Synthesis and Characterization of Silica, Silver-Silica, and Zinc Oxide-Silica Nanoparticles for Evaluation of Blood Biochemistry, Oxidative Stress, and Hepatotoxicity in Albino Rats.

Evaluation of nanoparticles (NPs) for biomedical applications has received a lot of attention for detailed study on pharmacokinetics prior to clinical application. In this study, pure C-SiO2 (crystalline silica) NPs and SiO2 nanocomposites with silver (Ag) and zinc oxide (ZnO) were prepared by utilizing different synthesis routes such as sol-gel and co-precipitation techniques. The prepared NPs showed highly crystalline nature as confirmed by X-ray diffraction analysis where average crystallite sizes of 35, 16, and 57 nm for C-SiO2, Ag-SiO2, and ZnO-SiO2 NPs, respectively, were calculated. Fourier transform infrared analysis confirmed the presence of functional groups related to the chemicals and procedures used for sample preparation. Due to agglomeration of the prepared NPs, the scanning electron microscope images showed large particle sizes when compared to their crystalline sizes. The optical properties of the prepared NPs such as absorption were obtained with UV-Vis spectroscopy. For in vivo biological evaluation, albino rats, both male and female, kept in different groups were exposed to NPs with 500 µg/kg dose. Hematological, serum biochemistry, histo-architecture, oxidative stress biomarkers, and antioxidant parameters in liver tissues along with various biomarkers for the evaluation of erythrocytes were estimated. The results on hemato-biochemistry, histopathological ailments, and oxidative stress parameters exhibited 95% alteration in the liver and erythrocytes of C-SiO2 NPs-treated rats while 75 and 60% alteration in the liver tissues of rats due to exposure to Ag-SiO2 and ZnO-SiO2 NPs, respectively, when compared with the albino rats of the control (untreated) group. Therefore, the current study showed that the prepared NPs had adverse effects on the liver and erythrocytes causing hepatotoxicity in the albino rats in respective order C-SiO2 > Ag SiO2 > ZnO-SiO2. As the C-SiO2 NPs appeared to be the most toxic, it has been concluded that coating SiO2 on Ag and ZnO reduced their toxicological impact on albino rats. Consequently, it is suggested that Ag-SiO2 and ZnO-SiO2 NPs are more biocompatible than C-SiO2 NPs.

Computational Insights into the Structural and Functional Impacts of nsSNPs of Bone Morphogenetic Proteins.

BMPs (bone morphogenetic proteins) are multipurpose (transforming growth factor)TGF-superfamily released cytokines. These glycoproteins, acting as disulfide-linked homo- or heterodimers, are highly potent regulators of bone and cartilage production and repair, cell proliferation throughout embryonic development, and bone homeostasis in the adults. Due to the fact that genetic variation might influence structural functions, this study is aimed to determine the pathogenic effect of nonsynonymous single-nucleotide polymorphisms (nsSNPs) in BMP genes. The implications of these variations, investigated using computational analysis and molecular models of the mature TGF-ß domain, revealed the impact of modifications on the function of BMP protein. The three-dimensional (3D) structure analysis was performed on the nsSNP Y316S, V386G, E387G, C389G, and C391G nsSNP in the TGF-ß domain of chicken BMP2 and H344P, S347P, V357A nsSNP in the TGF-ß domain of chicken BMP4 protein that was anticipated to be harmful and of high risk. The ability of the proteins to perform variety of tasks interact with other molecules depends on their tertiary structural composition. The current analysis revealed the four most damaging variants (Y316S, V386G, E387G, C389G, and C391G), highly conserved and functional and are located in the TGF-beta domain of BMP2 and BMP4. The amino acid substitutions E387G, C389G, and C391G are discovered in the binding region. It was observed that the mutations in the TGF-beta domain caused significant changes in its structural organization including the substrate binding sites. Current findings will assist future research focused on the role of these variants in BMP function loss and their role in skeletal disorders, and this will possibly help to develop practical strategies for treating bone-related conditions.

