User:Mohammed Abdul Majeed

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Curriculum Vitae

Contact Info

Abdul Majeed

<html><b>Mohammed Abdul Majeed</b></html> <html><br></html> 311 MD hall, Johns Hopkins University, Baltimore, Maryland, USA. <html><br>Email:<a href="mailto:amohamm8@jhu.edu">amohamm8@jhu.edu</a></html> <html><br>Email:<a href="mailto:m.abdul.majeed1@gmail.com">m.abdul.majeed1@gmail.com</a><br></html>

Education

<html> <ul> <li><b>Graduate Studies PhD. (2016), Johns Hopkins University</b></li> <a href="http://schulmanlab.jhu.edu/">Schulman Lab</a>. <li><b>Master of technology in Biotechnology, IIT Madras (2011)<br> Bachelor of technology in Biotechnology, IIT Madras (2011)</b></li> Graduated with GPA: 8.93/10 (Branch ranking – 2nd)<br> <li><b>Board of Intermediate Education (2006)</b></li>

 Graduated with 93.4%<br>

<li><b>Board of Secondary Education (2004)</b></li>

 Graduated with 85.4%<br>

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Research Projects

<html> <ul> <li><b>Biochemical Characterization of Human Phospholipid Scramblase 1</b></li> [Dr. Sathyanarayana N Gummadi's Lab, IIT Madras, Jan 2010 - April 2011]<br> <ol type:"1"> <li><b>Recovery of functionally active recombinant human phospholipid scramblase 1 from inclusion bodies using N-Lauroyl Sarcosine</b></li> <p><b>Abstract:</b> Human phospholipid scramblase (hPLSCR1) is a transmembrane protein involved in rapid bidirectional scrambling of phospholipids across the plasma membrane in response to elevated intracellular Ca<sup>2+</sup> levels. Over-expression of recombinant hPLSCR1 in <i>E. coli</i> BL21(DE3) leads to its accumulation as misfolded, aggregated protein and forms as inclusion bodies (IBs). Varying amounts N-Lauroyl sarcosine were used to solubilise IBs and correctly folded hPLSCR1 was extracted from them. In Vitro reconstitution studies confirm the functional activity of the protein. Far UV–CD studies reveal the secondary structure of protein is predominantly an alpha–helix. High recovery yields of purified hPLSCR1 were obtained without applying any renaturation techniques. NLS solubilised IBs can be directly used for scramblase assay without any further purification.</p>

<li><b>Predicted transmembrane helix of hPLSCR1 is required for scramblase activity and Ca<sup>2+</sup> coordination: a spectroscopic study</b></li> <p><b>Abstract:</b> hPLSCR1 belonging to ATP independent class of phospholipid (PL) translocators possesses a single EF hand like Ca<sup>2+</sup> binding motif and also a putative single transmembrane helix at the C terminal end. We have determined the functional consequence of this deletion without the loss of its ability to interact with Ca<sup>2+</sup> and studied conformation changes associated with it. Deletion of TM helix caused a twofold a decrease in binding affinity of Ca<sup>2+</sup> for (del)TM hPLSCR1 (K<sub>a</sub> = 19 uM) than hPLSCR1 (K<sub>a</sub> = 39 uM). In vitro reconstitution studies reveal that predicted TM helix is indeed required for membrane insertion and scrambling activity. Far UV-CD studies reveal that hPLSCR1 in presence of Ca<sup>2+</sup> undergo transition to adopt a beta–sheet conformation. ANS binding studies reveal that in presence of Ca<sup>2+</sup>, the hydrophobicity pattern of hPLSCR1 and (del)TM hPLSCR1 changes and also self associates a possible mechanism by which these proteins function. Quenching studies reveal that in the absence of TM helix, hPLSCR1 losses its compact conformation. Based on our results, we conclude that predicted TM helix is indeed a true TM domain required for the compact conformation of hPLSCR1 and the TM helix could be involved in Ca<sup>2+</sup> coordination.</p>

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Presented at the 7th Asian Biophysics Association (ABA) Symposium & Annual Meeting of the Indian Biophysical Society (IBS)

