA) to probe the maximum potential of C. reinhardtii for current output and identify the metabolic mechanisms supporting a high current generation in three different cultivation conditions, i.e., heterotrophic, photoautotrophic and mixotrophic growth. The results showed that flux balance limitations allow the highest current output for C. reinhardtii in the mixotrophic growth mode (2.368 A/gDW), followed by heterotrophic growth (1.141 A/gDW) and photoautotrophic growth the lowest (0.7035 A/gDW). The significantly higher mediated electron transfer (MET) rate in the mixotrophic mode is in complete contrast to previous findings for a photosynthetic cyanobacterium, and was attributed to the fact that for C. reinhardtii the photophosphorylation improved the efficiency of converting the acetate into biomass and NADH production. Overall, the cytosolic NADH-dependent current production was mainly associated with five reactions in both mixotrophic and photoautotrophic nutritional modes, whereas four reactions participated in the heterotrophic mode. The mixotrophic and photoautotrophic metabolisms were alike and shared the same set of reactions for maximizing current production, whereas in the heterotrophic mode, the current production was additionally contributed by the metabolic activities in the two organelles: glyoxysome and chloroplast. In conclusion, C. reinhardtii has a potential to be exploited in MFCs of MET mode to produce a high current output.
    Journal of Bioscience and Bioengineering 05/2014;
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    ABSTRACT: Acetate kinase (AK) generally utilizes ATP as a phosphoryl donor, but AK from Entamoeba histolytica (PPi-ehiAK) uses pyrophosphate (PPi), not ATP, and is PPi-specific. The determinants of the phosphoryl donor specificity are unknown. Here, we inferred 5 candidate amino acid residues associated with this specificity, based on structural information. Each candidate residue in Escherichia coli ATP-specific AK (ATP-ecoAK), which is unable to use PPi, was substituted with the respective PPi-ehiAK amino acid residue. Each variant ATP-ecoAK had an increased Km for ATP, indicating that the 5 residues are the determinants for the specificity to ATP in ATP-ecoAK. Moreover, Asn-337 of ATP-ecoAK was shown to be particularly significant for the specificity to ATP. The 5 residues are highly conserved in 2625 PPi-ehiAK homologs, implying that almost all organisms have ATP-dependent, rather than PPi-dependent, AK.
    Journal of Bioscience and Bioengineering 05/2014;
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    ABSTRACT: Tannases are important enzymes in the antioxidant potential of tea leaves. In this study, we evaluated the effect of two tannases (T1 and T2) on biotransformation of tea polyphenols and antioxidative activities from catechins in green tea extract (GTE). The T1 tannase-catalyzed reaction was inhibited by the addition of >2.0% GTE substrate, whereas the T2-catalyzed reaction was not inhibited, even by addition of 5.0% GTE. Furthermore, the T1 tannase-catalyzed reaction was inhibited by addition of 10 mg mL(-1) EGCG, whereas the T2 tannase-catalyzed reaction did not display any inhibitory effect. These results indicate that T2 tannase was more tolerant than T1 tannase to substrate inhibition in degallation reactions. Specifically, the substrate EGCG (90,687.1 μg mL(-1)) was transformed into gallic acid (50,242.9 μg mL(-1)) and EGC (92,598.3 μg mL(-1)) after 1-h treatment with T2 tannase (500 U g(-1)). The tannase-mediated product displayed higher in vitro radical-scavenging activity than the control. IC50 value of GTE on ABTS and DPPH radicals (46.1 μg mL(-1) and 18.4 μg mL(-1), respectively) decreased markedly after T2 tannase treatment (to 35.8 μg mL(-1) and 15.1 μg mL(-1), respectively). These results indicate that T2 tannase treatment of GTE enhanced its radical-scavenging activity, an increase that was also observed in the reaction using EGCG substrate. Taken together, our results revealed that T2 tannase is more suitable for biotransformation of catechins in GTE than T1 tannase, and T2 treatment provides an enhanced radical-scavenging effect.
