Types of spectroscopy and microscopy techniques for cancer diagnosis: a review

Cancer is a life-threatening disease that has claimed the lives of many people worldwide. With the current diagnostic methods, it is hard to determine cancer at an early stage, due to its versatile nature and lack of genomic biomarkers. The rapid development of biophotonics has emerged as a potential tool in cancer detection and diagnosis. Using the fluorescence, scattering, and absorption characteristics of cells and tissues, it is possible to detect cancer at an early stage. The diagnostic techniques addressed in this review are highly sensitive to the chemical and morphological changes in the cell and tissue during disease progression. These changes alter the fluorescence signal of the cell/tissue and are detected using spectroscopy and microscopy techniques including confocal and two-photon fluorescence (TPF). Further, second harmonic generation (SHG) microscopy reveals the morphological changes that occurred in non-centrosymmetric structures in the tissue, such as collagen. Again, Raman spectroscopy is a non-destructive method that provides a fingerprinting technique to differentiate benign and malignant tissue based on Raman signal. Photoacoustic microscopy and spectroscopy of tissue allow molecule-specific detection with high spatial resolution and penetration depth. In addition, terahertz spectroscopic studies reveal the variation of tissue water content during disease progression. In this review, we address the applications of spectroscopic and microscopic techniques for cancer detection based on the optical properties of the tissue. The discussed state-of-the-art techniques successfully determines malignancy to its rapid diagnosis.

A theoretical development of improved cosine similarity measure for interval valued intuitionistic fuzzy sets and its applications

This study mainly focuses on developing a new flexible technique for interval-valued intuitionistic fuzzy cosine similarity measures, which significantly analyzes the strength of the relationship between two objects. Based on the notion of a cosine similarity measure between IVIFSs, the proposed measure is formulated. Then, the measure is demonstrated to satisfy some essential properties, which prepare the ground for applications in different areas. Finally, the study uses the proposed measure to solve real-world decision problems such as pattern recognition, medical diagnosis, and multi-criteria decision-making problems with interval-valued intuitionistic fuzzy information. The numerical examples of the mentioned applications are delivered to validate the effectiveness of the developed approach in solving real-life problems.

Localization of sensor nodes in wireless sensor networks using bat optimization algorithm with enhanced exploration and exploitation characteristics

Wireless sensor networks (WSNs) contain sensor nodes in enormous amount to accumulate the information about the nearby surroundings, and this information is insignificant until the exact position from where data have been collected is revealed. Localization of sensor nodes in WSNs plays a significant role in several applications such as detecting the enemy movement in military applications. The major aim of localization problem is to find the coordinates of all target nodes with the help of anchor nodes. In this paper, two variants of bat optimization algorithm (BOA) are proposed to localize the sensor nodes in a more efficient way and to overcome the drawbacks of original BOA, i.e. being trapped in local optimum solution. The exploration and exploitation features of original BOA are modified in the proposed BOA variants 1 and 2 using improved global and local search strategies. To validate the efficiency of the proposed BOA variants 1 and 2, several simulations have been performed for various numbers of target nodes and anchor nodes, and the results are compared with original BOA and other existing optimization algorithms applied to node localization problem. The proposed BOA variants 1 and 2 outperform the other algorithms in terms of mean localization error, number of localized nodes and computing time. Further, the proposed BOA variants 1 and 2 and original BOA are also compared in terms of various errors and localization efficiency for several values of target and anchor nodes. The simulations results signify that the proposed BOA variant 2 is superior to the proposed BOA variant 1 and existing BOA in terms of several errors. The node localization based on the proposed BOA variant 2 is more effective as it takes less time to perform computations and has less mean localization error than the proposed BOA variant 1, BOA and other existing optimization algorithms.

