Induction of Paraquat-Mediated Parkinsonian Phenotype in Zebrafish

Paraquat (PQ) is a well-known neurotoxin closely associated with neurodegenerative Parkinson's disease (PD). Zebrafish are utilized as a model for PD research because of their well-defined neuropathology and locomotor behavior. Here, we highlight protocols for inducing PD using PQ and analyzing locomotor activity in adult zebrafish. Basic Protocol 1 details the treatment of adult male zebrafish with 60 mg/kg PQ via intraperitoneal injection to induce a PD-like phenotype, followed by the steps to perform a locomotor assay. Basic Protocol 2 provides step-by-step guidance for processing the acquired videos in ToxTrac software to understand the locomotor parameters of 0.9% saline- and 60 mg/kg PQ-injected adult zebrafish. The simplicity of the treatment strategy, low-cost video acquisition setup, and free video processing make these protocols accessible without prior experience. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Development of Parkinson's disease features in adult zebrafish Basic Protocol 2: ToxTrac analysis for locomotor assay.

Identification of key genes and signalling pathways in clear cell renal cell carcinoma: An integrated bioinformatics approach

BACKGROUND

Clear cell Renal Cell Carcinoma (ccRCC) is one of the most prevalent types of kidney cancer. Unravelling the genes responsible for driving cellular changes and the transformation of cells in ccRCC pathogenesis is a complex process.

OBJECTIVE

In this study, twelve microarray ccRCC datasets were chosen from the gene expression omnibus (GEO) database and subjected to integrated analysis.

METHODS

Through GEO2R analysis, 179 common differentially expressed genes (DEGs) were identified among the datasets. The common DEGs were subjected to functional enrichment analysis using ToppFun followed by construction of protein-protein interaction network (PPIN) using Cytoscape. Clusters within the DEGs PPIN were identified using the Molecular Complex Detection (MCODE) Cytoscape plugin. To identify the hub genes, the centrality parameters degree, betweenness, and closeness scores were calculated for each DEGs in the PPIN. Additionally, Gene Expression Profiling Interactive Analysis (GEPIA) was utilized to validate the relative expression levels of hub genes in the normal and ccRCC tissues.

RESULTS

The common DEGs were highly enriched in Hypoxia-inducible factor (HIF) signalling and metabolic reprogramming pathways. VEGFA, CAV1, LOX, CCND1, PLG, EGF, SLC2A1, and ENO2 were identified as hub genes.

CONCLUSION

Among 8 hub genes, only the expression levels of VEGFA, LOX, CCND1, and EGF showed a unique expression pattern exclusively in ccRCC on compared to other type of cancers.

Angiogenesis Assay for Live and Fixed Zebrafish Embryos/Larvae

Angiogenesis is the process of new blood vessel formation from preexisting vasculature. It is an integral component in normal embryonic development and tissue repair. Dysregulation of angiogenesis might lead to tissue ischemia (resulting from reduced blood vessel formation) or major diseases such as cancer (abnormal vascular growth). This makes angiogenesis an excellent area of research for cancer therapeutics, and various animal models including zebrafish are used to study blood vessel development. As most of the techniques used to study angiogenesis are complex and cumbersome, in this chapter, we provide two simple assays to study angiogenesis with live and fixed zebrafish embryos/larvae.

A π-π Bonding-Assisted Molecular-Wiring of Folded-Cytochrome c and Naphthoquinone and Its Electron-Relay-Based Bioelectrocatalytic H2O2 Reduction Reaction Visualized by Redox-Competitive Scanning Electrochemical Microscopy

