James Nakas - Academia.edu (original) (raw)
Papers by James Nakas
Biotechnology Progress, Dec 1, 2009
... 1995;128:219228. 9. Martina M, Hutmacher DW. Biodegradable polymers applied in tissue engine... more ... 1995;128:219228. 9. Martina M, Hutmacher DW. Biodegradable polymers applied in tissue engineering research: a review. Polym Int. ... 28. Gerngross TU, Martin DP. Enzyme-catalyzed synthesis of poly[(R)-(-)3-hydroxybutyratel]: formation of macroscopic granules in vitro. ...
![Research paper thumbnail of System development for linked-fermentation production of solvents from algal biomass. [Dunaliella tertiolecta, D. primolecta, D. parva, D. bardawil, D. salina]](https://attachments.academia-assets.com/44604570/thumbnails/1.jpg)
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Applied and Environmental Microbiology
Soil Science Society of America Journal, 1982
ABSTRACT
In an effort to devise inexpensive and sustainable production of ethanol fuel, experiments were c... more In an effort to devise inexpensive and sustainable production of ethanol fuel, experiments were conducted to establish conditions for Pichia stipitis NRRL Y-7124 to ferment a membrane treated wood hydrolysate derived from sugar maple to produce ethanol. The degree of aeration required to effectively utilize xylose, produce ethanol, and minimize xylitol formation as well as the optimal hydrolysate concentration were
Journal of Industrial Microbiology & Biotechnology, 2011
In order to improve the fermentative efficiency of sugar maple hemicellulosic hydrolysates for fu... more In order to improve the fermentative efficiency of sugar maple hemicellulosic hydrolysates for fuel ethanol production, various methods to mitigate the effects of inhibitory compounds were employed. These methods included detoxification treatments utilizing activated charcoal, anion exchange resin, overliming, and ethyl acetate extraction. Results demonstrated the greatest fermentative improvement of 50% wood hydrolysate (v/v) by Pichia stipitis with activated charcoal treatment. Another method employed to reduce inhibition was an adaptation procedure to produce P. stipitis stains more tolerant of inhibitory compounds. This adaptation resulted in yeast variants capable of improved fermentation of 75% untreated wood hydrolysate (v/v), one of which produced 9.8 g/l ± 0.6 ethanol, whereas the parent strain produced 0.0 g/l ± 0.0 within the first 24 h. Adapted strains RS01, RS02, and RS03 were analyzed for glucose and xylose utilization and results demonstrated increased glucose and decreased xylose utilization rates in comparison to the wild type. These changes in carbohydrate utilization may be indicative of detoxification or tolerance activities related to proteins involved in glucose and xylose metabolism.
Biotechnology Letters - BIOTECHNOL LETT, 1997
Laccase from Botrytis cinereacatalyzes benzylic oxidations and cleavage of lignin-related dipheny... more Laccase from Botrytis cinereacatalyzes benzylic oxidations and cleavage of lignin-related diphenylmethanes. Selective reactions with non-phenolic monomeric or b-1-dimeric model compounds using O 2 and redox mediators can also be carried out. At substrate to mediator ratios of 5:1, 1-hydoxybenzotriazole (HOBT) is 8-20 fold more effective than 2,2-azinobis-3-ethylthiazoline-6-sulfonate (ABTS) for such biotransformations. With unblocked phenols, ring couplings are the dominant endproducts either with or without mediators.
