Institute of Food Biotechnology and Genomics

With the rapid expansion of industrialization, agricultural intensification, and urbanization, environmental pollution has become a major global ecological challenge. Consequently, the development of effective, economically feasible, and sustainable remediation strategies has emerged as a key research priority in environmental biotechnology. In this context, mycoremediation is a fungal based bioremediation approach that exploits the biological capabilities of fungi such as biodegradation, biosorption, enzymatic detoxification, and symbiotic interactions. It has gained increasing attention as a low cost and environmentally friendly alternative for pollutant removal. This review provides a comprehensive and critical synthesis of the mechanisms underlying mycoremediation, with particular emphasis on ligninolytic and oxidative enzymatic pathways, fungal metabolic functions, and pollutant specific transformation processes. The performance of representative fungal species, including Phanerochaete chrysosporium, Trametes versicolor, Pleurotus ostreatus, Aspergillus niger, and Ganoderma lucidum, is comparatively evaluated across major pollutant groups such as heavy metals, pesticides, hydrocarbons, synthetic dyes, and pharmaceutical contaminants, drawing on recent quantitative findings. In addition, mycoremediation is assessed from environmental, economic, and social sustainability perspectives, with attention to its feasibility for large scale applications. Key limitations including enzyme instability, environmental sensitivity, biomass scalability, and microbial competition are critically discussed. Finally, the integration of advanced biotechnological tools such as genetic engineering, multi omics approaches, nanotechnology, and microbial consortia is highlighted as a promising pathway to enhance system robustness and field applicability. Overall, this review positions mycoremediation as a versatile and scalable component of future sustainable environmental management strategies, with significant potential for ecosystem restoration and public health protection.

Leucyl-tRNA synthetase (LeuRS) activates cognate leucine and wrongly activates norvaline (and other proteinogenic and non-proteinogenic amino acids), but then mischarges tRNA. Here, we studied the editing mechanisms of Thermus thermophilus LeuRS (TthLeuRS) by combination of biochemical and computational investigations with the appropriate substrate, norvalyl-tRNA, as previously reported for E. coli LeuRS (EcLeuRS). Based on DFT (density functional theory) calculations, we have proposed three alternative hydrolysis mechanisms. These mechanisms differ according to which group of water molecules present in the editing site of the enzyme-substrate complex participates in the chemical reaction of ester bond cleavage. The main feature of the proposed deacylation pathways is direct assistance by the substrate in the hydrolysis process. In all three cases, the 3'-OH group of the substrate directly participates in the reaction. To confirm the proposed models, the experimental substitution of the 76 3'-OH group of the tRNALeu was constructed yielding a tRNA that is devoid of editing activity. QM and metadynamics have shown that hydrolysis occurs via a common underlying catalysis mechanism involving more than one water molecule. An important element of hydrolysis is the involvement of several amino acid residues of the active centre of enzymatic editing (Asp-347/Asp-344 and Thr-247) in the process of catalytic deacylation. In conclusion, it was noted that the possibility of several alternative hydrolysis pathways may indicate that a sufficiently protected and flexible error-editing mechanism has been implemented for prokaryotic leucyl-tRNA synthetase.

Yellow (stripe) rust, the agent of which is a biotrophic fungus, Puccinia striiformis West. f. sp. tritici (Pst), is one of the most harmful diseases of wheat. Creating resistant genotypes is considered an ecologically safe and economically profitable technology for plant protection. At present, there are over 80 known and officially recognized genes of resistance to stripe rust (Yr) as well as dozens of genes with temporary labeling. Some Yr genes were characterized, and the corresponding molecular markers to them were selected. An urgent direction of studies is the search for effective quantitative trait loci (QTL) to be used in breeding programs for resistance to yellow rust. In current views, the genetic resistance of wheat to yellow rust is divided into adult seedling resistance (ASR) and adult plant resistance (APR). Most identified genes of resistance to yellow rust are considered race-specific ASR-genes. At present, the unification and systematization of all races were performed using the global pathogen collections, which allowed for the practical application of approximately 20 identified genetic groups of Pst. Triticum aestivum L. is believed to be the source of most genes of resistance to yellow rust: more than 50 Yr genes originate from bread wheat. Relevant sources of resistance genes can also be found in wild and cultivated Triticum species and genetically related plants, including different species of goat grass. The localization of Yr genes of the chromosomes of genomes А, B, and D of T. aestivum L. demonstrated their highest number in genome В. The genotypes with a complex of genes, controlling resistance to several diseases, are considered especially valuable and widely used in breeding programs worldwide.

