indian institute of technology delhi department of biochemical...

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Indian Institute of technology Delhi

Department of Biochemical Engineering and

Biotechnology

PhD project

Project details Project title Experimental and computational techniques for metabolic analysis and

engineering of microbes

Project description

Background: The analysis of metabolic pathways provides information about

the metabolic landscape of an organism. This project proposes to apply

combined metabolic flux and pathway analyses techniques for determining

genetic interventions for redirecting metabolic fluxes in microbial host(s).

Specific objectives and methodologies: This proposal aims to employ

experimental and computational techniques to determine genetic intervention

strategies for improving production of target molecules as outlined below.

(i) GC-MS analysis of 13C based labelling experiments followed by

computational determination of pathway fluxes.

(ii) In silico pathway analyses for suggesting changes in pathway fluxes to

improve product yields (Extreme pathways and flux balance).

(iii) Genetic engineering of microbial host(s) by cloning and expression of

plasmids for redirecting metabolic fluxes.

Instruments required

Shaker Incubator, PCR machine, GC-MS, Workstation,

Any other comments

PhD supervisors

Role Faculty Academic unit at IITD E-mail

Supervisor Ashish Misra DBEB [email protected]

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Skills required

Qualification Bachelors/Masters in Chemical/Biochemical Engineering or Biotechnology

Skills Programming language like MATLAB or PYTHON; Analytical techniques like

HPLC & GC-MS; Basic molecular biology techniques like PCR and cloning.

References

A Misra, MF Conway, J Johnnie, TM Qureshi, B Lige, AM Derrick, EC Agbo, G Sriram, ‘Metabolic

Analyses Elucidate Non-Trivial Gene Targets for Amplifying Dihydroartemisinic Acid Production in

Yeast’, Frontiers in Microbiology 4:200 (2013)

S Nargund, A Misra, X Zhang, GD Coleman, G Sriram, ‘Flux and Reflux: Metabolite Reflux in Plant

Suspension Cells and its Implications on Isotope-Assisted Metabolic Flux Analysis’, Molecular

BioSystems DOI: 10.1039/C3MB70348G (2013)

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Biotechnology

PhD project

Project details Project title Kinetics of recombinant protein synthesis on mixtures of carbon sources in

Komagataella phaffi

Project description

Objectives and Methodology: The goal is to characterize the kinetics of recombinant protein production during growth of K. phaffi on mixtures of the inducer (methanol) and various carbon sources. Chemostat studies will be performed to to quantify the recombinant protein production rate and the rates of consumption of glucose and other carbon sources under well-defined steady state conditions Background: To reduce heat generation and oxygen consumption, recombinant proteins are produced in K. pfaffi in the presence of methanol and a second carbon source. The identity of the optimal second carbon source is a subject of debate. Some authors recommend the non-repressing carbon sources and others find that the carbon source does affect the outcome. The results of this study will help settle the debate.


Bio-reactors

Any other comments

PhD supervisors

Role Faculty Academic unit at IITD E-mail Supervisor Prof. Atul Narang DBEB [email protected]

Skills required Qualification

2

Skills

References

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Indian Institute of Technology Delhi Department of Biochemical Engineering and

Biotechnology

PhD project

Project details Project title Eating electrons: investigating microbial cathodic extracellular electron transfer

Project description

Electroactive microorganisms are known to exchange electrons with solid conductive surfaces in a process termed extracellular electron transfer1,2. In this way, microorganisms can interact with metal oxides in nature and electrodes in the laboratory. However, efforts to understand this phenomenon have primarily focused on anodic electron transfer, where the electrode acts as a solid terminal electron acceptor. Less frequently investigated is electron flow in the opposite direction, termed cathodic electron transfer, whereby the microorganisms are fed electrons. It has been found that the manner in which microbes interact with solid electron donors may not just be a simple reversal of the known pathways they use to interact with solid electron acceptors as seen in anodic electron transfer3. This project aims to enhance current knowledge of the mechanisms employed by these “electric microbes” while eating electrons. Insights into this mode of living will eventually find application in microbial electrosynthesis4.


Potentiostat, additional equipment as required via core facilities.

Any other comments

Floated as PhD or MSR topic.

PhD supervisors Role Faculty Academic unit at IITD E-mail Supervisor Lucinda Elizabeth Doyle Department of Biochemical

Engineering & Biotechnology [email protected]

Skills required Qualification Minimum B.Tech or equivalent.

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Skills Understanding of microbiology and biochemistry.

References 1. Koch, C., & Harnisch, F. (2016). Is there a specific ecological niche for electroactive microorganisms?

ChemElectroChem, 3(9), 1282-1295. 2. Doyle, L. E., & Marsili, E. (2018). Weak electricigens: a new avenue for bioelectrochemical research.

Bioresource Technology, 258, 354-364. 3. Rowe, A.R., Rajeev, P., Jain, A., Pirbadian, S., Okamoto, A., Gralnick, J.A., El-Naggar, M.Y. and

Nealson, K.H. (2018). Tracking electron uptake from a cathode into Shewanella cells: implications for energy acquisition from solid-substrate electron donors. mBio, 9(1), e02203-17.

4. Glaven, S. M. (2019). Bioelectrochemical systems and synthetic biology: more power, more products. Microbial Biotechnology, 12(5), 819.

