BACKGROUND: Russian aquaculture develops rapidly in terms of commercial rainbow trout production that requires massive juvenile stocks. In the last decade, the industry for the production of juvenile trout from fertilized eggs has been formed and is now expanding. Most fish farmers are striving to carry out this stage under a fully controlled water regime in recirculating aquaculture system. Today, the problem of ongoing monitoring of the bacterial pathogens and control of their numbers in such recirculating aquaculture system does not have a solution for practical fish farms. Given that the use of antibiotics is strictly regulated in food production, a project was launched to develop a bacteriophage specifically targeting highly pathogenic bacterial species. AIM: Study various samples taken from the recirculating aquaculture system to determine the optimal site and method for bacteria collection and nucleic acid extraction. METHODS: Samples were collected during 2025 at recirculating aquaculture system for rainbow trout Oncorhynchus mykiss in the Leningrad Region and the Republic of Karelia. The bacteria studied in this article are Aeromonas hydrophila. The bacterial content was assessed using traditional bacterial cultivation methods. DNA was extracted from various sample types and subjected to isothermal amplification targeting A. hydrophila. For samples confirmed to contain A. hydrophila, additional processing methods were employed following initial lysis in a buffer composed SDS and NaOH. Both chemical techniques, such as precipitation with alcohols and nanoparticles, and physical methods, including heating and syringe pipetting, were utilized in this procedure. RESULTS: The study found that certain chemical methods (nanoparticle precipitation) for isolating bacterial DNA from the pre-lysed samples were just as effective as physical methods (syringe pipetting and heating). The most informative sample types for pathogen detection sites from the recirculating aquaculture system were swabs taken from pipes of the fish tanks drain. CONCLUSION: The ability to obtain microorganism identification results using nucleic acid amplification methods outside the laboratory makes them highly promising for use as rapid diagnostics for bacterial pathogens in practical aquaculture. Following the completion of sample collection and the creation of a collection of pathogenic organisms, the development plan includes the development of a genetically modified bacteriophage for bacterial population control.
Potassium channels constitute the most diverse group of ion channels and play a key role in regulating neuronal excitability and cardiac electrical activity. Despite significant progress in understanding their structure and function, the relationship between specific genetic alterations and disease phenotypes remains insufficiently systematized, which underscores the relevance of a comprehensive analysis of available data. This review summarizes findings from studies of animal models carrying mutations in potassium channel genes, aimed at elucidating their physiological roles and the molecular mechanisms of pathogenesis. Knockout models of kcna1, kcna2, and kcnq2 reproduce key features of human epileptic syndromes, including neuronal hyperexcitability, spontaneous seizures, and early mortality. Deficiency of kcnma1 is associated with impaired motor coordination and the development of cerebellar ataxia. Mutations in kcnq1 and kcne1 result in cardiac and auditory abnormalities characteristic of Jervell and Lange-Nielsen syndrome, whereas double knockout of kcne1/kcnh2 leads to a pronounced susceptibility to ventricular arrhythmias. In addition, deletion of kcnd2 and kcnd3, encoding Kv4 family channel subunits, reveals their critical role in shaping the early phase of cardiac repolarization. Thus, the systematization of data on genetically modified animal models enables the establishment of links between molecular defects in potassium channels and clinical manifestations of disease, and highlights their importance as tools for the development and testing of novel therapeutic approaches.