Soil Biology and Biochemistry, 1984
Nucleic Acids Research, 1990
Journal of Industrial Microbiology & Biotechnology, 2006
The potential for the use of woody biomass in poly-beta-hydroxyalkanoate (PHA) biosynthesis is re... more The potential for the use of woody biomass in poly-beta-hydroxyalkanoate (PHA) biosynthesis is reviewed. Based on previously cited work indicating incorporation of xylose or levulinic acid (LA) into PHAs by several bacterial strains, we have initiated a study for exploring bioconversion of forest resources to technically relevant copolymers. Initially, PHA was synthesized in shake-flask cultures of Burkholderia cepacia grown on 2.2% (w/v) xylose, periodically amended with varying concentrations of levulinic acid [0.07-0.67% (w/v)]. Yields of poly(beta-hydroxybutyrate-co-beta-hydroxyvalerate) [P(3HB-co-3HV)] from 1.3 to 4.2 g/l were obtained and could be modulated to contain from 1.0 to 61 mol% 3-hydroxyvalerate (3HV), as determined by 1H and 13C NMR analyses. No evidence for either the 3HB or 4HV monomers was found. Characterization of these P(3HB-co-3HV) samples, which ranged in molecular mass (viscometric, Mv) from 511-919 kDa, by differential scanning calorimetry and thermogravimetric analyses (TGA) provided data which were in agreement for previously reported P(3HB-co-3HV) copolymers. For these samples, it was noted that melting temperature (Tm) and glass transition temperature (Tg) decreased as a function of 3HVcontent, with Tm demonstrating a pseudoeutectic profile as a function of mol% 3HV content. In order to extend these findings to the use of hemicellulosic process streams as an inexpensive carbon source, a detoxification procedure involving sequential overliming and activated charcoal treatments was developed. Two such detoxified process hydrolysates (NREL CF: aspen and CESF: maple) were each fermented with appropriate LA supplementation. For the NREL CF hydrolysate-based cultures amended with 0.25-0.5% LA, P(3HB-co-3HV) yields, PHA contents (PHA as percent of dry biomass), and mol% 3HV compositions of 2.0 g/l, 40% (w/w), and 16-52 mol% were obtained, respectively. Similarly, the CESF hydrolysate-based shake-flask cultures yielded 1.6 g/l PHA, 39% (w/w) PHA contents, and 4-67 mol% 3HV compositions. These data are comparable to copolymer yields and cellular contents reported for hexose plus levulinic acid-based shake-flask cultures, as reported using Alcaligenes eutrophus and Pseudomonas putida. However, our findings presage a conceivable alternative, forestry-based biorefinery approach for the production of value-added biodegradable PHA polymers. Specifically, this review describes the current and potential utilization of lignocellulosic process streams as platform precursors to PHA polymers including hemicellulosic hydrolysates, residual cellulose-derived levulinic acid, tall oil fatty acids (Kraft pulping residual), and lignin-derived aromatics.
Journal of Industrial Microbiology & Biotechnology, 2012
Journal of Industrial Microbiology, 1992
Summary Purified xylanase A ofTrichoderma longibrachiatum was active on one of two carboxymethyl ... more Summary Purified xylanase A ofTrichoderma longibrachiatum was active on one of two carboxymethyl cellulose (CMC) preparations used as cellulase assay substrates. The pattern of enzyme activity, and analysis of the substrate by acid hydrolysis and thin-layer chromatography (TLC) suggested that the enzyme had acted on xylan present in the CMC.
Journal of Industrial Microbiology, 1987
Page 1. Journal of lndustfialMicrobiology, 2 (1987) 9-13 9 Elsevier SIM00056 Production of myceli... more Page 1. Journal of lndustfialMicrobiology, 2 (1987) 9-13 9 Elsevier SIM00056 Production of mycelial protein and hydrolytic enzymes from paper mill sludges by cellulolytic fungi John C. Royer and James P. Nakas SUNY College ...
Journal of Industrial Microbiology, 1991
ABSTRACT
Journal of Applied Polymer Science, 2013
Gene, 1994
There are no reports of gene sequences coding for extracellular chitinolytic enzymes from filamen... more There are no reports of gene sequences coding for extracellular chitinolytic enzymes from filamentous fungi, even though these enzymes are considered critical to the biological control of plant pathogenic fungi. The purpose of this paper was to report the isolation of a gene (ThEn-42) encoding endochitinase (Ech) from Trichoderma harzianum strain P1, describe its sequence, and to determine whether it was related to genes coding for enzymes with similar functions from prokaryotic or other eukaryotic sources. A clone containing a 1096-bp foreign cDNA fragment was isolated from thalli grown under induced conditions. This cDNA molecule was sequenced and found to lack a portion of the 5' terminus. Polymerase chain reaction (PCR) was used to isolate a fragment from the lambda gt11 library which contained the 5' terminus plus an overlap region with the 1096-bp cDNA clone. The full-length cDNA sequence, consisting of 1554 bp, contained an open reading frame (ORF) expressing a protein of 424 amino acids (aa). Southern analysis of genomic DNA indicated that there is only a single gene in strain P1 with sequence identity to the sequence described in this report. One region within the protein, thought to be required for catalytic activity of the enzyme, was highly conserved between genes coding for Ech from Th, Serratia marcescens, Bacillus circulans, Streptomyces plicatus, Vibrio parahemolyticus and Kluyveromyces lactis.
