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Protein folding under force is an integral source of generating mechanical energy in various cellular processes, ranging from protein translation to degradation. Although chaperones are well known to interact with proteins under mechanical force, how they respond to force and control cellular energetics remains unknown. To address this question, we introduce a real-time magnetic tweezer technology herein to mimic the physiological force environment on client proteins, keeping the chaperones unperturbed. We studied two structurally distinct client proteins--protein L and talin with seven different chaperones─independently and in combination and proposed a novel mechanical activity of chaperones. We found that chaperones behave differently, while these client proteins are under force, than their previously known functions. For instance, tunnel-associated chaperones (DsbA and trigger factor), otherwise working as holdase without force, assist folding under force. This process generates an additional mechanical energy up to ∼147 zJ to facilitate translation or translocation. However, well-known cytoplasmic foldase chaperones (PDI, thioredoxin, or DnaKJE) do not possess the mechanical folding ability under force. Notably, the transferring chaperones (DnaK, DnaJ, and SecB) act as holdase and slow down the folding process, both in the presence and absence of force, to prevent misfolding of the client proteins. This provides an emerging insight of mechanical roles of chaperones: they can generate or consume energy by shifting the energy landscape of the client proteins toward a folded or an unfolded state, suggesting an evolutionary mechanism to minimize energy consumption in various biological processes.

Polypeptide chains experiences mechanical tension while translocating through cellular tunnel. In this scenario, interaction of tunnel-associated chaperones with the emerging polypeptide occurs under force; however, this force-regulated chaperone behaviour is not fully understood.We studied the mechanical chaperone activity of two tunnel-associated chaperones BiP and ERdj3 both in the absence and presence of force; and compared to their respective cytoplasmic homologs DnaK and DnaJ. We found that BiP/ERdj3 shows strong foldase activity under force; whereas their cytoplasmic homolog DnaK/DnaJ behave as holdase. Importantly, these tunnel-associated chaperones (BiP/ERdj3) revert to holdase in the absence of force, suggesting that mechanical chaperone activity differs depending on the presence or absence of force. This tunnel-associated chaperone-driven folding event generates additional mechanical energy of up to 54 zJ that could help protein translocation. The mechanical-chaperone behaviour can be explained by strain theory: chaperones with higher intrinsic deformability function as mechanical foldase (BiP, ERdj3), while chaperones with lower intrinsic deformability act as holdase (DnaK and DnaJ). Our study thus unveils the underlying mechanism of mechanically regulated chaperoning activity and provides a novel mechanism of co-translocational protein folding.SignificanceThe mechanical-activity of chaperones, located at the edge of a tunnel, could be different from their cytoplasmic homologs. Translocating substrates within the tunnel are known to experience mechanical constraints, whereas the cytosolic substrates interact with the chaperones in the absence of force.To understand this phenomenon, we investigated two tunnel-associated chaperones BiP/ERdj3 and their cytosolic homologs-DnaK/DnaJ. We observed that BiP/ERdj3 possess strong foldase activity while their substrates are under force; whereas DnaK/DnaJ possess holdase function. Notably all these chaperones function as holdase in the absence of force, which suggest that mechanical chaperone activity is different with and without force. We explained this mechanical behaviour using strain theory, providing a physical mechanism of chaperone-assisted co-translocational protein folding.

The structure-function dynamics of a protein as a flexible polymer is essential to describe its biological functions. Here, using single-molecule magnetic tweezers, we have studied the effect of ionic strength on the folding mechanics of protein L, and probed its folding-associated physical properties by re-measuring the same protein in a range of ammonium sulfate concentrations from 150 mM to 650 mM. We observed an electrolyte-dependent conformational dynamics and folding landscape of the protein in a single experiment. Salt increases the refolding kinetics, while decreasing the unfolding kinetics under force, which in turn modifies the barrier heights towards the folded state. Additionally, salt enhances the molecular compaction by decreasing the Kuhn length of the protein polymer from 1.18 nm to 0.58 nm, which we have explained by modifying the freely jointed chain model. Finally, we correlated polymer chain physics to the folding dynamics, and thus provided an analytical framework for understanding compaction-induced folding mechanics across a range of ionic strengths from a single experiment.