The electron-transfer (ET) reaction of cytochrome c (Cytc) protein with biomolecules is a cutting-edge research area of interest in understanding the functionalities of natural systems. Several electrochemical biomimicking studies based on Cytc-protein-modified electrodes prepared via electrostatic interaction and covalent bonding approaches have been reported. Indeed, natural enzymes involve multiple types of bonding, such as hydrogen, ionic, covalent, and π-π, etc. In this work, we explore a Cytc-protein chemically modified glassy carbon electrode (GCE/CB@NQ/Cytc) prepared via π-π bonding using graphitic carbon as an underlying surface and an aromatic organic molecule, naphthoquinone (NQ), as a cofactor for an effective ET reaction. A simple drop-casting technique-based preparation of GCE/CB@NQ showed a distinct surface-confined redox peak at a standard electrode potential (E°) = -0.2 V vs Ag/AgCl (surface excess = 21.3 nmol cm-2) in pH 7 phosphate buffer solution. A control experiment of modification of NQ on an unmodified GCE failed to show any such unique feature. For the preparation of GCE/CB@NQ/Cytc, a dilute solution of Cytc-pH 7 phosphate buffer was drop-cast on the GCE/CB@NQ surface, wherein the protein folding and denaturalization-based complication and its associated ET functionalities were avoided. Molecular dynamics simulation studies show the complexation of NQ with Cytc at the protein binding sites. The protein-bound surface shows an efficient and selective bioelectrocatalytic reduction performance of H2O2, as demonstrated using cyclic voltammetry and amperometric i-t techniques. Finally, the redox-competition scanning electrochemical microscopy (RC-SECM) technique was adopted for in situ visualization of the electroactive adsorbed surface. The RC-SECM images clearly show the regions of highly bioelectrocatalytic active sites of Cytc-proteins bound to NQ molecules on a graphitic carbon surface. The binding of Cytc with NQ has significant implications for studying the biological electron transport mechanism, and the proposed method provides the requisite framework for such a study.

Insights on the Role of α- and β-Tubulin Isotypes in Early Brain Development

Tubulins are the highly conserved subunit of microtubules which involve in various fundamental functions including brain development. Microtubules help in neuronal proliferation, migration, differentiation, cargo transport along the axons, synapse formation, and many more. Tubulin gene family consisting of multiple isotypes, their differential expression and varied post translational modifications create a whole new level of complexity and diversity in accomplishing manifold neuronal functions. The studies on the relation between tubulin genes and brain development opened a new avenue to understand the role of each tubulin isotype in neurodevelopment. Mutations in tubulin genes are reported to cause brain development defects especially cortical malformations, referred as tubulinopathies. There is an increased need to understand the molecular correlation between various tubulin mutations and the associated brain pathology. Recently, mutations in tubulin isotypes (TUBA1A, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB3, and TUBG1) have been linked to cause various neurodevelopmental defects like lissencephaly, microcephaly, cortical dysplasia, polymicrogyria, schizencephaly, subcortical band heterotopia, periventricular heterotopia, corpus callosum agenesis, and cerebellar hypoplasia. This review summarizes on the microtubule dynamics, their role in neurodevelopment, tubulin isotypes, post translational modifications, and the role of tubulin mutations in causing specific neurodevelopmental defects. A comprehensive list containing all the reported tubulin pathogenic variants associated with brain developmental defects has been prepared to give a bird's eye view on the broad range of tubulin functions.

Simple and High-Throughput Rheotaxis Behavioral Assay for Zebrafish Larva

Zebrafish (Danio rerio) is used as a model for studying sensorineural hearing loss. The damage to the hair cells can be assessed by scoring rheotaxis behavior in zebrafish. In this study, we newly designed a rheotaxis behavioral assay protocol capable of quantifying rheotaxis behavior in zebrafish larvae. We chemically induced ototoxicity in the larvae using copper sulfate, a well-known ototoxin, and determined rheotaxis at different flow velocities. The simple, cost-effective, and high-throughput rheotaxis assay system can provide great insights into drug development and other behavioral studies.

