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7 results on '"Kalpani De Silva"'

1. PARP1 Regulates Circular RNA Biogenesis though Control of Transcriptional Dynamics

Author

Rebekah Eleazer, Kalpani De Silva, Kalina Andreeva, Zoe Jenkins, Nour Osmani, Eric C. Rouchka, and Yvonne Fondufe-Mittendorf

Subjects
circRNAs, transcription elongation, poly (ADP-ribose) polymerase, splicing, backsplicing, gene architecture, Cytology, QH573-671
Abstract

Circular RNAs (circRNAs) are a recently discovered class of RNAs derived from protein-coding genes that have important biological and pathological roles. They are formed through backsplicing during co-transcriptional alternative splicing; however, the unified mechanism that accounts for backsplicing decisions remains unclear. Factors that regulate the transcriptional timing and spatial organization of pre-mRNA, including RNAPII kinetics, the availability of splicing factors, and features of gene architecture, have been shown to influence backsplicing decisions. Poly (ADP-ribose) polymerase I (PARP1) regulates alternative splicing through both its presence on chromatin as well as its PARylation activity. However, no studies have investigated PARP1’s possible role in regulating circRNA biogenesis. Here, we hypothesized that PARP1’s role in splicing extends to circRNA biogenesis. Our results identify many unique circRNAs in PARP1 depletion and PARylation-inhibited conditions compared to the wild type. We found that while all genes producing circRNAs share gene architecture features common to circRNA host genes, genes producing circRNAs in PARP1 knockdown conditions had longer upstream introns than downstream introns, whereas flanking introns in wild type host genes were symmetrical. Interestingly, we found that the behavior of PARP1 in regulating RNAPII pausing is distinct between these two classes of host genes. We conclude that the PARP1 pausing of RNAPII works within the context of gene architecture to regulate transcriptional kinetics, and therefore circRNA biogenesis. Furthermore, this regulation of PARP1 within host genes acts to fine tune their transcriptional output with implications in gene function.

Published
2023
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2. Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: proceedings

Author

L. Leon Dent, Sammed N. Mandape, Siddharth Pratap, Jianan Dong, Jamaine Davis, Jennifer A. Gaddy, Kofi Amoah, Steve Damo, Dana R. Marshall, Jacob Jones, Toni Brandt, Gilberto Diaz, Qingguo Wang, Todd Gary, Ashwini Yenamandra, Marina Z. Ghattas, Marwa Elrakaiby, Ramy K. Aziz, Hamdallah H. Zedan, Moamen Elmassry, Marwa ElRakaiby, Mariam Lotfy, Jarrad Marcel, Rania A. Khattab, Maha M. Abdelfattah, Jack A. Gilbert, Pouya Dini, Shavahn C. Loux, Kirsten E. Scoggin, Alejandro Esteller-Vico, Edward L. Squires, Mats H. T. Troedsson, Peter Daels, Barry A. Ball, Kalpani De Silva, Ernest Bailey, Joel C. Stephens, Theodore S. Kalbfleisch, Christine E. Dolin, Lauren G. Poole, Daniel W. Wilkey, Eric C. Rouchka, Gavin E. Arteel, Michelle T. Barati, Michael L. Merchant, Richard M. Higashi, Teresa W-M Fan, Hunter Moseley, and Andrew N Lane

Subjects
Medicine, Science
Published
2017
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4. Disruption of the mouse liver epitranscriptome by long-term aroclor 1260 exposure

Author

Kellianne M. Piell, Belinda J. Petri, Kimberly Z. Head, Banrida Wahlang, Raobo Xu, Xiang Zhang, Jianmin Pan, Shesh N. Rai, Kalpani de Silva, Julia H. Chariker, Eric C. Rouchka, Min Tan, Yan Li, Matthew C. Cave, and Carolyn M. Klinge

Subjects
Pharmacology, Health, Toxicology and Mutagenesis, General Medicine, Toxicology
Published
2023

5. Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016: Cadiz, KY, USA. 8-10 April 2016.