Objectives Mitochondrial dysfunction has long been associated with the pathogenesis of lung cancer (LC). Mitochondrial DNA (mtDNA) haplogroups have been reported to modify the risk of LC in a few different populations; however, no study has been done among the Indians. Here, we explore the relationship between mtDNA haplogroups and LC in a representative eastern Indian sample set. Methods Different combinations of six mtDNA SNPs, which define the major Asian mtDNA haplogroups M and N, and their sub-haplogroups D, G, M7, R, and F were genotyped via polymerase chain reaction (PCR) – restriction fragment length polymorphism (RFLP) – sequencing approach in 94 smoker LC patients and 100 healthy smoker controls from an eastern Indian cohort. Results The distribution of 7 mtDNA haplogroups did not show any significant differences between patients and controls (p Conclusions Our study is the first to indicate that the major Asian mtDNA haplogroups have no significant (p<0.05) association with LC in East Indian population.

Recent single-molecule studies have recognized talin as a mechanosensitive hub in focal adhesion, where its function is strongly regulated by mechanical force. For instance, at low force (below 5 pN), folded talin binds RIAM for integrin activation; whereas at high force (above 5 pN), it unfolds to activate vinculin binding for focal adhesion stabilization. Being a cytoplasmic protein, talin might interact with several cytosolic chaperones: however, the role of chaperones in talin mechanics is unknown.To address this question, we investigated the force response of a mechanically stable talin domain with a set of well-known holdase (DnaJ, DnaK, Hsp70, and Hsp40) and foldase (DnaKJE, DsbA) chaperones, using single-molecule magnetic tweezers. Our findings demonstrate that chaperone could affect adhesion proteins stability by changing their folding mechanics; while holdase chaperones reduce their unfolding force to ~6 pN, foldase chaperones shift it up to ~15 pN. Since talin is mechanically synced within 2 pN force ranges, these changes are significant in cellular condition. Furthermore, we determined the fundamental mechanism of this altered mechanical stability, where chaperones directly reshape their energy landscape: unfoldase chaperone (DnaK) decreases the unfolding barrier height from 26.8 to 21.7 kBT, while foldase chaperone (DsbA) increases it to 33.5 kBT. We reconciled our observations with eukaryotic Hsp70 and Hsp40 chaperones and observed their similar function of decreasing the talin unfolding barrier to 23.1 kBT. The quantitative mapping of this chaperone-induced talin folding landscape directly illustrates that chaperones perturb the adhesion protein stability under physiological force, thereby influencing their force-dependent interactions and adhesion dynamics.

Recent single-molecule studies have recognized talin as a mechanosensitive hub in focal adhesion, where its function is strongly regulated by mechanical force. For instance, at low force (below 5 pN), folded talin binds RIAM for integrin activation; whereas at high force (above 5 pN), it unfolds to activate vinculin binding for focal adhesion stabilization. Being a cytoplasmic protein, talin might interact with several cytosolic chaperones: however, the role of chaperones in talin mechanics is unknown.To address this question, we investigated the force response of a mechanically stable talin domain with a set of well-known holdase (DnaJ, DnaK, Hsp70, and Hsp40) and foldase (DnaKJE, DsbA) chaperones, using single-molecule magnetic tweezers. Our findings demonstrate that chaperone could affect adhesion proteins stability by changing their folding mechanics; while holdase chaperones reduce their unfolding force to ∼6 pN, foldase chaperones shift it up to ∼15 pN. Since talin is mechanically synced within 2 pN force ranges, these changes are significant in cellular condition. Furthermore, we determined the fundamental mechanism of this altered mechanical stability, where chaperones directly reshape their energy landscape: unfoldase chaperone (DnaK) decreases the unfolding barrier height from 26.8 to 21.7 kBT, while foldase chaperone (DsbA) increases it to 33.5 kBT. We reconciled our observations with eukaryotic Hsp70 and Hsp40 chaperones and observed their similar function of decreasing the talin unfolding barrier to 23.1 kBT. The quantitative mapping of this chaperone-induced talin folding landscape directly illustrates that chaperones perturb the adhesion protein stability under physiological force, thereby influencing their force-dependent interactions and adhesion dynamics.