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Biotechnology

PhD project

Project details Project title Electroactive India: profiling electrochemically-active microorganisms from across the

subcontinent

Project description

Electroactive microorganisms are capable of exchanging electrons with solid conductive surfaces, including metal oxides in nature and electrodes in the laboratory. This phenomenon is termed extracellular electron transfer and results in an extracellular current (i.e. microbially-derived electricity). These “electric microbes” are the foundation of electromicrobiology; an interdisciplinary field at the nexus of microbiology, electrochemistry and engineering. Electroactive microorganisms have been found in diverse regions1 and are considered to have functionalities not yet completely understood2,3. Nonetheless, the resident community of such microorganisms in India and abroad is not fully elucidated, as work has primarily focused on waste water as a source of inoculum with comparatively few studies exploring alternative sites4. This project aims to generate a profile of the native electroactive microorganisms of India by performing enrichment and isolation from diverse environments. A key aim is to grow novel isolates and consortia which are electroactive in a range of physicochemical conditions, with the potential to increase fundamental understanding of extracellular electron transfer and to identify strains potentially useful in bioelectrochemical systems.



Any other comments





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Bioresource Technology, 258, 354-364. 3. Keogh D., Lam L.N., Doyle L.E., Matysik A., Pavagadhi S., Umashankar S., Low P.M., Dale J.L., Song

Y., Ng S.P., Boothroyd C.B. (2018) Extracellular electron transfer powers Enterococcus faecalis biofilm metabolism. mBio, 9(2):e00626-17.

4. Doyle, L. E., & Marsili, E. (2015). Methods for enrichment of novel electrochemically-active microorganisms. Bioresource Technology, 195, 273-282.

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Biotechnology

PhD project

Project details Project title Extracellular electron transfer at the extremes: investigating the limits of electroactive

microorganisms

Project description

Electroactive microorganisms are capable of deriving an electric current in a process termed extracellular electron transfer1,2. However, the manner in which these “electric microbes” exchange electrons with solid conductive surfaces has primarily been studied at circumneutral pH and mesophilic temperatures, representative of the waste water treatment plants which they were originally predicted to be able to partially power3. This project aims to identify the limits of this mode of respiration and to explore the potential for extremophile extracellular electron transfer which has been understudied4. A range of conditions will be investigated, including extremes of growth temperature, pH and salinity. The findings will increase the current understanding of the specific mechanisms by which cells carry out extracellular electron transfer, in addition to informing potential industrial applications of such microorganisms.



Any other comments





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Bioresource Technology, 258, 354-364. 3. Doyle, L. E., & Marsili, E. (2015). Methods for enrichment of novel electrochemically-active

microorganisms. Bioresource Technology, 195, 273-282. 4. Lusk, B. G. (2019). Thermophiles; or, the Modern Prometheus: The Importance of Extreme

Microorganisms for Understanding and Applying Extracellular Electron Transfer. Frontiers in Microbiology, 10, 818.

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Biotechnology

PhD project

Project details Project title Carbon nanodots for anticancer drug delivery and bioimaging

Project description

1. To synthesize fluorescent carbon nanodots from biological

macromolecules

2. To functionalize cabon nanodots with anticancer peptides for

targeted delivery

3. To study the efficacy of these peptides as theranostics

4. To develop carbon dot based biosensors for detection of prostate

cancer.

Background: Due to high PL quantum yield carbon nano dots have

gained significance. Interestingly, they have photostability,

biocompatibility and resistance to metabolic breakdown when used under

in vivo conditions. In addition, one can tune these carbon nanodots with

various agents to incorporate functional groups such as amino, carboxyl

or hydroxyl group, which allows incorporation of various drugs on the

surface of these dots. We have already developed protocols in lab to

purify proteins that had targeted delivery due to cell penetrating peptides

specific to cancer cells over normal cells. Developing functionalized

carbon nanodots with these peptides/ protein will allow them to be used

as theronostics.

Methodology: Various carbon based organic and biological materials

have been developed and employed for low cost production of cabon

nonodots. Amongst these materials toluene, citric acids and various

carbohydrates have gained popularity for making these nanodots. The

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passivation and functionalization of these nanodots enables their

application as drug delivery vehicle as well as for diagnosis.


All equipment required are available with me at Nano Research Facility as Principal Investigator.

Any other comments

For detailed publication see: http://scholar.google.co.in/citations?user=pCOEvOIAAAAJ http://web.iitd.ac.in/~pmishra/

PhD supervisors

Role Faculty Academic unit at IITD E-mail Supervisor Prashant Mishra DBEB [email protected]

Skills required Qualification B.Tech. or M.SC. Biochemistry/Microbiology/Molecular Biology/Biotechnology/ or Life

Sciences

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Skills Background in Life Sciences/ Biotechnology

References Details of Publications in past: In past we have developed biological molecules based sensors, sensors for detection of bacteria and Developed various delivery vehicles

Vancomycin functionalized WO3 thin film-based impedance sensor for efficient capture and

highly selective detection of Gram-positive bacteria

Singh S, Moudgil A, Mishra N, Das S, Mishra P

Biosensors and Bioelectronics 136, 23-30 (2019) IF 9.518

Surface Molecularly-Imprinted Biomimetic Magnetic Nanoparticles for Enantiosepar Goyal G, Bhakta S, Mishra P ACS Applied Nano Materials 2 (2019) 6747-6756.

Thymoquinone loaded mesoporous silica nanoparticles retard cell invasion and enhance in

vitro cytotoxicity due to ROS mediated apoptosis in HeLa and MCF-7 cell lines

Goel S, Mishra P

Materials Science & Engineering C (2019) 109881 IF 4.959

Smartphone based dual mode in situ detection of viability of bacteria using Ag nanorods

array.