Clinicohematological, Mutagenic, and Oxidative Stress Induced by Pendimethalin in Freshwater Fish Bighead Carp (Hypophthalmichthys nobilis).

Currently, aquatic and terrestrial ecosystems are continuously and chronically polluted by cocktails of countless chemical compounds. The susceptibility to infections is tremendously increasing in a variety of organisms due to exposure to environmental pollutants. Pendimethalin, an herbicide, is continuously used in agriculture to remove unwanted broadleaf weeds across the globe. Therefore, this study investigates the mechanisms of toxicity of pendimethalin in freshwater fish bighead carp upon exposure to low and environmentally relevant concentrations. For this purpose, 48 fish without any clinical abnormalities were kept in a glass aquarium in different experimental groups (T0, T1, T2, and T3). These groups were treated with pendimethalin at 0.00, 0.25, 0.50, and 0.75 mg/L, respectively. Four fish were randomly picked from each experimental group and killed at 72, 96, and 120 hours of the trial to study hematobiochemical parameters and visceral tissues including the brain, liver, heart, gills, and kidneys for histopathology. Herbicide-treated fish indicated various physical and behavioral abnormalities including hypersecretion of mucus, erratic swimming, operculum movement, air gulping, tremors of fins, loss of equilibrium, and increased surface breathing. Histopathologically, gills tissues of treated fish indicated atrophied lamellae, uplifting of secondary lamellae, necrosis of primary and secondary lamellar epithelial cells, telogenesis, congestion, and lamellar fusion. Histopathological examination of liver tissues of treated fish showed mild to moderate congestion, necrosis of hepatocytes, and atrophy of hepatocytes while kidneys revealed degeneration of renal tubules, glomerular atrophy, ceroid, and necrosis of renal tubules. The erythrocyte counts, monocyte and lymphocyte counts, and hemoglobin values were significantly (P < 0.05) reduced in pendimethalin-treated fish. Results on serum biochemistry showed that the biomarkers of kidneys, heart, and liver were significantly higher in fish of treated groups. In addition, values of different biochemical reactions like reactive oxygen species (ROS), thiobarbituric acid reactive species (TBARS), total proteins, and quantity of different antioxidant enzymes including reduced glutathione (GSH), catalase, and superoxide dismutase (SOD) were significantly different when compared to untreated fish. Moreover, the percentile of different nuclear abnormalities in red blood cells and frequency of DNA damage increased significantly in treated fish. It can be concluded from the findings that pendimethalin causes its toxic effects via disruption of physiological and hematobiochemical reactions of fish.

Structural and Evolutionary Adaptations of Nei-Like DNA Glycosylases Proteins Involved in Base Excision Repair of Oxidative DNA Damage in Vertebrates.

Oxidative stress is a type of stress that damages DNA and can occur from both endogenous and exogenous sources. Damage to DNA caused by oxidative stress can result in base modifications that promote replication errors and the formation of sites of base loss, which pose unique challenges to the preservation of genomic integrity. However, the adaptive evolution of the DNA repair mechanism is poorly understood in vertebrates. This research aimed to explore the evolutionary relationships, physicochemical characteristics, and comparative genomic analysis of the Nei-like glycosylase gene family involved in DNA base repair in the vertebrates. The genomic sequences of NEIL1, NEIL2, and NEIL3 genes were aligned to observe selection constraints in the genes, which were relatively low conserved across vertebrate species. The positive selection signals were identified in these genes across the vertebrate lineages. We identified that only about 2.7% of codons in these genes were subjected to positive selection. We also revealed that positive selection pressure was increased in the Fapy-DNA-glyco and H2TH domain, which are involved in the base excision repair of DNA that has been damaged by oxidative stress. Gene structure, motif, and conserved domain analysis indicated that the Nei-like glycosylase genes in mammals and avians are evolutionarily low conserved compared to other glycosylase genes in other "vertebrates" species. This study revealed that adaptive selection played a critical role in the evolution of Nei-like glycosylase in vertebrate species. Systematic comparative genome analyses will give key insights to elucidate the links between DNA repair and the development of lifespan in various organisms as more diverse vertebrate genome sequences become accessible.

