Comparative analysis of cyto-genotoxicity of zinc using the comet assay and chromosomal abnormality test.

In this study, the toxicity of the trace element zinc (Zn) in Allium cepa L. test material was examined. Toxicity was investigated in terms of physiological, cytogenetic, biochemical, and anatomical aspects. Germination percentage, root length, weight gain, mitotic index (MI), micronucleus (MN) frequency, chromosomal abnormalities (CAs), malondialdehyde (MDA), proline and chlorophyll levels, superoxide dismutase (SOD) and catalase (CAT) enzyme activities, and meristematic cell damage were used as indicators of toxicity. Additionally, the comet test was used to measure the degree of DNA damage. Four groups of A. cepa bulbs-one for control and three for applications-were created. While the bulbs in the treatment groups were germinated with Zn at concentrations of 35, 70, and 140 mg/L, the bulbs in the control group were germinated with tap water. Germination was carried out at room temperature for 72 h and 144 h. When the allotted time was over, the root tips and leaf samples were collected and prepared for spectrophotometric measurements and macroscopic-microscopic examinations. Consequently, Zn treatment led to significant reductions in physiological indicators such as weight gain, root length, and germination percentage. Zn exposure caused genotoxicity by decreasing the MI ratios and increasing the frequency of MN and CAs (p < 0.05). Zn promoted various types of CAs in root tip cells. The most observed of CAs was the sticky chromosome. Depending on the dose, Zn was found to cause an increase in tail lengths in comet analyses, which led to DNA damage. Exposure to Zn led to a significant decrease in chlorophyll levels and an increase in MDA and proline levels. It also promoted significant increases in SOD and CAT enzyme activities up to 70 mg/L dose and statistically significant decreases at 140 mg/L dose. Additionally, Zn exposure caused different types of anatomical damage. The most severe ones are epidermis and cortex cell damage. Besides, it was found that the Zn dose directly relates to all of the increases and decreases in physiological, cytogenetic, biochemical, and anatomical parameters that were seen as a result of Zn exposure. As a result, it has been determined that the Zn element, which is absolutely necessary in trace amounts for the continuation of the metabolic activities of the organisms, can cause toxicity if it reaches excessive levels.

Direct and indirect toxicity mechanisms of the natural insecticide azadirachtin based on in-silico interactions with tubulin, topoisomerase and DNA.

Natural pesticides, which attract attention with safe properties, pose a threat to many non-target organisms, so their toxic effects should be studied extensively. In this study, the toxic effects of Azadirachtin, a natural insecticide derived from Azadirachta indica, were investigated by in-vivo and in-silico methods. In-vivo toxic effects were determined using the Allium test and bulbs were treated with 5 mg/L (0.5x EC50), 10 mg/L (EC50), and 20 mg/L (2xEC50) Azadirachtin. In the groups treated with Azadirachtin, there was a decline in germination-related parameters and accordingly growth was delayed. This regression may be related to oxidative stress in the plant, and the increase in malondialdehyde and proline levels in Azadirachtin-applied groups confirms oxidative stress. Azadirachtin toxicity increased dose-dependently and the most significant toxic effect was observed in the group administered 20 mg/L Azadirachtin. In this group, the mitotic index decreased by 43.4% and sticky chromosomes, vagrant chromosomes and fragments were detected at rates of 83.1 ± 4.01, 72.7 ± 3.46 and 65.1 ± 3.51, respectively. By comet analysis, it was determined that Azadirachtin caused DNA fragmentation, and tail DNA, which was 0.10 ± 0.32% in the control group, increased to 34.5 ± 1.35% in the Azadirachtin -treated groups. These cytotoxic and genotoxic effects of Azadirachtin may be due to direct interaction with macromolecules as well as induced oxidative stress. Azadirachtin has been found to interact in-silico with alpha-tubulin, beta-tubulin, topoisomerase I and II, and various DNA sequences. Possible deteriorations in macromolecular structure and functions as a result of these interactions may cause cytotoxic and genotoxic effects. These results suggest that natural insecticides may also be unreliable for non-target organisms, and the toxic effects of compounds presented as "natural" should also be investigated.

LC-MS/MS phenolic profileand remedial role of Urtica dioica extract against Li2CO3-induced toxicity.

