Minneapolis, MN, United States
Minneapolis, MN, United States
SEARCH FILTERS
Time filter
Source Type

Shah A.R.,Pondicherry University | Ahmad A.,Systems Biology for Biofuels Group | Ahmad A.,Advanced BioEnergy | Srivastava S.,Systems Biology for Biofuels Group | And 2 more authors.
Algal Research | Year: 2017

Nannochloropsis gaditana is a promising marine microalga for biotechnological applications due to its capacity to accumulate large amounts of lipids and to synthesize valuable chemicals for the food industry. To identify the metabolic capabilities of this organism, a broad-level understanding of its metabolism is needed, which can be accomplished by a large-scale metabolic model. In this work, we present the first functional compartmentalized genome-scale metabolic model of this microalga, which we call iRJ1321. It includes 1321 genes, 1918 reactions, and 1862 metabolites and is thus the largest algal genome scale metabolic model to date in terms of number of genes and percentage gene coverage. The model-predicted growth rate matches reasonably well with the literature reported growth rate for photoautotrophic growth. The model was applied to capture the role of nitrogen limitation in remodeling N. gaditana metabolism. The flux distribution in iRJ1321 predicts C4-like carbon-concentrating co-existing with Calvin cycle. This model will be useful to researchers interested in understanding capabilities and limitations of N. gaditana metabolism and devising metabolic engineering strategies for synthetic pathway design for production of diverse molecules. © 2017 Elsevier B.V.


Milne C.B.,Urbana University | Eddy J.A.,Urbana University | Raju R.,University of Minnesota | Ardekani S.,Urbana University | And 7 more authors.
BMC Systems Biology | Year: 2011

Background: Solventogenic clostridia offer a sustainable alternative to petroleum-based production of butanol--an important chemical feedstock and potential fuel additive or replacement. C. beijerinckii is an attractive microorganism for strain design to improve butanol production because it (i) naturally produces the highest recorded butanol concentrations as a byproduct of fermentation; and (ii) can co-ferment pentose and hexose sugars (the primary products from lignocellulosic hydrolysis). Interrogating C. beijerinckii metabolism from a systems viewpoint using constraint-based modeling allows for simulation of the global effect of genetic modifications.Results: We present the first genome-scale metabolic model (iCM925) for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and utilized computational algorithms with manual curation to improve model completeness. Interestingly, we found only a 34% overlap in reactions collected from the three databases--highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To validate iCM925, we conducted fermentation experiments using the NCIMB 8052 strain, and evaluated the ability of the model to simulate measured substrate uptake and product production rates. Experimentally observed fermentation profiles were found to lie within the solution space of the model; however, under an optimal growth objective, additional constraints were needed to reproduce the observed profiles--suggesting the existence of selective pressures other than optimal growth. Notably, a significantly enriched fraction of actively utilized reactions in simulations--constrained to reflect experimental rates--originated from the set of reactions that overlapped between all three databases (P = 3.52 × 10-9, Fisher's exact test). Inhibition of the hydrogenase reaction was found to have a strong effect on butanol formation--as experimentally observed.Conclusions: Microbial production of butanol by C. beijerinckii offers a promising, sustainable, method for generation of this important chemical and potential biofuel. iCM925 is a predictive model that can accurately reproduce physiological behavior and provide insight into the underlying mechanisms of microbial butanol production. As such, the model will be instrumental in efforts to better understand, and metabolically engineer, this microorganism for improved butanol production. © 2011 Milne et al; licensee BioMed Central Ltd.