In recent years, research on the therapeutic potential of mushroom species has notably expanded, and the effects of these organisms on cancer treatment have come to the forefront. The present review examines the anticancer and antitumor effects of various edible and medicinal mushroom species on different human cancer cell lines and summarizes the biological mechanisms underlying these effects. The reviewed studies show that polysaccharides (particularly β-glucans), triterpenoids, phenolic compounds, protein-polysaccharide complexes and other bioactive components contained in mushrooms are effective on apoptosis induction, cell cycle arrest, activation of the immune system, reduction of oxidative stress, inhibition of metastasis and angiogenesis. In vitro and in vivo studies, especially on species such as Ganoderma lucidum, Cordyceps militaris, Lentinula edodes, Hericium erinaceus, and Grifola frondosa, have shown that these mushrooms exhibit significant cytotoxic, antiproliferative, and immunomodulatory effects against various types of cancer (including breast, colon, lung, liver, prostate, cervical, etc.). These findings indicate that mushroom-derived natural products should be evaluated not only as adjunctive therapies, but also as potential pharmaceutical agents. However, most of the available data are at the preclinical level, and more comprehensive toxicological and pharmacokinetic studies are needed to ensure clinical applicability.

Plants display several biological activities as a result of the production of various chemicals inside their metabolic processes. In recent times, the growing prevalence of alternative medicine uses has elevated the significance of plants. The present work aimed to assess the biological activities, phenolic and chemical compositions, applicability, mineral composition, and overall characteristics of Citrullus colocynthis (L.) Schrad. as documented in existing literature. Literature study revealed that it possesses significant antioxidant, antibacterial, and anticancer properties. Furthermore, it has been observed that it may serve as a potential reservoir for the minerals documented inside its structure. It is also thought to be an important source, especially in terms of potassium. From this perspective, it became evident that the fruit components of the plant, in particular, could serve as a significant natural resource for promoting health.

BackgroundFalse flax, or gold-of-pleasure (Camelina sativa) is an oilseed that has received renewed research interest as a promising vegetable oil feedstock for liquid biofuel production and other non-food uses. This species has also emerged as a model for oilseed biotechnology research that aims to enhance seed oil content and fatty acid quality. To date, a number of genetic engineering and gene editing studies on C. sativa have been reported. Among the most common targets for this research are genes, encoding fatty acid desaturases, elongases, and diacylglycerol acyltransferases. However, the majority of these genes in C. sativa are present in multiple copies due to the allohexaploid nature of the species. Therefore, genetic manipulations require a comprehensive understanding of the diversity of such gene targets.ResultsHere we report the detailed analysis of FAD2, FAD3 and FAE1 gene diversity in five Camelina species, including hexaploid C. sativa and four diploids, namely C. neglecta, C. laxa, C. hispida var. hispida and var. grandiflora. It was established that FAD2, FAD3 and FAE1 homeologs in C. sativa retain very high conservancy, despite their allohexaploid inheritance. High sequence conservancy of the identified genes along with their different expression patterns in C. sativa suggest that subfunctionalization of these homeologs is mainly grounded on the transcriptional balancing between subgenomes. Finally, fatty acid composition of seed lipids in different Camelina species was characterized, suggesting potential variability in the activity of fatty acid elongation/desaturation pathways may vary among these taxa.ConclusionIt was shown that the FAD2, FAD3 and FAE1 genes retain high conservation, even in allohexaploid C. sativa after polyploidzation, in which the subfunctionalization of the described homeologs is mainly grounded on the expressional differences. The major differences in FA accumulation patterns within the seeds of different species were identified as well. These results provide a foundation for future precise gene editing, which would be based on targeting of particular FAD2, FAD3 and FAE1 gene copies in C. sativa that allow regulating the dosage of the mentioned genes, thus shaping the desired FA composition in cultivated false flax.

