Saroj Kumar

Saroj Kumar
All India Institute of Medical Sciences | AIIMS

PhD, Biophysics

About

67
Publications
21,916
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928
Citations
Introduction
Development of a new tool "Infrared imaging" for biomedical applications. Here I am focusing on various diseases including cancer, neurodegenrative diseases ( Multiple sclerosis, chronic pain). Goal is to provide automated early diagnosis on the basis of chemical changes during the progression of disease. I am also focusing on to use the infrared spectroscopy for drug development and for the basic research on bio-molecules.
Additional affiliations
May 2014 - December 2015
Canadian Light Source Inc. (CLS)
Position
  • CIHR-THRUST postdoctoral fellow
December 2011 - present
Université Libre de Bruxelles
Position
  • Microenvironment of Breast cancer by FTIR Imaging
Description
  • Breast cancer is a global public health issue. Fourier transform infrared (FTIR) imaging is a suitable technique for the quantitative analysis of tissue in the clinical routine.
March 2007 - March 2011
Stockholm University
Position
  • spectroscopy of biological molecules
Education
August 1997 - June 2003
All India Institute of Medical Sciences, New Delhi, India
Field of study
  • Human Biology, Biophysics

Publications

Publications (67)
Article
A person suspected of having Alzheimer’s disease (AD) is clinically diagnosed for the presence of principal biomarkers, especially misfolded amyloid-beta (Aβ) and tau proteins in the brain regions. Existing radiotracer diagnostic tools, such as PET imaging, are expensive and have limited availability for primary patient screening and pre-clinical a...
Article
Full-text available
Parkinson's disease (PD) is a neurological disorder that affects the movement of the human body. It is primarily characterized by reduced dopamine levels in the brain. The causative agent of PD is still unclear but it is generally accepted that α-synuclein has a central role to play. It is also known that gap-junctions and associated connexins are...
Preprint
Parkinson’s disease is generally asymptomatic at earlier stages. The pressing need is for the susceptibility risk biomarkers, that can aid in better diagnosis and therapeutics as well can objectively serve to measure the endpoint of disease progression. The role of exosomes in progression of neurodegenerative diseases is already reported and its ca...
Article
Full-text available
The pandemic caused by SARS-CoV-2 (SCoV-2) has impacted the world in many ways and the virus continues to evolve and produce novel variants with the ability to cause frequent global outbreaks. Although the advent of the vaccines abated the global burden, they were not effective against all the variants of SCoV-2. This trend warrants shifting the fo...
Article
Purpose: To compare osteocalcin and crestal bone loss in implants placed under an immediate loading (IL) compared to a delayed loading (DL) protocol. Materials and methods: This preliminary, split-mouth, randomized controlled trial included 14 participants who required replacement of both mandibular first molars opposing a completely dentate max...
Article
Full-text available
The elusiveness encircling around the domain of cognition, its impairment, and the poor prognosis of Alzheimer’s disease has made early diagnosis a necessity. The noticeable symptoms in these conditions appear years later after the neuropathological changes occur in the brain. Exosomes, a small-sized extracellular vesicle facilitate intercellular c...
Article
Alzheimer's disease (AD) is an age-related multifactorial neurodegenerative disorder characterized by severe central cholinergic neuronal loss, gradually contributing to cognitive dysfunction and impaired motor activity, resulting in the brain's cell death at the later stages of AD. Although the etiology of AD is not well understood, however, sever...
Article
Full-text available
Neurodegenerative diseases (ND) remains to be one of the biggest burdens on healthcare systems and serves as a leading cause of disability and death. Alzheimer's disease (AD) is among the most common of such disorders, followed by Parkinson's disease (PD). The basic molecular details of disease initiation and pathology are still under research. Onl...
Article
Background The p53, tumor suppressor protein is inactivated upon mutation in the DNA-binding domain and the non-functional protein leads to cancers. The p53Y220C is one of the most frequently observed mutations in p53 with a scope of rescuing the protein function using small molecules. Methods Using computational modeling, biophysical, and experim...
Article
Full-text available
Abstract Background Cognitive impairment is an prominent aspect of aging and a common accomplice of dementia. Majority of dementia cases are dictated by Alzheimer’s disease (AD) pathology. There are many neuroimaging and molecular biomarkers to differentiate between cognitive impairment and dementia however, these are either invasive or expensive;...
Article
Full-text available
