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Vishma Pratap Sur
Postdoctoral Researcher
Vestec
Summary
An experienced Post Doctoral Researcher with a PhD in Chemistry with research expertise across a broad range of areas including molecular biology, biochemistry, cell culture, microbiology, drug molecule synthesis and testing, infection biology, host-pathogen interaction, and structural biology.
In addition, have experience in nanoparticle, quantum dots, and magnetic particle synthesis, ligand-based particle modification, and peptide designing. Also demonstrated the ability to identify alternative antibiotic approaches against resistant pathogenic bacterial strains.
Proficiency in homology modeling, docking, molecular dynamics simulations, has been instrumental in contribution to numerous successful projects including Testicular Germ cell tumor, histopathology, molecular analysis, QD and magnetic particle-based sperm imaging and selection, and the study of trans-membrane proteins' role in different protein interactions. Postdoctoral Fellow with extensive knowledge of molecular biology, infection biology, structural biology and cancer biology. Hardworking with strong understanding of research processes, methodology and implementation as publications or patent. Adaptable and hardworking individual with excellent problem-solving skills.
Overview
8
8
years of professional experience
7
7
years of post-secondary education
2
2
Certifications
5
5
Languages
Work History
Postdoctoral Research Fellow
Institute of Biotechnology, Czech Academy of Sciences
Vestec
07.2020 - Current
- Pathogenicity and severity of Testicular germ cell tumor.
- Sperm quality, metabolic activity with seahorse, oxygraph, and two-photon microscopy, gene regulation analysis and proteomics study in TGCT patient samples.
- Molecular dynamics simulation for protein-protein-protein, protein-ligand and drug screening.
- Python coding.
- QD- based spermatozoa imaging.
- Published research results in 6 high impacted peer-reviewed journals, 3 is under review and 4 is under preparation.
- Presented poster in 5 and talk in 4 international conferences.
- Maintained accurate records of research findings and provided statistical analysis of data results.
- Contributed to and actively participated in research conception, design and execution to address defined problems.
- Leveraged interpersonal and communication skills to mentor PhD, graduate and undergraduate students.
- Designed research projects and alternative approaches and discussed results with professor.
- Acquired two different grants.
- Collaborated with 4 multidisciplinary team members to accomplish our specific research goals.
- Attended research seminars and collegiate meetings to discover and discuss new technologies and research.
Doctoral Student
Mendel University in Brno
Brno
11.2017 - 07.2020
- Nanoparticle synthesis, Quantum dots synthesis, Coordinate compound synthesis as an alternative of antibiotics.
- In vivo and in vitro antimicrobial activity checking against resistant S. aureus.
- In vivo and in vitro host-microbe interactions imaging.
- Quantum dots synthesis for bacterial detection and imaging.
- Molecular Dynamics for protein-ligand interaction for drug screening.
- Published research results in 7 high impacted peer-reviewed journals.
- Presented poster in 2 conferences.
- Contributed to and actively participated in research conception, design and execution to address defined problems.
- Designed research projects and alternative approaches and discussed results with professor.
- Acquired one research grant.
Research Technician
CEITEC-BUT
Brno
11.2017 - 07.2020
- Nanoparticle characterization.
- Bacteria specific imaging technique development.
- Assisted with training junior team members in laboratory techniques and operation of equipment.
Visiting Research Scholar
Utah State University
Logan
11.2019 - 02.2020
- Sugar-based compound synthesis and modification.
- Green QD synthesis.
- Algal Protein extraction.
- NMR for organic molecules.
- LC-MS.
- Prepared complete documentation of research activities for reference purposes.
- Evaluated existing research techniques to recommend improvements.
- Preserved samples by labeling each sample and administering solutions to samples.
Senior Research Fellow
Indian Institute of Chemical Biology
Kolkata
05.2017 - 11.2017
- Drug molecules testing and their various roles on mammalian vision system analysis through various molecular biological approaches in vitro and in vivo.
- Real-time PCR for various inflammatory gene regulation analysis from in vivo and in vitro sources.
- Neuronal PSD protein isolation in various treatment scenarios and analysis through LC-MS and Western Blot.
- IHC and ICC of the whole cornea, corneal epithelial cells, keratocyte cells.
- Primary and secondary cell culture.
- Oversaw studies, documented data and extrapolated results.
- Generated 5 high-quality, professional papers for submission to scientific publications.
Junior Project Fellow
Indian Institute of Chemical Biology
Kolkata
11.2015 - 03.2017
- Drug molecules testing and their various roles on mammalian vision system analysis through various molecular biological approaches in vitro and in vivo.