Hematobiochemical, Oxidative Stress, and Histopathological Mediated Toxicity Induced by Nickel Ferrite (NiFe2O4) Nanoparticles in Rabbits.

From the past few decades, attention towards the biological evaluation of nanoparticles (NPs) has increased due to the persistent and extensive application of NPs in various fields, including biomedical science, modern industry, magnetic resonance imaging, and the construction of sensors. Therefore, in the current study, magnetic nickel ferrite (NiFe2O4) nanoparticles (NFNPs) were synthesized and evaluated for their possible adverse effects in rabbits. The crystallinity of the synthesized NFNPs was confirmed using X-ray diffraction (XRD) technique. The saturation magnetization (46.7 emug-1) was measured using vibrating sample magnetometer (VSM) and 0.35-tesla magnetron by magnetic resonance imaging (MRI). The adverse effects of NFNPs on blood biochemistry and histoarchitecture of the liver, kidneys, spleen, brain, and heart of the rabbits were determined. A total of sixteen adult rabbits, healthy and free from any apparent infection, were blindly placed in two groups. The rabbits in group A served as control, while the rabbits in group B received a single dose (via ear vein) of NFNPs for ten days. The blood and visceral tissues were collected from each rabbit at days 5 and 10 of posttreatment. The results on blood and serum biochemistry profile indicated significant variation in hematological and serum biomarkers in NFNP-treated rabbits. The results showed an increased quantity of oxidative stress and depletion of antioxidant enzymes in treated rabbits. Various serum biochemical tests exhibited significantly higher concentrations of different liver function tests, kidney function tests, and cardiac biomarkers. Histopathologically, the liver showed congestion, edema, atrophy, and degeneration of hepatocytes. The kidneys exhibited hemorrhages, atrophy of renal tubule, degeneration, and necrosis of renal tubules, whereas coagulative necrosis, neutrophilic infiltration, and severe myocarditis were seen in different sections of the heart. The brain of the treated rabbits revealed necrosis of neurons, neuron atrophy, and microgliosis. In conclusion, the current study results indicated that the highest concentration of NPs induced adverse effects on multiple tissues of the rabbits.

Bisphenol A Induces Histopathological, Hematobiochemical Alterations, Oxidative Stress, and Genotoxicity in Common Carp (Cyprinus carpio L.).

Bisphenol A (BPA) is one of the environmental endocrine disrupting toxicants and is widely used in the industry involving plastics, polycarbonate, and epoxy resins. This study was designed to investigate the toxicological effects of BPA on hematology, serum biochemistry, and histopathology of different organs of common carp (Cyprinus carpio). A total of 60 fish were procured and haphazardly divided into four groups. Each experimental group contained 15 fish. The fish retained in group A was kept as the untreated control group. Three levels of BPA 3.0, 4.5, and 6 mg/L were given to groups B, C, and D for 30 days. Result indicated significant reduction in hemoglobin (Hb), lymphocytes, packed cell volume (PCV), red blood cells (RBC), and monocytes in a dose-dependent manner as compared to the control group. However, significantly higher values of leucocytes and neutrophils were observed in the treated groups (P < 0.05). Results on serum biochemistry revealed that the quantity of glucose, cholesterol, triglycerides, urea, and creatinine levels was significantly high (P < 0.05). Our study results showed significantly (P < 0.05) increase level of oxidative stress parameters like reactive oxygen species (ROS) and thiobarbituric acid reactive substances (TBARS) and lower values of antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) in treated groups (4.5 mg/L and 6 mg/L)) in the brain, liver, gills, and kidneys. Our study depicted significant changes in erythrocytes (pear shaped erythrocytes, leptocytes, microcytes, spherocytes, erythrocytes with broken, lobed, micronucleus, blabbed, vacuolated nucleus, and nuclear remnants) among treated groups (4.5 mg/L and 6 mg/L). Comet assay showed increased genotoxicity in different tissues including the brain, liver, gills, and kidneys in the treated fish group. Based on the results of our experiment, it can be concluded that the BPA exposure to aquatic environment is responsible for deterioration of fish health, performance leading to dysfunction of multiple vital organs.