In this study, the protective role of Urtica dioica extract (Udex) against Li2CO3 toxicity in Allium cepa L. was investigated using various parameters such as germination rates, root growth, weight gain, mitotic index (MI), malondialdehyde (MDA), micronucleus (MN), antioxidant enzyme activity, chromosomal abnormalities (CAs) and anatomical changes. As the biological activity of Udex is related to its active content, the profile of phenolic compounds was determined by LC-MS/MS analysis. Li2CO3 caused abnormalities in the tested parameters and serious regressions in germination parameters. Application of 100 mg/L Li2CO3 reduced the chlorophyll a and b contents by 73.04% and 65.7%, respectively. Li2CO3 application exhibited a cytotoxic effect by inducing significant decreases in MI and increases in the frequency of MN, and also showed a genotoxic effect by causing CAs. After 100 mg/L Li2CO3 treatment, MDA, proline, superoxide dismutase, and catalase levels increased by 54.9%, 58.5%, 47.8%, and 52.3%, respectively. Li2CO3 and Udex co-administration resulted in a regression in increased biochemical parameters and genotoxicity parameters, and an improvement in germination parameters. Furthermore, Udex demonstrated efficacy in mitigating the detrimental effects of Li2CO3 on the root tip, particularly in the 200 µg/mL Udex-treated group. The thickening of the cortex cell wall and conduction tissue, which is commonly induced by Li2CO3, was not observed in the Udex-treated group. The protective effect of Udex can be explained by the phenolic compounds it contains. Rutin was detected as the major component in Udex and other phenolics were listed according to their presence rate as protecatechuic acid > caffeic acid > p-coumaric acid > syringic acid > rosemarinic acid > epicatechin. Li ions, which increase in the environment after industrialization, are an important environmental pollutant and exhibit toxicity that affects many pathways in organisms. Scientific research should not only detect these toxic effects but also develop solutions to such problems. In this study, it was determined that the Udex application had a toxicity-reducing role against Li2CO3 toxicity. Also, it has been demonstrated that A. cepa is an important indicator in determining this toxicity and toxicity-reducing applications.

Investigation of the protective role of Ginkgo biloba L. against phytotoxicity, genotoxicity and oxidative damage induced by Trifloxystrobin.

Trifloxystrobin (TFS) is a widely used strobilurin class fungicide. Ginkgo biloba L. has gained popularity due to its recognized medicinal and antioxidant properties. The aim of this study was to determine whether Ginkgo biloba L. extract (Gbex) has a protective role against TFS-induced phytotoxicity, genotoxicity and oxidative damage in A. cepa. Different groups were formed from Allium cepa L. bulbs subjected to tap water (control), 200 mg/L Gbex (Gbex1), 400 mg/L Gbex (Gbex2), 0.8 g/L TFS solution (TFS), 200 mg/L Gbex + 0.8 g/L TFS (TFS + Gbex1) and 400 mg/L Gbex + 0.8 g/L TFS (TFS + Gbex2), respectively. The phenolic composition of Gbex and alterations in the morphological, physiological, biochemical, genotoxicity and anatomical parameters were evaluated. Rutin, protocatechuic acid, catechin, gallic acid, taxifolin, p-coumaric acid, caffeic acid, epicatechin, syringic acid and quercetin were the most prevalent phenolic substances in Gbex. Rooting percentage, root elongation, weight gain, chlorophyll a and chlorophyll b decreased by approximately 50%, 85%, 77%, 55% and 70%, respectively, as a result of TFS treatment compared to the control. In the TFS group, the mitotic index fell by 28% compared to the control group, but chromosomal abnormalities, micronuclei frequency and tail DNA percentage increased. Fragment, vagrant chromosome, sticky chromosome, uneven chromatin distribution, bridge, vacuole-containing nucleus, reverse polarization and irregular mitosis were the chromosomal abnormalities observed in the TFS group. The levels of proline (2.17-fold) and malondialdehyde (2.71-fold), as well as the activities of catalase (2.75-fold) and superoxide dismutase (2.03-fold) were increased by TFS in comparison to the control. TFS-provoked meristematic disorders were damaged epidermis and cortex cells, flattened cell nucleus and thickened cortex cell wall. Gbex combined with TFS relieved all these TFS-induced stress signs in a dose-dependent manner. This investigation showed that Gbex can play protective role in A. cepa against the phytotoxicity, genotoxicity and oxidative damage caused by TFS. The results demonstrated that Gbex had this antioxidant and antigenotoxic potential owing to its high phenolic content.

A comprehensive analysis of royal jelly protection against cypermethrin-induced toxicity in the model organism Allium cepa L., employing spectral shift and molecular docking approaches.

In this study, the toxicity of the pesticide cypermethrin and the protective properties of royal jelly against this toxicity were investigated using Allium cepa L., a model organism. Toxicity was evaluated using 6 mg/L cypermethrin, while royal jelly (250 mg/L and 500 mg/L) was used in combination with cypermethrin to test the protective effect. To comprehend toxicity and protective impact, growth, genotoxicity, biochemical, comet assay and anatomical parameters were employed. Royal jelly had no harmful effects when applied alone. On the other hand, following exposure to cypermethrin, there was a reduction in weight increase, root elongation, rooting percentage, mitotic index (MI), and chlorophyll a and b. Cypermethrin elevated the frequencies of micronucleus (MN) and chromosomal aberrations (CAs), levels of proline and malondialdehyde (MDA), and the activity rates of the enzymes catalase (CAT) and superoxide dismutase (SOD). A spectral change in the DNA spectrum indicated that the interaction of cypermethrin with DNA was one of the reasons for its genotoxicity, and molecular docking investigations suggested that tubulins, histones, and topoisomerases might also interact with this pesticide. Cypermethrin also triggered some critical meristematic cell damage in the root tissue. At the same time, DNA tail results obtained from the comet assay revealed that cypermethrin caused DNA fragmentation. When royal jelly was applied together with cypermethrin, all negatively affected parameters due to the toxicity of cypermethrin were substantially restored. However, even at the maximum studied dose of 500 mg/L of royal jelly, this restoration did not reach the levels of the control group. Thus, the toxicity of cypermethrin and the protective function of royal jelly against this toxicity in A. cepa, the model organism studied, were determined by using many different approaches. Royal jelly is a reliable, well-known and easily accessible protective functional food candidate against the harmful effects of hazardous substances such as pesticides.