    Journal of Bioscience and Bioengineering 05/2014;
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    ABSTRACT: Production of pharmaceutical glycoproteins, such as therapeutic antibodies and cytokines, in plants has many advantages in safety and reduced costs. However, plant-made glycoproteins have N-glycans with plant-specific sugar residues (core β-1,2-xylose and α-1,3-fucose) and a Lewis a (Le(a)) epitope, Galβ(1-3)[Fucα(1-4)]GlcNAc. Because it is likely that these sugar residues and glycan structures are immunogenic, many attempts have been made to delete them. Previously, we reported the simultaneous deletion of the plant-specific core α-1,3-fucose and α-1,4-fucose residues in Le(a) epitopes by repressing the GDP-d-mannose 4,6-dehydratase (GMD) gene, which is associated with GDP-l-fucose biosynthesis, in Nicotiana benthamiana plants (rGMD plants, renamed to ΔGMD plants) (Matsuo and Matsumura, Plant Biotechnol. J., 9, 264-281, 2011). In the present study, we generated a core β-1,2-xylose residue-repressed transgenic N. benthamiana plant by co-suppression of β-1,2-xylosyltransferase (ΔXylT plant). By crossing ΔGMD and ΔXylT plants, we successfully generated plants in which plant-specific sugar residues were repressed (ΔGMDΔXylT plants). The proportion of N-glycans with deleted plant-specific sugar residues found in total soluble protein from ΔGMDΔXylT plants increased by 82.41%. Recombinant mouse granulocyte/macrophage-colony stimulating factor (mGM-CSF) and human monoclonal immunoglobulin G (hIgG) harboring N-glycans with deleted plant-specific sugar residues were successfully produced in ΔGMDΔXylT plants. Simultaneous repression of the GMD and XylT genes in N. benthamiana is thus very useful for deleting plant-specific sugar residues.
    Journal of Bioscience and Bioengineering 05/2014;
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    ABSTRACT: We investigated the autonomous bottom-up fabrication of three-dimensional honeycomb cellulose structures, using Gluconacetobacter xylinus as a bacterial nanoengine, on cellulose honeycomb templates prepared by casting water-in-oil emulsions on glass substrates(Kasai and Kondo, Macromol. Biosci., 4, 17-21, 2004). The template film had a unique molecular orientation state along the honeycomb frames, but was non-crystalline. When G. xylinus, used as a nanofiber-producing bacterium, was incubated on the honeycomb scaffold in a culture medium, it secreted cellulose nanofibers only on the upper surface of the honeycomb frame. The movement was regulated by a selective interaction between the synthesized nanofiber and the surface of the honeycomb frames of the template. The relationship between directed deposition of synthesized nanofibers and ordered fabrication from the nano- to the micro-scale could provide a novel bottom-up methodology, using bacteria, for the design of three-dimensional honeycomb structures as functional materials with nano/micro hierarchical structures, with low energy consumption.
    Journal of Bioscience and Bioengineering 05/2014;
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    ABSTRACT: We enriched an anaerobic, soil-free 4-chlorophenol (4-CP)-degrading culture under iron-reducing conditions. The [ring-(14)C(U)]4-CP tracer experiment showed that 65 μM 4-CP mineralized to CO2 and CH4 through phenol, 4-hydroxybenzoate, and benzoate intermediates over 60 days. 16S rRNA gene analyses suggested the involvement of Dehalobacterium in the 4-CP dechlorination in the culture.
    Journal of Bioscience and Bioengineering 04/2014;
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    ABSTRACT: Fibrin polymers are widely used in the tissue engineering field as biomaterials. Although numerous researchers have studied the fabrication of scaffolds using fibrin glue (FG) and bone powder, the effects of varied fibrinogen content during the fabrication of scaffolds on human mesenchymal stem cells (hMSCs) and bone regeneration remain poorly understood. In this study, we formulated scaffolds using demineralized bone powder and various fibrinogen concentrations and analyzed the microstructure and mechanical properties. Cell proliferation, cell viability, and osteoblast differentiation assays were performed. The ability of the scaffold to enhance bone regeneration was evaluated using a rabbit calvarial defect model. Micro-computed tomography (micro-CT) showed that bone powders were uniformly distributed on the scaffolds, and scanning electron microscopy (SEM) showed that the fibrin networks and flattened fibrin layers connected adjacent bone powder particles. When an 80 mg/mL fibrinogen solution was used to formulate scaffolds, the porosity decreased 41.6 ± 3.6%, while the compressive strength increased 1.16 ± 0.02 Mpa, when compared with the values for the 10 mg/mL fibrinogen solution. Proliferation assays and SEM showed that the scaffolds prepared using higher fibrinogen concentrations supported and enhanced cell adhesion and proliferation. In addition, mRNA expression of alkaline phosphatase and osteocalcin in cells grown on the scaffolds increased with increasing fibrinogen concentration. Micro-CT and histological analysis revealed that newly formed bone was stimulated in the scaffold implantation group. Our results demonstrate that optimization of the fibrinogen content of fibrin glue/bone powder scaffolds will be beneficial for bone tissue engineering.
    Journal of Bioscience and Bioengineering 04/2014;

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