BACKGROUND: Breakthroughs in genome editing technology have made it possible to precisely alter target nucleotides in plant DNA/RNA. Such changes can be identical or comparable to natural mutations, or achieved through conventional mutagenesis, providing the scientific basis for recognizing gene-edited (GE) plants of this category as analogous to plants created through traditional breeding. Risk assessment of off-target editing effects, as well as the methodology and criteria for distinguishing GE plants from transgenic ones, remain unresolved issues for the scientifically based regulation of plant genetic engineering in Russia. AIM: This study aimed to develop methodological approaches and a decision-making tree for determining the status of plants obtained using genome editing technology, allowing for the registration of the GE plant and its subsequent cultivation. METHODS: The objects of this analytical study are GE organisms of plant origin. RESULTS: The result of this work is a comprehensive strategy for minimizing the risks of off-target editing effects and assessing the biosafety of GE plant, namely: a) “safe design” at the concept stage; b) molecular genetic analysis of the obtained GE plants using instrumental methods; c) analysis of the data required for the biosafety assessment of SDN-1 and SDN-2 types of GE plants; d) criteria and a decision-making tree for determining the status of plants obtained using genome editing technology. For instrumental confirmation a modified plant’s status, we proposed to analyze by PCR/RT-PCR of the regions around target editing sites with a length of 1000 base pairs, centered relative to the break site, with subsequent sequencing, and for a more in-depth analysis, the k-mer method. CONCLUSION: The developed methodological approaches, criteria, requirements, and decision tree will enable the classification of plants obtained using genome editing technology. Thus, the ability to determine whether a plant is transgenic (SDN-3) or gene-edited (SDN-1, SDN-2) will enable the establishment of appropriate regulatory and control measures.
BACKGROUND: Preeclampsia is a serious pregnancy disorder that arises after 20 weeks’ gestation and is characterized by hypertension, proteinuria and edema; it can progress to eclampsia with severe complications and death. Several studies have reported amyloid like aggregates in placenta and urine from preeclampsia patients that stain with Congo red. Mass spectrometry of these aggregates identified Albumin, Ceruloplasmin, Interferon alpha inducible protein 6, Serotransferrin, Alpha 1 antitrypsin, immunoglobulin light chains (κ) and Aβ peptides. Except for Aβ, and immunoglobulin light chains, the ability of these proteins to form amyloids in vivo has not been demonstrated. AIM: To evaluate the in vivo amyloidogenic potential of proteins identified in preeclampsia associated urinary aggregates using the yeast based assay. METHODS: Candidate human proteins (including Aβ42 as positive control) were cloned in frame with the N-terminal prion domain of S. cerevisiae Sup35 (Sup35N) into a yeast expression plasmid. Constructs were under control the copper inducible CUP1 promoter. The constructs were transformed into a S. cerevisiae ade1-14 strain (nonsense mutation in ADE1) and lacking endogenous prions. Expression was induced by growth colonies on −Ura medium containing 150 µM CuSO4 for 48 h. Colonies were then replica plated to adenine deficient (−Ade) medium, and growth was monitored up to 21 days as a readout of Sup35 conversion to the [PSI+] prion and of the amyloidogenicity of the Sup35N fusion. RESULTS: Analysis indicates that none of the human proteins tested—except the Aβ42 peptide—have demonstrated amyloidogenic potential in vivo. CONCLUSION: None of the full-length human proteins detected in urine from preeclampsia patients–albumin, ceruloplasmin, IFN-α-inducible protein 6, serotransferrin, and alpha-1-antitrypsin showed amyloidogenic activity in a yeast-based phenotypic assay; only Aβ42 functioned as an effective seed. Future work will assess amyloidogenicity of individual domains of these proteins.
The Fifth International Conference “Genetically Modified Organisms: History, Achievements, and Social and Environmental Risks” was successfully held on December 1–3, 2025, at Saint Petersburg State University (Russia). The hybrid event brought together both in-person and online participants, including researchers from Russia, Moldova, and Turkmenistan. The conference was dedicated to the anniversary of Professor Lyudmila A. Lutova, whose research in plant biotechnology and genetic engineering is widely recognized both in Russia and internationally. This issue of the journal Ecological Genetics presents selected articles contributed by conference participants.