Differential effects of moderate chronic ethanol consumption on neurobehavior, white matter glial protein expression, and mTOR pathway signaling with adolescent brain maturation.

Background: Adolescent brains are highly vulnerable to heavy alcohol exposure. Increased understanding of how alcohol adversely impacts brain maturation may improve treatment outcomes.Objectives: This study characterizes short-term versus long-term effects of ethanol feeding on behavior, frontal lobe glial proteins, and mTOR signaling.Methods: Adolescent rats (8/group) were fed liquid diets containing 26% or 0% ethanol for 2 or 9 weeks, then subjected to novel object recognition (NOR) and open field (OF) tests. Frontal lobes were used for molecular assays.Results: Significant ethanol effects on OF performance occurred in the 2-week model (p < .0001). Further shifts in OF and NOR performance were unrelated to ethanol exposure in the 9-week models (p < .05 to p < .0001). Ethanol inhibited MAG1 (p < .01) and MBP (p < .0001) after 2 but not 9 weeks. However, both control and ethanol 9-week models had significantly reduced MAG1 (p < .001-0.0001), MBP (p < .0001), PDGFRA (p < .05-0.01), and PLP (p < .001-0.0001) relative to the 2-week models. GFAP was the only glial protein significantly inhibited by ethanol in both 2- (p < .01) and 9-week (p < .05) models. Concerning the mTOR pathway, ethanol reduced IRS-1 (p < .05) and globally inhibited mTOR (p < .01 or p < .001) in the 9- but not the 2-week model.Conclusions: Short-term versus long-term ethanol exposures differentially alter neurobehavioral function, glial protein expression, and signaling through IRS-1 and mTOR, which have known roles in myelination during adolescence. These findings suggest that strategies to prevent chronic alcohol-related brain pathology should consider the increased maturation-related vulnerability of adolescent brains.

Investigation of multidirectional toxicity induced by high-dose molybdenum exposure with Allium test.

In this study, the multifaceted toxicity induced by high doses of the essential trace element molybdenum in Allium cepa L. was investigated. Germination, root elongation, weight gain, mitotic index (MI), micronucleus (MN), chromosomal abnormalities (CAs), Comet assay, malondialdehyde (MDA), proline, superoxide dismutase (SOD), catalase (CAT) and anatomical parameters were used as biomarkers of toxicity. In addition, detailed correlation and PCA analyzes were performed for all parameters discussed. On the other hand, this study focused on the development of a two hidden layer deep neural network (DNN) using Matlab. Four experimental groups were designed: control group bulbs were germinated in tap water and application group bulbs were germinated with 1000, 2000 and 4000 mg/L doses of molybdenum for 72 h. After germination, root tips were collected and prepared for analysis. As a result, molybdenum exposure caused a dose-dependent decrease (p < 0.05) in the investigated physiological parameter values, and an increase (p < 0.05) in the cytogenetic (except MI) and biochemical parameter values. Molybdenum exposure induced different types of CAs and various anatomical damages in root meristem cells. Comet assay results showed that the severity of DNA damage increased depending on the increasing molybdenum dose. Detailed correlation and PCA analysis results determined significant positive and negative interactions between the investigated parameters and confirmed the relationships of these parameters with molybdenum doses. It has been found that the DNN model is in close agreement with the actual data showing the accuracy of the predictions. MAE, MAPE, RMSE and R2 were used to evaluate the effectiveness of the DNN model. Collective analysis of these metrics showed that the DNN model performed well. As a result, it has been determined once again that high doses of molybdenum cause multiple toxicity in A. cepa and the Allium test is a reliable universal test for determining this toxicity. Therefore, periodic measurement of molybdenum levels in agricultural soils should be the first priority in preventing molybdenum toxicity.

LC-MS/MS, GC-MS and molecular docking analysis for phytochemical fingerprint and bioactivity of Beta vulgaris L.