Novel insights on acetylcholinesterase inhibition by Convolvulus pluricaulis, scopolamine and their combination in zebrafish

Acetylcholinesterase (AChE) inhibitors increase the retention of acetylcholine (ACh) in synapses. Although they alleviate cognitive deficits in Alzheimer's disease, their limited benefits warrant investigations of plant extracts with similar properties. We studied the anti-AChE activity of Convolvulus pluricaulis (CP) in a zebrafish model of cognitive impairment induced by scopolamine (SCOP). CP is a perennial herb with anti-amnesiac and anxiolytic properties. It contains alkaloid, anthocyanin, coumarin, flavonoid, phytosterol and triterpenoid components. Isoxazole (ISOX) was used as a positive control for AChE inhibition. CP-treated 168 hpf larvae showed a similar pattern of AChE inhibition (in the myelencephalon and somites) as that of ISOX-treated larvae. CP was superior to ISOX as evidenced by the retention of avoidance response behavior in adult zebrafish. Molecular docking studies indicated that ISOX binds Ser203 of the catalytic triad on the human AChE. The active components of CP-scopoletin and kaempferol-were bound by His447 of the catalytic triad, the anionic subsite of the catalytic center, and the peripheral anionic site. This suggested the ability of CP to mediate both competitive and non-competitive modes of inhibition. Surprisingly, SCOP showed AChE inhibition in larvae, possibly mediated via the choline-binding sites. CP + SCOP induced a concentration-dependent increase in AChE inhibition and ACh depletion. Abnormal motor responses were observed with ISOX, CP, ISOX + SCOP, and CP + SCOP, indicative of undesirable effects on the peripheral cholinergic system. Our study proposes the examination of CP, SCOP, and CP + SCOP as potential AChE inhibitors for their ability to modulate cognitive deficits.

Chemically induced models of Parkinson's disease

Environmental toxins are harmful substances detrimental to humans. Constant exposure to these fatal neurotoxins can cause various neurodegenerative disorders. Although poisonous, specific neurotoxins at optimal concentrations mimic the clinical features of neurodegenerative diseases in several animal models. Such chemically-induced model systems are beneficial in deciphering the molecular mechanisms of neurodegeneration and drug screening for these disorders. One such neurotoxin is 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), a widely used chemical that recapitulates Parkinsonian features in various animal models. Apart from MPTP, other neurotoxins like 6-hydroxydopamine (6-OHDA), paraquat, rotenone also induce specific clinical features of Parkinson's disease in animal models. These chemically-induced Parkinson's disease models are playing a crucial role in understanding Parkinson's disease onset, pathology, and novel therapeutics. In this review, we provide a concise overview of various neurotoxins that can recapitulate Parkinsonian features in different in vivo and in vitro model systems specifically focusing on the different treatment methodologies of neurotoxins.

Identification of zebrafish fumarate hydratase active site by molecular docking and simulation studies

Fumarate hydratase (FH), one of the members of TCA cycle, acts as a catalyte for the synthesis of malate from fumarate. FH has been proposed to play as a tumour suppressor leading to the pathogenicity of leiomyomas, renal cell carcinoma and paraganglioma. Mutations in the active site of FH lead to alteration in the protein structure. Similarly, binding of several chemical inhibitors to the active site also leads to the disruption of protein structural integrity thereby leading to protein dysfunction. Therefore, in order to address this mechanism leading to cancer, the binding efficiency of potential human FH inhibitor citrate to zebrafish fh has been extensively analysed in this study by molecular docking and simulation experiments followed by quantification of fumarate hydratase enzyme activity to validate and confirm the findings. Molecular docking revealed stronger interaction of zebrafish fh protein with inhibitor citrate when compared to natural substrate fumarate. Study on the dynamics of docked structures further confirmed that citrate was found to possess more binding affinity than fumarate. In vitro biochemical analysis also revealed concentration dependent potential inhibitory effect of citrate on zebrafish fh, thus confirming the findings of the in-silico experiments.Communicated by Ramaswamy H. Sarma.

