Indranil Mitra

Roche Pharma AG (Germany)

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Co-Authors

Gila E. Stein

University of Tennessee at Knoxville

Prasun Nandy

PricewaterhouseCoopers (South Korea)

Stephen C. Jacobson

Indiana University Bloomington

Sisir Roy

National Institute of Advanced Studies

Nikhila Mahadevapuram

University of Houston

Joseph Strzalka

Argonne National Laboratory

Jayanta Mandi

KU Leuven

Miloš V. Novotný

Indiana University Bloomington

Rovshan G. Sadygov

The University of Texas Medical Branch at Galveston

Neelam Patodia

Vellore Institute of Technology University

Cooperative Institutions

Indiana University Bloomington

Roche Pharma AG (Germany)

University of Oxford

Indiana University – Purdue University Indianapolis

University of Houston

PricewaterhouseCoopers (South Korea)

The University of Texas at Austin

University of Tennessee at Knoxville

Indiana University

University of Freiburg

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A New Class of Exact Solutions to a Generalized form of Charap’s Nonlinear Chiral Field Equations of Field Theory

Annals of Pure and Applied Mathematics (2017)

Indranil Mitra Pranab K. Chanda

Exact solutions to a generalized form of the Charap's nonlinear Chiral field equations have been presented for different values of the coupling constants.In most of the situations the solutions could not be obtained as the equations led to non-integrable expressions.In one situation the solutions were exact and complex.In the rest of the situations the solutions were well behaved.

Coupling constant

10.22457/apam.v14n3a8

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In situ characterization of the mTORC1 during adipogenesis of human adult stem cells on chip

Proceedings of the National Academy of Sciences (2016)

Xuanye Wu Nils Schneider Alina Platen Indranil Mitra Matthias Blazek

Significance Adipogenesis is vital for animals to maintain energy balance by storing lipid. As a crucial integrator of nutrient, energy, and metabolite signals, mammalian target of rapamycin (mTOR) reportedly regulates adipogenesis. However, conventional cell cultures are limited to mimicking in vivo conditions, and previous reports do not provide the localization information of mTOR during adipogenesis. Here, we developed an automated microfluidic large-scale integration platform for differentiating human adult stem cells into mature adipocytes with standardized nutrient availability over weeks. With an integrated multiplexed immunoassay, we detected interaction, phosphorylation, and abundance changes of mTOR under the defined conditions. High-content analysis of single-cell data revealed that mTOR complex 1 changes its subcellular position in a temporally synchronized process with lysosomes during adipogenesis.

10.1073/pnas.1601207113

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Generalized linear and mixed models for label-free shotgun proteomics

Statistics and Its Interface (2012)

Matthew C. Leitch Indranil Mitra Rovshan G. Sadygov

Label-free shotgun proteomics holds great promise, and has already had some great successes in pinpointing which proteins are up or down regulated in certain disease states.However, there are still some pressing issues concerning the statistical analysis of label-free shotgun proteomics, and this field has not enjoyed as much dedication of statistical research towards it as microarray research has.Here we reapply previously used statistical methods, the QSpec and quasi-Poisson, as well as apply the negative binomial distribution to both a control data set and a data set with known differential expression to determine the successes and failure of each of the three methods.

Shotgun proteomics

Shotgun

Binomial distribution

Statistical Analysis

10.4310/sii.2012.v5.n1.a8

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Co-operativity in neurons and the role of noise in brain

arXiv (Cornell University) (2007)

Indranil Mitra Sisir Roy Gary Hastings

In view of some recent results in case of the dopaminergic neurons exhibiting long range correlations in VTA of the limbic brain we are interested to find out whether any stochastic nonlinear response may be reproducible in the nano scales usimg the results of quantum mechanics. We have developed a scheme to investigate this situation in this paper by taking into consideration the Schrodinger equation (SE) in an arbitrary manifold with a metric, which is in some sense a special case of the heat kernel equation. The special case of this heat kernel equation is the diffusion equation, which may reproduce some key phenomena of the neural activities. We make a dual equivalent circuit model of SE and incorporate non commutativity and noise inside the circuit scheme. The behaviour of the circuit elements with interesting limits are investigated. The most bizarre part is the long range response of the model by dint of the Central Limit Theorem, which is responsible for coherent behaviour of a large assembly of neurons.

10.48550/arxiv.0708.2384

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Stochastic Polynomial Dynamic Models of the Yeast Cell Cycle

Bulletin of the American Physical Society (2010)

Indranil Mitra Elena Dimitrova Abdul Salam Jarrah

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Understanding molecular recognition and epitope prediction from Information

Indranil Mitra Yan Cui

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In‐plane and out‐of‐plane defectivity in thin films of lamellar block copolymers

Journal of Polymer Science Part B Polymer Physics (2015)

Nikhila Mahadevapuram Indranil Mitra Alona Bozhchenko Joseph Strzalka Gila E. Stein