Enzyme and Microbial Technology, 1989
Biotechnology Progress, Dec 1, 2009
... 1995;128:219228. 9. Martina M, Hutmacher DW. Biodegradable polymers applied in tissue engine... more ... 1995;128:219228. 9. Martina M, Hutmacher DW. Biodegradable polymers applied in tissue engineering research: a review. Polym Int. ... 28. Gerngross TU, Martin DP. Enzyme-catalyzed synthesis of poly[(R)-(-)3-hydroxybutyratel]: formation of macroscopic granules in vitro. ...
Applied and Environmental Microbiology
Soil Science Society of America Journal, 1982
ABSTRACT
In an effort to devise inexpensive and sustainable production of ethanol fuel, experiments were c... more In an effort to devise inexpensive and sustainable production of ethanol fuel, experiments were conducted to establish conditions for Pichia stipitis NRRL Y-7124 to ferment a membrane treated wood hydrolysate derived from sugar maple to produce ethanol. The degree of aeration required to effectively utilize xylose, produce ethanol, and minimize xylitol formation as well as the optimal hydrolysate concentration were
Journal of Industrial Microbiology & Biotechnology, 2011
In order to improve the fermentative efficiency of sugar maple hemicellulosic hydrolysates for fu... more In order to improve the fermentative efficiency of sugar maple hemicellulosic hydrolysates for fuel ethanol production, various methods to mitigate the effects of inhibitory compounds were employed. These methods included detoxification treatments utilizing activated charcoal, anion exchange resin, overliming, and ethyl acetate extraction. Results demonstrated the greatest fermentative improvement of 50% wood hydrolysate (v/v) by Pichia stipitis with activated charcoal treatment. Another method employed to reduce inhibition was an adaptation procedure to produce P. stipitis stains more tolerant of inhibitory compounds. This adaptation resulted in yeast variants capable of improved fermentation of 75% untreated wood hydrolysate (v/v), one of which produced 9.8 g/l ± 0.6 ethanol, whereas the parent strain produced 0.0 g/l ± 0.0 within the first 24 h. Adapted strains RS01, RS02, and RS03 were analyzed for glucose and xylose utilization and results demonstrated increased glucose and decreased xylose utilization rates in comparison to the wild type. These changes in carbohydrate utilization may be indicative of detoxification or tolerance activities related to proteins involved in glucose and xylose metabolism.
Biotechnology Letters - BIOTECHNOL LETT, 1997
Laccase from Botrytis cinereacatalyzes benzylic oxidations and cleavage of lignin-related dipheny... more Laccase from Botrytis cinereacatalyzes benzylic oxidations and cleavage of lignin-related diphenylmethanes. Selective reactions with non-phenolic monomeric or b-1-dimeric model compounds using O 2 and redox mediators can also be carried out. At substrate to mediator ratios of 5:1, 1-hydoxybenzotriazole (HOBT) is 8-20 fold more effective than 2,2-azinobis-3-ethylthiazoline-6-sulfonate (ABTS) for such biotransformations. With unblocked phenols, ring couplings are the dominant endproducts either with or without mediators.
