Synthetic Biology and Biofuels Group

Delhi, India

Synthetic Biology and Biofuels Group

Delhi, India

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Garg S.,Malaria Group | Agarwal S.,Malaria Group | Kumar S.,Plant Biology Plant Transformation Group | Shams Yazdani S.,Synthetic Biology and Biofuels Group | And 3 more authors.
Nature Communications | Year: 2013

Clinical malaria is associated with proliferation of blood-stage parasites. During the blood stage, Plasmodium parasites invade host red blood cells, multiply, egress and reinvade uninfected red blood cells to continue the life cycle. Here we demonstrate that calcium-dependent permeabilization of host red blood cells is critical for egress of Plasmodium falciparum merozoites. Although perforin-like proteins have been predicted to mediate membrane perforation during egress, the expression, activity and mechanism of action of these proteins have not been demonstrated. Here, we show that two perforin-like proteins, perforin-like protein 1 and perforin-like protein 2, are expressed in the blood stage. Perforin-like protein 1 localizes to the red blood cell membrane and parasitophorous vacuolar membrane in mature schizonts following its Ca2+ -dependent discharge from micronemes. Furthermore, perforin-like protein 1 shows Ca2+ -dependent permeabilization and membranolytic activities suggesting that it may be one of the effector proteins that mediate Ca2+ -dependent membrane perforation during egress. © 2013 Macmillan Publishers Limited. All rights reserved.


Koigoora S.,Indian Institute of Chemical Technology | Koigoora S.,University of Averio | Ahmad I.,University of Averio | Pallela R.,Synthetic Biology and Biofuels Group | Janapala V.R.,Indian Institute of Chemical Technology
Environmental Monitoring and Assessment | Year: 2013

Marine sediments of the Gulf of Mannar (GoM), India are contaminated by potential toxic elements (PTEs) due to anthropogenic activities posing a risk to the existing fragile coral ecosystem and human health. The current study aimed to assess the distribution of PTEs (arsenic - As; cobalt - Co; copper - Cu, molybdenum - Mo; lead - Pb; and zinc - Zn) in marine sediments of different grain size fractions, viz.; medium sand (710 μm), fine sand (250 μm), and clay (<63 μm) among the different coastal regions of Pamban, Palk Bay, and Rameswaram coasts of GoM, using grain size as one of the key factor controlling their concentrations. The concentrations of PTEs were measured in the different size fractions of sediment using inductively coupled plasma mass spectrophotometer. The order of accumulation of all PTEs in the three fractions was ranked as Zn > Cu > Pb > As > Co > Mo and in the three locations as Rameswaram > Palk Bay > Pamban. The concentration of PTEs in Palk Bay and Rameswaram coast was significantly different (P < 0.05), when compared to Pamban coast. Measured geoaccumulation index (I geo) and contamination factor (CF) indicated significant enrichment of Co and Pb from Rameswaram coast when compared to other two coasts. Although the concentration of Co was low but the measured I geo and CF values indicated significant enrichment of this PTE in Rameswaram coast. The increased input of PTEs in the coastal regions of GoM signifies the need to monitor the coast regularly using suitable monitoring tools such as sediments to prevent further damage to the marine ecosystem. © 2013 Springer Science+Business Media Dordrecht.


Venkatesan J.,Pukyong National University | Pallela R.,Synthetic Biology and Biofuels Group | Kim S.-K.,Pukyong National University
Journal of Biomedical Nanotechnology | Year: 2014

In the biomedical field, remarkable advancements have been made in artificial biomaterials for treating bone loss or defects. A variety of synthetic polymers, natural polymers and bioceramics are being used to develop artificial bones. Many natural and synthetic biomaterials, which are being investigated for their physiochemical role in vivo, are currently in the clinical trial stage. Carbon-based prostheses are promising materials that mimic the natural function of bone, e.g., mechanical strength. Recently, carbon-based bone materials, such as carbon nanotubes and graphene, have been widely investigated as potential solutions to several biomedical problems. This review summarizes the biophysicochemical and biomedical properties of carbon nanomaterials composed of polymer and ceramic structures and discusses their functionality in bone tissue engineering. Copyright © 2014 American Scientific Publishers All rights reserved.