Bidirectional crosstalk between Hypoxia-Inducible Factor and glucocorticoid signalling in zebrafish larvae

In the last decades in vitro studies highlighted the potential for crosstalk between Hypoxia-Inducible Factor-(HIF) and glucocorticoid-(GC) signalling pathways. However, how this interplay precisely occurs in vivo is still debated. Here, we use zebrafish larvae (Danio rerio) to elucidate how and to what degree hypoxic signalling affects the endogenous glucocorticoid pathway and vice versa, in vivo. Firstly, our results demonstrate that in the presence of upregulated HIF signalling, both glucocorticoid receptor (Gr) responsiveness and endogenous cortisol levels are repressed in 5 days post fertilisation larvae. In addition, despite HIF activity being low at normoxia, our data show that it already impedes both glucocorticoid activity and levels. Secondly, we further analysed the in vivo contribution of glucocorticoids to HIF activity. Interestingly, our results show that both glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) play a key role in enhancing it. Finally, we found indications that glucocorticoids promote HIF signalling via multiple routes. Cumulatively, our findings allowed us to suggest a model for how this crosstalk occurs in vivo.

Investigation of the role of VHL-HIF signaling in DNA repair and apoptosis in zebrafish

pVHL is a tumor suppressor. The lack of its function leads to various tumors, among which ccRCC (clear cell renal cell carcinoma) has the most serious outcome due to its resistance to chemotherapies and radiotherapies. Although HIF promotes the progression of ccRCC, the precise mechanism by which the loss of VHL leads to tumor initiation remains unclear. We exploited two zebrafish vhl mutants, vhl and vll, and Tg (phd3:: EGFP)ⁱ¹⁴⁴ fish to identify crucial functions of Vhl in tumor initiation. Through the mutant analysis, we found that the role of pVHL in DNA repair is conserved in zebrafish Vll. Interestingly, we also discovered that Hif activation strongly suppressed genotoxic stress induced DNA repair defects and apoptosis in vll and brca2 mutants and in embryos lacking ATM activity. These results suggest the potential of HIF as a clinical modulator that can protect cells from accumulating DNA damage and apoptosis which can lead to cancers and neurodegenerative disorders.

Effect of Fadrozole Exposure on Socioreproductive Behaviors and Neurochemical Parameters in Betta splendens

Induction of all-male population in Siamese fighting fish, Betta splendens, has potential application in ornamental fish trade. In addition, the sexually dimorphic nature of aggressive behavior exhibited by this species has made it into an emerging model for behavioral studies. Fadrozole, an aromatase inhibitor, which has been used widely in masculinization, has captivated us to use it in this study. Twenty one days postfertilization (dpf), B. splendens fry were subjected to discrete immersion treatment with various concentrations of fadrozole, and eventually, analyses of various socioreproductive behaviors and analyses of stress markers such as dopamine in brain samples, sex hormones, cortisol, and glucose in plasma samples were performed. We observed that 91% of 50 μg/L fadrozole treated fish developed as males. Interestingly, reproductive analyses of these males gave rise to two subgroups (A and B). Subsequent sociobehavioral analyses demonstrated a timid and subdued behavior in subgroup B males. Furthermore, estimation of stress markers such as dopamine levels in the brain tissue, cortisol, and glucose levels in blood plasma and sex hormone levels in blood plasma exhibited an endocrine disruption-mediated stress leading to altered behavior in these males. These findings will help in understanding the fadrozole-mediated masculinization and behavioral alterations following endocrine disruption.

Transition Metal Ion (Mn2+, Fe2+, Co2+, and Ni2+)-Doped Carbon Dots Synthesized via Microwave-Assisted Pyrolysis: A Potential Nanoprobe for Magneto-fluorescent Dual-Modality Bioimaging