Green synthesis of nickel oxide nanoparticles using Allium cepa peels for degradation of Congo red direct dye: an environmental remedial approach.

Direct dyes are used in different textile operations and processings. The textile industries are disposing of unused direct dyes into the aquatic environment which is posing a serious alarming threat to aquatic lives. The current study deals with the synthesis of nickel oxide nanoparticles using Allium cepa peels aqueous extract. Nickel oxide nanoparticles (NiO-NPs) were characterized by scanning electron microscopy (SEM). Synthesized NiO-NPs were used to remove Congo red direct dye. Various experimental factors like concentration of dye and nanoparticles, pH, and temperature were optimized. Congo red direct dye was decolorized up to 90% at optimized conditions (Congo Red Direct dye concentration 0.02%, catalyst dose 0.003 g·L-1, pH 6, and temperature 50 °C). The real textile industry effluent disclosed 70% decolorization at optimized conditions. The percent reduction in total organic carbon (TOC) and chemical oxygen demand (COD) was found to be 73.24% and 74.56% in the case of Congo red dye catalytic treatment and the percent reduction in TOC and COD was found to be 62.47% and 60.23%, respectively, in the treatment of textile effluent using nickel oxide nanoparticles as a catalyst. Treated and untreated dye samples were exposed to Fourier transform infrared (FTIR) and UV-Visible spectral analyses too. The reaction products were studied by degradation pathway.

In Silico Structural, Functional, and Phylogenetic Analysis of Cytochrome (CYPD) Protein Family.

Cytochrome (CYP) enzymes catalyze the metabolic reactions of endogenous and exogenous compounds. The superfamily of enzymes is found across many organisms, regardless of type, except for plants. Information was gathered about CYP2D enzymes through protein sequences of humans and other organisms. The secondary structure was predicted using the SOPMA. The structural and functional study of human CYP2D was conducted using ProtParam, SOPMA, Predotar 1.03, SignalP, TMHMM 2.0, and ExPASy. Most animals shared five central motifs according to motif analysis results. The tertiary structure of human CYP2D, as well as other animal species, was predicted by Phyre2. Human CYP2D proteins are heavily conserved across organisms, according to the findings. This indicates that they are descended from a single ancestor. They calculate the ratio of alpha-helices to extended strands to beta sheets to random coils. Most of the enzymes are alpha-helix, but small amounts of the random coil were also found. The data were obtained to provide us with a better understanding of mammalian proteins' functions and evolutionary relationships.

Investigation of Hypoglycemic Peptides Derived from Conserved Regions of adMc1 to Reveal Their Antidiabetic Activities.

Diabetes mellitus is the most common chronic disorder and leading cause of renal, neurological, and gastrointestinal manifestations in developed and developing countries. Despite of many drugs and combinational therapies, the complications of diabetes are still listed due to severe consequences of those drugs. In past few years, plant-derived drugs draw special attention due to their higher efficacy and fewer side-effects. Momordica charantia also known as bitter melon is referred as an antidiabetic and hypoglycemic plant in native populations of Asia and East Africa. In current study, an in silico approach was used to evaluate the interactions and binding patterns of plant-derived peptides devised from a hypoglycemic protein adMc1 of M. charantia as potential inhibitor of DPP-IV, SGLT1, and GLUT2 receptor proteins. The study has described a novel approach to investigate hypoglycemic peptides to cure diabetes. A total of eighty tetra-, penta-, and hexapeptides were devised from conserved regions of adMc1 homologs. The molecular docking approach using MOE software was employed to reveal inhibiting potentials of devised peptides against three selected proteins. Out of 30 shortlisted ligands six peptides (i.e. SMCG, DECC, TTIT, RTTI, ARNL and TVEV) accomplished the criteria of being good drug candidates against selected receptor proteins following the drugability assessment test. The overall results are acceptable on the basis of ADMET profiling for being good drug candidates against selected proteins.