Mattam A.J.,Synthetic Biology and Biofuels Group | Yazdani S.S.,Synthetic Biology and Biofuels Group
Biotechnology for Biofuels | Year: 2013

Background: Recent progress in production of various biofuel precursors and molecules, such as fatty acids, alcohols and alka(e)nes, is a significant step forward for replacing the fossil fuels with renewable fuels. A two-step process, where fatty acids from sugars are produced in the first step and then converted to corresponding biofuel molecules in the second step, seems more viable and attractive at this stage. We have engineered an Escherichia coli strain to take care of the second step for converting short chain fatty acids into corresponding alcohols by using butyrate kinase (Buk), phosphotransbutyrylase (Ptb) and aldehyde/alcohol dehydrogenase (AdhE2) from Clostridium acetobutylicum. Results: The engineered E. coli was able to convert butyric acid and other short chain fatty acids of chain length C3 to C7 into corresponding alcohols and the efficiency of conversion varied with different E. coli strain type. Glycerol proved to be a better donor of ATP and electron as compared to glucose for converting butyric acid to butanol. The engineered E. coli was able to tolerate up to 100 mM butyric acid and produced butanol with the conversion rate close to 100% under anaerobic condition. Deletion of native genes, such as fumarate reductase (frdA) and alcohol dehydrogenase (adhE), responsible for side products succinate and ethanol, which act as electron sink and could compete with butyric acid uptake, did not improve the butanol production efficiency. Indigenous acyl-CoA synthetase (fadD) was found to play no role in the conversion of butyric acid to butanol. Engineered E. coli was cultivated in a bioreactor under controlled condition where 60 mM butanol was produced within 24 h of cultivation. A continuous bioreactor with the provision of cell recycling allowed the continuous production of butanol at the average productivity of 7.6 mmol/l/h until 240 h. Conclusions: E. coli engineered with the pathway from C. acetobutylicum could efficiently convert butyric acid to butanol. Other short chain fatty acids with the chain length of C3 to C7 were also converted to the corresponding alcohols. The ability of engineered strain to convert butyric acid to butanol continuously demonstrates commercial significance of the system. © 2013 Mattam and Yazdani; licensee BioMed Central Ltd.


Bashir Z.,Synthetic Biology and Biofuels Group | Kondapalli V.K.,Synthetic Biology and Biofuels Group | Adlakha N.,Synthetic Biology and Biofuels Group | Sharma A.,Insect Resistance Group | And 3 more authors.
Scientific Reports | Year: 2013

Arthropods living on plants are able to digest plant biomass with the help of microbial flora in their guts. This study considered three arthropods from different niches-termites, pill-bugs and yellow stem-borers-and screened their guts for cellulase producing microbes. Among 42 unique cellulase-producing strains, 50% belonged to Bacillaceae, 26% belonged to Enterobacteriaceae, 17% belonged to Microbacteriaceae, 5% belonged to Paenibacillaceae and 2% belonged to Promicromonosporaceae. The distribution of microbial families in the three arthropod guts reflected differences in their food consumption habits. Most of the carboxymethylcellulase positive strains also hydrolysed other amorphous substrates such as xylan, locust bean gum and β-D-glucan. Two strains, A11 and A21, demonstrated significant activity towards Avicel and p-nitrophenyl-β-D-cellobiose, indicating that they express cellobiohydrolase. These results provide insight into the co-existence of symbionts in the guts of arthropods and their possible exploitation for the production of fuels and chemicals derived from plant biomass.


