User:Aman Kumar

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Contact Info

Aman Kumar
Room no. 4009, Alakananda Hostel, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India.
Email:amank.iitm@gmail.com
Email:bt10b003@smail.iitm.ac.in


Education

  • Master of technology in Biotechnology, IIT Madras (2015)
    Bachelor of technology in Biotechnology, IIT Madras (2014)
  • Board of Higher Secondary Education (2009)
    School: Patna Central School
  • Graduated with 91% (Class ranking = 1st (among 100 students)) (School ranking = 7th (among 1200 students))
  • Board of Secondary Education (2007)
    School: Patna Central School
  • Graduated with 87.2%


Conferences

Aman Kumar representing iGEM'13 IIT Madras team at CUHK, Hong Kong
Aman Kumar representing iGEM'13 IIT Madras team at CUHK, Hong Kong

Research Projects

  • Summer Research: Production and purification of human ATP citrate Lyase protein for determining its function using structural analysis
  • [ Dr. Marie Fraser ; May 2014 - Aug 2014]

    Abstract: ATP-citrate lyase (ACLY) is the enzyme that 1) links energy metabolism from carbohydrates to the production of acetyl-CoA in the cytoplasm of animals and 2) closes the reductive citric acid cycle in bacteria that use this cycle to fix carbon dioxide. The crystal structure of two-thirds of ACLY in complex with the substrate citrate, the inhibitor tartrate and the product ADP-Mg2+ has been already determined. These structures answered the question of where the organic acid bound to this member of the family of succinyl-CoA synthetase-related enzymes; but the truncated protein did not bind CoA. Our goal is to determine the structure of a longer form of ACLY, which will also show the binding sites of CoA and acetyl-CoA. The motivation for the study is that acetyl-CoA is one of the most important substrate of various pathways like mevalonate pathway, fatty acid synthesis pathways etc. Thus, imbalance in the activity of the enzyme can lead to several diseases including Tumor cell growth, Type 2 Diabetes, Obesity, Hypocitraturia etc. Hence, our goal is to elucidate the function and catalytic sites of the enzyme using structural analysis.

  • International Genetically Engineered Machine (iGEM) Project 2013: Combating Shiga-toxin: A synthetic biology approach
  • [ Dr. Nitish Mahapatra , Dr. Karthik Raman ; Mar 2013 - Sept 2013]

    Abstract: Shiga toxin, a worldwide menace, has killed over 1 million people to date and continues to afflict almost 150 million people each year. Currently, there is no treatment for Shiga toxicosis and it leads to complications in the human system like hemolytic uremic syndrome (HUS) and renal failure. Here, we propose a two-fold, novel synthetic biology approach to combat the lethal effect of the toxin. We aim to neutralize the already produced toxin through a nine amino acid Gb3 mimic peptide. We have engineered the Gb3 mimic along with a cellular export signal (ompF) downstream of AHL(quorum sensing molecule) inducible promoter (pLuxR). We also plan to prevent further toxin production by inhibiting the biofilm formation of shigatoxigenic E.coli using indole-3-acetaldehyde (I3A). We expect to validate our approach through functional assays and in silico modelling. Our findings can potentially initiate a new perspective of tackling Shiga toxicosis using synthetic biology tools.
    Please visit our official iGEM'13 website for more information.

  • Characterization of Chromogranin A protein and studying its interaction with Hsp.
  • [ Dr. Nitish Mahapatra ; Dec 2012 - Till Date]

    Abstract: Cardiovascular diseases (coronary heart disease, heart failure, stroke etc.) affect a large section of the adult population and are the leading causes of morbidity and mortality in many countries including India. Chromogranin A (CHGA) is ubiquitously expressed in secretory cells of the endocrine, neuroendocrine, and neuronal tissues. Although this protein has long been known as a marker for neuroendocrine tumors, its role in cardiovascular disease states including essential hypertension (EH) has only recently been recognized. Our plan focuses on purifying and investigating the functional behaviour of the protein and studying its interactions with heat shock proteins (Hsp 70).