BACKGROUND: Chlamydomonas reinhardtii P.A. Dang. is a model organism for studying the genetics of green algae. To expand and improve the genetic engineering toolkit for microalgae, we used the binary plant vector pKSE401, based on the CRISPR/Cas9 system, to knock out the PSY1 (PHYTOENE SYNTHASE 1) gene in C. reinhardtii, which encodes a key enzyme in the metabolic pathway of carotenoid biosynthesis. Mutations in this gene result in the appearance of a characteristic white or pale-green colony phenotype, which allows the selection of transformants with disruptions in the PSY1 gene based on phenotype. AIM: To evaluate the feasibility of using the binary plant vector pKSE401 for CRISPR/Cas9-mediated gene knockout in the microalga C. reinhardtii. METHODS: The vector pKSE401-PSY1 was constructed containing a previously used guide RNA spacer targeting the PSY1 gene of C. reinhardtii. Two wild-type strains were used in this study: CC-124 (wt, mt–) and 137c (wt, mt+). Experiments were performed in three biological and three technical replicates. Cell cultivation and transformation conditions (electroporation method), as well as the screening protocol for psy1 transformants (white/pale-green colony phenotype as a selection system, PCR and sequencing for verification of genome editing), were carried out according to published protocols. RESULTS: A total of 164 transformant colonies were obtained and analyzed, of which 29 displayed the white or pale-green phenotype (17.7%). Sequencing confirmed the presence of insertions/deletions in the target site of the PSY1 gene in 13 mutants, whereas PCR amplification failed for three mutants. The overall efficiency of targeted editing of the PSY1 gene (across all experimental variants) reached 7.9%. CONCLUSION: The preliminary results demonstrate the feasibility of using the plant binary vector pKSE401 for gene knockout in the green alga C. reinhardtii, thereby expanding the range of potential target species for its application. The system has substantial limitations (random plasmid integration into the genome and relatively low editing efficiency). However, further optimization of the protocol may help overcome some of these limitations.
Cystinuria is a hereditary nephropathy caused by defects in the SLC3A1 and SLC7A9 genes, which encode the subunits of the heterodimeric transporter rBAT–b0,+AT. This complex mediates cystine reabsorption in the proximal renal tubules. Consequently, dysfunction of this complex leads to cystine accumulation in urine and the formation of cystine stones. A major challenge in patient management still remains delayed diagnosis, typically after the manifestation of urolithiasis, which particularly underscores the need to develop preventive and molecularly oriented approaches. The absence of effective therapies capable of modifying the course of the disease thus highlights the relevance of establishing adequate experimental models. Animal models—primarily murine—are clearly indispensable tools for both dissecting the molecular basis of cystinuria and for preclinical evaluation of potential novel therapeutic strategies. This comprehensive review summarizes all current data on animal models of cystinuria, with emphasis on their ability to reproduce important key aspects of the disease associated with dysfunction of the rBAT–b0,+AT transport complex.
BACKGROUND: The CRISPR/Cas9 technology enables the generation of genetically modified founder animals (F0 generation) already at the stage of zygote editing. However, the resulting offspring are often mosaic, meaning they carry different mutations in different cells, which complicates accurate genotyping using standard tissue samples. To establish a stable knockout line, it is necessary to identify F0 individuals carrying the target mutations, which requires subsequent crossing with wild-type mice and a large-scale analysis of the F1 offspring, involving significant costs. Therefore, the efficient prediction of inheritable mutations at the F0 generation stage is a critical task. AIM: A comparative evaluation of the efficiency of the TIDE and ICE bioinformatic algorithms for analyzing Sanger sequencing data to accurately predict inheritable mutations in the vldlr gene in F0 mosaic mice. METHODS: The study was conducted on five F0 mosaic mice with mutations in the vldlr gene, obtained by microinjection of CRISPR/Cas9 components into zygotes. Genomic DNA was isolated from ear tissue, the target region of the vldlr gene was amplified by PCR and sequenced by the Sanger method. The resulting chromatograms were analyzed using the TIDE and ICE algorithms. The predictions were validated by crossing the F0 mice with wild-type mice and analyzing the inheritance of mutations in the F1 generation. RESULTS: The comparison of the algorithms showed that both programs correctly predicted all mutations that were subsequently detected in the F1 generation. In total, 31 F1 offspring were analyzed. CONCLUSION: Both tools are suitable for primary screening. The analysis of the offspring confirmed that all actually inherited mutations were predicted by both methods.
