Description of Research Expertise

The work in the lab is focused in three areas: elucidating the genetic and metabolic regulatory networks that allow tuberculosis to persist in the human host for years, determination of the molecular basis of serine protease inhibition and mathematical modeling of complex biomolecular systems. We also work on national and international policy issues relating to infectious diseases


Research:

Pathogenesis of dormancy in Mycobacterium tuberculosis.
It is widely believed that oxygen limitation, amino acid starvation and carbon source restriction are involved in establishing and maintaining Mycobacterium tuberculosis in a dormant state. Correspondingly, emergence from dormancy is related to a partial or complete amelioration of these conditions. We have identified and are studying three genetic and enzyme systems that comprise regulatory networks in Mtb that may be invovled in Mtb pathogenesis. These are: 1) ribonucleotide reductase systems that carry out the reduction of ribonucleotides to deoxyribonucleotides--the rate limiting enzymatic step in DNA synthesis, 2) the cytochrome system and, 3) the stringent response system that regulates the expression of a complex network of genes. This work is supported by the NIH.

Biomolecular Computation.
A new area of investigation known as biomolecular computation where complex computational operations are carried out using biomolecules, in particular using DNA. We showed how macromolecules can be manipulated to carry out fundamental logical operations and can be wired together as reversible logic gates. We are currently collaborating with members of the School of Engineering on modeling complex biological behavior using a hybrid systems approach that combines continuous and stochastic modalities. This work wa\s supported by the NSF and DARPA

Enzymology and cell biology of serine proteases and serine protease inhibitors.
Serine proteases and serine protease inhibitors (serpins) play critical roles in a wide variety of biological processes including inflammation, coagulation and growth and development. We have proposed a general model for the mechanism of inhibition of serine proteases by serine protease inhibitors based on site directed mutagenesis, atomic resolution crystal structures and NMR spectroscopic analyses. We are currently exploring the consequences and extensions of this model. This work is supported by the NIH.

Selected Publications

Abhiraman B, Fotis R, Eskin L, Rubin H.: Fault Detection for Vaccine Refrigeration via Convolutional Neural Networks Trained on Simulated Datasets. International Journal of Refrigeration. Volume 149, May 2023, Pages 274-285. : 2023.

Kim .J, Xin Chen X, Nikpey. H, Rubin. H, Bidokhti SS, Sarkar S.: Tracing and testing multiple generations of contacts to COVID-19 cases: cost-benefit trade-offs. R Soc Open Sci . 2022 Oct 12;9(10):211927. doi: 10.1098/rsos.211927. eCollection 2022 Oct. : 2022.

Chowdhury SR, Rafayat S, Yasir MT, Hossain S, Shetty S, Tahsin S, Rubin H, Rahaman A.: Vaccine Storage and Distribution in Rural Bangladesh. International Journal of Medicine and Public Health,2022,12,2,56-64. DOI:10.5530/ijmedph.2022.2.12. : 2022.

Ali RN, Rubin H, Sarkar S: Countering the potential re-emergence of a deadly infectious disease—Information warfare, identifying strategic threats, launching countermeasures.: PLoS ONE 16(8) : 2021.

Dutta NK, Klinkenberg LG, Vazquez M-J, Segura-Carro D, Colmenarejo G, Ramon F, Rodriguez-Miquel B, Mata-Cantero L, Porras-De Francisco E, Chuang Y-M, Rubin H, Lee JJ, Eoh H, Bader JS, Perez-Herran E, Mendoza-Losana A, Karakousis PC: Inhibiting the stringent response blocks entry into quiescence and reduces persistence Science advances 5 (3): eaav2104,2019.

Harbut MB, Yang B, Liu R, Yano T, Vilchèze C, Cheng B, Lockner J, Guo H, Yu C, Franzblau SG, Petrassi HM, Jacobs WR, Rubin H, Chatterjee AK, Wang F: Small Molecules Targeting Mycobacterium tuberculosis Type II NADH Dehydrogenase Exhibit Antimycobacterial Activity Angewandte Chemie (International ed. in English) 57 (13): 3478-3482,2018.

Ogura M, Wakaiki M, Rubin H, Preciado VM: Delayed bet-hedging resilience strategies under environmental fluctuations Physical Review E 95 (5-1): 052404,2017.

Tantry SJ, Markad SD, Shinde V, Bhat J, Balakrishnan G, Gupta AK, Ambady A, Raichurkar A, Kedari C, Sharma S, Mudugal NV, Narayan A, Naveen KCN, Nanduri R, Bharath S, Reddy J, Panduga V, Prabhakar KR, Kandaswamy K, Saralaya R, Kaur P, Dinesh N, Guptha S, Rich K, Murray D, Plant H, Preston M, Ashton H, Plant D, Walsh J, Alcock P, Naylor K, Collier M, Whiteaker J, McLaughlin RE, Mallya M, Panda M, Rudrapatna S, Ramachandran V, Shandil R, Sambandamurthy VK, Mdluli K, Cooper CB, Rubin H, Yano T, Iyer P, Narayanan S, Kavanagh S, Mukherjee K, Balasubramanian V, Hosagrahara VP, Solapure S, Ravishankar S, Hameed PS: Discovery of Imidazo[1,2-a]pyridine Ethers and Squaramides as Selective and Potent Inhibitors of Mycobacterial Adenosine Triphosphate (ATP) Synthesis J Med Chem 60 (4): 1379-1399,2017.

Chuang YM, Dutta NK, Hung CF, Wu TC, Rubin H, Karakousis PC: The stringent response factors PPX1 and PPK2 play an important role in Mycobacterium tuberculosis metabolism, biofilm formation, and sensitivity to isoniazid in vivo Antimicrob Agents Chemother : pii: AAC.01139-16. ,2016.

Chuang YM, Bandyopadhyay N, Rifat D, Rubin H, Bader JS, Karakousis PC.: Deficiency of the novel exopolyphosphatase Rv1026/PPX2 leads to metabolic downshift and altered cell wall permeability in Mycobacterium tuberculosis MBio 6 (2): e02428,2015.

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Academic Contact Information

502C Johnson Pavilion
Philadelphia, PA 19104
Patient appointments: 800-789-7366