Molecular Docking of Phytochemicals Targeting GFRs as Therapeutic Sites for Cancer: an In Silico Study

Drug delivery in a safe manner is a major challenge in the drug development process. Growth factor receptors (GFRs) are known to have profound roles in the growth and progression of cancerous cells making these receptors a therapeutic target in the effective treatment of cancer. This work focused on exploring bioactive compounds that can target GFRs using in silico method. In this study, 50 bioactive compounds from different plant sources were screened as anticancer agent against GFRs using drug likeness parameters of Lipinski's rule of five. The molecular docking was performed between phytochemicals and GFRs. Ligands with acceptable drug likeness and binding energy comparable to the standard drugs were further screened to determine their pharmacokinetic activities. This study showed phytochemicals with the binding energy comparable with the standard drugs (Dovitinib and Gefitinib), while ADME, bioactivity score, and bioavailability radar analysis gave further insight on these compounds as potent anticancer agents.

COVID-19: an In Silico Analysis on Potential Therapeutic Uses of Trikadu as Immune System Boosters

Corona virus pandemic outbreak also known as COVID-19 has created an imbalance in this world. Scientists have adopted the use of natural or alternative medicines which are consumed mostly as dietary supplements to boost the immune system as herbal remedies. India is famous for traditional medicinal formulations which includes 'Trikadu'-a combination of three acrids, namely Zingiber officinale, Piper nigrum and Piper longum which have antioxidant properties that boost our immune system hence acting as a strong preventive measure. In this study, AutoDock 4.0 was used to study interaction between the phytocompounds of Trikadu with RNA-dependent polymerase protein and enveloped protein of the SARS-CoV-2 virus. Analysis of the results showed that coumarin, coumaperine and bisdemethoxycurcumin showed strong bonding interactions with both the proteins. We can conclude that Trikadu has the potential molecules; hence, it can be incorporated in the diet to boost the immune system as a preventive measure against the virus.

Interaction of various types of bisphenols with enzymes involved in melanin synthesis

Objectives

Bisphenol is one of the commercial chemical compounds which finds application in the manufacture of phenol, polyesters, polycarbonates, epoxy resins, etc. Bisphenol A is the most commonly found bisphenol derivative, although there are various analogues such as Bisphenol S, Bisphenol B, Bisphenol C, Bisphenol E, Bisphenol AF, which vary with their structures. Bisphenols majorly get into us by means of food as they are found in food packaging and beverage containers and can be easily absorbed by the body. They can make way into the body systems either by direct means like skin contact or by indirect means through food that is stored in a bisphenol-coated containers. Exposure of the human system to this compound may bring about mild to adverse ailments ranging from skin irritations to infertility. Pigmentation disorder is one such health condition that occurs due to melanocyte destruction and is caused by bisphenol exposures. They interact with various proteins and enzymes that have been involved in the melanocyte synthesis pathway, thereby disrupting their normal functions.

Methods

In silico analysis has been done to predict the interaction and other descriptive binding parameters when the bisphenol derivatives BPA. BPB, BPC, BPE, BPS and BPAF have been docked with some of the essential proteins for melanin synthesis such as tyrosinase, tyrosinase-related protein 1(TRP-1), dopachrome tautomerase/tyrosinase-related protein-2(TRP-2).

Results

The interaction has been quantified with the binding energies, and the interacting amino acid residues have also been identified. The results showed strong interactions for both the proteins TRP-1 and TRP-2 with BPA. BPB, BPC, BPE, BPS and BPAF.

Conclusions

The risk and threats caused by the commercial products made of bisphenol are at higher levels, and thereby, the need for a safe and desirable alternative has been insisted.

The lysosome as an imperative regulator of autophagy and cell death

Lysosomes are single membrane-bound organelles containing acid hydrolases responsible for the degradation of cellular cargo and maintenance of cellular homeostasis. Lysosomes could originate from pre-existing endolysosomes or autolysosomes, acting as a critical juncture between autophagy and endocytosis. Stress that triggers lysosomal membrane permeabilization can be altered by ESCRT complexes; however, irreparable damage to the membrane results in the induction of a selective lysosomal degradation pathway, specifically lysophagy. Lysosomes play an indispensable role in different types of autophagy, including microautophagy, macroautophagy, and chaperone-mediated autophagy, and various cell death pathways such as lysosomal cell death, apoptotic cell death, and autophagic cell death. In this review, we discuss lysosomal reformation, maintenance, and degradation pathways following the involvement of the lysosome in autophagy and cell death, which are related to several pathophysiological conditions observed in humans.