The plants that we consume in our daily diet and use as a risk preventer against many diseases have many biological and pharmacological activities. In this study, the phytochemical fingerprint and biological activities of Beta vulgaris L. leaf extract, which are widely consumed in the Black Sea region, were investigated. The leaf parts of the plant were dried in an oven at 35 °C and then ground into powder. The main constituents in B. vulgaris were identified by LC-MS/MS and GC-MS analyses. Phenolic content, betaxanthin and betacyanin levels were investigated in the extracts obtained using three different solvents. The biological activity of the extract was investigated by anti-microbial, anti-mutagenic, anti-proliferative and anti-diabetic activity tests. Anti-diabetic activity was investigated by in vitro enzyme inhibition and in-silico molecular docking was performed to confirm this activity. In the LC-MS analysis of B. vulgaris extract, a major proportion of p_coumaric acid, vannilin, protecatechuic aldehyde and sesamol were detected, while the major essential oils determined by GC-MS analysis were hexahydrofarnesyl acetone and phytol. Among the solvents used, the highest extraction efficiency of 2.4% was obtained in methanol extraction, and 36.2 mg of GAE/g phenolic substance, 5.1 mg/L betacyanin and 4.05 mg/L betaxanthin were determined in the methanol extract. Beta vulgaris, which exhibited broad-spectrum anti-microbial activity by forming a zone of inhibition against all tested bacteria, exhibited anti-mutagenic activity in the range of 35.9-61.8% against various chromosomal abnormalities. Beta vulgaris extract, which did not exhibit mutagenic, sub-lethal or lethal effects, exhibited anti-proliferative activity by reducing proliferation in Allium root tip cells by 21.7%. 50 mg/mL B. vulgaris extract caused 58.9% and 55.9% inhibition of α-amylase and α-glucosidase activity, respectively. The interactions of coumaric acid, vanniline, hexahydrofarnesyl acetone and phytol, which are major compounds in phytochemical content, with α-amylase and α-glucosidase were investigated by in silico molecular docking and interactions between molecules via various amino acids were determined. Binding energies between the tested compounds and α-amylase were obtained in the range of - 4.3 kcal/mol and - 6.1 kcal/mol, while for α-glucosidase it was obtained in the range of - 3.7 kcal/mol and - 5.7 kcal/mol. The biological activities of B. vulgaris are closely related to the active compounds it contains, and therefore studies investigating the phytochemical contents of plants are very important. Safe and non-toxic plant extracts can help reduce the risk of various diseases, such as diabetes, and serve as an alternative or complement to current pharmaceutical practices.

Metronidazole promotes oxidative stress and DNA fragmentation-mediated myocardial injury in albino mice.

The purpose of the present study was to investigate the cardiotoxic effects of Metronidazole (Mtz) in albino mice. The mice were divided into four experimental groups: Gp.I (control group): saline, Gp.II:125 mg/kg b.w Mtz, Gp.III:250 mg/kg b.w, Gp.IV:500 mg/kg b.w Mtz. Heart weight ratio, markers of cardiac injury, markers of oxidative stress, histopathological examinations, DNA fragmentation and spectral analysis were used to determine cardiotoxicity. Administration of 125-500 mg/kg Mtz caused an increase in heart weight and a decrease in body weight. Administration of 500 mg/kg Mtz increased heart weight by 35.5% and decreased body weight by 21.9% compared with control. Mtz-treated mice showed a significant increase in cardiac injury biomarkers and serious alterations in cardiac oxidative stress markers. Histopathological changes of cardiac tissues observed in mice treated with Mtz include myocardial hypertrophy, fibrosis, myocarditis, separation of the muscle fibers, congestion-narrowing in vessels, necrosis, myocardium-vacuolation, myocytolysis, myocyte degeneration, nuclear aggregation, cytoplasmic fragmentation and prevalent nuclei. Mtz treatment already resulted in a significant decrease in the percentage of head DNA and an increase in the percentage of tail DNA. The most striking tail formation among the Mtz-treated groups was observed in the group receiving 500 mg/kg Mtz. In the presence of Mtz, there was a hypochromic shift in the absorption spectrum of DNA, and the potential DNA-Mtz interaction was found to occur in the intercalation mode. These results show that Mtz used against anaerobic bacteria and protozoa in gastrointestinal infections can cause severe cardiotoxic findings in albino mice and cause fragmentation in DNA.

In-vivo and in-silico studies to identify toxicity mechanisms of permethrin with the toxicity-reducing role of ginger.