ABSTRACT We investigate the ordering of poly(styrene‐ b ‐methyl methacrylate) (PS‐PMMA) lamellar copolymers (periodicity L 0 = 46 nm) confined between a free surface and brushed poly(styrene‐ r ‐methyl methacrylate) silicon substrate. The processing temperature was selected to eliminate wetting layers at the top and bottom interfaces, producing approximately neutral boundaries that stabilize perpendicular domain orientations. The PS‐PMMA film thickness ( t = 0.5 L 0 − 2.5 L 0 ) and brush grafting density (Σ = 0.2–0.6 nm −2 ) were systematically varied to examine their impacts on in‐plane and out‐of‐plane ordering. Samples were characterized with a combination of high‐resolution microscopy, X‐ray reflectivity, and grazing‐incidence small‐angle X‐ray scattering. In‐plane order at the top of the film (quantified through calculation of orientational correlation lengths) improved with t n , where the exponent n increased from 0.75 to 1 as Σ decreased from 0.6 to 0.2 nm −2 . Out‐of‐plane defects such as tilted domains were detected in all films, and the distribution of domain tilt angles was nearly independent of t and Σ. These studies demonstrate that defectivity in perpendicular lamellar phases is three‐dimensional, comprised of in‐plane topological defects and out‐of‐plane domain tilt, with little or no correlation between these two types of disorder. Strong interactions between the block copolymer and underlying substrate may trap both kinds of thermally generated defects. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 339–352

Film plane

10.1002/polb.23937

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Improved Mass Defect Model for Theoretical Tryptic Peptides

Analytical Chemistry (2012)

Indranil Mitra Alexey V. Nefedov Allan R. Brasier Rovshan G. Sadygov

Improvements in the mass accuracy and resolution of mass spectrometers have greatly aided mass spectrometry-based proteomics in profiling complex biological mixtures. With the use of innovative bioinformatics approaches, high mass accuracy and resolution information can be used for filtering chemical noise in mass spectral data. Using our recent algorithmic developments, we have generated the mass distributions of all theoretical tryptic peptides composed of 20 natural amino acids and with masses limited to 3.5 kDa. Peptide masses are distributed discretely, with well-defined peak clusters separated by empty or sparsely populated trough regions. Accurate models for peak centers and widths can be used to filter peptide signals from chemical noise. We modeled mass defects, the difference between monoisotopic and nominal masses, and peak centers and widths in the peptide mass distributions. We found that peak widths encompassing 95% of all peptide sequences are substantially smaller than previously thought. The result has implications for filtering out larger stretches of the mass axis. Mass defects of peptides exhibit an oscillatory behavior which is damped at high mass values. The periodicity of the oscillations is about 14 Da which is the most common difference between the masses of the 20 natural amino acids. To determine the effects of amino acid modifications on our findings, we examined the mass distributions of peptides composed of the 20 natural amino acids, oxidized Met, and phosphorylated Ser, Thr, and Tyr. We found that extension of the amino acid set by modifications increases the 95% peak width. Mass defects decrease, reflecting the fact that the average mass defect of natural amino acids is larger than that of oxidized Met. We propose that a new model for mass defects and peak widths of peptides may improve peptide identifications by filtering chemical noise in mass spectral data.

Monoisotopic mass

Mass

Tandem mass tag

10.1021/ac203255e

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Early developments toward HbA1c determination in whole blood by high-speed sample preparation and LC–MS/MS analysis

Analytical and Bioanalytical Chemistry (2024)

Indranil Mitra Andreas Leinenbach Andrea Geistanger Andreas Huber Thomas Dülffer

Abstract We report a method to determine HbA 1c (glycated hemoglobin) where whole blood samples are prepared by fast hemolysis (dilution with deionized water and vortex mixing), digestion with 0.6 mg/mL endoproteinase Glu C (Glu C) in 30 mM ammonium acetate buffer (pH 4.3) at 37 °C for 45 min, and termination of the digestion by diluting with 0.1% formic acid in water, and then analysis by a gradient liquid chromatography-tandem mass spectrometry (LC–MS/MS) method with a run time of 36 s. The method is linear between 0 and 200 HbA 1c /mol Hb (IFCC) with a correlation coefficient of 0.999, providing an inter-day reproducibility between 1.3 and 2.3% CV, and comparable with results from analysis of the same samples on the Roche Cobas® c 513 clinical analyzer with a correlation coefficient of 0.998. In two alternative detection workflows that were not characterized in detail, the same digested samples were purified by a magnetic bead-based solid-phase extraction (SPE) method requiring about 10 min and then analyzed using either an isocratic LC–MS/MS method or a flow injection analysis (FIA)-MS/MS method with run times of 12 s and 18 s, respectively. Our work demonstrates the feasibility of LC–MS-based methods for HbA 1c determination that minimize the time required for sample preparation and measurement while preserving analytical performance and are thereby more suitable for routine clinical settings compared to traditional methods which require up to 25 h and 23 min, respectively, to prepare and measure samples. Graphical abstract

Sample Preparation

Sample (material)

Medical laboratory

10.1007/s00216-024-05601-5

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Multivariate Analysis of Conformational Changes Induced by Macromolecular Interactions

APS (2009)

Indranil Mitra Emil Alexov

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