In recent years, studies on mineralized tissues are becoming increasingly popular not only due to the diverse mechanophysical properties of such materials but also because of the growing need to understand the intricate mechanism involved in their assembly and formation. The biochemical mechanism that results in the formation of such hierarchical s...
Article
Background: Cognition is the ability of a person to think, remember, and interconnect ideas from various dimensions to strive for solutions. Cognitive defects accompany all forms of dementia and the decline in cognition is a most feared aspect. Mild cognitive impairment is considered as a transitional phase and the progressive loss in cognition ca...
Article
Biomineralization can be considered as nature's strategy to produce and sustain biominerals, primarily via creation of hard tissues for protection and support. This review examines the biomineralization process within the hard tissues of the human body with special emphasis on the mechanisms and principles of bone and teeth mineralization. We descr...
Article
All mRNAs cannot be translated into full-length proteins due to ribosome-stalling that leads to release of peptidyl-tRNA which can be lethal for bacterial survival. The enzyme peptidyl-tRNA hydrolase (PtH) hydrolyses the ester bond between nascent peptide and tRNA of peptidyl-tRNA and rescues the cells from toxicity. PtH is an essential enzyme in b...
Article
Full-text available
Serine racemase (SR) converts the free form of L-serine into D-serine (DS) in the mammalian brain. The DS functions as a co-agonist of N-methyl D-aspartate (NMDA) receptor. The over- activation of NMDA receptor leads to many neurological disorders like stroke, amyotrophic lateral sclerosis, Alzheimer’s disease and an effective inhibitor of SR could...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
A growing body of evidence supports the hypothesis that intrinsically disordered proteins often mediate host‐pathogen interactions and modulate host functions for pathogen survival and virulence. Mycobacterium tuberculosis (M.tb) has evolved largely through reductive evolution, with a few exceptions such as the glycine‐alanine rich PE‐PPE/PGRS prot...
Article
Full-text available
The importance of whole protein extracts from different types of human teeth in modulating the process of teeth biomineralization is reported. There are two crucial features in protein molecules that result in efficient teeth biomineralization. Firstly, the unique secondary structure characteristics within these proteins i.e. the exclusive presence...
Conference Paper
Full-text available
Proteins are the biomacromolecules that work downstream to genes in every living system. It is these protein molecules that are responsible for a plethora of functions in our body, ranging from building skeleton tissues to transmitting signal from one place to others. There was a period when biologists have the view that for a protein to function,...
Article
Full-text available
The present study describes an efficient method for isolation and purification of protein extracts from four types of human teeth i.e. molar, premolar, canine, and incisor. Detailed structural characterization of these protein extracts was done by Fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) which showed that a major f...
Article
Linked Article: De Bruyne et al. Br J Dermatol 2019; 180:637–646.
Article
The Mycobacterium tuberculosis (Mtb) Rv2747 gene encodes for a functional protein known as ArgA, which plays an important role in the first step of the L-arginine biosynthesis pathway. ArgA transfers the acetyl group from the acetyl-CoA to either L-glutamate or L-glutamine, which are the known substrates. Here, we present two crystal structures of...
Article
We employed Fourier Transform Infrared Microspectroscopy to examine, in situ, the effects of waterborne Cu, Cd and Zn, alone and in binary mixtures, during acute exposure on the integrity of major lipid and protein constituents of the gill of a model teleost species, rainbow trout (Oncorhynchus mykiss). Our findings demonstrated that acute exposure...
Article
Full-text available
Clubroot disease is a serious threat to canola production in western Canada and many parts of the world. Rcr1 is a clubroot resistance (CR) gene identified recently and its molecular mechanisms in mediating CR have been studied using several omics approaches. The current study aimed to characterize biochemical changes in the cell wall of canola roo...
Article
Full-text available
Background: Cancer is a major global health issue. It causes extensive individual suffering and gives a huge burden on the health care in society. Despite extensive research and different tools have been developed it still remains a challenge for early detection of this disease. FTIR imaging has been used to diagnose and differentiate the molecula...
Article
Full-text available
The tumor microenvironment changes chemically and morphologically during cancer progression. Cancer stimulated fibroblasts promote tumor growth, yet, the mechanism explaining the transition to a cancer-stimulated fibroblast remains elusive. Here, we have used multi-modal spectroscopic modalities such as Fourier transform infrared imaging (FTIRI), X...
