Mohan Vivekanandan has 5 years of experience in bioanalytical assay development and quality control for biotherapeutics and vaccines. He has a PhD in Biochemistry and expertise in protein characterization, stability testing, method development and validation. His most recent role was as a Research Scientist at Theragen Biologics where he developed ELISA and other assays to characterize a novel Fab protein. He is looking for a challenging career in a progressive organization.
Predicting volume of distribution for drug compounds using decision treesNithyakalyani Chinnaiah
The project is about improving the prediction accuracy of numerical value of volume of
distribution (VD), which is a proportionality constant for drug compounds. While there have been many approaches using regression with decision trees to predict VD, very few research studies have been carried out using classification scheme. This project proposes a method where the two approaches are combined with the addition of a classification confidence measure. The two stage classification-regression approach is studied with six different data divisions. In the proposed approach, a test drug’s class is predicted using molecular structures as attributes and if the prediction confidence is higher than a predetermined threshold, the log VD value is obtained using regression decision tree built for the particular class. If the classification prediction is not high, then the approach resorts to standard regression to obtain log VD value. This two stage approach seems to be promising as the cross validated performances are improved as compared to standard regression approach for two of the studied data divisions (one third and one fifth divisions) that gave geometric mean fold errors (GMFE) of 2.1502 and 2.2013 as compared to the standard regression GMFE of 2.2373 and 2.2356, respectively.
This lecture outlines the different strategies for finding a fragment hit and the subsequent elaboration strategies used in order to increase potency to develop a lead compound in drug discovery.
Prescribing practices of antibiotics in outpatient setting of a tertiary care...SriramNagarajan19
Antibiotic resistance is a form of drug resistance whereby certain sub-populations of a microorganism, usually a bacterial species, are able to survive after exposure to one or more antibiotics; pathogens resistant to multiple antibiotics are considered multidrug resistant (MDR) and the issue is the subject of ongoing investigation these days. The present study observed the rationality of antibiotics prescribed in an outpatient setting in a tertiary care hospital.
A prospective cohort study was conducted for 2 months on the patients who were prescribed antibiotics in a tertiary care hospital in outpatient setting. The prescriptions of patients were evaluated with respect to the medical condition of the patient. A total of 500 prescriptions were evaluated for rationality out of which 240 prescriptions (48%) were rational and 260 prescriptions (52%) were found to be irrational. The misuse of antibiotics continues to haunt the health care system of Pakistan and pose a threat of pandemic of bacterial resistance due to irrational use. Interventions by clinical pharmacists in the given situation are the need of the hour.
Predicting volume of distribution for drug compounds using decision treesNithyakalyani Chinnaiah
The project is about improving the prediction accuracy of numerical value of volume of
distribution (VD), which is a proportionality constant for drug compounds. While there have been many approaches using regression with decision trees to predict VD, very few research studies have been carried out using classification scheme. This project proposes a method where the two approaches are combined with the addition of a classification confidence measure. The two stage classification-regression approach is studied with six different data divisions. In the proposed approach, a test drug’s class is predicted using molecular structures as attributes and if the prediction confidence is higher than a predetermined threshold, the log VD value is obtained using regression decision tree built for the particular class. If the classification prediction is not high, then the approach resorts to standard regression to obtain log VD value. This two stage approach seems to be promising as the cross validated performances are improved as compared to standard regression approach for two of the studied data divisions (one third and one fifth divisions) that gave geometric mean fold errors (GMFE) of 2.1502 and 2.2013 as compared to the standard regression GMFE of 2.2373 and 2.2356, respectively.
This lecture outlines the different strategies for finding a fragment hit and the subsequent elaboration strategies used in order to increase potency to develop a lead compound in drug discovery.
Prescribing practices of antibiotics in outpatient setting of a tertiary care...SriramNagarajan19
Antibiotic resistance is a form of drug resistance whereby certain sub-populations of a microorganism, usually a bacterial species, are able to survive after exposure to one or more antibiotics; pathogens resistant to multiple antibiotics are considered multidrug resistant (MDR) and the issue is the subject of ongoing investigation these days. The present study observed the rationality of antibiotics prescribed in an outpatient setting in a tertiary care hospital.
A prospective cohort study was conducted for 2 months on the patients who were prescribed antibiotics in a tertiary care hospital in outpatient setting. The prescriptions of patients were evaluated with respect to the medical condition of the patient. A total of 500 prescriptions were evaluated for rationality out of which 240 prescriptions (48%) were rational and 260 prescriptions (52%) were found to be irrational. The misuse of antibiotics continues to haunt the health care system of Pakistan and pose a threat of pandemic of bacterial resistance due to irrational use. Interventions by clinical pharmacists in the given situation are the need of the hour.