Positive Selection Drives the Adaptive Evolution of Mitochondrial Antiviral Signaling (MAVS) Proteins-Mediating Innate Immunity in Mammals.

The regulated production of filamentous protein complexes is essential in many biological processes and provides a new paradigm in signal transmission. The mitochondrial antiviral signaling protein (MAVS) is a critical signaling hub in innate immunity that is activated when a receptor induces a shift in the globular caspase activation and recruitment domain of MAVS into helical superstructures (filaments). It is of interest whether adaptive evolution affects the proteins involved in innate immunity. Here, we explore and confer the role of selection and diversification on mitochondrial antiviral signaling protein in mammalian species. We obtined the MAVS proteins of mammalian species and examined their differences in evolutionary patterns. We discovered evidence for these proteins being subjected to substantial positive selection. We demonstrate that immune system proteins, particularly those encoding recognition proteins, develop under positive selection using codon-based probability methods. Positively chosen regions within recognition proteins cluster in domains involved in microorganism recognition, implying that molecular interactions between hosts and pathogens may promote adaptive evolution in the mammalian immune systems. These significant variations in MAVS development in mammalian species highlights the involvement of MAVS in innate immunity. Our findings highlight the significance of accounting for how non-synonymous alterations affect structure and function when employing sequence-level studies to determine and quantify positive selection.

Adaptive evolution of peptidoglycan recognition protein family regulates the innate signaling against microbial pathogens in vertebrates.

The innate immune system is the first line of defense in vertebrates against microbial pathogens. This defense system depends on the peptidoglycan pathogen recognition of receptors (PGRPs) existing in both invertebrates and vertebrates. Although some studies revealed the structural and functional differences between them, however, the evolutionary history and the selection pressures on these genes during adaptive evolution are poorly understood. In this study, we examined four (PGLYRP1, PGLYRP2, PGLYRP3, and PGLYRP4) genes of 127 vertebrates' species, conserved across vertebrates to evaluate positive selection pressure drives by adaptive evolution. The codons under positive selection were recognized through likelihood tests by comparing different models based on ω ratios in these genes across the vertebrate species. The positive selection test used two sets of models M1a vs. M2a and M7 vs. M8. The results showed that the test of these genes in M1a vs. M2a was not significant with the likelihood value 2ΔlnL = 0, while the likelihood ratios (2ΔlnL) were 2ΔlnL = 12.386, 2ΔlnL = 4.9283, 2ΔlnL = 24.031, and 2ΔlnL = 103.39 for PGLYRP1, PGLYRP2, PGLYRP3, and PGLYRP4 in M7 vs. M8, respectively. Our study identified the evidence of robust positive selection for these four genes across the vertebrates. These protuberant changes in PGRPs evolution of vertebrates reveal their role in innate immunity. Our study provides an insight based on PGRP genes to understand the evolution of host and pathogens interaction that leads to the progress of the novel conducts for immune diseases that include proteins linked to the recognition of pathogens.

Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates.