Fatma Z.,Synthetic Biology and Biofuels Group | Jawed K.,Synthetic Biology and Biofuels Group | Mattam A.J.,Synthetic Biology and Biofuels Group | Yazdani S.S.,Synthetic Biology and Biofuels Group | Yazdani S.S.,Advanced BioEnergy
Metabolic Engineering | Year: 2016

Long chain fatty alcohols have wide application in chemical industries and transportation sector. There is no direct natural reservoir for long chain fatty alcohol production, thus many groups explored metabolic engineering approaches for its microbial production. Escherichia coli has been the major microbial platform for this effort, however, terminal endogenous enzyme responsible for converting fatty aldehydes of chain length C14-C18 to corresponding fatty alcohols is still been elusive. Through our in silico analysis we selected 35 endogenous enzymes of E. coli having potential of converting long chain fatty aldehydes to fatty alcohols and studied their role under in vivo condition. We found that deletion of ybbO gene, which encodes NADP+ dependent aldehyde reductase, led to >90% reduction in long chain fatty alcohol production. This feature was found to be strain transcending and reinstalling ybbO gene via plasmid retained the ability of mutant to produce long chain fatty alcohols. Enzyme kinetic study revealed that YbbO has wide substrate specificity ranging from C6 to C18 aldehyde, with maximum affinity and efficiency for C18 and C16 chain length aldehyde, respectively. Along with endogenous production of fatty aldehyde via optimized heterologous expression of cyanobaterial acyl-ACP reductase (AAR), YbbO overexpression resulted in 169 mg/L of long chain fatty alcohols. Further engineering involving modulation of fatty acid as well as of phospholipid biosynthesis pathway improved fatty alcohol production by 60%. Finally, the engineered strain produced 1989 mg/L of long chain fatty alcohol in bioreactor under fed-batch cultivation condition. Our study shows for the first time a predominant role of a single enzyme in production of long chain fatty alcohols from fatty aldehydes as well as of modulation of phospholipid pathway in increasing the fatty alcohol production. © 2016 International Metabolic Engineering Society.


Chlamydomonas reinhardtii is the mostextensively studied eukaryotic model microalgae havingessentialbiological pathwayssuch as biomass production, photosynthesis, carbon concentrating mechanisms (CCMs), carbohydrate metabolism (CM), lipid metabolism (LM), and response towards nutritional stresses, with fine-tuned physiological data and genome sequence available publicly. During nitrogen (N) deprivation, C. reinhardtii accumulates oil (triacylglycerols, TAG) as storage reserves and studies to understand the entire global regulatory network is still not clear. Recent studies showed that they have identified and characterizedentire set of genes encoding transcription factors (TFs) and transcriptional regulators (TRs)that control lipid metabolism relative to other genes under different stress responses using combined omics analysis but evaluation of common TFs and TRs under normal conditions involvingLMand CCM in combination is essential for understanding regulatory network that may lead to identification of several regulatory hubs that controls these essential cellular processes. Our study will focus on reconstruction of a regulatory network from publicly available databases such as PlnTFDB, STRING and elucidate common TFs and TRs essential for both these mechanisms. We have identified new TFs and TRssuch as, SET, PHD, FHA, Myb, Myb-related, and HMGthat play an important role in different functions such as control of chromatin and/or transcription, methylation of lysine residues, DNA repair, signal transduction etc. Also, our findings demonstrate that these TFs and TRs areinvolved in photoreceptor-like activities in the model microalga, whichhasthe maximum degree of interactions with different genes and thus have relevant physiological importance in both these mechanisms. © 2016 IEEE.


Shihadeh J.K.,Advanced BioEnergy | Huang H.,Advanced BioEnergy | Rausch K.D.,Advanced BioEnergy | Tumbleson M.E.,Advanced BioEnergy | Singh V.,Advanced BioEnergy
Transactions of the ASABE | Year: 2013