Gahlaut SK, Kalyan N, Sharan C, Mishra P, Singh JP

Biosensors and Bioelectronics 126, 478-484 (2019) IF 9.518 Azurin-TiO 2 hybrid nanostructure field effect transistor for efficient ultraviolet detection Moudgil A, Kalyani N, Mishra P, Das S

Nanotechnology 30 (2019) 495205 IF 3.399

MoS2/TiO2 Hybrid Nanostructure‐Based Field‐Effect Transistor for Highly

Sensitive, Selective, and Rapid Detection of Gram‐Positive Bacteria

Moudgil A, Singh S, Mishra N, Mishra P, Das S Advanced Materials Technologies (2019) 1900615 IF:5.395

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S-Layer Protein for Resistive Switching and Flexible Nonvolatile Memory Device Moudgil A, Kalyani N, Sinsinbar G, Das S and Mishra P ACS Applied Materials and Interfaces 10 (5), 4866–4873 (2018) IF 8.09 Co-delivery of curcumin and serratiopeptidase in HeLa and MCF cells through nanoparticles show improved cancer activity Jaiswal S and Mishra P Material Science and Engineering C 92, 673-684 (2018) IF 4.959 Metalloprotein based scalable field effect transistor with enhanced switching behaviour Kalyani N, Moudgil A, Das S and Mishra P. Sensors and Actuators B 246: 363–369 (2017). IF 5.66 Facile method for fabrication of buckled PDMS silver nanorod arrays as active 3D SERS cage for bacterial sensing Kumar S, Lodhi DK, Goel P, Neeti, Mishra P and Singh J.P. Chem. Commun 51: 12411-12414 (2015) IF 6.29

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Biotechnology

PhD project

Project details Project title Fabrication of bioactive peptide loaded multifunctional mesoporous silica

nanoparticles for cancer treatment

Project description

Objectives: 1. To synthesis mesoporous silica nanoparticles (MSNs) 2. To fabricate gate/ homing for silica nanoparticles for delivery peptide drugs 3. Testing these nanoparticles for their in vitro efficacy 4. To have dual drug loading and delivery strategies for MSNs Background: The current global crisis of people suffering from cancer and long term

treatment burden is rising and hence sustainable nanoparticle based drug

delivery systems are being developed. In this proposal, a novel strategy to

design a mesoporous silica nanoparticle (MSNs) based nano-carrier (NC)

system with iron as the core is planned. The MS have well-ordered internal

mesopores, larger pore volume and surface area, tunable size and shape,

robustness make them an ideal platform to design multifunctional nanosystems.

Their high drug loading capacity can deliver the effective concentration of drug

to the target cell and released smartly via external stimuli such as change in pH,

wherein tumors (pH~6.5) and endosomes and lysosomes (pH~5–6). It is

anticipated that precisely engineered nanoparticles will emerge as the next-

generation platform for cancer therapy. The gated NPs will provide additional

tool for sustainable delivery.

Methodology Well established protocols developed in lab will be used

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All equipment required are available with me at Nano Research Facility as Principal Investigator.

Any other comments

For detailed publication see: http://scholar.google.co.in/citations?user=pCOEvOIAAAAJ http://web.iitd.ac.in/~pmishra/

PhD supervisors


Supervisor Prashant Mishra DBEB [email protected]

Skills required

Qualification B.Tech /MSc/M.Tech Biotechnology/Biochemistry/Microbiology/Life sciences

Skills Background in Life Sciences/Biotechnology

References

Thymoquinone loaded mesoporous silica nanoparticles retard cell invasion and enhance in vitro cytotoxicity due to ROS mediated apoptosis in HeLa and MCF-7 cell lines

Goel S, Mishra P Materials Science & Engineering C (2019) 109881 IF 4.959

Surface Molecularly-Imprinted Biomimetic Magnetic Nanoparticles for Enantioseparation Goyal G, Bhakta S, Mishra P ACS Applied Nano Materials 2 (2019) 6747-6756.

Asparaginase conjugated magnetic nanoparticles used for reducing acrylamide formation in food model system

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Alam S, Ahmad R, Kumar P, Mishra P and Khare SK Bioresource Technology 269, 121-126 (2018) IF 6.669 Co-delivery of curcumin and serratiopeptidase in HeLa and MCF cells through nanoparticles show improved cancer activity Jaiswal S and Mishra P Material Science and Engineering C 92, 673-684 (2018) IF 4.959 Thymoquinone inhibits biofilm formation and has selective antibacterial activity due to ROS generation Goel S and Mishra P Applied Microbiology and Biotechnology 102, 1955–1967 (2018) IF 3.67

Antimicrobial and antibiofilm activity of curcumin-silver nanoparticles with improved stability and selective toxicity to bacteria over mammalian cells Jaiswal S and Mishra P Med Microbiol Immunol 207, 39-53 (2018) IF 2.96

Permeation behavior of lysozyme-loaded poly(lactic-co-glycolic acid) nanoparticle through procine oesophageal mucosa and its microscopic studies. Shankarayan R and Mishra P J Nanopharmaceutics Drug Delivery 3: 85-96 (2016)

Modulation of toxic assembly of human gelsolin amyloids by emetine and curcumin-conjugated PLGA-nanoparticles. Srivastava A, Arya P, Goel S, Kundu B, Mishra P and Ashish FNU PLoS One 10 (5)e0127011 (2015) IF 2.766