- Real-time PCR for various inflammatory gene regulation analysis from in vivo and in vitro sources.
- Conducted experiments to evaluate the efficacy of drug treatments .
- Gathered and evaluated quality assurance data to identify issues and improve process efficiency.
- Measured and assessed antibodies for fluorescence imaging.
- Analyzed cell cultures using molecular-based and biochemical techniques.
University Research Assistant
Presidency University
Kolkata
05.2015 - 11.2015
- Fungal Culture and metabolite purification.
- Nanoparticle synthesis coated with fungal toxins.
- Worked well in a team setting, providing support.
- Used strong analytical and problem-solving skills to develop effective solutions for challenging situations.
- Gained strong leadership skills by managing projects from start to finish.
Biotech Industrial Trainee
GCC Biotech-DBT Government of India
Kolkata
11.2014 - 05.2015
- Bacterial identification with 16s rDNA sequencing.
- Fungal identification with 18s rDNA sequencing.
- Cloning and Protein Purification, to be precise Taq Polymerase purification.
- Various isolation kit development.
- Worked effectively in fast-paced environments.
- Resolved problems, improved operations and provided exceptional service.
- Self-motivated, with a strong sense of personal responsibility.
Education
Ph.D. - Chemistry
Mendel University in Brno
Brno 11.2017 - 07.2020
Master of Science - Biotechnology
University of Burdwan
Burdwan 09.2012 - 08.2014
Bachelor of Science - Molecular Biology And Biotechnology
University of Kalyani
Kalyani, India. 07.2009 - 06.2012
Skills
Molecular Biology, Biochemistry, Microbiology, Cell culture, PCR, qPCR, Magnetic particle, Nanoparticle, and QD Synthesis, Homology modeling, Molecular Dynamics Simulation (NAMD, GROMACS), Docking, Fluorescence imaging 2-Photon Imagin, Animal experimentation, pathogenic Bacteria - human epithelial cells co-culture, Biosensor designing and bacterial sensing, Live cell imaging - confocal microscopy, In vivo infection model
undefinedSoftware
Gromacs, NAMD, MODELLER, Chimera, Discovery Studio Visualizer
Adobe Illustrator, Adobe Photoshop
Certification
OsakaUx: CNR101x Cognitive Neuroscience Robotics - Part A
Work Availability
monday
tuesday
wednesday
thursday
friday
saturday
sunday
morning
afternoon
evening
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Grants
1. Two photon microscopy as a tool for analysis of the metabolic status of human sperm in physiological and pathological
conditions. Medical Imaging under Czech Bioimaging grant programme. 2023.
2. IGA for PhD student, Mendel University. 01/2019 to 12/2019.
3. IGA for PhD student, Mendel University. 01/2018 to 12/2018.
4. Team IGA, Mendel University. 01/2018 to 12/2018.
Scholarship
1. Post-Doctoral Support form Czech Academy of Sciences (Prospective human resources support program - postdoctoral
students). From 01/01/2022 To 31/12/2024.
2. Visiting scholar grant for USA, Utah State University. 11/2019 to 02/2020.
3. Senior Reserch Fellow, CSIR, IICB. 03/2017 to 11/2017.
4. DBT-BCIL scholarship for industrial training. 11/2014 to 05/2015.
Publication
Under Consideration, Submission and in preparation:
1. In silico Benzimidazole based ligands identification, and their antibacterial activities determination with docking and Molecular Dynamics Simulation. Vishma Pratap Sur, Aninda Mazumdar, Madhab Kumar Sen, Katerina Komarskova. Journal: eLife (IF 8.14).
2. RNA-seq transcriptome profiling identified diverse gene families involved in pyroxsulum resistance in Bromus sterilis. Madhab Kumar Sen, Katerina Hamouzová, Vishma Pratap Sur, Ram Kumar, Jakub Mikulka, Pavlina Košnarová, Amit Roy, Josef Soukup. Journal: Proceedings of the royal society b-biological sciences (IF 5.349).
3. Juno and CD9 Protein network organization in mouse oolemma captured by 3D STED imaging. Michaela Frolikova and Ivan Novotny, Ondrej Simonik, Michaela Blazikova, Vishma Pratap Sur, Eliska Valaskova, Jana Svobodová, Lukas Ded, Pavla Postlerova, Ondrej Horvath, Katerina Komrskova. Journal: Frontiers in Cell and Developmental Biology (IF 6.684).
4. Mitochondrial activity of sperm analysis by Seahorse, approach to understand the OCR and ECR by sperm mitochondria. Ondrej Simonik and Vishma Pratap Sur, Katerina Komrskova. Journal Bio Protocol (IF 5.78).