  • Summer Internship: Investigating the function of Mom protein using site-directed mutagenesis.
  • [ Prof. V Nagaraja; May'12 - Jun'12]

    Abstract: Bacteriophage Mu or phage Mu is a temperate bacteriophage that infects Escherichia coli and a wide range of other gram-negative enteric bacteria. Mu is a phage that replicates by transposition, which happens on induction of the quiescent phage or during lytic infection. Thus, replication of Mu phage occurs through a series of replicative transposition events. There is one novel feature of Mu that expands its host range which happens through unusual host-range expansion mechanism because of the gene of our interest, the mom gene. The gene mom stands for modification of mutator. This gene helps in modifying the DNA of the phage and acts as a saviour to the phage. The mechanism of modification is a post-replicative DNA modification. This function helps the viral genome resistant to cleavage by a wide variety of restriction endonucleases. Thus, mom gene acts as a protective sheath against nucleolytic attack when the Mu genome infects a bacterial cell possessing host specificity or RM (restriction modification) system different from the one in which the phage had been last grown. Our objective is to purify the Mom protein and investigate its function using site-directed mutagenesis with wild-type as the control.

Please feel free to contact me in case you want a more detailed report/poster for any of my research projects

Course Projects

  • Boolean Modelling of Catecholamine synthesis and degradation pathways
  • [Dr. Karthik Raman; Jan'14- May'14]

    Abstract: Catecholamines are the common name used for the hormones like epinephrine (adrenaline), norepinephrine (noradrenaline), and dopamine. Catecholamines are neurotransmitters which are involved in various regulatory processes and its involvement in various disorders like cardiovascular, neurological, psychiatric has been extensively studied. The qualitative dynamics of the catecholamine synthesis and degradation pathway is studied here using synchronous and asynchronous analysis with the help of Boolean modelling. The effect of various inhibitors on the key enzyme viz. Monoamine oxidase (MAO) of the degradation pathway was also studied and the network was validated. The results obtained gives an important insight into the state cycle and steady state of the catecholamine regulatory network.
    The research article for the project can be found here.

  • A study on the Kinetic modeling for polyhydroxybutyrate (PHB) production by Hydrogenophaga pseudoflava
  • [Prof. K B Ramachandran; Apr'14-May'14]

    Abstract: Biodegradable plastics are the necessity of today’s world. Polyhydroxybutyrate (PHB) is a biopolymer belonging to the class of esters that can be used as a biodegradable thermoplastic material and can find several applications for waste management strategies and biocompatibility in medical devices. The idea of the project was to repeat the experiments originally done by Mahmoudi et al. 2010. The experimental data points were taken from the paper and the coding was performed using MATLAB to replicate it. On rigorous study, an improvement to the model was proposed (Gompertz model) and the results were compared with that of logistic model which was used in the paper. The report for the project can be found here.

  • Testing the purity of water from various sources inside campus of Indian Institute of Technology Madras, India
  • [Prof. G. K. Suraish Kumar; Oct'13-Nov'13]

    This project was done as a part of Laboratory course (Downstream Processing). As a primary experiment the aim was to find the cake resistance using conventional filtration. We as a team of 6 members developed an approach to make conventional filtration more efficient and also we also tested the purity of water inside IIT Madras campus using conventional filtration. The report for the project can be found here. The project involving testing the water purity was highly appreciated by the assessor and the evaluation report can be seen here.

Academic and Related Achievements

  • MITACS Scholar 2014- one of 120 students from India to be awarded Mitacs scholarship for carrying out summer research internship at University of Calgary, Canada
  • Recipient of gold medal at the prestigious Internationally Genetically Engineered Machine (iGEM) competition at the regional jamboree held at Chinese University of Hong Kong (CUHK) (2013)
  • Recipient of a grant of INR 2lakh from Industrial Consultancy & Sponsored Research (ICSR) to carry out a research project on the topic entitled “ Combating Shiga-toxin: A synthetic biology approach"
  • Recipient of the prestigious Summer Research Fellowship Program from Indian Academy of Sciences to carry out research project at Indian Institute of Science (IISc) Banagalore(2012)
  • Among top 1% in the state in STD XII & 7th rank holder in my school(2009)
  • Among top 2% to clear world's 5th toughest examination and to get admission into the prestigious Indian Institute of Technology Madras (2010)
  • Co-Curricular Activities

  • Conducted awareness drive for safe meat processing all over India using our project "Code Red" which was awarded as the best Human Practices Advance prize at the iGEM competition (2013)
  • Formulated questionnaire and conducted an event “BIODOCKS” at IIT Madras Biotechnology Departmental festival "Biofest" which dealt with substrate ligand binding studies using AutoDock (2012)
  • Taught Disadvantaged Children basic Mathematics & Science as a team member of National Service Scheme (2010)
  • Aman Kumar

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