Differential permeation of piroxicam- loaded PLGA micro/nanoparticles and their in vitro enhancement Shankarayan R, Kumar S and Mishra P J Nanopart Res 15 1496-1502 (2013) IF 2.009

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Biotechnology

PhD project

Project details Project title Molecular basis of asphaltene biotransformation by a microbial consortium

Project description

A 9-membered microbial consortium which can biotransform asphaltene has been isolated in our lab. The members have been characterized and the asphaltene biotransformation and viscosity reduction potential has been determined. The biotransformation pathway is not known. To the best of our knowledge, there are no reports on the asphaltene biotransformation pathway till date. In the present study, we aim to perform secretome analysis of the growing consortium with respect to time. This will be done by analyzing the proteome on an SDS-PAGE and identifying the proteins by MALDI-ToF or ESI MS/MS. The enzyme(s) catalyzing the initial steps for asphaltene biotransformation will be characterized in detail. The genes encoding for the putative enzyme will be cloned, expressed and purified. Biotransformation will be performed by pure enzyme. Selected genes encoding for the protein(s) will be deleted/overexpressed to determine their role. The broad outcome of the study will be pathway elucidation for asphaltene biotransformation. This will form the basis for improving the biotransformation process further.


FTIR, GC-MS, NMR, GPC

Any other comments

PhD supervisors


Supervisor Preeti Srivastava DBEB [email protected]

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Skills required

Qualification M.Sc Biotechnology/Life Sciences/Biochemistry, M.Tech/B. Tech Biotechnology

Skills Molecular biology

References

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Biotechnology

PhD project

Project details Project title

Deciphering the mechanism of regulation of the dsz operon for

biodesulfurization of organosulfurs

Project description

Research on biodesulfurization of petroleum fractions began in the year 1993 and since then several research papers have been published. Several microorganisms were isolated for biodesulfurization and their genes were characterized. There was one thing common amongst all the microorganisms; all the microorganisms showed repression of biodesulfurization activity in the presence of inorganic sulfur. This severely affects the overall process of biodesulfurization. The mechanism of this repression is not known. We have recently isolated a transcription regulator belonging to TetR family and named it as DszR as it could specifically activate the dsz operon at low concentrations. At high concentrations it repressed the operon. The site of activation was found to be located at upstream region between -385 to -305bp with respect to the translation start site. The underlying mechanism for this long-distance activation is not known. Thus, the broad aim of the study is to determine the mechanism of regulation of dsz operon. We hypothesize that the binding of the DszR to the promoter region and its interaction with RNA polymerase requires other proteins. In the present study we aim to isolate and identify the DszR interacting proteins, which together with DszR are responsible for the activation or repression of biodesulfurization operon.


They are available in RNA I lab

Any other comments

PhD supervisors


Supervisor Preeti Srivastava DBEB [email protected]

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Skills required

Qualification M.Sc in Life Sciences/Biochemistry/Biotechnology or M.Tech in Biotechnology

Skills Molecular biology

References

1. Pooja Murarka (2019) Isolation and characterization of proteins involved in regulation of dsz operon for biodesulfurization of organosulfurs . PhD thesis

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Biotechnology

PhD project

Project details Project title Development of siderophores immobilized magnetic material for the recovery of

germanium from industrial wastewater and solid waste

Project description

Siderophores are low molecular weight molecules (500 – 1500 Da) produced by micro-organisms, fungi and plants for complexing Fe3+ in low iron environment. These siderophores has shown remarkable ability to selectively complex gallium and germanium at very low concentrations of these metals even when impurities are present in much higher concentrations. Among these metals, germanium is particularly interesting due to its high commercial value and use in fiber optics cable, photo voltaics and PET catalyst. Further more, the germanium has no direct mining and is primarily recovered from coal ash and recycling. The application of siderophores for the recovery of germanium is interesting, however, the solid-liquid separation of germanium-siderohore complex is a challenge. This project proposes to immobilize siderophores onto magnetic material while ensuring the activity of the siderophores towards germanium and stability of the magnetic material. This would involve testing several strategy for optimization of immobilization. After successful immobilization, few reactor design will be evaluated for achieving a good solid-liquid separation. Eventually, a scale-up would be attempted for the recovery of germanium. To understand the process of complexation, stability of germanium-siderophore complex will be evaluated using density functional theory calculations and spectroscopic technques.


HPLC, chemistry laboratory, LC-MS, Gaussian 16 software

Any other comments

PhD supervisors

Role Faculty Academic unit at IITD E-mail PI Rohan Jain DBEB [email protected]

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Skills required Qualification Master’s in chemical engineering, Master of Engineering in Biotechnology

Skills Experience in HPLC, LC-MS Understanding of immobilization chemistry Experience or understanding of modelling is beneficial

References (1) Jain, R.; Cirina, F.; Kaden, P.; Pollmann, K. Investigation of the Ga Complexation Behaviour of the

Siderophore Desferrioxamine B. Solid State Phenom. 2017, 262, 643–646. https://doi.org/10.4028/www.scientific.net/SSP.262.643.

(2) Jain, R.; Fan, S.; Kaden, P.; Tsushima, S.; Foerstendorf, H.; Barthen, R.; Lehmann, F.; Pollmann, K. Recovery of Gallium from Wafer Fabrication Industry Wastewaters by Desferrioxamine B and E Using Reversed-Phase Chromatography Approach. Water Res. 2019, 158 (2019), 203–212. https://doi.org/10.1016/j.watres.2019.04.005.