In this study, the toxic effects of permethrin on Allium cepa L. and the protective role of Zingiber officinale rhizome extract (Zoex) were investigated. In this context, 6 different groups were formed. While the control group was treated with tap water, the groups II and III were treated with 10 µg/mL and 20 µg/mL Zoex, respectively, and the group IV was treated with 100 µg/L permethrin. The protective effect of Zoex against permethrin toxicity was studied as a function of dose, and groups V and VI formed for this purpose were treated with 10 µg/mL Zoex + 100 µg/L permethrin and 20 µg/mL Zoex + 100 µg/L permethrin, respectively. After 72 h of germination, cytogenetic, biochemical, physiological, and anatomical changes in meristematic cells of A. cepa were studied. As a result, permethrin application decreased the mitotic index (MI) and increased the frequency of micronuclei (MN), and chromosomal abnormalities. The increase in malondialdehyde (MDA), superoxide dismutase (SOD), and catalase (CAT) and the decrease in glutathione (GSH) indicate that permethrin causes oxidative damage. Compared to the control group, a 68.5% decrease in root elongation (p < 0.05) and an 81.8% decrease (p < 0.05) in weight gain were observed in the permethrin-treated group. It was found that the application of Zoex together with permethrin resulted in regression of all detected abnormalities, reduction in the incidence of anatomical damage, MN and chromosomal aberrations, and improvement in MI rates. The most significant improvement was observed in group VI treated with 20 µg/mL Zoex, and Zoex was also found to provide dose-dependent protection. The toxicity mechanism of permethrin was also elucidated by molecular docking and spectral studies. From the data obtained during the study, it was found that permethrin has toxic effects on A. cepa, a non-target organism, while Zoex plays a protective role by reducing these effects.

Effect of Melissa officinalis L. leaf extract on manganese-induced cyto-genotoxicity on Allium cepa L.

Although the antioxidant properties of Melissa officinalis extract (Mox) are widely known, little work has focused on its protective capacity against heavy metal stress. The primary objective of this study was to determine the potential of Mox to mitigate manganese (II) chloride (MnCI2)-induced cyto-genotoxicity using the Allium and comet assays. Physiological, genotoxic, biochemical and anatomical parameters as well as the phenolic composition of Mox were examined in Allium cepa (L.). Application of 1000 µM MnCl2 reduced the rooting percentage, root elongation, weight gain, mitotic index and levels of chlorophyll a and chlorophyll b pigments compared to the control group. However, it increased micronuclei formation, chromosomal abnormality frequencies, tail DNA percentage, proline amount, lipid peroxidation level and meristematic damage severity. The activities of superoxide dismutase and catalase also increased. Chromosomal aberrations induced by MnCl2 were fragment, sticky chromosome, vagrant chromosome, unequal distribution of chromatin and bridge. Application of 250 mg/L Mox and 500 mg/L Mox along with MnCl2 significantly alleviated adverse effects dose dependently. The antioxidant activity bestowed by the phenolic compounds in Mox assisted the organism to combat MnCl2 toxicity. Consequently, Mox exerted remarkable protection against MnCl2 toxicity and it needs to be investigated further as a potential therapeutic option.

DNA fragmentation, chromosomal aberrations, and multi-toxic effects induced by nickel and the modulation of Ni-induced damage by pomegranate seed extract in Allium cepa L.

This study was designed to assess the recovery effect of pomegranate seed extract (PSEx) against nickel (Ni)-induced damage in Allium cepa. Except for the control group treated with tap water, five experimental groups were exposed to 265 mg L-1 PSEx, 530 mg L-1 PSEx, 1 mg L-1 NiCI2, 265 mg L-1 PSEx + 1 mg L-1 NiCI2, and 530 mg L-1 PSEx + 1 mg L-1 NiCI2, respectively. The toxicity of Ni was examined through the analysis of physiological (germination percentage, weight gain, and root length), cytotoxicity (mitotic index), genotoxicity (micronucleus, chromosomal anomalies, and Comet test), and biochemical (malondialdehyde, proline, chlorophyll a and chlorophyll b contents, the activities of superoxide dismutase and catalase) parameters. Meristematic cell defects were also investigated. The NiCl2-DNA interaction was evaluated through spectral shift analysis. Values of all physiological parameters, mitotic index scores, and chlorophyll contents decreased while micronucleus frequency, DNA tail percentage, chromosomal anomalies, proline, MDA, and enzyme activities increased following Ni administration. According to the tail DNA percentage scale, Ni application caused "high damage" to DNA. Ni-induced chromosomal anomalies were fragment, sticky chromosome, vagrant chromosome, bridge, unbalanced chromatin distribution, reverse polarization, and nucleus with bud. NiCl2-DNA interaction caused a hyperchromic shift in the UV/Vis spectrum of DNA by spectral profile analysis. Ni exposure impaired root meristems as evidenced by the formation of epidermis cell damage, flattened cell nucleus, thickened cortex cell wall, and blurry vascular tissue. Substantial recovery was seen in all parameters with the co-administration of PSEx and Ni. Recovery effects in the parameters were 18-51% and 41-84% in the 265 mg L-1 PSEx + 1 mg L-1 NiCI2 and 530 mg L-1 PSEx + 1 mg L-1 NiCI2 groups, respectively. The Comet scale showed that PSEx applied with Ni reduced DNA damage from "high" to "moderate." Ni-induced thickened cortex cell wall and blurry vascular tissue damage disappeared completely when 530 mg L-1 PSEx was mixed with Ni. PSEx successfully reduced the negative effects of Ni, which can be attributed to its content of antioxidants and bioactive ingredients.

In silico interactions and deep neural network modeling for toxicity profile of methyl methanesulfonate.

