◊ Prof. N. Yathindra
- Shodhaka: A company founded by Dr. Kshitish Acharya
◊ Dr. Bibha
◊ Dr. S.
◊ Dr. R.
◊ GANIT Labs
students at IBAB
◊ Info for training/projects
Background: Dr. Kshitish K Acharya completed most of his basic education within Karnataka and worked in a wild life research project for one year in Western Ghats (Mangalore University) after his MSc. He qualified CSIR-NET and completed PhD in reproductive biology in 1996 at BHU, Varanasi. He used several approaches such as behavioral observations and physiological/endocrinological experiments to study the pheromonal influences on implantation in mice, during his doctoral work. He continued working in the field of reproductive biology during his post-doctoral research work, extensively using molecular biology / cell-culture techniques in the Indian Institute of Science, Bengaluru (~ 2 years) and University of Virginia, Charlottesville, USA (~ 4 years). He then worked in a biotech company as the head of the production unit for one year.
Role in IBAB: Dr. Kshitish joined IBAB as a faculty in 2003. Apart from involving in regular teaching and research, he conceptualized and developed a unique 14-months diploma. This laboratory course trained students in multiple aspects of research methodologies, mainly focusing on the abilities to perform molecular biology experiments. He convened 8 batches of this Laboratory Course in Bio-Techniques (LCBT) successfully and placed the students. The placement records (95%, across batches) and feedback from industry have been extremely positive for this program. He has also organized many short-term courses. Dr. Kshitish has recently founded a company (Shodhaka Life Sciences Pvt. Ltd., being incubated inside IBAB) that focuses on biological data analysis (services), product development (database and software) and bioinformatics-training for biologists. He currently has 2 PhD students: Mr. Darshan SC and Ms. Neelima Ch.
RESEARCH: He has been trying to understand the transcription regulatory mechanisms in the mammalian tissues. One of the immediate goals of his group is to establish and complete molecular portrait of the mammalian testis tissue, including the transcriptional regulatory network. He intends to do this by making a better use of already available gene expression data. After completing the work with mammalian testis, the same work would be extrapolated to other tissues, and his group has already begun working on uterus, ovary, prostate, liver and kidney.
His group is also using these profiles to identify potential biomarkers. His current group includes collaborators from other organizations such as the NIRRH (Mumbai), KMIOal (Bengalooru), VIT (Vellore), Ankur hospitals (Bengalooru) and Shodhaka Life Sciences Pvt. Ltd. (Bengalooru).
Extensive biocuration and data analysis are being used. The analysis is applied to wide variety to understand the testis as a system, and include SNPs from genome sequencing data, meta analysis of microarray data, alternative splice forms from RNA-seq & microarrays, protein interactions, pathways and miRNAs. The research methodology also involves molecular techniques such as cloning, RT-PCR, qRT-PCR, microarray and Next Generation Sequencing (NGS) are being employed by Dr. Kshitish and his team.
His team is currently finalizing highly reliable clusters of mammalian genes based on their expression status across normal tissues and trying to use them to,
a) identify potential biomarkers for tissue/disease-specific biomarkers, at the gene and transcript levels, and
b) analyze sequence-features in potential promoter regions to find out how gene-expression is regulated.
They have completed data compilation (mostly by biocuration) and development of specific databases and a few tools. They are also performing experimental validations and promoter analysis.
Following are some of the bioinformatics resources developed by Dr. Kshitish and his group:
- Mammalian gene expression databases:
- A tool to design primers from exon-exon junctions: Ex-Ex Primer
- A tool to detect position-specific motifs: MotDet
- Also see a useful portal for most bioinformatics databases & tools: startbioinfo.com (From ‘Shodhaka’)
Please scroll-down or click here for a list of publications.
Glimpses of research work / background of Dr. Kshitish Acharya
The novel meta analysis approach developed by the group helps to make maximum use of available gene expression data, and identify which genes are crucial for specific tissues and conditions, and thereby identify more promising potential biomarkers.
After completing the work on testis, Kshitish intends to study other tissues and catalog crucial genes for various functions. The combination of meta-analysis and the biocuration helped his team to create a series of robust Mammalian Gene Expression Databases (MGEx-dbs) for multiple tissues. Their overall performance is superior to any other similar databases reported before.
A revisit to probe and primer designing strategies:
It is important to assess the variations in existing gene expression data. There could be inefficiencies in primer / probe designing by previous researchers. Results of Dr. Kshitish’s group emphasize thoroughness required for microarray probe designing. They are creating new tools for primer and probe designing, and experimentally validating the output of the tools.
