Genomes often contain multiple copies of the same gene, either identical or slightly altered. The functional role of such redundancy is poorly understood. For example, in addition to multiple copies of the same tRNA gene, genomes may contain more than one tRNA isoacceptor for the same amino acid although only a subset is sufficient for protein synthesis. Understanding the functional basis of genome redundancy is important, both to rationalize the phenomenon and for the implications it may have on the current efforts of creating artificial synthetic life forms that are based on minimalist genomes without any redundancy. I will discuss a new functional role of tRNA isoacceptor redundancy in the genome. Specifically, I will show how isoacceptor redundancy of tRNA(Gln) in proteobacteria facilitated the functional evolution of glutamyl-tRNA synthetase (GluRS) â€” evolving to become tRNA(Glu)-specific from an ancestral version which was capable of aminoacylating both tRNA(Glu) and tRNA(Gln).
Understanding the Nano-Bio Interface: The key for Translation
Nanotechnology is an enabling technology with its wide spread application in different industries, energy sector, agriculture, food, packaging and medicine. The unique properties acquired by the materials can be intelligently exploited for different innovative applications with high translational value. The field of nanomedicine is rapidly advancing which can revolutionize the current medical practice. The areas of nanomedicine can be broadly divided into 3 categories: Laboratory Diagnosis, Imaging and Therapy. In cosmetic industry there is also a large scale use of titanium dioxide and zinc oxide for sun screen products. Any nanomaterial being used in health care apart from in-vitro diagnostics has to be proven safe. Nanomaterial used in any industry and agriculture may contaminant environment leading adverse effects to ecosystems and enter into food chain affecting our health. So understanding of life cycle of any nanoparticle is very important with reference to its biological interaction. Non-biodegradable systems will have more concern as they can have a long life and sequestrate. However it will be unwise to label all non-biodegradable nanomaterial unsafe unless we have science based evidence. For biodegradable nanomaterial one has to focus on its degradation product and mechanism of degradation. Biocompatibility is needed for any system for human use. Let us focus on human system as we may be potentially exposed to any engineered nanomaterial used for any purpose. The simplest concept for life cycle of nanomaterial is ADME (A= Absorption/port of entry in the body, D = Distribution, M = Metabolism and E = Excretion ). The port of entry may be oral, parenteral (intravenous/ intramuscular/ subcutaneous/ intraperitoneal â€“ injectable), respiratory and through skin. Now suppose we have injected your engineered nanomaterial intravenously. It will be in the blood where it will interact with blood cells (red blood cells), white blood cells, platelets), serum proteins, coagulation factors, circulating immune complexes, complement components, opsonin etc and endothelial cells in the wall of the blood vessels. Its interaction in the blood will depend on its Size, Shape, Surface Charge and Flexibility. The cationic surface can lead to more haemolysis, platelet and leukocyte activation. All engineered nanoparticles are foreign to our body. So our immune system specially mononuclear and macrophage system will try to engulf these circulating particles and sequestrate them in Reticulo-Endothelial System (liver, spleen, lymphoid system, bone marrow etc.). The most popular method to reduce macrophage uptake is to coat the surface with PEG. Size and shape are also important factors. Approximately 150 to 350nm size is avidly taken up by the macrophages. Macrophage is comfortable to engulf spherical system, but they may be uncomfortable with long tube like structure (carbon nano tube) or 2-dimentional structure like graphene. For cancer due to the presence of leaky blood vessels accumulation of nanomaterial may happen passively by Enhanced Permeability and Retention (EPR) effect. There are large number of publications on receptor targeted nanoparticles for cancer. However for any kind of nanomedicine for cancer off target sequestration and side effect should be avoided. In the nanomedicine sector major R&D world over is nano-drug delivery system. In the simplest form we load the drug/active molecule inside a nanoparticle. This makes a nano-depot of the freely diffusible small molecule. The release of free drug (bioavailable) will depend on degradation kinetics of nanoparticle. Thus the phamcokinetic model of the drug changes when we use the nanodrug delivery system. For any nanodrug delivery for human use from regulatory point of view we have to prove the (1) Biological Equivalence, (2) Pharmacologic Equivalence and (3) Therapeutic Equivalence compared to drug (Active Pharmaceutical Ingredient/ API). The safety data including immunotoxicity data have to be generated. Those working on inorganic/ metal system may be encouraged with great potential for in-vitro diagnostic system, imaging and areas like metalbiotics (use of metal nanoparticle as antimicrobials). We can discuss about how our extensive research and innovation in the area of nano can be translated beyond publication with greater economic and social impact with reference to Nano-Bio Interface.