BACKGROUND: Breakthroughs SARS-CoV-2 main protease (Mpro) remains a central antiviral target due to its essential role in viral replication and high conservation among coronaviruses. Early-stage prioritization of candidate inhibitors, particularly from complex natural matrices, requires functional systems that are experimentally accessible, biosafe, and compatible with crude preparations. We previously developed a bacterial colorimetric reporter assay that couples intracellular Mpro activity to β-galactosidase output in a genetically engineered Escherichia coli strain. AIM: The present study aimed to evaluate juice preparations derived from four closely-related and widely consumed Vaccinium species: northern highbush blueberry (Vaccinium corymbosum L.), lingonberry (Vaccinium vitis-idaea L.), swamp cranberry (Vaccinium oxycoccos L.), and American cranberry (Vaccinium macrocarpon Ait.) for the potential to produce a functional inhibitory signal against Mpro using our previously established assay. METHODS: The evaluation was performed using our previously developed bacterial colorimetric reporter assay that couples intracellular Mpro activity to β-galactosidase output in E. coli. RESULTS: Under identical experimental conditions, northern highbush blueberry, lingonberry, and swamp cranberry juices did not restore reporter signal at any tested concentration. In contrast, American cranberry juice produced a detectable gain-of-signal response at two lower concentrations, whereas higher concentrations resulted in reporter-specific interference confirmed by internal controls. This pattern suggests the presence of bioactive compounds in cranberry juice that may modulate galactosidase-associated readout at higher concentrations. CONCLUSION: Such observations are relevant for future studies aimed at identifying anti-COVID drug candidates and evaluating potential biological effects associated with complex plant-derived preparations. Collectively, these findings prioritize American cranberry as a candidate for further evaluation within defined experimental boundaries.
BACKGROUND: Rice coleoptiles were used to investigate the importance of V H+-ATPase in vacuolization during elongation growth under normoxic and hypoxic conditions. AIM of the study was to find out a link between growth intensity, protein amount of subunits B and E and transcription of genes encoding those proteins. MATERIALS AND METHODS: The investigation was carried out on two rice varieties of domestic selection, fast-growing Kuban 3 and slow-growing Amethyst. Seedlings were grown in etiolated conditions at normoxia and submergence. Western-blot analysis was employed to evaluate amount of subunits B and E in microsomal fraction. qRT-PCR was used to distinguish differences in expression of genes encoding subunits B and E of V H+-ATPase. RESULTS: The growth under aerobic conditions was more consistent with the changes in subunits B and E of V H+-ATPase which was determined at the proteomic level, while the hypoxic growth had a stronger correspondence with changes in OsVHAs gene expression. Varietal differences were revealed only when comparing the transcription intensity, which did not affect the growth dynamics of coleoptiles. Obtained data suggested the existence of differences in the regulation of the enzyme at the transcriptional and proteomic levels during coleoptile elongation. CONCLUSIONS: The importance of the B and E subunits of V-ATPase involvement in vacuolization during the growth process of rice coleoptiles under different oxygen level was demonstrated.
Due to oncoming climate changes, droughts, high salinity, extreme temperatures became quite common stressors universally occurring in the most of terrestrial habitats. Expansions of these changes are often accompanied with strong herbivore attacks. Due to the outstanding impact of these factors on sustainable agriculture, since several last decades, the biochemistry and molecular biology of plant stress response remains in the focus of the research interest worldwide. Thus, bottom-up proteomics became a versatile tool of plant research in general and of stress biology in particular. As plant-derived materials are recognized as an extremely complex matrix, which is rich in polysaccharides, polyphenols and hardly water-soluble proteins, their proteome is typically analyzed by gel-based techniques. However, recent advances in sample preparation techniques (first of all — protein solubilization and digestion) allowed establishment of gel-free methods for plant-derived samples. Implementation of high-throughput nano-flow reversed phase-high performance liquid chromatography coupled on-line to electrospray ionization mass spectrometry (nanoRP-HPLC-ESI-MS) gave access to data-rich datasets giving high protein identification rates. Moreover, high reproducibility of HPLC allows highly sensitive and precise quantification. Therefore, over the recent decade, shotgun proteomics became the method of choice in the study of adaptive stress responses of plant proteome. Here we address the bottom-up shotgun proteomics strategy in plant biology and discuss its application to the study of plant stress response. We also discuss the main steps of the plant proteome analysis pipeline and address emerging problems and future perspectives.