(3) Hider, R. C.; Kong, X. Chemistry and Biology of Siderophores. Nat. Prod. Rep. 2010, 27 (5), 637–657. https://doi.org/10.1039/b906679a.

(4) Frenzel, M.; Mikolajczak, C.; Reuter, M. A.; Gutzmer, J. Quantifying the Relative Availability of High-Tech by-Product Metals – The Cases of Gallium, Germanium and Indium. Resour. Policy 2017, 52 (October 2016), 327–335. https://doi.org/10.1016/j.resourpol.2017.04.008.

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Biotechnology

PhD project

Project details Project title Identification and production of siderophores that can selectively and sensitively bind to

rare earth elements

Project description

Rare earth elements have large application in photo voltaics, wind energy, electric vehicles and more. Further, there is no mining for these metals and they are recovered as by-product. Due to their large requirement in future, several agencies has predicted their lack of availability. One way to overcome this is through recycling. The main challenge in economic recycling is the low concentration of target metals and presence of large amount of impurities. Thus, a highle sensitive and selective method is required. Siderophores are low molecular weight molecules (500 – 1500 Da) produced by micro-organisms, fungi and plants for complexing Fe3+ in low iron environment. These siderophores has shown remarkable ability to selectively complex gallium and germanium at very low concentrations of these metals even when impurities are present in much higher concentrations. The high binding strength of the siderophores towards iron, gallium or germanium is due to their similar ionic radius. However, siderophores such as desferrioxamine cannot bind to rare earth elements due to their large ionic radius. But there are more than 500 types of siderophores known and some with the larger trapping “hole” for the metals. This project proposes to apply molecular modeling and quantum modeling (MM + DFT) for identifying the siderophores that can bind to the rare earth metals. After the successful identification, it will be produced and complexed with the rare earth metals.


ICP-MS, HPLC, chemistry laboratory, LC-MS, Gaussian 16 software

Any other comments

PhD supervisors


2

Skills required Qualification Master’s in chemical engineering, Master of Engineering in Biotechnology

Skills Experience in HPLC, LC-MS Understanding of immobilization chemistry Experience or understanding of modelling is beneficial

References (1) Hennebel, T.; Boon, N.; Maes, S.; Lenz, M. Biotechnologies for Critical Raw Material Recovery from

Primary and Secondary Sources: R&D Priorities and Future Perspectives. N. Biotechnol. 2013, 32 (1), 121–127. https://doi.org/10.1016/j.nbt.2013.08.004.

(2) Jain, R.; Fan, S.; Kaden, P.; Tsushima, S.; Foerstendorf, H.; Barthen, R.; Lehmann, F.; Pollmann, K. Recovery of Gallium from Wafer Fabrication Industry Wastewaters by Desferrioxamine B and E Using Reversed-Phase Chromatography Approach. Water Res. 2019, 158 (2019), 203–212. https://doi.org/10.1016/j.watres.2019.04.005.

(3) Song, L.; Zhao, X.; Fu, J.; Wang, X.; Sheng, Y.; Liu, X. DFT Investigation of Ni(II) Adsorption onto MA-DTPA/PVDF Chelating Membrane in the Presence of Coexistent Cations and Organic Acids. J. Hazard. Mater. 2012, 199–200, 433–439. https://doi.org/10.1016/j.jhazmat.2011.11.046.

(4) Gückel, K.; Tsushima, S.; Foerstendorf, H. Structural Characterization of the Aqueous Dimeric Uranium(vi) Species: (UO2)2CO3(OH)3-. Dalt. Trans. 2013, 42 (28), 10172–10178. https://doi.org/10.1039/c3dt50814e.

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Biotechnology

PhD project

Project details Project title Understanding the mechanism of elemental selenium nanoparticles interactions with

extracellular polymeric substances/proteins

Project description

Selenium (Se) is reduced to form biogenic selenium nanoparticles (BioSeNPs). These BioSeNPs are stabilized by the presence of extracellular polymeric substances (EPS)/proteins on their surface. This leads to their colloidal properties and hence present in the discharge of the wastewater treatment plants. Thus, understanding the interaction of elemental selenium with EPS/proteins is important to understand the fate of BioSeNPs. In the on-going research, it has been identified that the not only the type but the length of amino acids capping the BioSeNPs is important. However, the exact role of the length/type of amino acids is not well understood. This project proposes to unravel the interaction of elemental selenium with amino acids using modeling and spectroscopy approach. The modeling with consist of molecular simulations and DFT calculations. For the spectroscopic approach, the student will be required to carry out the experiments analyzing the interaction of chemically produced elemental selenium nanoparticles with amino acids/peptides. The produced CheSeNPs interacting with amino acids/peptides will be investigated with Raman/IR/UV and X-ray Absorption Spectroscopy.


ICP-MS, Gaussian 16, Particle size analyzer,

Any other comments

Short visits to European Synchrotan facility as well as Indore facility

PhD supervisors


2

Skills required Qualification Master’s in chemical engineering

Skills Experience in nanoparticles Understanding/experience in X-ray Absorption spectroscopy, Raman, IR

References (1) Jain, R.; Jordan, N.; Tsushima, S.; Hübner, R.; Weiss, S.; Lens, P. Shape Change of Biogenic

Elemental Selenium Nanoparticles from Nanospheres to Nanorods Decreases Their Colloidal Stability.