<html><br><ul> <li><b>Constraint-Based Network Analysis of Sugar Fermentation in <i>Saccharomyces cerevisiae</i></b></li> [Dr.Jennifer L. Reed's Lab, University of Wisconsin, Madison, June - July 2009] <p><b>Abstract: </b>There is considerable interest in recent years in the bioconversion of forestry and agricultural residues into ethanol and value added chemicals. High ethanol yields from lignocellulosic residues are dependent on efficient use of all the available sugars including glucose and xylose. The well-known fermentative yeast Saccharomyces cerevisiae is the preferred microorganism for ethanol production and various genome scale metabolic networks have been reconstructed for S. cerevisiae in the recent years. In this study, S. cerevisiae’s network is analyzed by constraint based modeling techniques and the organism’s inability to ferment xylose is studied. This inability is due to the cofactor imbalance occurring at the XR and XDH reactions in the xylose uptake pathway. <!--Two genes were found when up-regulated in the regulatory network; xylitol secretion was not predicted.--> Also, various strains were designed computationally for improving the S. cerevisiae’s ethanol yield on glucose fermentation.</p> </ul> <!--<a href="http://openwetware.org/images/5/57/Abdul_report_wisc.pdf">Click here to view the report</a>. <br>--></html> <html><!--[[Image:Poster_Abdul_wisconsin.jpg|1050 px]]--></html> Poster Abdul wisconsin.jpg

Industrial Experience

<html> <ul> <li><b>Small scale cell culture performance of recombinant Chinese Hamster Ovary cells – A study of metabolite profiles</b></li> [Dr. Reddy’s Laboratories; Hyderabad, May – July 2008] <ol type:"1"> <li>Study of growth characteristics and metabolic profiles of rCHO cells in Spinner flask (250ml and 500ml) and fermenter (2l).</li> <li>Study of growth characteristics and metabolite profiles when the initial media had different ratio of fresh to spent media volume.</li> <li>Study of growth characteristics and metabolite profiles when the initial media had different initial glutamine concentration. </li> <li>Determination of glutamine degradation rate in a pfCHO media incubated at 37 degC.</li> </ol> </ul> <a href="http://openwetware.org/images/4/47/Dr_reddys_Abdul_report.pdf">Click here to view the report</a>. <br> </html>

International Competitions/Conferences

<html><ul> <li><b>iGEM (International Genetically Engineered Machines Competition) 2009; Team: IIT Madras</b></li> [M.I.T., Boston] <b>[Won Silver]</b><br> <b>Project Title:</b> P.L.A.S.M.I.D. - Plasmid Locking Assembly for Sustaining Multiple Inserted DNA <p><b>Abstract:</b> Any episome introduced into the cell shows a segregational asymmetry accompanied with differential growth rates in the absence and presence of episome leading to an overall loss of the episomal unit in the absence of any selective pressure. We have designed a new versatile system which can maintain any given plasmid DNA in E.coli by using user defined selection pressures, limited only by the presence of a response element to said pressure, such as most antibiotics, certain chemical and physical conditions. Depending on this selection pressure, a custom plasmid retaining system can be designed and co-transformed along with the plasmid of interest which will maintain this plasmid. A similar system can be used to “lock up” the function of a certain gene of interest, thus functioning as a combination lock, which is unlocked only when the cultures are grown in a pre-determined order of external selection pressures. In principle, using this locking system, a large number of plasmids can be maintained using a single selection pressure instead of all the selection pressures required to maintain each individual plasmid. Directed evolution, inter-species symbioses are applications that illustrate our plasmid protection system as a powerful tool for a wide range of functions.</p> <a href="http://2009.igem.org/Team:IIT_Madras">Click here to view the IIT Madras iGEM wiki 2009</a>.<br> <a href="http://openwetware.org/images/3/36/Igem09_final_one_ppt.pdf">Click here to view the IIT Madras iGEM Presentation 2009</a>.<br><br> </ul></html>

Presented at the iGEM Jamboree 2009, MIT

<html><br> <ul> <li><b>33rd Steenbock Symposium</b></li> [Biochemistry, University of Wisconsin, Madison, 30th July - 2nd August]<br> <ul> <li>Poster presentation of my work at Dr. Jennifer Reed's Lab.</li> <li>Honored as a <a href="http://www.biochem.wisc.edu/faculty/ansari/khorana_program/fellows/2009Fellows.aspx">Khorana Scholar</a>.</li> </ul></ul></html>