Article
Clubroot disease, caused by Plasmodiophora brassicae Woronin, is a serious soil-borne disease of crucifer crops worldwide. It poses a serious threat to canola production in western Canada. Rcr1 is a new clubroot resistance gene identified in Brassica rapa. A multifaceted approach was employed to understand the molecular changes in canola plant cell...
Data
Fluorescent (A–D) microscope images from cross section (10 μm) of control and inoculated wheat cultivars Sumai3 (SU3, A,B) and Muchmore (MM, C,D) after 4 days of infection with FHB. Red arrows show changes in cell wall thickness following the pathogenic infection with FHB. Scale bar = 75 μm.
Data
Asymptomatic and symptomatic infected rachis of the resistant and susceptible cultivars Sumai3 and Muchmore in comparison with control rachis at 10 days post-inoculation with FHB. Scale bar 4 mm. (A): control Sumai3, (B): inoculated Sumai3 with FHB, (C) control Muchmore, and (D) inoculated Muchmore with FHB.
Data
Confocal microscope movie showing cell wall structures of the infected wheat rachis of the resistant cultivar Sumai3 (A) and the susceptible cultivar Muchmore (B) with Fusarium head blight at 4 days post-inoculation.
Article
Full-text available
Fusarium head blight (FHB) is a serious disease of wheat worldwide. Cultivar resistance to FHB depends on biochemical factors that confine the pathogen spread in spikes. Breeding for cultivar resistance is considered the most practical way to manage this disease. In this study, different spectroscopy and microscopy techniques were applied to discri...
Article
The effect of microwave treatment to reduce the cooking times of five pulses namely red lentil, chickpea, pigeon pea, mung bean and pinto bean were determined in this study. Pulses from 10 to 18% moisture contents were treated using 400 to 600 W microwaves for 14 to 56 s. The cooking times of microwave treated pulses were significantly lower than t...
Article
Development of modern infrared spectroscopy and imaging technique has wide range of applications in health and plant sciences. Initially, it was extensively used for the study of proteins, nucleotides, lipids and carbohydrates. With time, it extended to the disease assessment to discriminate healthy and diseased samples on the basis of chemical cha...
Conference Paper
Full-text available
Clubroot disease, caused by Plasmodiophors brassicae Woronin, is a serious threat to canola production in western Canada. Rcr1 is a new clubroot resistance (CR) gene identified in Brassica rapa. The purpose of this study was to understand biochemical changes associated with Rcr1-mediated clubroot resistance and the expression of defense-related gen...
Conference Paper
Full-text available
Fusarium Head Blight (FHB) is the major disease of wheat in North America, causing severe losses in grain yield and quality. Breeding for cultivar resistance is considered the most practical way to manage this disease. In this study, different spectroscopy and microscopy techniques were applied to discriminate resistance in wheat genotypes against...
Conference Paper
Full-text available
Background: Breast cancer is a global public health issue. It is the second cause of mortality in western women. Surgery is the primary treatment in the majority of cases, alone or in combination with radiotherapy, chemotherapy etc. However around 50% of these cases will develop metastatic disease (incurable). The mechanism involved in the progress...
Article
Pea (Pisum sativum L.) is a major legume crop grown in a semi-arid climate in western Canada, where heat stress affects pollination, seed set and yield. Seed set and pod growth characteristics, along with in vitro percentage pollen germination, pollen tube growth, and pollen surface composition, were measured in two pea cultivars (CDC Golden and CD...
Article
Full-text available
Fusarium head blight (FHB) is a serious disease of wheat worldwide. Cultivar resistance to FHB depends on biochemical factors that confine the pathogen spread in spikes. In the current study, Fourier transform infrared (FTIR) spectroscopy (4000–800 cm−1 ) was used of bulk samples of florets and rachises to better understand the mechanism of FHB res...
Poster
Full-text available
Mid-Infrared and high energy X-ay spectroscopy were used to analyze the organic and mineral composition of pea seeds from two genotypes of peas that differ in phytic acid content. Mid-IR absorption spectra of bulk pea seed samples were used to assess the spectral differences between the two pea genotypes and identify the absorption maxima of spectr...
Article
Full-text available
With climate change, pea will be more frequently subjected to heat stress in semi-arid regions like Saskatchewan during flowering. The pollen germination percentage of two pea cultivars was reduced by heat stress (36°C) with an important decrease in cultivar ‘CDC Golden’ compared to ‘CDC Sage’. Lipids, protein and other pollen coat compositions of...
Article
Full-text available