Programmed cell death-1 (PD-1) and its ligands, particularly PD-L1 and PD-L2, are the most important proteins responsible for signaling T-cell inhibition and arbitrating immune homeostasis and tolerance mechanisms. However, the adaptive evolution of these genes is poorly understood. In this study, we aligned protein-coding genes from vertebrate species to evaluate positive selection constraints and evolution in the PD1, PD-L1 and PD-L2 genes conserved across up to 166 vertebrate species, with an average of 55 species per gene. We determined that although the positive selection was obvious, an average of 5.3% of codons underwent positive selection in the three genes across vertebrate lineages, and increased positive selection pressure was detected in both the Ig-like domains and transmembrane domains of the proteins. Moreover, the PD1, PD-L1 and PD-L2 genes were highly expressed in almost all tissues of the selected species indicating a distinct expression pattern in different tissues among most species. Our study reveals that adaptive selection plays a key role in the evolution of PD1 and its ligands in the majority of vertebrate species, which is in agreement with the contribution of these residues to the mechanisms of pathogen identification and coevolution in the complexity and novelties of vertebrate immune systems.

Adaptation to host-specific bacterial pathogens drive rapid evolution of novel PhoP/PhoQ regulation pathway modulating the virulence.

The presence of the PhoP-PhoQ system is usually different in various bacterial groups, suggesting that PhoP can control the expression of different genes in species. However, little is known about the evolution of the PhoP-PhoQ system among bacterial pathogens. Here, we study the evolution of PhoP and PhoQ regulation in 15 species of Enterobacteriaceae family. We have determined that the regulatory objectives adopted by PhoP and PhoQ are mainly different, due to the result of horizontal gene transfer events and even the change in the genetic content between closely related species. We have compared many possibilities tests (M1 vs. M2 and M7 with M8) to determine the positive selection. Estimating parameters at M1 and M2, with positive selection in M2 of the two proteins. The proportions of positive selection sites significant with ω = 4.53076 for PhoP and ω = 4.21041 PhQ. M8 was significant for PhoP and PhQ proteins. To further confirm the positive selection results, we used the Selecton server to confer positive selection on individual sites using the Mechanistic-Empirical Combination model, and we noticed that several sites had been identified under selection pressure during the evolution. There was a strong indication for the positive selection in bacterial genes of PhoP and PhoQ showed the results. By the use of REL and IFEL, the positive selection for PhoP was detected 14 and 11 sites respectively at different codon positions. The positively selected sites of amino acids such as Arginine, Alanine, Lysine, and Leucine are more important for the production of signals. Our results suggest that the positive selection of PhoP-PhoQ genes in host adaptation during evolution raises an intriguing possibility causes subtle variations in actions of PhoP-PhoQ and also increases the opportunities that cause modification in protein structure for the evolution of increasing pathogenicity in bacterial pathogens.

Anticancer, antithrombotic, antityrosinase, and anti-α-glucosidase activities of selected wild and commercial mushrooms from Pakistan.

Mushrooms have been accepted as nutraceutical foods because of their high nutritional and functional values. They have also gained interest due to their medicinal properties, economic importance, and organoleptic merit. In this study, wild Ganoderma lucidum and four commercial mushrooms, that is, Pleurotus ostreatus, Volvariella volvacea, Hericium erinaceus, and Lentinus edodes from Pakistan were screened for their biological activities such as anticancer, antityrosinase, anti-α-glucosidase, and antithrombotic activities from their methanol, ethanol, and water extracts. Enzyme inhibition assay showed that selected mushrooms are potent inhibitors with %age inhibition ranging from 19.00% to 80.91%, and 32.85% to 83.38% for tyrosinase and α-glucosidase, respectively. The best tyrosinase inhibition was shown by P. ostreatus whereas L. edodes was found best as α-glucosidase inhibitor. These mushrooms were tested against cancer cell lines including HT-29 colon and H-1299 lungs carcinoma cell lines. G. lucidum showed 29% and 24% viability of cells against HT-29 and H-1299 cell lines, respectively. This antiproliferative effect was in dose-dependent manner, and the maximum inhibition was observed at 200 µg/ml. Mushrooms extracts were also found effective against clot lysis. The percentage of clot lysis was in the range of 27%-29%. The research would provide knowledge to the people of Pakistan about the importance of locally available commercial mushrooms and wild mushrooms for health improvement and prevention against different kinds of diseases.