Heteroatom-doped carbon dots (C-dots) have captured widespread research interest owing to high fluorescence and biocompatibility for multimodal bioimaging applications. Here, we exemplify a rapid, facile synthesis of ethylenediamine (EDA)-functionalized transition metal ion (Mn²⁺, Fe²⁺, Co²⁺, and Ni²⁺)-doped C-dots via one-pot microwave (MW)-assisted pyrolysis at 800 W within 6 min using Citrus limon (lemon) extract as a carbon source. During MW pyrolysis, the precursor extract undergoes simultaneous carbonization and doping of metal ions onto C-dot surfaces in the presence of EDA. The EDA-functionalized transition metal ion-doped C-dots (i.e., Mn/C, Fe/C, Co/C, and Ni/C-dots) are collectively termed as TMCDs. The water-soluble TMCDs exhibited a size of 3.2 ± 0.485 nm and were enriched with amino and oxo functionalities and corresponding metal-oxide traces on the surfaces, as revealed from Fourier transfer infrared and X-ray photoelectron spectroscopy analyses. Interestingly, TMCDs demonstrated excitation-wavelength-dependent emission with brighter photoluminescence (PL) at 460 nm. Compared to pristine C-dots with a PL quantum yield (QY) of 48.31% and a fluorescence lifetime of 3.6 ns, the synthesized Mn/C, Fe/C, Co/C, and Ni/C-dots exhibited PL QY values of 35.71, 41.72, 75.07, and 50.84% as well as enhanced fluorescence lifetimes (τ_av) of 9.4, 8.6, 9.2, and 8.9 ns, respectively. The TMCDs significantly exhibited enhanced biocompatibility in human colon cancer cells (SW480) for fluorescence bioimaging and showed ferromagnetic and superparamagnetic behavior with vibrant T₁-contrast ability. Interestingly, the maximum longitudinal (r₁) relaxivity of 0.341 mM^-1 s^-1 was observed for Mn/C-dots in comparison to that of 3.1-3.5 mM^-1 s^-1 of clinically used Gd-DTPA magnetic resonance (MR)-contrast agent in vitro (1.5 T). Similarly, the maximum longitudinal relaxivity (r₁) of 0.356 mM^-1 s^-1 was observed for Ni/C-dots (1.5 T) with respect to 4.16 ± 0.02 mM^-1 s^-1 attained for Gd-DTPA in vivo (8.45 T). Thus, the rapid, energy-efficient MW-assisted pyrolysis presents lemon extract derived, EDA-functionalized TMCDs with enhanced PL and efficient T₁ contrast as potential magneto-fluorescent nanoprobes for dual-modality bioimaging applications.

Isolation of quercetin from the methanolic extract of Lagerstroemia speciosa by HPLC technique, its cytotoxicity against MCF-7 cells and photocatalytic activity

The flavonoids present in the leaves of Lagerstroemia speciosa were extracted, characterized by spectral methods and studied for its cytotoxicity activity against MCF-cell lines and photocatalytic activity against azo dye. Direct and sequential soxhlet extraction was performed and its concentrated crude extract was subjected to high performance liquid chromatography. The yield obtained by the isolated compound (MEI-quercetin) from leaves of L. speciosa was found to be 1.8g from the methanolic extract. The phytochemical analysis and the Rf value of the isolated flavonoid was found to be 3.59. The isolated compound was characterized by Infrared Spectroscopy, NMR and Mass. Based on the characterization, the structure was elucidated as quercetin - a flavonoid. The isolated compound showed the significant in vitro cytotoxicity activity against MCF-7 cell lines at 500μg/ml when compared to the crude extract. Among the various concentrations (25, 50, 100, 250, and 500μg/ml), at higher concentration the cell viability was pronounced and also compared with that of the control. It was first time to report that the isolated flavonoid showed photocatalytic against azo dye-methyl orange. The dye degradation was monitored by UV-Vis spectrophotometry. The isolated compound showed dye degradation of 91.66% with the crude extract 82.47% at 160min. Hence in the present findings, the photocatalytic degradation of MO dye under UV irradiation was investigated over isolated compound of L. speciosa. Hence we expect that this can be used to treat the waste water in near future based on the photocatalytic technique.