Environ. Sci. Nano 2017, 4, 1054–1063. https://doi.org/10.1039/C7EN00145B.

(2) Jain, R.; Jordan, N.; Weiss, S.; Foerstendorf, H.; Heim, K.; Kacker, R.; Hübner, R.; Kramer, H.; van

Hullebusch, E. D.; Farges, F.; et al. Extracellular Polymeric Substances Govern the Surface Charge of

Biogenic Elemental Selenium Nanoparticles. Environ. Sci. Technol. 2015, 49, 1713–1720.

https://doi.org/10.1021/es5043063.

(3) Winkel, L. H. E.; Johnson, C. A.; Lenz, M.; Grundl, T.; Leupin, O. X.; Amini, M.; Charlet, L.

Environmental Selenium Research: From Microscopic Processes to Global Understanding. Environ. Sci.

Technol. 2012, 46 (2), 571–579. https://doi.org/10.1021/es203434d.

(4) Lenz, M.; van Hullebusch, E. D.; Farges, F.; Nikitenko, S.; Corvini, P. F. X.; Lens, P. N. L. Combined

Speciation Analysis by X-Ray Absorption near-Edge Structure Spectroscopy, Ion Chromatography, and

Solid-Phase Microextraction Gas Chromatography-Mass Spectrometry to Evaluate Biotreatment of

Concentrated Selenium Wastewaters. Environ. Sci. Technol. 2011, 45 (3), 1067–1073.

https://doi.org/10.1021/es1022619.

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Biotechnology

PhD project

Project details Project title Molecular source tracking of AMR pathogens based on Whole Genome

Sequencing

Project description

Background: Antibiotic resistance has been reported as one of the greatest threats to global health and food security today by World Health Organization (WHO). It has been indicated that new resistance mechanisms are emerging and spreading globally, threatening the ability to treat common infectious diseases. Use of antibiotics has become a major cause of water pollution in aquaculture as this is changing the structure of the environmental microbiota due to the accumulation of antibiotics in water environments. Project plan: With the rapid development of the global aquaculture industry, the presence of antibiotics and ARGs in aquaculture environment is of increasing concern. Therefore, in recent years, much attention has been paid to ARGs in farming processes, which are regarded as one of the main human activities that contributes to the selection and dissemination of ARGs (Durso LM et al., 2014). To our knowledge, few studies have evaluated the diversity and abundance of ARGs in aquaculture environment. Moreover, the mechanisms by which ARGs are transferred among fish, shrimp guts, the sediment and pond water of their aquatic environment remain unknown. Therefore, understanding the molecular mechanisms of antimicrobial resistance prevalent in aquaculture environment is important to design effective disease treatment strategies, to prioritize the use and registration of antimicrobials for aquaculture use, and to assess and minimize potential risks to public health. Due to the large-scale, high-density use of antibiotics in Indian aquaculture, we deemed it necessary to conduct an extensive investigation of the main aquaculture areas in India in order to understand the levels of antibiotics being used in Indian aquaculture. Objectives: 1) To investigate the comprehensive profiles of ART populations associated with different types of samples acquired from the aquaculture farm 2) Identification of a new resistant variant from domestic aquaculture products. Methodology: DNA extraction and library preparation :Samples will be concentrated by filtering through a 0.22 µm membrane, and then the bacteria will be suspended in 10 ml of 0.1% peptone water using a vortex mixer. All samples will be subjected to total DNA extraction (Ref.). Extracted DNA of samples from different sources/ponds will be subjected to NGS assessment. Illumina shotgun DNA library construction will be prepared. High-throughput metagenomic sequencing and data analysis High-throughput sequencing on a Miseq 2000 sequencer (Illumina, San Diego, CA, USA) will be done. The generated quality-filtered reads will be aligned using

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the basic local alignment search tool (BLASTx) with databases downloaded for ARGs (from the Antibiotic Resistance Genes Database (ARDB), http://ardb.cbcb.umd.edu/index.html), MGEs and integrons (from INTEGRALL, http://integrall.bio.ua.pt/), insertion sequences (ISs) (from IS Finder, https://www-is.biotoul.fr/) and plasmids (from the NCBI RefSeq database; 2408 plasmid genome sequences).


High-throughput sequencing on a Miseq 2000 sequencer (Illumina, San Diego, CA, USA

Any other comments

PhD supervisors


Supervisor Ravikrishnan Elangovan

DBEB [email protected]


3

Skills

References

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Biotechnology

PhD project

Project details Project title Optimization of light sheet microscopy for large clinical specimen analysis

Project description

Background: Histopathological examination of tissues remains as current gold standard in Cancer diagnostics. Current histopathological techniques are based on paraffin embedded thinly cut tissues sections for microscopy evaluations. This is due to limitation in the current microscopy methods to visualize thick samples. Current thin section based histopathology has many limitations, i.e., tumor hetrogenity across the volume of tissue sample can not be identified; sample is lost due to thin section processing; with limited volume imaging there is high error rate in the results. Project plan: Light sheet microscopy is recent technique that illuminate samples at an orthogonal angle. Sample is immersed with refractive index matching liquid to clear the sample for deep penetration. In this project, we propose to develop and optimize sample preparation methods for large clinical specimen clearing and imaging with light sheet microscopy. Objectives:

1. Develop tissue clearing protocol for large clinical samples 2. Develop sample labeling protocol for large clinical samples 3. Develop 3D rendering of images of large volume samples

Methodology:

1. Development of tissue clearing protocol: Small tissue samples from poultry chicken will be used to optimize tissue clearing protocol optimization. Samples will be immersed in PBS with triton X for 6 hours, following with treatment with eoysin Y and DRAQ5. Finally appropriate amount of 2,2'-thiodiethanol will be added to match the refractive index.