PhD students with Dr. Kshitish Acharya K
Mr. Darshan SC has been a PhD student at IBAB for 3.5 years. He is working to establish expression-based gene clusters for prediction of mammalian promoters and expression patterns, and has published three papers (PLoS One. 2013;8(3):e58419; PLoS One. 2012;7(5):e36776. BMC Genomics. 2010 Aug 11;11:467). He has also won the best poster award two international conferences. After BSc (Biotechnology, Zoology and Computer Science, 2005; DVS Arts & Science College, Shivamogga, Kuvempu University, Karnataka), he completed MSc in Bioinformatics (2007, Jnana Sahyadri, Kuvempu University, Karnataka) with 2nd rank to the University.
Mr. Darshan was one of the 2 candidates selected among 25 applicants screened with a practical programming test followed by an interview (by Dr. Kshitish Acharya K). After 15 months of research work with Dr. Kshitish K Acharya, he proposed his work to the research team (all faculty and other researchers) at IBAB. After qualifying the scrutiny process at IBAB, and at Manipal University, he has registered with Manipal University, Manipal, Karnataka. His research work (at IBAB) is in the final stages, and is expected to submit the thesis soon.
Ms. Neelima Ch has been a PhD student at IBAB for about 3.5 years. She intends to understand differences in the preliminary stages of gene expression regulation in healthy and unhealthy mammalian tissues, and identificaty potential markers for some of the conditions. She has published one research article so far (BMC Genomics. 2010 Aug 11;11:467). After BSc (Agriuculture, 2003; Acharya N.G Ranga Agricultural University, Baptala, Andhra Pradesh), she completed MSc in bioinformatics (2006, SRM college, Madras university, Chennai, Tamilnadu)
Ms. Neelima was one of the very few candidates selected via written test and interview (by Dr. Kshitish Acharya K) for a 'Research Assistant' position. She joined in December 2006. After 2 years of research, she decided to register for PhD, qualified the written test and interview at IIIT, Hyderabad in 2008. Under the guidance of Dr. Kshitish Acharya K (IBAB, Bengaluru), and the co-guidance of Dr. Abhijit Mitra (IIIT, Hyderbad) her registration was completed in February 2009. She is in the final stages of her doctoral work. She is also in the process of submitting two of her first author manuscripts for publication.
Shweta Bhagwat, Veena Dalvi, Darshan Chandrasekhar , Tinsu Matthew, Kshitish Acharya, Rahul Gajbhiye, Vijay Kulkarni, Shobha Sonawane, Manish Ghosalkar, Priyanka Parte; Acetylated alpha tubulin is reduced in individuals with poor sperm motility; Fertility and Sterility – accepted Sept 2013
Bhagwat SR, Chandrashekar DS, Kakar R, Davuluri S, Bajpai AK, Nayak S, Bhutada S, Acharya KK, Sachdeva G. Endometrial receptivity: a revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb. PLoS One, 8(3), e58419 (2013)
Bajpai, AK, Davuluri, S, Chandrashekar, D S, Ilakya, S, Dinakaran, M and Acharya, KK MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer PLoS One, 7(5), e36776 (2012).
Acharya, KK, Kasliwal, G and Haritha, H How do you choose your literature search tool(s)? Nature Precedings 2011;
- Kshitish K Acharya, Darshan S Chandrashekar, Neelima Chitturi, Hardik Shah, Varun Malhotra, Sreelakshmi KS, Deepti H, Akhilesh Bajpai, Sravanthi Davuluri, Pranami Bora, Leena Rao A novel tissue-specific meta-analysis approach for gene-expression predictions, initiated with a mammalian gene expression testis database. BMC Genomics, 11, 467-476 (2010).
- Acharya, KK. Book review: Career development in bioengineering and biotechnology. By Madhavan, G., Oakley, B. and Ken, L. (eds) Springer Science + Business Media (New York) Current Science, 96, 293 (2009).