Optimizing extraction conditions can help maximize the efficiency and yield of the extraction process while minimizing negative impacts on the environment and human health. For the purpose of the current study, an artificial neural network (ANN) combined with a genetic algorithm (GA) was utilized for that the extraction conditions of Hypericum spectabile were optimized. In this particular investigation, the main objective was to get the highest possible levels of total antioxidant status (TAS) for the extracts that were obtained. In addition to this, conditions of the extract that exhibited the maximum activity have been determined and the biological activity of the extract that was obtained under these conditions was analyzed. TAS values were obtained from extracts obtained using extraction temperatures of 30–60 °C, extraction times of 4–10 h, and extract concentrations of 0.25-2 mg/mL. The best model selected from the established ANN models had a mean absolute percentage error (MAPE) value of 0.643%, a mean squared error (MSE) value of 0.004, and a correlation coefficient (R) value of 0.996, respectively. The genetic algorithm proposed optimal extraction conditions of an extraction temperature of 59.391 °C, an extraction time of 8.841 h, and an extraction concentration of 1.951 mg/mL. It was concluded that the integration of ANN-GA can successfully be used to optimize extraction parameters of Hypericum spectabile. The total antioxidant value of the extract obtained under optimum conditions was determined as 9.306 ± 0.080 mmol/L, total oxidant value as 13.065 ± 0.112 µmol/L, oxidative stress index as 0.140 ± 0.001. Total phenolic content (TPC) was 109.34 ± 1.29 mg/g, total flavonoid content (TFC) was measured as 148.34 ± 1.48 mg/g. Anti-AChE value was determined as 30.68 ± 0.77 µg/mL, anti-BChE value was determined as 41.30 ± 0.48 µg/mL. It was also observed that the extract exhibited strong antiproliferative activities depending on the increase in concentration. As a result of LC-MS/MS analysis of the extract produced under optimum conditions in terms of phenolic content. The presence of fumaric, gallic, protocatechuic, 4-hydroxybenzoic, caffeic, 2-hydoxycinamic acids, quercetin and kaempferol was detected. As a result, it was determined that the H. spectabile extract produced under optimum conditions had significant effects in terms of biological activity.

Acid-sensing ion channels (ASICs) play a key role in the perception and response to extracellular acidification changes. These proton-gated cation channels are critical for neuronal functions, like learning and memory, fear, mechanosensation and internal adjustments like synaptic plasticity. Moreover, they play a key role in neuronal degeneration, ischemic neuronal injury, seizure termination, pain-sensing, etc. Functional ASICs are homo or heterotrimers formed with (ASIC1-ASIC3) homologous subunits. ASIC1a, a major ASIC isoform in the central nervous system (CNS), possesses an acidic pocket in the extracellular region, which is a key regulator of channel gating. Growing data suggest that ASIC1a channels are a potential therapeutic target for treating a variety of neurological disorders, including stroke, epilepsy and pain. Many studies were aimed at identifying allosteric modulators of ASIC channels. However, the regulation of ASICs remains poorly understood. Using all available crystal structures, which correspond to different functional states of ASIC1, and a molecular dynamics simulation (MD) protocol, we analyzed the process of channel inactivation. Then we applied a molecular docking procedure to predict the protein conformation suitable for the amiloride binding. To confirm the effect of its sole active blocker against the ASIC1 state transition route we studied the complex with another MD simulation run. Further experiments evaluated various compounds in the Enamine library that emerge with a detectable ASIC inhibitory activity. We performed a detailed analysis of the structural basis of ASIC1a inhibition by amiloride, using a combination of in silico approaches to visualize its interaction with the ion pore in the open state. An artificial activation (otherwise, expansion of the central pore) causes a complex modification of the channel structure, namely its transmembrane domain. The output protein conformations were used as a set of docking models, suitable for a high-throughput virtual screening of the Enamine chemical library. The outcome of the virtual screening was confirmed by electrophysiological assays with the best results shown for three hit compounds.