Soil Biology and Biochemistry, 1984
Nucleic Acids Research, 1990
Journal of Industrial Microbiology & Biotechnology, 2006
The potential for the use of woody biomass in poly-beta-hydroxyalkanoate (PHA) biosynthesis is re... more The potential for the use of woody biomass in poly-beta-hydroxyalkanoate (PHA) biosynthesis is reviewed. Based on previously cited work indicating incorporation of xylose or levulinic acid (LA) into PHAs by several bacterial strains, we have initiated a study for exploring bioconversion of forest resources to technically relevant copolymers. Initially, PHA was synthesized in shake-flask cultures of Burkholderia cepacia grown on 2.2% (w/v) xylose, periodically amended with varying concentrations of levulinic acid [0.07-0.67% (w/v)]. Yields of poly(beta-hydroxybutyrate-co-beta-hydroxyvalerate) [P(3HB-co-3HV)] from 1.3 to 4.2 g/l were obtained and could be modulated to contain from 1.0 to 61 mol% 3-hydroxyvalerate (3HV), as determined by 1H and 13C NMR analyses. No evidence for either the 3HB or 4HV monomers was found. Characterization of these P(3HB-co-3HV) samples, which ranged in molecular mass (viscometric, Mv) from 511-919 kDa, by differential scanning calorimetry and thermogravimetric analyses (TGA) provided data which were in agreement for previously reported P(3HB-co-3HV) copolymers. For these samples, it was noted that melting temperature (Tm) and glass transition temperature (Tg) decreased as a function of 3HVcontent, with Tm demonstrating a pseudoeutectic profile as a function of mol% 3HV content. In order to extend these findings to the use of hemicellulosic process streams as an inexpensive carbon source, a detoxification procedure involving sequential overliming and activated charcoal treatments was developed. Two such detoxified process hydrolysates (NREL CF: aspen and CESF: maple) were each fermented with appropriate LA supplementation. For the NREL CF hydrolysate-based cultures amended with 0.25-0.5% LA, P(3HB-co-3HV) yields, PHA contents (PHA as percent of dry biomass), and mol% 3HV compositions of 2.0 g/l, 40% (w/w), and 16-52 mol% were obtained, respectively. Similarly, the CESF hydrolysate-based shake-flask cultures yielded 1.6 g/l PHA, 39% (w/w) PHA contents, and 4-67 mol% 3HV compositions. These data are comparable to copolymer yields and cellular contents reported for hexose plus levulinic acid-based shake-flask cultures, as reported using Alcaligenes eutrophus and Pseudomonas putida. However, our findings presage a conceivable alternative, forestry-based biorefinery approach for the production of value-added biodegradable PHA polymers. Specifically, this review describes the current and potential utilization of lignocellulosic process streams as platform precursors to PHA polymers including hemicellulosic hydrolysates, residual cellulose-derived levulinic acid, tall oil fatty acids (Kraft pulping residual), and lignin-derived aromatics.
Journal of Industrial Microbiology & Biotechnology, 2012
Journal of Industrial Microbiology, 1992
Summary Purified xylanase A ofTrichoderma longibrachiatum was active on one of two carboxymethyl ... more Summary Purified xylanase A ofTrichoderma longibrachiatum was active on one of two carboxymethyl cellulose (CMC) preparations used as cellulase assay substrates. The pattern of enzyme activity, and analysis of the substrate by acid hydrolysis and thin-layer chromatography (TLC) suggested that the enzyme had acted on xylan present in the CMC.
Journal of Industrial Microbiology, 1987
Page 1. Journal of lndustfialMicrobiology, 2 (1987) 9-13 9 Elsevier SIM00056 Production of myceli... more Page 1. Journal of lndustfialMicrobiology, 2 (1987) 9-13 9 Elsevier SIM00056 Production of mycelial protein and hydrolytic enzymes from paper mill sludges by cellulolytic fungi John C. Royer and James P. Nakas SUNY College ...
Journal of Industrial Microbiology, 1991
ABSTRACT
Journal of Applied Polymer Science, 2013
Gene, 1994
There are no reports of gene sequences coding for extracellular chitinolytic enzymes from filamen... more There are no reports of gene sequences coding for extracellular chitinolytic enzymes from filamentous fungi, even though these enzymes are considered critical to the biological control of plant pathogenic fungi. The purpose of this paper was to report the isolation of a gene (ThEn-42) encoding endochitinase (Ech) from Trichoderma harzianum strain P1, describe its sequence, and to determine whether it was related to genes coding for enzymes with similar functions from prokaryotic or other eukaryotic sources. A clone containing a 1096-bp foreign cDNA fragment was isolated from thalli grown under induced conditions. This cDNA molecule was sequenced and found to lack a portion of the 5' terminus. Polymerase chain reaction (PCR) was used to isolate a fragment from the lambda gt11 library which contained the 5' terminus plus an overlap region with the 1096-bp cDNA clone. The full-length cDNA sequence, consisting of 1554 bp, contained an open reading frame (ORF) expressing a protein of 424 amino acids (aa). Southern analysis of genomic DNA indicated that there is only a single gene in strain P1 with sequence identity to the sequence described in this report. One region within the protein, thought to be required for catalytic activity of the enzyme, was highly conserved between genes coding for Ech from Th, Serratia marcescens, Bacillus circulans, Streptomyces plicatus, Vibrio parahemolyticus and Kluyveromyces lactis.
Enzyme and Microbial Technology, 1989