- Acharya, KK, Govind, C.K., Shore, A.N., Stoler, M.H. and Reddi, P.P. cis-Requirement for the maintenance of round spermatid-specific transcription. Dev. Biol., 295, 781-790 (2006)
- Acharya KK The biotech-bioinfo interface in the context of education and growth of the biotechnology industry in India today. Biovistas, 1, 7-13 (2006)
- Sreekumar, A, Acharya, KK, Lalitha, HS, Indi, SS, Bali, P and Seshagiri, PB Germ cell-specific localization of immunoreactive riboflavin carrier protein in the male golden hamster: appearance during spermatogenesis and role in sperm function. Reproduction, 129, 577-587 (2005)
- Sandhu, K S and Acharya, KK, ExPrimer: to design primers from exon-exon junctions. Bioinformatics, 21, 2091-2092 (2005)
- Reddi PP., Shore A., Shapiro JA, Anderson A, Stoler MH and Acharya KK and Herr JC. Spermatid-specific promoter of the SP-10 gene functions as an insulator in somatic cells. Developmental Biology 262,173-182 (2003)
- Reddi PP., Shore A., Acharya KK and Herr JC. Transcriptional regulation of spermiogenesis: Insights from the study of SP-10 gene, which codes for an acrosomal protein. Journal of Reproductive Immunology. 53, 25-36 (2002)
- Seshagiri PB, Acharya, KK, Jayaprakash, D, Satish, KS and Shetty, G. Ovarian hyperstimulation in bonnet monkeys using gonadotrophins. In: Follicular Growth, Ovulation and Fertilization: Molecular and Clinical Basis. A. Kumar and A.K. Mukhopadhyay (Eds.). Narosa Publishing House. New Delh. (2002)
- Acharya KK, Roy A and Amitabh K. Relative role of olfactory cues and certain non-olfactory factors in foraging of fruit-eating bats. Behavioural Processes. 44, 59-64 (1998)
- Acharya KK and Dominic CJ. Duration of the luteotrophic memory of the stud male odours formed in female mouse. J. Exp. Zool. 279, 626-632 (1997)
- Acharya KK and Dominic CJ. Male-induced post-implantation pregnancy failure in the laboratory mouse: A re-investigation. J. Reprod. Biol. Comp. Endocrinol. 6, 69-75 (1994)
- Acharya KK and Dominic CJ. Male-induced acceleration of sexual maturation in female mice: Absence in the Parkes (P) strain. Indian J. Exp. Biol. 32, 906-907 (1994)
Dr. Kshitish has been teaching many aspects of general biology, research methodology, molecular biology and bioinformatics subjects (mainly technologies such as NGS, microarray, ESTs etc, related data analsys, and resource usage for genomics, transcriptomics and proteomics). He has also been teaching a few general topics such as career planning, presentation skills, Intelligent Property Rights (IPR) and Good Laboratory/Manufacturing Practices (GLPs/GMPs). He has taught the students of 10 batches of the post graduate diploma (18 months program) and 8 batches of post graduate diploma (14 months program) for research methodologies, which was referred to as the Laboratory Course in Bio-Techniques (LCBT). This laboratory training program was conceptualized, planned, initiated, organized by him. He also placed the students directly (95% placement records across 8 batches). He has also taught in many short-term courses and even organized some of them.
Examples of the short-courses organized by Dr. Kshitish K Acharya:
Dr. Kshitish has experience in certain industrial aspects of the life sciences sector, including management and organizational activities and is keen to be a consultant for
(a) specific research projects in biotechnology or bioinformatics organizations,
(b) training employees in specific areas including general professional skills, and
(c) setting molecular biology / cell culture laboratories
Examples of his consultancy are:
- Wipro (in the area of microarray data analysis) and
- Microtest Innovation (in the area of quality tests and stability studies of certain molecular products).
- Scinnovation Consultants Pvt. Ltd. (selection and placement criteria in the biotechnology/bioinformatics area; 2005-2006)
- A research group in a leading US University
Following is a summary of his experiences:
Experience (20 years of research, including Ph.D.):
Academic, India: Slightly more than 16 years of research.
Academic USA:~4 years of patent-oriented research (molecular biology).
Industry, India: An year as scientist & head of the production unit in a
growing Indian Biotechnology company, and now director of his
own company – Shodhaka Life Sciences Pvt. Ltd. for 3 years
Teaching: 11 years of teaching ( molecular biology, bioinformatics and general professional skills at IBAB.
Shodhaka Life Sciences Pvt. Ltd. is founded by Dr. Kshitish K Acharya. The company is currently being incubated inside IBAB. The activities
began in the middle of 2009.
The current R & D goal for this company is to identify potential biomarkers by applying a novel algorithm on huge amounts of transcriptomics and proteomics data. But ‘Shodhaka’ has also been spending quite a bit of time and effort in systematically comparing bioinformatics resources from biologists perspective, as providing the best the custom-designed training and services to scientists in biology has been among its main goals. Using the new insights obtained during its in-house research, a new useful portal has been created for the scientific community by Shodhaka: startbioinfo.com
Shodhaka intends to provide service to scientists in the area of biological data analysis, and other aspects of bioinformatics. It has also developed software products in the areas of literature search, online test for job/course-suitability in life sciences sector, primer designing etc.
Shodhaka has also collaborated with IBAB and other organizations on some of the research projects.