Author

Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park, Xueyuan Cao, Stanley Pounds, Susana C. Raimondi, James R. Downing, Raul C. Ribeiro, Jeffrey Rubnitz, Jatinder Lamba, Bernie J. Daigle Jr., Deborah Burgess, Stephanie Gehrlich, John C. Carmen, Nicholas Johnson, Chandrakanth Emani, Kalpani De Silva, Michael P. Heaton, Theodore S. Kalbfleisch, Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun Ajayi, Fatih Sen, Eunice Y. Huang, Mohammad Mohebbi, Luaire Florian, Douglas J. Jackson, John F. Naber, Akm Sabbir, Sally R. Ellingson, Yuping Lu, Charles A. Phillips, Michael A. Langston, Rahul Kumar Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui 0001, Mohammed Sayed, Jing Wang 0026, Qi Liu 0024, Yu Shyr, Xiaofei Zhang, Naresh Prodduturi, Gavin R. Oliver, Diane Grill, Jie Na, Jeanette Eckel-Passow, Eric W. Klee, Michael M. Goodin, Mark L. Farman, Harrison Inocencio, Chanyong Jang, Jerzy W. Jaromczyk, Neil Moore, Kelly L. Sovacool, Leon Dent, Mike Izban, Sammed N. Mandape, Shruti S. Sakhare, Siddharth Pratap, Dana Marshall, M. Scotty Depriest, James N. MacLeod, Hanady Adam, Ethan Blandford, Joel Campbell, Joshua Castlen, Brittany Dixon, Ginger Gilbert, Aaron Hall, Philip Kreisle, Jessica Lasher, Bethany Oakes, Allison Speer, Maximilian Valentine, Naga Satya Venkateswara Ra Nagisetty, Rony Jose, Robert W. Rooney, and David Hains

Published
2016
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6. An Aggregate Production Plan for a Biscuit Manufacturing Plant Using Integer Linear Programming

Author

Dilishiya Kalpani De Silva and Wasantha Bandara Daundasekara

Subjects
Mathematical optimization, Idle, Simplex algorithm, Computer science, business.industry, Production cost, Scheduling (production processes), Overtime, ComputerApplications_COMPUTERSINOTHERSYSTEMS, Solver, Human resources, business, Integer programming
Abstract

Effective planning, scheduling, and synchronization of all production activ-ities are the key responsibilities of the management of a manufacturing plant. Therefore, it is necessary for the management of the plant to design the production process so that the total production cost is minimized, subject to the available resources that cannot be compromised. In this study, a biscuit manufacturing plant is selected and an integer linear programming (ILP) model is formulated to determine aggregate number of batches that the plant should produce from each product per month so that monthly demand is satisfied with available resources. The objective is to minimize the monthly production cost of the plant. The required data were collected from the production plant for a period of one month, and then, the objective function and constraints were formulated. The management has given a paramount importance in satisfying the demand so that there will not be any unsatisfied customer. According to the managerial requirement, any feasible solution obtained by the model must satisfy the demand. Therefore, demand constraint is considered as a hard constraint. The management is forced to adjust the labour and machine requirements more frequently according to the monthly demand. Thus, labour and machine hour constraints are considered as soft constraints. Formulated ILP model was implemented as a spreadsheet model in Excel and solved using Excel Solver which uses the simplex algorithm and incorporates the integer requirement of the model when finding the optimal solution. Total available labour and machine hours can be changed within a particular range until a feasible solution is found. The solved model determines the number of batches to be produced from each product and the corresponding minimum cost per month. By implementing this production plan, manufacturing excess of biscuits can be avoided and hence utilizes the physical and human resources to the optimum manner. Additionally, the machine and labour idle times and the needed overtime hours can be identified using the solution while the additional overtime cost will be added to the monthly production cost.

Published
2019

7. Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: proceedings

Author

Jarrad Marcel, Qingguo Wang, Gavin E. Arteel, Alejandro Esteller-Vico, Daniel W. Wilkey, Shavahn C. Loux, Richard M. Higashi, Andrew N. Lane, Joel C. Stephens, Moamen M. Elmassry, Maha M. Abdelfattah, Siddharth Pratap, Steve Damo, Hamdallah Zedan, Michelle T. Barati, Michael L. Merchant, Teresa W.-M. Fan, Jennifer A. Gaddy, Theodore S. Kalbfleisch, Pouya Dini, Barry A. Ball, Marwa T. ElRakaiby, Todd Gary, Kalpani De Silva, Hunter N. B. Moseley, Mariam Lotfy, Jack A. Gilbert, Kirsten E. Scoggin, Ernest Bailey, Jacob Jones, Jamaine Davis, Eric C. Rouchka, Leon Dent, Sammed N. Mandape, Christine E. Dolin, Edward L. Squires, Kofi Amoah, Jianan Dong, Marina Z. Ghattas, Gilberto Diaz, Mats H.T. Troedsson, Dana Marshall, Rania Abdelmonem Khattab, Ashwini Yenamandra, Ramy K. Aziz, Lauren G. Poole, Peter Daels, and Toni Brandt

Subjects
0301 basic medicine, 03 medical and health sciences, geography, 030104 developmental biology, Summit, geography.geographical_feature_category, business.industry, Medicine, Library science, General Medicine, business, General Biochemistry, Genetics and Molecular Biology
Published
2017

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