Stochastic formulation of multiwave pandemic: decomposition of growth into inherent susceptibility and external infectivity distributions

Many known and unknown factors play significant roles in the persistence of an infectious disease, but two that are often ignored in theoretical modelling are the distributions of (i) inherent susceptibility ( σ inh ) and (ii) external infectivity ( ι ext ), in a population. While the former is determined by the immunity of an individual towards a disease, the latter depends on the exposure of a susceptible person to the infection. We model the spatio-temporal propagation of a pandemic as a chemical reaction kinetics on a network using a modified SAIR (Susceptible-Asymptomatic-Infected-Removed) model to include these two distributions. The resulting integro-differential equations are solved using Kinetic Monte Carlo Cellular Automata (KMC-CA) simulations. Coupling between σ inh and ι ext are combined into a new parameter Ω, defined as Ω = σ inh × ι ext ; infection occurs only if the value of Ω is greater than a Pandemic Infection Parameter (PIP), Ω 0 . Not only does this parameter provide a microscopic viewpoint of the reproduction number R₀ advocated by the conventional SIR model, but it also takes into consideration the viral load experienced by a susceptible person. We find that the neglect of this coupling could compromise quantitative predictions and lead to incorrect estimates of the infections required to achieve the herd immunity threshold. The figure represents the network model for spread of infectious diseases considered in this work. It also shows the resultant multiwave infection graph by inclusion of inherent susceptibility and external infectivity distributions and migration of infected individuals.

Arms and ammunitions: effectors at the interface of rice and it's pathogens and pests

The plant immune system has evolved to resist attack by pathogens and pests. However, successful phytopathogens deliver effector proteins into plant cells where they hijack the host cellular machinery to suppress the plant immune responses and promote infection. This manipulation of the host cellular pathways is done by the pathogen using various enzymatic activities, protein- DNA or protein- protein interactions. Rice is one the major economically important crops and its yield is affected by several pathogens and pests. In this review, we summarize the various effectors at the plant- pathogen/ pest interface for the major pathogens and pests of rice, specifically, on the mode of action and target genes of the effector proteins. We then compare this across the major rice pathogens and pests in a bid to understand probable conserved pathways which are under attack from pathogens and pests in rice. This analysis highlights conserved patterns of effector action, as well as unique host pathways targeted by the pathogens and pests.

Identification of cancer stemness related miRNA(s) using integrated bioinformatics analysis and in vitro validation

The stemness property of cells allows them to sustain their lineage, differentiation, proliferation, and regeneration. MicroRNAs are small non-coding RNAs known to regulate the stemness property of cells by regulating the expression of stem cell signaling pathway proteins at mRNA level. Dysregulated miRNA expression and associated stem cell signaling pathways in normal stem cells give rise to cancer stem cells. Thus, the present study was aimed to identify the miRNAs involved in the regulation of major stem cell signaling pathways. The proteins (n = 36) involved in the signaling pathways viz., Notch, Wnt, JAK-STAT, and Hedgehog which is associated with the stemness property was taken into the consideration. The miRNAs, having binding sites for the targeted protein-encoding gene were predicted using an online tool (TargetScan) and the common miRNA among the test pathways were identified using Venn diagram analysis. A total of 22 common miRNAs (including 8 non-studied miRNAs) were identified which were subjected to target predictions, KEGG pathway, and gene ontology (GO) analysis to study their potential involvement in the stemness process. Further, we studied the clinical relevance of the non-studied miRNAs by performing the survival analysis and their expression levels in clinical breast cancer patients using the TCGA database. The identified miRNAs showed overall poor survival in breast cancer patients. The miR-6844 showed significantly high expression in various clinical subgroups of invasive breast cancer patients compared with the normal samples. The expression levels of identified miRNA(s) were validated in breast normal, luminal A, triple-negative, and stem cells in vitro models using qRT-PCR analysis. Further treatment with the phytochemical showed excellent down regulation of the lead miRNA. Overall the study first time reports the association of four miRNAs (miR-6791, miR-4419a, miR-4251 and miR-6844) with breast cancer stemness.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02994-3.