Wendy Cornell, Director, Chemistry Modeling and Informatics at Merck, moderates an expert
panel discussion on targets in drug discovery. The panelists are: Jamie Baumgartner, Ph.D.,
Senior Director of in vitro Pharmacology at MDS Pharma Services, Brian Lightbody, Vice President
of Business Development of Small Molecule Drug Discovery for MicroCal Products Group,
GE Healthcare, and Patrick Zarrinkar, Vice President of Technology Development at Ambit BioSciences
Wendy Cornell, Director, Chemistry Modeling and Informatics at Merck, moderates an expert
panel discussion on targets in drug discovery. The panelists are: Jamie Baumgartner, Ph.D.,
Senior Director of in vitro Pharmacology at MDS Pharma Services, Brian Lightbody, Vice President
of Business Development of Small Molecule Drug Discovery for MicroCal Products Group,
GE Healthcare, and Patrick Zarrinkar, Vice President of Technology Development at Ambit BioSciences
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Lateral Ventricles.pdf very easy good diagrams comprehensive
Resume
1. Mohan Vivekanandan, PhD
Profile (Update date:
20/3/20)
Scientist with 5 years of work experience in bio-analytical and assay development for antibody based bio-therapeutics
and vaccines. Strong knowledgein designing andexecuting stability studies, Quality controlprocedures, and developing
analytical/biophysical assays. Expertise in bio-molecular interaction and thermodynamics studies, protein biophysical
studies, HPLC methods for protein characterization and aggregation analysis. Looking for a challenging career in a
progressive organization.
Education
Ph.D., Biochemistry
University of Houston, TX, USA August 2009 - August
2014
M.S (by Research) June 2006 – July 2009
Anna University, Chennai
B.Tech, Biotechnology
PSG College of Technology, Coimbatore June 2001 - May
2005
Awards
1. Best poster award at 27th International Symposium on Preparative and Process Chromatography (PREP),
Boston, 2014
2. Best poster award at the 3rd
Bioscience Graduate Society Symposium, University of Houston, 2012
Fellowship
1. Cleared Junior research fellowship exam (CSIR-JRF NET), Council of scientific and industrial research (CSIR),
India, 2008.
Work Experience
Research Scientist Dec 2019 – Present
Theragen Biologics, Chennai
Team lead in bio-analytical lab. Performed characterization and stability testing of novel Fab (antigen binding
fragment) for treating diabetic retinopathy.
1) ELISA based technique for quantification of Fab protein for process optimization of DSP and USP process and
purified proteins
2) Performed competitive assay based Affinity ELISA to determine theoretical EC50
3) Performed kinetic Turbidometric assay to estimate Endotoxin levels in Drug substance and drug product
4) Studying purity and integrity of Fab using various HPLC: RP-HPLC, SEC-HPLC and IEX-HPLC
Sr. Scientist Oct 2014 – July 2019
Center for Vaccine Development, Baylor College of Medicine
1) Quality control:
• Developed and performed method validation of biophysical and biochemical assays (RP-HPLC, SEC-HPLC) as
per ICH/FDA guidelines
• Performed stability testing (long term regulated and accelerated studies) on recombinant vaccines
2) Biophysical/Analytical method development:
2. • Developed biophysical and biochemical methods for protein purity analysis and quantification
• Performed routine characterization of in-process samples, Drug substance and Drug product to study protein
purity and integrity
• Development of direct protein quantification assay for Alhydrogel formulated proteins using fluorescent
immuno-assay
Additional projects:
Upstream Process development:
• Expression and purification of recombinant SARS RBD protein from P. pastoris with 80 % recovery in 10L scale
fermenter
Performed reproducibility studies for evaluation of the optimized process which resulted in successful cGMP
production
Identifying the origin for decrease in potency of Becaplermin during storage (Contract project):
Performed IsoThermal Calorimetry (ITC) to study the nature and energetics of interaction between thickener
(carboxymethyl cellulose) and human Platelet derived growth factor. Designed experiments, performed ITC, and
performed data analysis.
Graduate Research Assistant
University of Houston, Texas, August 2009 –
August 2014
1) Kinetics of anti-IgE-aptamer IgE antibody interaction:
• Developed study design and performed characterization and kinetic studies of anti IgE aptamer-IgE antibody
interactions using fluorescence anisotropy technique and stopped flow technique
• Performed ITC for determination of Kd and binding stoichiometry of IgE aptamer-IgE antibody
2) Evaluating performance of cluster charge Ion-exchange chromatography using single molecule techniques:
• Designed and developed experiments including an agarose based ion exchange resin
Skills
Molecular biology and biochemistry: Western blot, ELISA, Quantitative HCP slot blot assay, Iso-electric focusing
gel, and quantification of alhydrogel formulated proteins.