Academic Projects

<html><ul> <li><b>Analysis of Urinary Tract Infection (Pylonephritis) – a mathematical model</b></li> [Prof. G.K Sureishkumar, IIT Madras] <!--<p>Pyelonephritis – inflammatory infection process was understood with the aid of mathematical modelling. In my approach, I assumed that the only defence mechanism is through the flow of urine, which delays the bacterial migration towards the kidney. An equation giving the bacterial flux into the kidney was framed. The various conclusions in the analysis include that one should have adequate fluid intake, especially water (to increase the urinary flow rate). Also cranberry juice decrease the incidence of UTI (prevents association of bacteria to cell wall).</p>-->

<li><b>Kinetics of Ethanol Fermentation with high biomass concentration considering the effect of temperature</b></li> [Prof. K.B.Ramachandran, IIT Madras] <!--<p>The mathematical model describing the Kinetics of ethanol fermentation was solved using MATLAB for various Temperature conditions of the process. This solution was validated with reference to the results given in the paper (Applied Biochemistry and Biotechnology Vol. 91–93, 2001). The developed model considered substrate, product and biomass inhibition, as well as an active cell phase (viable) and an inactive (dead) phase. The kinetic parameters were described as functions of temperature.</p>-->

<b><li>Recovery of native folded proteins from inclusion bodies - A Review</b></li> [Prof. Sathyanarayana N. Gummadi, IIT Madras] <!--<p>The main objective of protein refolding from bacterial inclusion bodies is to recover a good amount of bioactive protein at low cost. Although understanding of inclusion body protein structure, novel solubilization and improved refolding methods has increased recently, a single straight forward method which satisfies all protein folding requirements remains the desired objective. Protein aggregation during different refolding step is the major bottle neck in recovering high amounts of protein from inclusion bodies. It is thus necessary to reduce the extent of protein aggregation at each step of refolding starting from isolation to final purification. Completely unfolded protein is more prone to aggregation than a partially folded intermediate polypeptide chain. It is essential to restore the native-like secondary structure of inclusion body protein during solubilization which renders protein less prone to aggregation. Besides refolding of proteins from inclusion bodies is affected by several factors, including solubilization of inclusion bodies by denaturants, removal of the denaturant, and assistance of refolding by small molecule additives It is expected that a novel solubilization process which reduces the propensity of protein aggregation followed by improved refolding will help in the high recovery of recombinant protein from inclusion bodies.</p>-->

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Scholastic Achievements

<html><ul> <li>Graduated with a <b>Branch Position 2</b> at IIT, Madras (in a class of 40 students).</li> <li><b>Khorana Scholar 2009:</b> Received a scholarship of $ 4100 through the DBT-Govt. of India, IUSSTF and UW-Madison to be amongst the top 15 students in India (out of over 1000 applicants) to undertake research at University of Wisconsin, Madison during May-July 2009.</li> <li><b>Indian National Physics Olympiad 2006 (INPhO):</b> Awarded to be among the top 1% (250 students) of 31,459 candidates enrolled.</li> <li>Awarded <b>Scholarship</b> of INR 25,000 in class X and XII for outstanding performance in high school (2002-2004).</li> <li>Secured a position in the <b>top 0.5% students in JEE 2006</b> (Joint Entrance Examination for IITs) written by over 300,000 students.</li> </ul></html>

Co-curricular & Extracurricular Activities

    <html> <li><b>Teaching Assistant</b> for the summer workshop on Bioprocess Technology (12th to 21st July 2010).</li> <li><b>Teaching Assistant</b> for the Downstream Processing Laboratory (Aug - Nov 2010).</li> <li>Served the <b>Spastic Society of India</b> as a part of NSS, 2006-07.</li> <li>Coordinated the <b>campus placements</b> for the academic year 2008-09.</li> <li>Organizer for the Department <b>Open House at Shaastra 2007.</b></li> <li><b>Won the Robotics competition</b> of the Civil Engineering department, IIT Madras 2007.</li> <li>Member of the hostel <b>soccer team.</b></li> </ul></html>