5. Human germ cell tumor pathophysiology and molecular understanding, A comprehensive review. Vishma Pratap Sur and Markéta Cimlerová, Ondrej Simoník, Pavel Skrobanek, Jiri Neuzil, Tomas Hradec, Libor Zamecnik, Tomas Buchler, Katerina Komrskova. Journal Annual Review of Cancer Biology (IF 9.391).
6. Standalone python script for protein analysis. Vishma Pratap Sur, Katerina Komrskova. SoftwareX. (IF 2.686).
7. Stabdalone python tool for fast image analysis with fluorescence intensity and percentage. Vishma Pratap Sur, Katerina Komrskova. SoftwareX. (IF 2.686).
8. SALL4 is expressed in the XY body of human pachytene spermatocytes: a possible role in male MSCI.
Published
1. Bharati, R.; Sen, M.K.; Kumar, R.; Gupta, A.; Sur, V.P.; Melnikovová, I.; Fernández-Cusimamani, E. Selection and Validation of the Most Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Salvia rosmarinus under In Vitro Conditions. Plants 2022, 11, 2878. https://doi.org/10.3390/plants11212878. (IF 4.658)
2. Sur, V.P.; Simonik, O.; Novotna, M.; Mazumdar, A.; Liska, F.; Vimberg, V.; Komrskova, K. Dynamic study of small toxic hydrophobic proteins PepA1 and PepG1 of Staphylococcus aureus. International Journal of Biological Macromolecules 2022, doi: https://doi.org/10.1016/j.ijbiomac.2022.07.192. (IF 8.025).
3. O. Simonik, F. Bubenickova, L. Tumova, M. Frolikova, V.P. Sur, J. Beran, K. Havlikova, L. Hackerova, D. Spevakova, K. Komrskova, P. Postlerova, Boar Sperm Cryopreservation Improvement Using Semen Extender Modification by Dextran and Pentaisomaltose, Animals 12(7) (2022) 868. https://doi.org/10.3390/ani12070868. (IF 3.231).
4. V.P. Sur, A. Mazumdar, V. Vimberg, T. Stefani, L. Androvic, L. Kracikova, R. Laga, Z. Kamenik, K. Komrskova, Specific Inhibition of VanZ-Mediated Resistance to Lipoglycopeptide Antibiotics, International Journal of Molecular Sciences 23(1) (2022) 97. https://doi.org/10.3390/ijms23010097. (IF 6.208).
5. R. Kumar, J. Mazakova, A. Ali, V.P. Sur, M.K. Sen, M.D. Bolton, M. Manasova, P. Rysanek, M. Zouhar, Characterization of the Molecular Mechanisms of Resistance against DMI Fungicides in Cercospora beticola Populations from the Czech Republic, Journal of Fungi 7(12) (2021) 1062. https://doi.org/10.3390/jof7121062. (IF 5.724)
6. V.P. Sur, M.K. Sen, K. Komrskova, In Silico Identification and Validation of Organic Triazole Based Ligands as Potential Inhibitory Drug Compounds of SARS-CoV-2 Main Protease, Molecules 26(20) (2021) 6199. https://doi.org/10.3390/molecules26206199. (IF 4.927).
7. A. Mazumdar, Y. Haddad, V.P. Sur, V. Milosavljevic, S. Bhowmick, H. Michalkova, R. Guran, R. Vesely, A. Moulick, Characterization and in vitro Analysis of Probiotic-Derived Peptides Against Multi Drug Resistance Bacterial Infections, Frontiers in Microbiology 11 (2020). (IF 6.064)
8. Sur, V.P.; Mazumdar, A.; Ashrafi, A.; Mukherjee, A.; Milosavljevic, V.; Michalkova, H.; Kopel, P.; Richtera, L.; Moulick, A. A Novel Biocompatible Titanium–Gadolinium Quantum Dot as a Bacterial Detecting Agent with High Antibacterial Activity. Nanomaterials 2020, 10, 778. https://doi.org/10.3390/nano10040778. (IF 5.719).
9. Sur, V.P.; Mazumdar, A.; Kopel, P.; Mukherjee, S.; Vítek, P.; Michalkova, H.; Vaculovičová, M.; Moulick, A. A Novel Ruthenium Based Coordination Compound Against Pathogenic Bacteria. International Journal of Molecular Sciences 2020, 21, 2656. https://doi.org/10.3390/ijms21072656. (IF 6.208).
10. Ghosh, T.; Maity, N.; Sur, V.P.; Konar, A.; Hazra, S. Mitigating fibrosis-An impediment to corneal re-innervation following lamellar flap surgery. Experimental Eye Research 2020, 194, 108009. https://doi.org/10.1016/j.exer.2020.108009. (IF 3.467).