Single-molecule technologies have expanded our ability to detect biological events individually, in contrast to ensemble biophysical technologies, where the result provides averaged information. Recent developments in atomic force microscopy have not only enabled us to distinguish the heterogeneous phenomena of individual molecules, but also allowed us to view up to the resolution of a single covalent bond. Similarly, optical tweezers, due to their versatility and precision, have emerged as a potent technique to dissect a diverse range of complex biological processes, from the nanomechanics of ClpXP protease–dependent degradation to force-dependent processivity of motor proteins. Despite the advantages of optical tweezers, the time scales used in this technology were inconsistent with physiological scenarios, which led to the development of magnetic tweezers, where proteins are covalently linked with the glass surface, which in turn increases the observation window of a single biomolecule from minutes to weeks. Unlike optical tweezers, magnetic tweezers use magnetic fields to impose torque, which makes them convenient for studying DNA topology and topoisomerase functioning. Using modified magnetic tweezers, researchers were able to discover the mechanical role of chaperones, which support their substrate proteinsby pulling them during translocation and assist their native folding as a mechanical foldase. In this article, we provide a focused review of many of these new roles of single-molecule technologies, ranging from single bond breaking to complex chaperone machinery, along with the potential to design mechanomedicine, which would be a breakthrough in pharmacological interventions against many diseases.

In today's world, we are on an express train to a cashless society which has led to a tremendous escalation in the use of credit card transactions. But the flipside of this is that fraudulent activities are on the increase; therefore, implementation of a methodical fraud detection system is indispensable to cardholders as well as the card-issuing banks. In this paper, we are going to use different machine learning algorithms like random forest, logistic regression, Support Vector Machine (SVM), and Neural Networks to train a machine learning model based on the given dataset and create a comparative study on the accuracy and different measures of the models being achieved using each of these algorithms. Using the comparative analysis on the F_1 score, we will be able to predict which algorithm is best suited to serve our purpose for the same. Our study concluded that Artificial Neural Network (ANN) performed best with an F_1 score of 0.91.

Protein folding under force is an integral source of generating mechanical energy in various cellular processes, ranging from protein translation to degradation. Although chaperones are well known to interact with proteins under mechanical force, how they respond to force and control cellular energetics remains unknown. To address this question, we introduce novel real-time microfluidics-magnetic-tweezers technology to apply physiological force pulses on client proteins, keeping the chaperones unperturbed. Interestingly, we observe that chaperones behave differently under force than its previously known functions. For instance, tunnel associated chaperones (trigger factor and DsbA), otherwise working as holdase without force, assist folding under force. This process generates an additional mechanical energy up to ~65 zJ to facilitate translation or translocation. However, other cytoplasmic oxidoreductases (PDI, thioredoxin) or well-known foldase chaperone (DnaKJE) does not possess this mechanical folding ability. Notably, the transferring chaperones (DnaK, DnaJ, SecB), act as unfoldase and slow down folding process to prevent misfolding of the client proteins. This provides an emerging insight of mechanical roles of chaperones: they can generate or consume energy by shifting energy landscape of the client proteins towards folded or unfolded state; suggesting an evolutionary mechanism to minimize the energy consumption in various biological processes.