It is well known that the micro-environment plays a major role in breast cancer progression. Yet, the mechanism explaining the transition from normal to cancer-stimulated fibroblasts remains to be elucidated. Here we report a FTIR imaging study of the effects of three different breast cancer cell lines on normal fibroblasts in culture. Fibroblast a...
Article
Infrared spectroscopy was used to characterise recombinant sarcoplasmic reticulum Ca(2+)-ATPase (SERCA1a). In the amide I region, its spectrum differed from that of Ca(2+)-ATPase prepared from rabbit fast twitch muscle below 1650 cm(-1). A band at 1642 cm(-1) is reduced in the spectrum of the recombinant protein and a band at 1631 cm(-1) is more pr...
Article
Thermally cleavable solubilizing groups have been introduced on a π-conjugated core, which can be cleaved and volatilized via heat treatment directly after the thin film fabrication. The X-ray and atomic force microscopic investigations of “3,6-di(2,2′-bithiophen-5-yl)pyrrolo[3,4-c]pyrrole-1,4-(2H,5H)-dione” (DPP-4T) synthesized from its precursor...
Article
This brief review focuses on the information that can be obtained for biomolecules, especially proteins, by using the technique infrared-induced difference spectroscopy.
Article
Full-text available
Fourier transform infrared (FTIR) imaging was applied on histopathological specimens of breast cancer of different tumor histological grades. Focus was given to the extracellular matrix. FTIR spectral changes were observed when examining the extracellular matrix close to and far from carcinoma. Major changes were observed, in particular in the rela...
Article
Recombinant Ca(2+) -ATPase was expressed in Saccharomyces cerevisiae with a biotin acceptor domain (BAD) linked to its C terminus by a thrombin cleavage site. We obtained 200 μg of ~70% pure recombinant sarco-endoplasmic reticulum Ca(2+) -ATPase isoform 1a (SERCA1a) from a 6 L yeast culture. The catalytic cycle of SERCA1a was followed in real time...
Article
Fourier transform infrared (FTIR) spectroscopy was used to study the structure of the recombinant antibodies 1E10, anti-CD20 and hR3, which are used as anti-cancer therapeutic drugs. We tested their sensitivity against different conditions and treatments such as pH, temperature, freeze-thaw cycles and drying, which are relevant for the practical us...
Article
Drug development is impeded by the need to design for each drug target a test that detects the binding of drug candidate molecules to the target protein. Therefore a general method to detect ligand binding is highly desirable. Here we present an observation towards developing such a method which is based on monitoring a change in water absorption b...
Article
Pyruvate kinase exhibits allosteric properties. The allosteric effect of fructose 1,6-bisphosphate (FBP) on phosphoenolpyruvate (PEP) binding to rabbit muscle pyruvate kinase (PK) in the presence of various ions (Mg(2+), Mn(2+), K(+), Na(+)) was studied by attenuated total reflection infrared spectroscopy in combination with a dialysis accessory. T...
Article
The effects of mono- and divalent ions (Li(+), K(+), Na(+), Cs(+), Mg(2+), Ca(2+), Mn(2+), Zn(2+)) on the binding of phosphoenolpyruvate (PEP) to rabbit muscle pyruvate kinase (PK) were studied by attenuated total reflection infrared spectroscopy in combination with a dialysis accessory. The experiments assessed the structural change of the protein...
Book
Infrared spectroscopy is a valuable technique for the study of ligand induced changes in biomolecules. Our development of a dialysis accessory to attenuated total reflection infrared spectroscopy makes this technique more universal for ligand binding studies. We use this method to understand the binding of phosphoenolpyruvate (PEP) and Mg2+ to pyru...
Article
Structural changes in rabbit muscle pyruvate kinase (PK) induced by phosphoenolpyruvate (PEP) and Mg(2+) binding were studied by attenuated total reflection Fourier transform infrared spectroscopy in combination with a dialysis accessory. The experiments indicated a largely preserved secondary structure upon PEP and Mg(2+) binding but also revealed...
Article
Full-text available
Fourier transform infrared (FTIR) spectroscopy provides a direct, "on-line" monitor of enzymatic reactions. Measurement of enzymatic activity is based on the fact that the infrared spectra of reactants and products of an enzymatic reaction are usually different. Several examples are given using the enzymes pyruvate kinase, fumarase and alcohol dehy...
Article
The infrared spectrum of phosphoenol pyruvate (PEP) in aqueous solution was studied experimentally and theoretically in its fully ionized, singly protonated and doubly protonated form. The density functional theory with the B3LYP functional and with the 6-31G(d,p), 6-31++G(d,p), and 6-311++G(d,p) basis sets were used in the theoretical study. The c...
Article
Full-text available
A dialysis accessory for attenuated total reflection (ATR) infrared spectroscopy is described together with an evaluation based on known systems with well-studied infrared spectra, such as chemical oxidation and reduction of cytochrome c and substrate binding to the Ca2+-ATPase. Changes in the infrared spectra of the two proteins are successfully m...