11. Sur, V.P.; Kominkova, M.; Buchtova, Z.; Dolezelikova, K.; Zitka, O.; Moulick, A. CdSe QD Biosynthesis in Yeast Using Tryptone-Enriched Media and Their Conjugation with a Peptide Hecate for Bacterial Detection and Killing. Nanomaterials 2019, 9, 1463. https://doi.org/10.3390/nano9101463. (IF 5.719).
12. Jelinkova, P.; Mazumdar, A.; Sur, V.P.; Kociova, S.; Dolezelikova, K.; Jimenez, A.M.J.; Koudelkova, Z.; Mishra, P.K.; Smerkova, K.; Heger, Z.; et al. Nanoparticle-drug conjugates treating bacterial infections. Journal of Controlled Release 2019, 307, 166-185. https://doi.org/10.1016/j.jconrel.2019.06.013. (IF 11.47).
13. Jelinkova P, Splichal Z, Jimenez Jimenez AM, Haddad Y, Mazumdar A, Sur VP, Milosavljevic V, Kopel P, Buchtelova H, Guran R, Zitka O, Richtera L, Hegerova D, Heger Z, Moulick A, Adam V. Novel vancomycin–peptide conjugate as potent antibacterial agent against vancomycin-resistant Staphylococcus aureus. Infect Drug Resist. 2018; 11:1807-1817. https://doi.org/10.2147/IDR.S160975. (IF 4.003).
14. Jha, R.; Sur, V.; Bhattacharjee, A.; Ghosh, T.; Kumar, V.; Konar, A.; Hazra, S. Intracameral Use of Nepafenac: Safety and Efficacy Study. Current Eye Research 2018, 43, 630-638, doi:10.1080/02713683.2017.1408129. https://doi.org/10.1080/02713683.2017.1408129. (IF 2.555).
15. Kumar, V.; Sur, V.P.; Guha, R.; Konar, A.; Hazra, S. Estrogen Modulates Corneal Nociception and Maintains Corneal Homeostasis in Rat Eye. Cornea 2018, 37. doi: 10.1097/ICO.0000000000001437. (IF 2.774).
16. Khanum, B.N.M.K.; Guha, R.; Sur, V.P.; Nandi, S.; Basak, S.K.; Konar, A.; Hazra, S. Pirfenidone inhibits post-traumatic proliferative vitreoretinopathy. Eye 2017, 31, 1317-1328, https://doi.org/10.1038/eye.2017.21. (IF 3.899).
17. Gupta, P.S.S.; Banerjee, S.; Islam, R.N.U.; Sur, V.P.; Bandyopadhyay, A.K. Substitutional Analysis of Orthologous Protein Families Using BLOCKS. Bioinformation 2017, 13, 1-7, https://doi.org/10.6026%2F97320630013001. (Pubmed Central and WOS Indexed).
18. Nayek, A.; Gupta, P.S.S.; Banerjee, S.; Sur, V.P.; Seth, P.; Das, S.; Islam, R.N.U.; Bandyopadhyay, A.K. ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2. Bioinformation 2015, 11, 413-415, https://doi.org/10.6026%2F97320630011413. (Pubmed Central and WOS Indexed).
19. Banerjee, S.; Gupta, P.S.S.; Nayek, A.; Das, S.; Sur, V.P.; Seth, P.; Islam, R.N.U.; Bandyopadhyay, A.K. PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2. Bioinformation 2015, 11, 366-368, https://doi.org/10.6026%2F97320630011366. (Pubmed Central and WOS Indexed).
20. Arnab Nayek, Parth Sarthi Sen Gupta, Shyamashree Banerjee, Sunit Das, Vishma Pratap Sur, Pratyay Seth, Rifat Nawaz Ul Islam and Amal K Bandyopadhyay Received: 28-04- 2015; Adsbet: automated determination of salt-bridge energy terms.Revised: 14-05-2015; Accepted: 15-05-2015 Volume 5, Issue 3 2015 (May - June) page- 28-36 http:// www.ijipls.com/uploaded/journal_files/150514030525.
21. Gupta, P.S.S.; Nayek, A.; Banerjee, S.; Seth, P.; Das, S.; Sur, V.P.; Roy, C.; Bandyopadhyay, A.K. SBION2: Analyses of Salt Bridges from Multiple Structure Files, Version 2. Bioinformation 2015, 11, 39-42, https://doi.org/10.6026%2F97320630011039. (Pubmed Central and WOS Indexed).