Cholesterol-induced Conformational Plasticity and Oligomerization of GPCRs: Novel Insights in Health and Disease
G protein-coupled receptors (GPCRs) are the largest class of molecules involved in signal transduction across membranes, and represent major drug targets in all clinical areas. The serotonin1A receptor is an important neurotransmitter receptor of the GPCR superfamily and is implicated in the generation and modulation of various cognitive, behavioral and developmental functions. We previously demonstrated that membrane cholesterol is necessary for ligand binding, and G-protein coupling of serotonin 1A receptors. Interestingly, recently reported crystal structures of GPCRs have shown structural evidence of cholesterol binding site(s). In this context, we reported the presence of cholesterol recognition/interaction amino acid consensus (CRAC) motifs in the serotonin1A receptor. We also showed that the receptor is more stable and compact in the presence of membrane cholesterol. Our recent results utilizing coarse-grain molecular dynamics simulations to analyze the molecular nature of receptor-cholesterol interaction offer interesting insight in cholesterol binding site(s) in the receptor and oligomerization of the receptor. We showed utilizing homo-FRET that the serotonin1A receptor is constitutively oligomerized in live cells, with the possibility of higher order oligomers of the receptor. Progress in deciphering molecular details of the nature of GPCR-cholesterol interaction in the membrane would lead to better insight into our overall understanding of GPCR function in health and disease.
Interfering with Interference: targeting the RNAi pathway: Opportunities and Challenges.
MicroRNAs (miRNAs) play crucial roles in regulating gene expression in many cellular context. Deregulation of miRNAs has been implicated in a number of disease conditions and thus, methods that can modulate mature miRNA levels in cells can have immense therapeutic potential. We describe a simple in vitro screening method using a DNA based molecular beacon which overcomes the limitations associated with earlier screens. With this proof of concept study we illustrate the utility of a scalable molecular beacon based screening strategy for miRNA inhibitors. We have identified potent molecules against several oncogenic microRNA as a candidate anticancer agent. Results of such studies will comprehensively be discussed during the presentation.
1) Enhanced and synergistic downregulation of oncogenic miRNAs by self-assembled branched DNA. Nahar S, Kayak AK, Ghosh A, Subudhi U, Maiti S. Nanoscale. 2017 Dec 21;10(1):195-202.
2) Systematic Evaluation of Biophysical and Functional Characteristics of Selenomethylene-Locked Nucleic Acid-Mediated Inhibition of miR-21. Nahar S, Singh A, Morihiro K, Moai Y, Kodama T, Obika S, Maiti S. Biochemistry. 2016 Dec 20;55(50):7023-7032.
3) Potent inhibition of miR-27a by neomycinâ€“bisbenzimidazole conjugates. Nahar S, Ranjan N, Ray A, Arya, DV. Maiti S. Chem. Sci., 2015,6, 5837-5846.
4) Selective inhibition of miR-21 by phage display screened peptide. Bose D, Nahar S, Rai MK, Ray A, Chakraborty K, Maiti S. Nucleic Acids Res. 2015, 43, 4342-52.
5) Nonconventional chemical inhibitors of microRNA: therapeutic scope. Jayaraj GG, Nahar S, Maiti S. Chem Commun. 2015, 51(5):820-31.
6) Anti-cancer therapeutic potential of quinazoline based small molecules via global upregulation of miRNAs. Nahar S, Bose D, Kumar Panja S, Saha S, Maiti S. Chem Commun . 2014, 50(35):4639-42.
7) A Molecular-Beacon-Based Screen for Small Molecule Inhibitors of miRNA Maturation. Bose D, Jayaraj GG, Kumar S, Maiti S. ACS Chem Biol. 2013, 17, 930-938.
8) The tuberculosis drug streptomycin as a potential cancer therapeutic: inhibition of miR-21 function by directly targeting its precursor. Bose D, Jayaraj G, Suryawanshi H, Agarwala P, Pore SK, Banerjee R, Maiti S. Angew Chem Int Ed Engl. 2012, 51, 1019-23.
9) Antagomirzymes: oligonucleotide enzymes that specifically silence microRNA function. Jadhav VM, Scaria V, Maiti S. Angew Chem Int Ed Engl. 2009; 48, 2557-60.
Understanding enzymes: Insights into structure and function from biophysical approaches.
Understanding enzyme function from the perspective of structure started with the first 3-diemnsional structure of an enzyme, lysozyme solved in 1965. However, even today mechanistic enzymology has many open and unanswered questions as each enzyme is a case study on its own. Over the past two decades, with the aim of understanding metabolism in the malarial parasite Plasmodium my laboratory has been simultaneously probing into the function of enzymes involved in nucleotide biosynthesis. In my talk, I will take up specific enzymes where understanding function has ranged from protein dynamics involving peptide bond isomerization, formation of channels to intramolecularly tunnel ammonia to identification of a unique peptide backbone modification that imparts structural stability.
January 04, 2018
Prof. Anindya Dutta, University of Virginia School of Medicine
Noncoding RNAs in regulation of differentiation and cancer
I will use examples from skeletal muscle differentiation and prostate and brain cancers to illustrate the importance of (a) short noncoding RNAs like microRNAs and (b) long noncoding RNAs (lncRNAs). We will begin our discussion of lncRNA with H19, which promotes muscle differentiation by producing a microRNA and MUNC lncRNA which is an eRNA,but also has an independent role in promoting the expression of several myogenic RNAs. We will then move to cancers to discuss the discovery of DRAIC and its importance in regulation of cancer progression (with significant contribution from an IACS alumnus, Dr. Shekhar Saha. Finally, if time permits, we will address the identification of tens of lncRNAs that predict outcome in gliomas and glioblastomas. Overall this talk will introduce the students to lncRNAs, but more important, will encourage them to ask questions during the seminar itself that will guide the direction in which the seminar will proceed.