In this study, the toxicity induced by the alkylating agent methyl methanesulfonate (MMS) in Allium cepa L. was investigated. For this aim, bulbs were divided into 4 groups as control and application (100, 500 and 4000 µM MMS) and germinated for 72 h at 22-24 °C. At the end of the germination period root tips were collected and made ready for analysis by applying traditional preparation methods. Germination, root elongation, weight, mitotic index (MI) values, micronucleus (MN) and chromosomal abnormality (CAs) numbers, malondialdehyde (MDA) levels, superoxide dismutase (SOD) and catalase (CAT) activities and anatomical structures of bulbs were used as indicators to determine toxicity. Moreover the extent of DNA fragmentation induced by MMS was determined by comet assay. To confirm the DNA fragmentation induced by MMS, the DNA-MMS interaction was examined with molecular docking. Correlation and principal component analyses (PCA) were performed to examine the relationship between all parameters and understand the underlying structure and relationships among these parameters. In the present study, a deep neural network (DNN) with two hidden layers implemented in Matlab has been developed for the comparison of the estimated data with the real data. The effect of MDA levels, SOD and CAT activities at 4 different endpoints resulting from administration of various concentrations of MMS, including MN, MI, CAs and DNA damage, was attempted to be estimated by DNN model. It is assumed that the predicted results are in close agreement with the actual data. The effectiveness of the model was evaluated using 4 different metrics, MAE, MAPE, RMSE and R2, which together show that the model performs commendably. As a result, the highest germination, root elongation, weight gain and MI were measured in the control group. MMS application caused a decrease in all physiological parameters and an increase in cytogenetic (except MI) and biochemical parameters. MMS application caused an increase in antioxidant enzyme levels (SOD and CAT) up to a concentration of 500 µM and a decrease at 4000 µM. MMS application induced different types of CAs and anatomical damages in root meristem cells. The results of the comet assay showed that the severity of DNA fragmentation increased with increasing MMS concentration. Molecular docking analysis showed a strong DNA-MMS interaction. The results of correlation and PCA revealed significant positive and negative interactions between the studied parameters and confirmed the interactions of these parameters with MMS. It has been shown that the DNN model developed in this study is a valuable resource for predicting genotoxicity due to oxidative stress and lipid peroxidation. In addition, this model has the potential to help evaluate the genotoxicity status of various chemical compounds. At the end of the study, it was concluded that MMS strongly supports a versatile toxicity in plant cells and the selected parameters are suitable indicators for determining this toxicity.

Deep neural network and molecular docking supported toxicity profile of prometryn.

In this study, the versatile toxicity profile of prometryn herbicide on Allium cepa was investigated. In this context, 4 different groups were formed. While the control group was treated with distilled water, Groups II, III and IV were treated with 200 mg/L, 400 mg/L and 800 mg/L prometryn, respectively. After 72 h of germination, cytogenetic, biochemical, physiological and anatomical changes were investigated. As a result increase in malondialdehyde levels, decrease in glutathione level, changes in superoxide dismutase and catalase activities in root tip cells show that prometryn causes oxidative stress. The decrease in mitotic index values and the increase in the frequency of micronucleus and chromosomal abnormalities observed after prometryn treatment indicate genotoxic effects. The genotoxic effects may be due to the induced oxidative stress as well as the promethryn-DNA interaction. Molecular docking analyses revealed that prometryn interacts with various bases in DNA. As a result of the Comet assay, exposure to prometryn was found to cause DNA fragmentation. In physiological parameters final weight, germination percentage and root length decreased by 23.8%, 59.1% and 87.3%, respectively, in the 800 mg/L prometryn applied group. Deep neural network (DNN) model was optimized to predict the effects of different doses of prometryn on 4 different endpoints: micronucleus, mitotic index, chromosomal abnormalities and DNA Damage. The predicted data was found to be very similar to the actual data. The performance of the model was evaluated using MAE, MAPE, RMSE and R2, and these metrics indicate that the model performed well. Overall, the findings of this study suggest that the DNN model developed here is a valuable tool for predicting genotoxicity biomarkers in response to the application doses of prometryn, and has the potential to contribute to the development of safer and more sustainable agricultural practices.

Phytochemical fingerprint and biological activity of raw and heat-treated Ornithogalum umbellatum.