Conference:
1. Genetic and proteomic aspects of testicular germ cell tumor in patients. Vishma Pratap Sur. PragueOnco 2023. (Talk).
2. Testicular germ Cell Tumor pathophysiology to molecular Insight. Vishma Pratap Sur, Ondrej Simonik, Eliska Vacurova, Zuzana Kratka, Radomir Kren, Pavel Skrobanek, Libor Zamecnik, Tomas Buchler, Jiri Neuzil, Katerina Komrskova. ECA Barcelona, 2022. (Poster)
3. Molecular Biology and pathology of TGCT. Vishma Pratap Sur. 26th Symposium of Biology and Immunology of Reproduction – SBIR2021. (Talk).
4. Drug screening against Penicillin-Binding Protein from MRSA with docking and Molecular Dynamic Simulation. Vishma Pratap Sur, Katerina Komrskova. NGS Conference 2022, Warsaw. (Poster)
5. Testicular germ Cell Tumor pathophysiology to molecular Insight. Vishma Pratap Sur, Ondrej Simonik, Eliska Vacurova, Zuzana Kratka, Radomir Kren, Pavel Skrobanek, Libor Zamecnik, Tomas Buchler, Jiri Neuzil, Katerina Komrskova. Biocev Days, 2022. (Poster).
6. Analysis of pathophysiological state of testicular tissue and sperm in patients with testicular germ cell tumour. Vishma Pratap Sur, Ondrej Simonik, Eliska Vacurova, Zuzana Kratka, Radomir Kren, Pavel Skrobanek, Libor Zamecnik, Tomas Buchler, Jiri Neuzil, Katerina Komrskova. 26th Symposium of Biology and Immunology of Reproduction – SBIR2021. (Poster).
7. Analysis of reproductive parameters in men with testicular germ cell tumour. Katerina Komrskova, Vishma Pratap Sur, Ondrej Simoník, Eliska Vacurova, Zuzana Kratka, Radomir Kren, Pavel Skrobanek, Jiri Neuzil, Libor Zamecnik & Tomas Buchler. 16th Annual Meeting of the European Society for Reproductive Immunology- ESRI2021. (Poster).
8. Novel diagnostic tool for assessment of human sperm acrosome integrity; Šimoník Ondřej , Frolíková Michaela , Sadílková Lucie, Vishma Pratap Sur, Postlerová Pavla, Komrsková Kateřina; 26th Symposium of Biology and Immunology of Reproduction – SBIR2021. (Poster).
9. VISHMA PRATAP SUR, ANINDA MAZUMDAR, PAVEL KOPEL, AMITAVA MOULICK; Novel antibacterial ruthenium-Schiff base combined with benzimidazole ligand coordinat compound alternative of antibiotics on resistant VRSA a n d M R S A ; M e n d e l N e t Conference Full paper. https://mendelnet.cz/artkey/mnt-201901-0126_Novel-Ruthenium-coordinate-compound-combined-with Schiff-base-and-benzimidazole-as-a-potent-antibacterial agent.php?back=/magno/mnt/2019/mn1.php?secid=4.
10. Abstract-ADSETMEAS: Automated Determination of Salt-bridge Energy Terms and Mic Environment from Atomic Structures using APBS method, version 1.0 Arnab Nayek, Shyamashree Banerjee, Parth Sarthi Sen Gupta, Biswa Pratap Sur, Pratay Seth, Sunit Das, Nathan A Baker, Amal K Bandyopadhya http:// www.barcelocongresos.com.es/protein2015/images/book_abstracts.pdf
Timeline
Postdoctoral Research Fellow
Institute of Biotechnology, Czech Academy of Sciences
07.2020 - Current
Visiting Research Scholar
Utah State University
11.2019 - 02.2020
Doctoral Student
Mendel University in Brno
11.2017 - 07.2020
Research Technician
CEITEC-BUT
11.2017 - 07.2020
Ph.D. - Chemistry
Mendel University in Brno
11.2017 - 07.2020
Senior Research Fellow
Indian Institute of Chemical Biology
05.2017 - 11.2017
OsakaUx: CNR101x Cognitive Neuroscience Robotics - Part A
03-2016
Cellular mechanisms of brain function.
03-2016
Junior Project Fellow
Indian Institute of Chemical Biology
11.2015 - 03.2017
University Research Assistant
Presidency University
05.2015 - 11.2015
Biotech Industrial Trainee
GCC Biotech-DBT Government of India
11.2014 - 05.2015
Master of Science - Biotechnology
University of Burdwan
09.2012 - 08.2014
Bachelor of Science - Molecular Biology And Biotechnology
University of Kalyani
07.2009 - 06.2012
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