Association studies on lung cancer have often yielded conflicting and inconclusive results. We performed a comprehensive meta-analysis to dissect the precise effects of the candidate variants. We searched for association studies on lung cancer from the Indian subcontinent. Cochran’s Q-test assessed heterogeneity. Both overall and histotype-stratified meta-analysis was done using fixed-effect and random-effects models. Smoking status stratified subgroup analysis and effect modification tests were done. An associated variant with significant heterogeneity was genotyped in an eastern Indian population to investigate the contribution of potential confounders followed by a comprehensive meta-analysis across world populations. Significant heterogeneity was observed for the 8 variants. Both fixed-effect and random-effects meta-analysis of 24 variants showed FDR-corrected associations of rs3547/XRCC1 and rs1048943/CYP1A1 with lung cancer along with 5 nominal associations. del1/GSTT1, rs4646903/CYP1A1, and rs10488943/CYP1A1 were associated with adenocarcinoma, squamous cell carcinoma, and both, respectively. rs4646903/CYP1A1 was associated with lung cancer among smokers with significant effect modification by smoking. rs10488943/CYP1A1 was associated with lung adenocarcinoma in the East Indian case-control study. rs1048943/CYP1A1 was associated with lung cancer across world populations. Our work confirms the risk loci for lung cancer and its subtypes in the context of smoking and other aetiological factors, which could aid in personalised treatment.

Protein folding under force is an integral source of generating mechanical energy in various cellular processes, ranging from protein translation to degradation. Although chaperones are well known to interact with proteins under mechanical force, how they respond to force and control cellular energetics remains unknown.To address this question, we introduce novel real-time magnetic-tweezers technology to mimic physiological force environment on client proteins, keeping the chaperones unperturbed. We studied two structurally distinct client proteins with seven different chaperones, independently and in combination, and proposed novel mechanical activity of chaperones. We found chaperones behave differently, while these client proteins are under force than its previously known functions. For instance, tunnel associated chaperones (DsbA and trigger factor), otherwise working as holdase without force, assist folding under force. This process generates an additional mechanical energy up to ∼147 zJ to facilitate translation or translocation. However, well-known cytoplasmic foldase chaperones (PDI, thioredoxin, or DnaKJE), does not possess the mechanical folding ability under force. Notably, the transferring chaperones (DnaK, DnaJ, SecB), act as unfoldase and slow down folding process, both in the presence and absence of force, to prevent misfolding of the client proteins. This provides an emerging insight of mechanical roles of chaperones: they can generate or consume energy by shifting energy landscape of the client proteins towards folded or unfolded state; suggesting an evolutionary mechanism to minimize the energy consumption in various biological processes.

As the scale of cloud infrastructure is augmenting, so is the number of instances that needs to be provisioned. As a result, there is a requirement for automating the process of managing infrastructure instances to facilitate development, staging, and production environments. The purpose of this paper is to understand ‘Infrastructure as a code’ (IaC) in relation to Software Defined Infrastructure. Using Azure Resource Manager (ARM) Templates we will demonstrate the benefit and importance of IaC by deploying a web application on Microsoft Azure using only code. The use of ARM templates was found to increase the agility of the deployment and management process. We will also demonstrate IaC using Terraform and Pulumi. The paper also discusses the correlation of IaC with the concept of code reusability and repeatability.

Studies of free energy, kinetics or elasticity are common to most disciplines of science. Detailed quantification of these properties demands number of specialized technologies. Furthermore, monitoring perturbation in any of these properties, in presence of external stimuli (protein/DNA/drugs/nanoparticles etc.), requires multiple experiments. However, none of these available technologies can monitor these perturbations simultaneously in real time on the very same molecule in a single shot experiment. Here we present real-time microfluidics-magnetic tweezers technology with the unique advantage of tracking a single protein dynamics for hours, in absence of any significant drift, with the flexibility of changing physical environment in real time. Remarkable stability of this technique allows us to quantify five molecular properties (unfolding kinetics, refolding kinetics, conformational change, chain flexibility, and ∆G for folding/unfolding), and most importantly, their dynamic perturbation upon interacting with salt on the same protein molecule from a single experiment. We observe salt reshapes the energy landscape by two specific ways: increasing the refolding kinetics and decreasing the unfolding kinetics, which is characterized as mean first passage time. Importantly, from the same trajectory, we calculated the flexibility of the protein polymer, which changes with salt concentration and can be explained by our modified electrolyte FJC model. The correlation between Delta G, kinetics and polymer elasticity strongly argues for a stiffness driven energy landscape of proteins. Having the advantage of sub nanometer resolution, this methodology will open new exciting window to study proteins , one such examples is demonstrated in this article: electrolyte driven conformational fluctuation under force, which was not studied before.