The plants that we use as food in our daily diet and as risk preventers against many diseases have many biological and pharmacological activities. The heat treatments applied during the cooking of the plants cause changes in the phytochemical content and bioactivity. In this study, the phytochemical fingerprint and biological activities of raw and heat-treated extracts of Ornithogalum umbellatum L., which is widely consumed in the Black Sea region, were investigated. The bulb and leaf parts of the plant consumed as food were dried in an oven at 35 °C and then ground into powder. For heat treatment, the plant was boiled at 100 °C for 20 min. Differences in phytochemical contents of raw and heat-treated extracts were determined by ICP-MS, LC-MS/MS, and FTIR analysis. Biological activity was investigated with antiradical, antimicrobial, antimutagenic and antiproliferative activity tests. In this way, the effect of heat treatment on both the phytochemical content and biological activity of the O. umbellatum extract was determined. Gallic acid, procateuic acid and caffeic acid were found as the main compounds in the O. umbellatum extract, while the presence of procateuic aldehyde, vanillin and kaempferol in minor proportions was determined. There was a significant decrease in phenolic compound levels after heat treatment and gallic acid content decreased by 92.6%, procateuic acid content by 90% and caffeic acid content by 84.8%. Significant differences were detected in macro and micro element levels after heat treatment in ICP-MS results. While Cd, Ba and Zn levels of the raw extract increased; Na, Mg, K, Fe, U, Co levels decreased significantly. In FTIR spectrum, shifts and disappearances were observed in some of the vibrations and the emergence of new vibrations was also determined after heat treatment. Raw extract exhibited strong scavenging activity against H2O2 and DPPH and had a broad spectrum antimicrobial property. As a result of heat application, regressions were detected in antiradicalic, antibacterial and antifungal activities. Antimutagenic and antiproliferative activities were determined by the Allium test and a significant decrease in both activities and loss of activity against some chromosomal abnormalities were determined after heat treatment. While the antiproliferative activity of the raw extract was 20%, the activity of the heat-treated extract decreased to 7.6%. The raw extract showed the strongest antimutagenic effect with 69.8% against the unequal distribution of chromatin. Similarly, the antimutagenic activity of the extract, which reduced the bridges by 56.1%, decreased to 0.74% after heat treatment and almost lost its antimutagenic activity. The biological activities of raw O. umbellatum are closely related to the major compounds it contains, and the decrease in the levels of these compounds with the effect of heat was reflected in the activity. Studies investigating the phytochemical contents of plants are very important and the studies investigating biological activities related to phytochemical content are more remarkable. In this study, the phytochemical fingerprint of O. umbellatum was determined, its biological activities were related to the compounds it contained, and the biological activity was found to be heat sensitive.

Surface characterization, electrochemical properties and in vitro biological properties of Zn-deposited TiO2 nanotube surfaces.

In this work, to improve antibacterial, biocompatible and bioactive properties of commercial pure titanium (cp-Ti) for implant applications, the Zn-deposited nanotube surfaces were fabricated on cp-Ti by using combined anodic oxidation (AO) and physical vapor deposition (PVD-TE) methods. Homogenous elemental distributions were observed through all surfaces. Moreover, Zn-deposited surfaces exhibited hydrophobic character while bare Ti surfaces were hydrophilic. Due to the biodegradable behavior of Zn on the nanotube surface, Zn-deposited nanotube surfaces showed higher corrosion current density than bare cp-Ti surface in SBF conditions as expected. In vitro biological properties such as cell viability, ALP activity, protein adsorption, hemolytic activity and antibacterial activity for Gram-positive and Gram-negative bacteria of all surfaces were investigated in detail. Cell viability, ALP activity and antibacterial properties of Zn-deposited nanotube surfaces were significantly improved with respect to bare cp-Ti. Moreover, hemolytic activity and protein adsorption of Zn-deposited nanotube surfaces were decreased. According to these results; a bioactive, biocompatible and antibacterial Zn-deposited nanotube surfaces produced on cp-Ti by using combined AO and PVD techniques can have potential for orthopedic and dental implant applications.

Detection of heavy metal contamination in Batlama Stream (Turkiye) and the potential toxicity profile.

In this study, heavy metal pollution in Batlama stream flowing into the Black Sea from Giresun (Turkiye) province and the toxicity induced by this pollution were investigated by Allium test. Heavy metal concentrations in stream water were analyzed by using ICP-MS. Germination percentage, weight gain, root length, micronucleus (MN), mitotic index (MI), chromosomal abnormalities (CAs), proline, chlorophyll, malondialdehyde (MDA), antioxidant enzyme activities were used as indicators of physiological, cytogenetic and biochemical toxicity. In addition, Comet assay was performed for detecting DNA fragmentation. Anatomical changes caused by heavy metals in the root meristem cells were observed under the microscope. A. cepa bulbs are divided into two groups as control and treatment. The bulbs in the control group were germinated with tap water and the bulbs in the treatment group were germinated with stream water. As a result, heavy metals such as Al, Ti and Co and radioactive heavy metals such as Rb, Sr, Sb and Ba were detected in the stream water above the acceptable parametric values. Heavy metals in the water caused a decrease in germination, root elongation, weight gain, MI and chlorophyll values, and an increase in MDA, proline, SOD, CAT, MN and CAs values. Comet assays indicated the presence of severe DNA damage. In addition, heavy metals in stream water caused different types of CAs and anatomical damage in root meristem cells. As a result, it was determined that there is intense heavy metal pollution in the stream water and this pollution promotes multi-dimensional toxicity in A. cepa, which is an indicator organism. For this reason, the first priority should be to prevent pollution of water resources in order to prevent heavy metal-induced toxicity in water.