Solar catalysed activity against methyl orange dye, cytotoxicity activity of MCF-7 cell lines and identification of marker compound by HPTLC of Lagerstroemia speciosa

The investigation was aimed to quantify the Gallic acid present in Lagerstroemia speciosa leaves (Lythraceae). The High-Performance Thin Layer Chromatography (HPTLC) quantification was performed for acetone (AE), methanolic (ME) and chloroform (CE) extract of leaves of L. speciosa. The pre-coated silica gel 60 F₂₅₄ was used for complete separation of compounds using the mobile phase pet. Ether: ethyl acetate: formic acid (5:5:1v/v).The validation of the extracts was carried out using ICH guidelines for precision, repeatability and accuracy showing the Rf 0.49 against standard Gallic acid. Linearity range for Gallic acid was done from 200 to 1000ng/spot (AE) and200 ng to 600ng/spot (ME), with Correlation, coefficient r=0.99 (AE) and 0.54 (ME) in the said concentrations. The composition in crude leaf extract was determined to be of 49.712mg (AE) and 20.125mg (ME), while it was not found in chloroform extract against standard Gallic acid. Hence the proposed method was very simple, precise, accurate and easy for the screening of the bioactive compounds present in the acetone and methanolic extracts of the leaves of L. speciosa. It was observed that the acetone extract subjected to cytotoxicity showed promising activity at higher concentrations (100 and 200μg/ml) showed 92.9% and 87.13% inhibition against MCF-7 cell lines respectively. The photocatalytic activity of the acetone and methanolic extracts of methyl orange was found to be 90.25% (190min) and 89.03% (180min) respectively. Therefore this can be used as an indicator of purity of herbal drugs and formulation containing L. speciosa.

Photocatalytic activity against azo dye and cytotoxicity on MCF-7 cell lines of zirconium oxide nanoparticle mediated using leaves of Lagerstroemia speciosa

Metal oxide nanoparticles are gaining interest in recent years. The present paper explains about the green synthesis of zirconium oxide nanoparticles (ZrO NPs) mediated from the leaves of Lagerstroemia speciosa. The prepared ZrO NPs were characterized by UV-vis spectroscopy, FT-IR, X-ray diffraction analysis (XRD), Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Energy Dispersive X-ray spectroscopy (EDX) and Thermogravimetric Analysis (TGA). The photocatalytic activity of ZrO NPs was studied for azo dye by exposing to sunlight. The azo dye was degraded up to 94.58%. Also the ZrO NPs were studied for in vitro cytotoxicity activity against breast cancer cell lines-MCF-7 and evaluated by MTT assay. The cell morphological changes were recorded by light microscope. The cells viability was seen at 500μg/mL when compared against control. Hence the research highlights, that the method was simple, eco-friendly towards environment by phytoremediation activity of the azo dye and cytotoxicity activity against MCF-7 cell lines. Hence the present paper may help to further explore the metal nanoparticle for its potential applications.

Tbx2b is required for the development of the parapineal organ

Structural differences between the left and right sides of the brain exist throughout the vertebrate lineage. By studying the zebrafish pineal complex, which exhibits notable asymmetries, both the genes and the cell movements that result in left-right differences can be characterized. The pineal complex consists of the midline pineal organ and the left-sided parapineal organ. The parapineal is responsible for instructing the asymmetric architecture of the bilateral habenulae, the brain nuclei that flank the pineal complex. Using in vivo time-lapse confocal microscopy, we find that the cells that form the parapineal organ migrate as a cluster of cells from the pineal complex anlage to the left side of the brain. In a screen for mutations that disrupted brain laterality, we identified a nonsense mutation in the T-box2b (tbx2b) gene, which encodes a transcription factor expressed in the pineal complex anlage. The tbx2b mutant makes fewer parapineal cells, and they remain as individuals near the midline rather than migrating leftward as a group. The reduced number and incorrect placement of parapineal cells result in symmetric development of the adjacent habenular nuclei. We conclude that tbx2b functions to specify the correct number of parapineal cells and to regulate their asymmetric migration.