Efficiency gains in current grain ethanol processes are limited by limitations of the yeast biocatalyst. Yeast stress, including glucose concentrations (15% w/v) produced during liquefaction and saccharification and subsequent high ethanol concentrations (18% v/v) produced during fermentation, restrict slurry solids to 32% w/w for grain ethanol processes. A system was constructed to circumvent this solids limitation by combining two technologies: (1) granular starch hydrolyzing enzyme (GSHE), which can liquefy starch simultaneously with fermentation, and (2) reduced vapor pressure to remove ethanol from high-solids fermentations. GSHE eliminates the need for a separate liquefaction step because it gradually digests raw starch to glucose, which results in lower initial glucose concentrations (5% w/w). Vacuum was applied to remove ethanol as concentrations increased to near inhibition levels. An in situ ethanol removal system was constructed to conduct fermentation at 40% solid content. The vacuum flashing process successfully removed ethanol from the fermentation broth, thereby maintaining ethanol concentration in the broth below 10% to 12% v/v, while ethanol concentration in the control experiment without vacuum stripping was above 18% v/v. The final residual glucose concentrations in the fermentation broth for vacuum and non-vacuum treatments were 1.5% and 0.1%, respectively, indicating a more complete fermentation with vacuum flash. However, ethanol yields for vacuum and non-vacuum treatments were similar, 0.288 ±0.013 L kg-1 and 0.285 ±0.013 L kg-1, respectively. Neither removal of CO2 nor repressurization with unfiltered air affected final ethanol yields. © 2013 American Society of Agricultural and Biological Engineers.


Agrawal R.,Advanced BioEnergy | Verma A.K.,Govind Ballabh Pant University of Agriculture & Technology | Satlewal A.,Govind Ballabh Pant University of Agriculture & Technology
Innovative Food Science and Emerging Technologies | Year: 2016

Β-glucosidases are among the key enzymes for juice and beverage industries. They are responsible for the release of aromatic compounds in fruits and fermentation products. In this study, β-glucosidase was isolated, purified, and characterized from an indigenously developed Bacillus subtilis mutant PS-5CM-UM3. It is a 56 kDa protein monomer (isoelectric point of 5.6) belonging to 1 glycosyl hydrolase family. The purified β-glucosidase was immobilized on SiO2 nanoparticles (with 52% efficiency and 14.1% yield) to improve the thermostability and Michaelis constant (Km) value of β-glucosidase from 0.9 to 1.1mM. The immobilized enzyme showed improved storage stability and was reusable for up to 10 cycles with 70% residual activity. β-glucosidase treatment in sugarcane juice elevated the phenolics content with about 2.6 folds and 2.4 folds increase in p-hydroxy benzoic acid (PHBA) and gallic acid, respectively. The results show that recyclable immobilized enzyme system is a novel green approach for improving the sugarcane juice properties. Industrial relevance: In this study, β-glucosidase originally isolated and purified from an indigenously developed Bacillus subtilismutantwas immobilized on SiO2 nanoparticles. The immobilization has improved the thermostability, storage stability, and Michaelis constant (Km) value of the β-glucosidase. The immobilized β-glucosidase is nowreusable for 10 cycles with 70% residual activity. Further, β-glucosidase treatment in sugarcane juice elevated the phenolics content with about 2.6 folds and 2.4 folds increase in p-hydroxy benzoic acid (PHBA) and gallic acid, respectively. Hence, this study provides a green and sustainable approach for the food industry to efficiently enhance the juice properties. © 2016 Elsevier Ltd. All rights reserved.


Trademark
Advanced BioEnergy | Date: 2013-06-11

Biofuels. Generation of energy; Production of energy; Production, treatment and refinement of fuel, diesel fuel, biofuel and biodiesel fuel for others.


Trademark
Advanced BioEnergy | Date: 2013-06-11

Biofuels. Generation of energy; Production of energy; Production, treatment and refinement of fuel, diesel fuel, biofuel and biodiesel fuel for others.


Trademark
Advanced BioEnergy | Date: 2010-02-18

Biofuels. Generation of energy; Production of energy; Production, treatment and refinement of fuel, diesel fuel, biofuel and biodiesel fuel for others.


Loading Advanced BioEnergy collaborators
Loading Advanced BioEnergy collaborators