2. Samples will be labelled for nucleic acid stains and additional immune-labelling will be decided on the type of clinical sample processed.

3. Large 3D data set needs to be rendered to visualize and extract feature information.


Any other comments

2

PhD supervisors





Skills

References

1



Biotechnology

PhD project

Project details Project title Study of microRNA expression profile in exosomes derived from lung cells

Project description

Objective: 1. Study microRNA expression between healthy and lung cancer derived

exosomes 2. Identify key microRNA biomarkers to differentiate health and lung

cancer samples Background: Lung cancer is the second most common cancer globally, causing major proportion of deaths worldwide. In Indian scenario, out of 70,275 incidences 63,759 deaths were reported that represents more than 90% of patient population. However, Lung cancer can be treated successfully if detected early but unfortunately majority patients are detected in advanced stage and have dismal prognosis. Most clinical symptoms in early stages of lung cancer are similar to other common lung infections. In the proposed study we intend to look specifically at lung cancer derived exosomes to discover novel markers of disease. Methodology: In this attempt we intend to look specifically at lung cancer derived exosomes. As majority of exosomes released into the circulation are from normal physiological processes. So, purification of exosomes of a particular origin can assist in providing selectivity to study molecular signature of a particular tumor in more efficient and robust manner. Exosomes being the carrier keeps the integrity of DNA/RNA intact that ensures the higher copy number of the biomarker; sufficient for detection and analysis. Contrarily, when the RNA is extracted from whole plasma/serum samples, yield is low and their origin is not known. Thus, only an average molecular signature is obtained, that is not specific to the pathology being studied. However, exosomes provides selectivity to study the molecular content of disease of interest. Lung cancer derived exosome will be isolated using magnetic bead based enrichment protocol development in the lab. Total RNA from the exosomes will be isolated using MiVana RNA isolation kit protocol. Briefly, Exosome pellet will be dissolved in 700 µl QIAzol lysis solution and disrupted by vortexing for 15 seconds. Purified total RAN will be sequenced and analyzed for biomarker discovery and microRNA expression profiling.


Real time PCR machines

2

Any other comments

PhD supervisors

Role Faculty Academic unit at IITD E-mail Supervisor Ravikrishnan

Elangovan



Skills

References

1



Biotechnology

PhD project

Project details Project title Single cell imaging for rapid susceptibility assay

Project description

Objective: 1. Development of microfluidics channels to immobilize bacterial cells 2. Development of single cell imaging and analysis protocols 3. Correlating single cell membrane potential and susceptibility to

antibiotics Background: Rapid detection of susceptibility profile is very useful in prescribing appropriate antibiotics treatment. Current Antibiotics Susceptibility Test (AST) take a minimum of 8 hours and large number of cells to reliably identify the AST profile for a microbe. In this project, we would like to develop fundamental understanding on role of membrane potential in survival of the microorganism. We would like to image cells at single cell resolution and calculate the change in membrane potential vis-vis antibiotics concentration in the environment. Methodology: A microfluidics platform will be developed to immobilize microbial cells and add a gradient of antibiotics concentration. Membrane potential of the cells will be measure using fluorescent DiSc3 dyes and imaged using high numerical objectives.


Fluorescent microscope and BSL2 facilities

Any other comments

PhD supervisors




2


Skills

References

1

Indian Institute of Technology Delhi


Biotechnology

Ph.D. project

Project details Project title Designing a synthetic microbial community for biocontrol of pathogen

Project description Pigeon pea (Cajanus cajan) or Arhar is one of the most important pulse

crop grown in India due to its high nutritional value and protein content. The

crop’s productivity has remained stagnant despite major agricultural

breakthroughs in the country. Several biotic and abiotic constraints contribute to

this phenomenon. The crop is susceptible to a number of fungal pathogens

amongst which Fusarium udum causes heavy and major economic loss not

only in India but worldwide. Use of chemical pesticides despite having

suppressed target pathogen, exert non-target effects which hamper the growth

of resident soil microbes. Addition of bioinoculants individually or as a

consortium has not been fairly successful in the long run due to competition

from resident microbial communities in natural field conditions. Using diverse

set of microbes with defined function in a robust synthetic microbial community

(SMC) will be able to overcome the major limitation of bioinoculants’ persistence

and performance.


Real time cycler, vertical and horizontal gel electrophoresis units, HPLC, plant growth chamber etc

Any other comments

PhD supervisors


Supervisor Dr. Shilpi Sharma Biochem Engg and Biotech [email protected]

Skills required

2

Qualification B.Tech. Biotech / M.Tech. Biotechnology / M.Sc. Life Sciences/Microbiology or the like

Skills Basic microbiology and molecular biology tools

References

• Vorholt, J.A., Vogel, C., Carlström, C.I. and Müller, D.B., 2017. Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host and Microbe, 22:142-155.