Biophysical/Analytical: HPLC and UPLC based analysis of purity and integrity, OLIS Fluorometer (fluorescence
anisotropy and stopped flow kinetics), Isothermal Titration calorimetry and protein melting curve analysis using
CD spectroscopy, DLS particle size estimation, and MALDI mass spectrometry.
Professional Training
1. Completed 2-day comprehensive certificate course (1.5 units), Regulatory compliance in the pharmaceutical
industry, at National Center for Therapeutics manufacturing (NCTM), College Station, TX, USA
2. Completed certificate course (1 unit) on Vaccine adjuvants and delivery system at Baylor college of Medicine,
May 27, 2015
3. Organized and presented a certificate course on Quality control in Vaccine development, April, 2016
Activities/Leadership
Secretary, Bioscience Graduate Society, University of Houston, August 2011-June
2012
Publications
1. Chen WH, Chag SM, Poongavanam MV, Biter AB, Rezende W, Seid CA, Hudspeth EM, Pollet J, McAtee CP,
Strych U, Bottazzi ME, Hotez PJ, Optimization of the production process and characterization of the yeast-
expressed SARS-CoV recombinant receptor-binding domain (RBD219-N1), a SARS vaccine candidate, J Pharm Sci.,
2017 Aug;106(8):1961-1970
3. 2. Lydia Kisley, Mohan-Vivekanandan Poongavanam, Katerina Kourentzi, Richard C. Willson, Christy F. Landes,
pH-dependence of single-protein adsorption and diffusion at a liquid chromatographic interface, J. Sep. Sci., 2015,
1–7
3. Mohan-Vivekanandan Poongavanam, Kisley L, Kourentzi K, Willson RC, Ensemble and Single-Molecule
Biophysical Characterization of D17.4 DNA Aptamer-IgE Interactions, Biochim Biophys Acta., 2015.
4. Adhikari, M; Strych, U; Kim, J; Dhamane, S; Mohan-Vivekanandan P; Hagström, A; Kourentzi, K; Conrad, J;
Willson, R Aptamer-phage reporters for ultrasensitive lateral flow assays., Anal. Chem. 2015 Dec 1;87(23):11660-5
5. Lydia Kisley,Jixin Chen, Andrea P. Mansur, Sergio Dominguez-Medina, Eliona Kulla, Marci Kang, Bo Shuang,
Katerina Kourentzi, Mohan-Vivekanandan Poongavanam, Sagar Dhamane, Richard C. Willson, Christy F.
Landes, High ionic strength narrows the population sites participating in protein ion-exchange adsorption. J
Chromatography A., 2014 May 23;1343:135-42.
6. Lydia Kisley, Jixin Chen, Andrea P. Mansur, Bo Shuang, Katerina Kourentzi, Mohan-Vivekanandan
Poongavanam, Wen-Hsiang Chen, Sagar Dhamane, Richard C. Willson, and Christy F. Landes, Unified
superresolution experiments and stochastic theory provide mechanistic insight into protein ion-exchange
adsorptive separations, PNAS, 2014 Feb 11;111(6):2075-80.
7. Kanakaraj I, Chen WH, Poongavanam MV, Dhamane S, Stagg LJ, Ladbury JE, Kourentzi K, Strych U, Willson
RC, Biophysical characterization of VEGF-aHt DNA aptamer interactions, Int J Biol. Macromol., 2013 Jun;57:69-75
8. Daniels CR, Kisley L, Kim H, Chen WH, Poongavanam MV, Reznik C, Kourentzi K, Willson RC, Landes CF,
Fluorescence correlation spectroscopy study of protein transport and dynamic interactions with clustered-charge
peptide adsorbents, J Mol. Recognition, 2012 Aug;25(8):435-4.
Presentations and Posters
Oral Presentations
“Studying protein transport and adsorption/desorption kinetics on IEX adsorbents using a single-molecule
approach”. 245th ACS National Meeting, New Orleans, LA, April 7, 2013.
Selected Posters
1. Best Poster award: Mechanistic Insights into Protein IEX Separations using Single-molecule, Super-resolution
Imaging.27th International Symposium on Preparative and Process Chromatography (PREP 2014), Boston, July
2014
2. Best Poster award: “Studying protein transport and adsorption/desorption kinetics on IEX adsorbents using a
single-molecule approach”. 3rd
Bioscience Graduate Society Symposium, University of Houston, 2012