Dubey R.,Synthetic Biology and Biofuels Group | Jakeer S.,Synthetic Biology and Biofuels Group | Gaur N.A.,Synthetic Biology and Biofuels Group
Journal of Bioscience and Bioengineering | Year: 2016

Robust microorganisms are required for sustainable second-generation biofuel production. We evaluated the growth and fermentation performance of six natural isolates that were derived from grape wine and medicinal herbs using a wide range of carbon sources, rice and wheat straw hydrolysates as well as stress conditions associated with second-generation ethanol production. Sequence analysis of the 5.8S internal transcribed spacer (ITS) and species-specific PCR amplification of the HO gene region assigned the natural isolates to Saccharomyces cerevisiae. Restriction fragment length polymorphism (RFLP) analysis of the mitochondrial DNA revealed that natural yeast isolates are genetically closer to the laboratory strain BY4741 than to the CEN.PK strains. Dextrose fermentation by a natural isolate, MTCC4780, under semi-anaerobic conditions produced maximum ethanol yields of 0.44 g/g and 0.39 g/g, respectively, with and without the stresses encountered during lignocellulosic ethanol fermentation. However, MTCC4780 produced ethanol yields of 0.48 g/g, 0.42 g/g and 0.45 g/g, respectively, with glucose, rice and wheat straw enzymatic hydrolysate fermentation in a bioreactor. The isolates MTCC4781 and MTCC4796 showed higher growth and fermentation performance than did MTCC4780 in the presence of elevated temperature and pre-treatment inhibitors. Taken together, the MTCC4780, MTCC4781 and MTCC4796 strains have the potential to serve as a platform for lignocellulosic ethanol production under stresses associated with second-generation biofuel production. © 2015 The Society for Biotechnology, Japan.


Adlakha N.,Synthetic Biology and Biofuels Group | Yazdani S.S.,Synthetic Biology and Biofuels Group
Journal of Industrial Microbiology and Biotechnology | Year: 2015

We report here the production of pure (R,R)-2,3-butanediol (2,3-BDO) isomer by the non-pathogenic Paenibacillus polymyxa ICGEB2008 using lignocellulosic hydrolysate as substrate. Experimental design based on Plackett-Burman resulted in identification of Mn and K as most crucial salt elements along with the yeast extract for 2,3-BDO production. Further experiments using Box-Behnken design indicated that both KCl and yeast extract together had major impact on 2,3-BDO production. Optimized medium resulted in 2,3-BDO production with 2.3-fold higher maximum volumetric productivity (2.01 g/L/h) and similar yield (0.33 g/g sugar) as compared to rich yeast extract-peptone-dextrose medium in the bioreactor studies. Considering that the balance substrate was channeled towards ethanol, carbon recovery was close to theoretical yield between the two solvents, i.e., 2,3-BDO and ethanol. Biomass hydrolysate and corn-steep liquor was used further to produce 2,3-BDO without impacting its yield. In addition, 2,3-BDO was also produced via simultaneous saccharification and fermentation, signifying robustness of the strain. © 2014, Society for Industrial Microbiology and Biotechnology.


Pallela R.,Synthetic Biology and Biofuels Group
Advances in Food and Nutrition Research | Year: 2014

Current day's research has been focusing much on the potential pharmacological or nutraceutical agents of selective health benefits with less toxicity. As a consequence of increased demand of nutritional supplements of great medicinal values, development of therapeutic agents from natural sources, in particular, marine environment are being considered much important. A diverse array of marine natural products containing medicinally useful nutritional substances, i.e., marine nutraceuticals have been focused to the benefit of mankind. Carbohydrates, by being constituted in considerable amount of many marine organisms display several nutraceutical and pharmaceutical behavior to defend from various diseases. Moreover, the carbohydrates from algae as well as from shellfish wastes, like chitosan and its derivatives, showed tremendous applications in biology and biomedicine. In the current chapter, several of marine carbohydrates from various marine flora and fauna have been covered with their applications and prospects in the development of nutraceuticals and pharmaceuticals. © 2014 Elsevier Inc.


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.


PubMed | Synthetic Biology and Biofuels Group and Advanced BioEnergy
Type: | Journal: 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 169mg/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 1989mg/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.

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