• Kong, Z., Hart, M.M., Liu, H., 2018 Paving the Way From the Lab to the Field: Using Synthetic Microbial Consortia to Produce High-Quality Crops. Frontiers in Plant Science, doi: 10.3389/fpls.2018.01467

https://www.semanticscholar.org/author/Zhaoyu-Kong/5885093

https://www.semanticscholar.org/author/Zhaoyu-Kong/5885093

https://www.semanticscholar.org/author/Miranda-M-Hart/36883184

https://www.semanticscholar.org/author/Miranda-M-Hart/36883184

https://www.semanticscholar.org/author/Hongguang-Liu/143789193

https://www.semanticscholar.org/author/Hongguang-Liu/143789193

1



Biotechnology

PhD project

Project details Project title AD doctor: Development of tools to assess health of anaerobic digester (AD)

Project description

Objective: different physicochemical and microbial factors will be assessed to develop rapid and reliable tools to assess health of high rate anaerobic digester Background: Anaerobic treatment is become popular due to the energy efficiency of treatment system. Poor resilience to fluctuation of operating conditions and delicate syntrophic balance of the sensitive microbial communities present in the anaerobic digester are the major hurdle to make AD as the most attractive option for treating wastewaters. Due to poor understanding of the behavior of the microbes frequent failure of AD is a common phenomena. Better understanding of the reactor behavior can help in making the AD more robust and acceptable in treating different wastewaters. Various key chemical, biochemical and molecular-microbial parameters will be monitored to better understand the health of AD. Appropriate reactor Management strategy will be developed to protect the reactors from failure. Methodology : Estimation of different chemical and microbial parameters Development of management strategy to operate the AD in more intelligent manner to better handle the operation ensuring no failure of the system. Equipment required : qPCR, HPLC, spectrophotometer, GC, Metagenomic sequencing (will be outsourced)

Special chemicals/reagents required: qPCR master mix, SPE column


qPCR system, GC

Any other comments

PhD supervisors


Supervisor T. R. Sreekrishnan DBEB [email protected]

2

Skills required

Qualification BE/BTech in Chemical Engg/ Biochemical Engg/Biotechnology or ME/MTech in Chemical Engg/ Biochemical Engg/Biotechnology or MSc in Microbiology

Skills

References

1



Biotechnology

PhD project

Project details Project title Understanding the auto-healing capability of Ganga river (in view of the reduction

efficacy of AMR burden)

Project description

Objective: Understand the dynamics of bacteriophage and bacteria in Ganga River water and to estimate the AMR burden reduction potential of its water at various sites. Background: Contamination of major water bodies is major threat to the user community of the water bodies. AMR is a challenging water contaminant which rapidly proliferate through different hosts by the use of contaminated water. India is the land of rivers where Ganga river holds an important place in the livelihood of 1/3rd of nations population. Presence of bacteriophage in its water is considered as one of the major reasons behind its self-cleansing property. Efforts will be made to understand the bacteriophage and bacterial population dynamics at various sites of the Ganga river. Effect of different pollutants and different environmental conditions on the dynamics will be studied. Potential of natural treatment of AMR by the bacteriophage present in the water will be estimated. Appropriate risk of the water use will assessed. Methodology : Estimation of different chemical and microbial parameters, Estimation of bacteriophage and bacterial community using flow-cytometry and qPCR and metagenomic sequencing. Estimation of ARB/ARGs, Development of risk assessment strategy in use of the river water for various purposes. Equipment required : qPCR, HPLC, MALDI-TOF, spectrophotometer, GC, Flow-cytometer Metagenomic sequencing (will be outsourced)

Special chemicals/reagents required: qPCR master mix, SPE column


qPCR system, GC-MS/MS, LC-MS/MS

Any other comments

PhD supervisors


Supervisor Shaikh Ziauddin Ahammad DBEB [email protected]

2

Skills required

Qualification BE/BTech in Chemical Engg/ Biochemical Engg/Biotechnology or ME/MTech in Chemical Engg/ Biochemical Engg/Biotechnology or MSc in Microbiology

Skills

References

1

Indian Institute of technology Delhi Department of Biochemical Engineering and

Biotechnology PhD project

Project details Project title Development of IoT enabled system for water quality surveillance in water bodies

Project description

Objective: Development of IoT enabled sensor assembly for efficient and rapid monitoring of conventional and emerging pollutants present in water bodies.

Background: Increase in water pollution and reduction of fresh water reserve is leading towards a situation of dire water scarcity. Global warming is also catalyzing the possibility. Rapid and efficient monitoring system can ensure rapid identification of pollution caused by different effluent and this can help in taking appropriate measures to protect receiving water bodies. IoT enabled monitoring system would help in remote monitoring and reduce the chance of mishandling of the monitoring system. An array of sensors will be developed and used in a compact housing to make easily deployable small sensor assembly for monitoring water quality. Predictive models will be developed based on the data obtained from the monitoring systems. Methodology : Estimation of abundance of conventional and emerging pollutants, estimation of kinetics of pollutants proliferation, neural network model to predict the water quality.

Special chemicals/reagents required: NA


Potentiostat, qPCR, MALDI-TOF, LC-MS, GC-MS, HPLC, spectrophotometer, GC

Any other comments

PhD supervisors


Supervisor Shaikh Ziauddin Ahammad DBEB [email protected]

Supervisor Brejesh Lal EE [email protected]

2

Skills required

Qualification BE/BTech in Chemical Engg/ Biochemical Engg/Biotechnology or ME/MTech in Chemical Engg/ Biochemical Engg/Biotechnology

Skills

References

indian institute of technology delhi department of biochemical...

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