Mechanotransduction from the extracellular matrix into the cell is primarily supervised by a transmembrane receptor, integrin, and a cytosolic protein, talin. Integrin binds ligands on the extracellular side, whereas talin couples integrin receptors to the actin cytoskeleton and later acts as a "force buffer". Talin and integrin together form a mechanosensitive signaling hub that regulates crucial cellular processes and pathways, including cell signaling and formation of focal adhesion complexes, which help cells to sense their mechano-environment and transduce the signal accordingly. Although both proteins function in tandem, most literature focuses on them individually. Here, we provide a focused review of the talin-integrin mechano-interactome network in light of its role in the process of mechanotransduction and its connection to diseases. While working under force, these proteins drive numerous biomolecular interactions and form adhesion complexes, which in turn control many physiological processes such as cell migration; thus, they are invariably associated with several diseases from leukocyte adhesion deficiency to cancer. Gaining insights into their role in the occurrence of these pathological disorders might lead us to establish treatment methods and therapeutic techniques.

In today's technologically advanced and highly digitalized world, huge amounts of raw images are being captured on a daily basis. Processing these images to extract useful information and/or manipulating them is a herculean task in itself. Image enhancement has been an important facet in image processing ever since images were captured on photographic paper using silver chlorides and other photosensitive chemicals. Earlier converting negatives took more than eight hours straight. Now with the advent of computers and digital images we can do this in milliseconds. One such problem was to enhance an image. In this paper, efforts have been made for performing digital image enhancement by using Histogram Equalization and Bilinear Interpolation to enhance the contrast and scaling of the image, so that, one can say at a cursory glance that the image quality has improved. The C programming language is a good algorithm description format as it is a widely used language and one can understand the basics of image processing and how image enhancement is done at a pixel level. This paper is intended to serve as a reference for developers and programmers who are keen on learning about image manipulation by directly working with the pixel information.

Human rights education is no longer considered an alien normative and discursive practice in the inter-governmental discussions and civil society actions because human rights have increasingly become more universal in the sense that they are held to be a guarantee of ideals of equality and enhance moral autonomy of rational human beings, irrespective of their own specific desires, identities or partial interests. Seen from this perspective, this chapter discusses ethnic conflict and sectarian violence in India in the context of human rights violations by the state and by non-state actors. Given the relative silence of discussion of sectarian violence in human rights literacy, we argue that interrogation of various types of ethnic violence is urgently required for understanding the evolution of universal and inalienable regime of human rights in varying institutional and cultural contexts across nations. Based on empirical data, we conclude that the case studies of sectarian and communal violence from a plural, diverse democracy like India have potential to contribute to reframing the discussion of human rights literacy in the universities and college/school class rooms.

Skin pigmentation in human is a complex trait, which varies widely, both within and between human populations. The exact players governing the trait of skin pigmentation remain elusive till date. Various Genome Wide Association Studies (GWAS) have shown the association of different genomic variants with normal human skin pigmentation, often indicating genes with no direct implications in melanin biosynthesis or distribution. Little has been explained in terms of the functionality of the associated Single-Nucleotide Polymorphisms (SNPs) with respect to modulating the skin pigmentation phenotype. In the present study, which, to our knowledge, is the first of its kind, we tried to analyze and prioritize 519 non-coding SNPs and 24 3'UTR SNPs emerging from 14 different human skin pigmentation-related GWAS, primarily using several ENCODE-based web-tools like rSNPBase, RegulomeDB, HaploReg, etc., most of which incorporate experimentally validated evidences in their predictions. Using this comprehensive, in-silico, analytical approach, we successfully prioritized all the pigmentation-associated GWAS-SNPs and tried to annotate pigmentation-related functionality to them, which would pave the way for deeper understanding of the molecular basis of human skin pigmentation variations.