Luteolin as a potential host-directed immunotherapy adjunct to isoniazid treatment of tuberculosis

Tuberculosis (TB) remains a major health problem throughout the world with one third of the population latently infected and ~1.74 million deaths annually. Current therapy consists of multiple antibiotics and a lengthy treatment regimen, which is associated with risk for the generation of drug-resistant Mycobacterium tuberculosis variants. Therefore, alternate host directed strategies that can shorten treatment length and enhance anti-TB immunity during the treatment phase are urgently needed. Here, we show that Luteolin, a plant-derived hepatoprotective immunomodulator, when administered along with isoniazid as potential host directed therapy promotes anti-TB immunity, reduces the length of TB treatment and prevents disease relapse. Luteolin also enhances long-term anti-TB immunity by promoting central memory T cell responses. Furthermore, we found that Luteolin enhances the activities of natural killer and natural killer T cells, both of which exhibit antitubercular attributes. Therefore, the addition of Luteolin to conventional antibiotic therapy may provide a means to avoid the development of drug-resistance and to improve disease outcome.

The current TB therapy is lengthy, expensive, and may induce severe hepatotoxicity in patients, often leading to premature withdrawal from therapy, which is associated with the risk of generating drug-resistant strains. We considered inclusion of a hepatoprotective immunomodulator, Luteolin, as a potential host directed adjunct to available therapy as a means to improve its efficacy by enhancing host protective immunity. Luteolin-Isoniazid combination therapy induces improved central memory T cell responses. The boosted immune responses permitted reduction of treatment duration, improved treatment outcome and efficiently prevented disease relapse. Luteolin treatment rendered the host resistant against reinfection and reactivation of the disease, which is a major challenge following conventional TB treatment. We conclude that Luteolin is an effective adjunctive immunomodulator for designing anti-TB immunotherapeutics that can provide superior host protection.

Plasmodium falciparum PhIL1-associated complex plays an essential role in merozoite reorientation and invasion of host erythrocytes

The human malaria parasite, Plasmodium falciparum possesses unique gliding machinery referred to as the glideosome that powers its entry into the insect and vertebrate hosts. Several parasite proteins including Photosensitized INA-labelled protein 1 (PhIL1) have been shown to associate with glideosome machinery. Here we describe a novel PhIL1 associated protein complex that co-exists with the glideosome motor complex in the inner membrane complex of the merozoite. Using an experimental genetics approach, we characterized the role(s) of three proteins associated with PhIL1: a glideosome associated protein- PfGAPM2, an IMC structural protein- PfALV5, and an uncharacterized protein—referred here as PfPhIP (PhIL1 Interacting Protein). Parasites lacking PfPhIP or PfGAPM2 were unable to invade host RBCs. Additionally, the downregulation of PfPhIP resulted in significant defects in merozoite segmentation. Furthermore, the PfPhIP and PfGAPM2 depleted parasites showed abrogation of reorientation/gliding. However, initial attachment with host RBCs was not affected in these parasites. Together, the data presented here show that proteins of the PhIL1-associated complex play an important role in the orientation of P. falciparum merozoites following initial attachment, which is crucial for the formation of a tight junction and hence invasion of host erythrocytes.

Invasion of Plasmodium merozoites into RBCs is a multistep process that involves initial attachment of merozoites to the RBC surface, their reorientation, and subsequent gliding into RBCs using glideosome machinery. The glideosome machinery lies between the plasma membrane and inner membrane complex (IMC) and consists of MyoA, its interacting protein; MTIP, gliding associated proteins (GAPs), and a Photosensitized INA labeled protein (PhIL1)-associated protein complex. Here, we demonstrate that the deletion of any of two components of the PhIL1-associated complex, PfPhIP or PfGAPM2, aborts merozoite reorientation and blocks their invasion into RBCs. The study thus provides new molecular and mechanistic insights into merozoite invasion of RBCs.