Questions

Questions (3)
Question
Need Suggestions
I am doing kinetics assays and binding studies of my protein which is an enzyme .There are two substrates for this enzyme: sub-A and sub B. I am getting discrepancies in the Kd and Km values. The sub-A has Kd: 54 and Km : 155 value. Sub-B: Kd: 23, Km: 25. The IC50 of SubA: 1.27 micro molar and Sub B: 27 micro molar. Please also provide the references.
Question
Is any has experiences with the Pro-Q dimond phospho protein staining? Is this dye can be reusable, if yes how many times?

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Projects (2)
Project
The interplay between autophagy, IAPs, and aging; their role in adult neurogenesis; and the contribution of autophagy as a regulatory strategy are being explored in the study, and discuss potential roles of autophagy in adult brain function. To understand this, the expression patterns of autophagic proteins, IAPs, aging-related proteins, and various markers of neural stem cells and neurogenesis will be studied in the presence of autophagic modulators in young and aged rats. Although several factors are known to affect neurogenesis, this study will make an understanding in the interplay between these mechanisms and their roles in regulating adult neurogenesis. Autophagy has an important role in cell survival during neurodegenerative diseases and brain injuries, and adult neurogenesis and neural stem cells have been shown to improve the outcomes of these pathologies. Therefore, this study will shed some light on the mechanism involving autophagic regulation of adult neurogenesis and neural stem cells which may contribute to enhancing the survival and differentiation of endogenous NSCs, will advance the clinical applications of NSC therapy.
Project
Biomarker based early detection in biodiagnosis based on chemical changes such as cancer, neuro-degenerative diseases. Understanding the protein mechanism and ligand (Drug) bindings.