Potential toxicity assessment of mycotoxin fusaric acid with the spectral shift profile on DNA.

In this study, the multiple toxicities induced by three different doses (1, 5, and 10 µM) of fusaric acid (FA), a mycotoxin, was investigated with Allium test. Physiological (percent germination, root number, root length, and weight gain), cytogenetic (micronucleus = MN, chromosomal abnormalities = CAs, and mitotic index = MI), biochemical (proline level, malondialdehyde = MDA level, catalase = CAT activity, and superoxide dismutase = SOD activity), and anatomical parameters were used as indicators of toxicity. Allium cepa L. bulbs were divided into four groups as one control and three applications. The bulbs in the control group were germinated with tap water for 7 days, and the bulbs in the treatment groups were germinated with three different doses of FA for 7 days. As a result, FA exposure caused a decrease in all physiological parameters examined at all three doses. Besides, all FA doses caused a decrease in MI and an increase in the frequency of MN and the number of CAs. FA promoted CAs such as nucleus with vacuoles, nucleus buds, irregular mitosis, bridge, and misdirection in root meristem cells. DNA and FA interactions, which are the possible causes of genotoxic effects, were examined by spectral analysis, and FA could interact with DNA through intercalation, causing bathochromic and hypochromic shifts in the spectrum. FA also causes toxicity by inducing oxidative stress in cells, confirming this; dose-related increases in root MDA and proline levels were measured as a result of FA exposure. In the root SOD and CAT enzyme activities, increases up to 5 µM doses and decreases at 10 µM doses were measured. FA exposure induced anatomical damage such as necrosis, epidermis cell damage, flattened cell nucleus, thickening of the cortex cell wall, and unclear vascular tissue in root tip meristem cells. As a result, FA caused a comprehensive toxicity by showing an inhibitory effect in A. cepa test material, and the Allium test was a very useful test in determining this toxicity.

DNA fragmentation and multifaceted toxicity induced by high-dose vanadium exposure determined by the bioindicator Allium test.

In this study, the toxicity of vanadium (VCI3) in Allium cepa L. was studied. Germination-related parameters, mitotic index (MI), catalase (CAT) activity, chromosomal abnormalities (CAs), malondialdehyde (MDA) level, micronucleus (MN) frequency and superoxide dismutase (SOD) activity were investigated. The effects of VCI3 exposure on the DNA of meristem cells were investigated with the help of comet assay, and the relationships between physiological, cytogenetic and biochemical parameters were revealed by correlation and PCA analyses. A. cepa bulbs were germinated with different concentrations of VCI3 for 72 h. As a result, the maximum germination (100%), root elongation (10.4 cm) and weight gain (6.85 g) were determined in the control. VCI3 treatment caused significant decreases in all tested germination-related parameters compared to the control. The highest percentage of MI (8.62%) was also observed in the control. No CAs were found in the control, except for a few sticky chromosomes and unequal distribution of chromatin (p > 0.05). VCI3 treatment caused significant decreases in MI and increases in the frequencies of CAs and MN, depending on the dose. Similarly, the comet assay showed that DNA damage scores increased with increasing VCI3 doses. The lowest root MDA (6.50 µM/g) level and SOD (36.7 U/mg) and CAT (0.82 OD240nmmin/g) activities were also measured in the control. VCI3 treatment caused significant increases in root MDA levels and antioxidant enzyme activities. Besides, VCI3 treatment induced anatomical damages such as flattened cell nucleus, epidermis cell damage, binuclear cell, thickening in the cortex cell wall, giant cell nucleus, damages in cortex cell and unclear vascular tissue. All examined parameters showed significant negative or positive correlations with each other. PCA analysis confirmed the relations of investigated parameters and VCI3 exposure.

Characterization and investigation of electrochemical and biological properties of antibacterial silver nanoparticle-deposited TiO2 nanotube array surfaces.

The one of main reasons of the premature failure of Ti-based implants is infections. The metal- and metal oxide-based nanoparticles have very high potential on controlling of infections. In this work, the randomly distributed AgNPs-deposited onto well-ordered TiO2 nanotube surfaces were fabricated on titanium by anodic oxidation (AO) and electrochemical deposition (ED) processes. AgNPs-deposited nanotube surfaces, which is beneficial for bone tissue growth exhibited hydrophilic behaviors. Moreover, the AgNPs-deposited nanotube surfaces, which prevent the leaching of metallic Ti ions from the implant surface, indicated great corrosion resistance under SBF conditions. The electrochemical corrosion resistance of AgNPs-deposited nanotube surfaces was improved up to about 145% compared to bare Gr2 surface. The cell viability of AgNPs-deposited nanotube surfaces was improved. Importantly, the AgNPs-deposited nanotube surfaces exhibited antibacterial activity for Gram-positive and Gram-negative bacteria. Eventually, it can be concluded that the AgNPs-deposited nanotube surfaces possess high stability for long-term usage of implant applications.