The review is devoted to the application of quantitative trait loci (QTL) analysis to study the interactions of common pea (Pisum sativum L.), one of the most important grain legumes, with soil microorganisms. Pea, like other legumes, forms symbioses with nodule bacteria and arbuscular mycorrhiza fungi. The formation of symbioses leads to improved nitrogen and phosphorus nutrition of plants, resulting in increased plant resistance to abiotic and biotic stress factors, in particular, to phytopathogens. The main objective of QTL analysis is to identify genomic regions whose allelic state affects the manifestation of quantitative traits, including such traits as nitrogen fixation efficiency and pathogen resistance. The identified QTLs and molecular markers created on their basis can be used in the selection of new pea varieties with improved agronomic characteristics, such as resistance to changing environmental conditions and high efficiency of symbiotic systems. This article reviews the historical stages of the emergence of QTL analysis, the basic principles of QTL mapping, and modern approaches. The need for an integrated approach to the analysis of the characteristics of symbiosis efficiency and stability is noted, and the use of integrated phenotypic assessments for working with such traits is discussed.
The dynamics of the composition of the Adalia bipunctata L. population in Arkhangelsk for 21 years has been studied. The proportion of black individuals decreased by almost 2 times; the average annual temperature at the same time increased from 1.92° to 2.95°. A comparison of the population composition with the average annual temperature showed that the proportion of black individuals in the population is negatively correlated with the average annual temperature. The observed change in population composition is probably the effect of global warming.
BACKGROUND: The efficiency of modern selection programs in poultry breeding largely depends on animal genotyping. The availability of genotyping data allows to perform genome-wide association studies (GWAS), a genotype array analysis that identifies relationships between phenotypic traits and genome. Establishing local poultry breeds for meat production, a crucial protein source for human nutrition, is a significant priority within the national poultry sector. Achieving this goal requires examination of available genetic resources and identification of genomic regions responsible for manifestation of meat productivity. AIM: the present research aimed to perform a GWAS for carcass traits in Tsarskoye Selo chicken breed to establish the genetic determinants of meat productivity. METHODS: Tsarskoye Selo chicken breed (n = 96) was used as material for the study. Genotyping data were obtained using the Illumina Chicken 60K SNP iSelectBeadChip (Illumina Inc., USA), and GWAS was performed using EMMAX with Bonferroni correction. Genome-wide significance was assessed using the simple method in R, the calculation of the effective number of independent tests was performed using the Meff program. Gene annotation was performed via ENSEMBL genome browser, using GRCg6a genome assembly. RESULTS: For 8 out of 12 traits, 11 suggestive SNPs (2,31E-05) were obtained on chromosomes 1,3,11,12,15,22,23 and 27. The highest number of SNPs was detected for the thigh muscles (TM)—3 SNPs, and for breast muscles (BM)—2 SNPs. For the remaining traits, 1 SNP each was detected. A total of 16 genes associated with immunity (SKAP1, DCAF1, ISCU, TRAFD1), metabolism (GPATCH1, CMKLR1, TBC1D15, RAB21), osteogenesis (GPM6B, RAB9A, TRAPPC2), protein synthesis (RPL6), serotonin biosynthesis and eating behavior (TPH2), myogenesis (AGO3), morphogenesis (UNC5D), and DNA damage response (CLSPN) were identified. CONCLUSION: The obtained results can be successfully used in selection programs of Tsarskoye Selo chicken breed, and can be recommended for approbation in other breeds.
BACKGROUND: According to modern concepts, the SWEET family may be the only family of plant sugar transporters that includes genes specifically expressed during the formation and development of plant symbiosis with fungi of arbuscular mycorrhiza. The data on the key genetic markers of the development of effective arbuscular mycorrhiza symbiosis can contribute an active development of organic agriculture in various conditions of phosphorus availability in the soil. AIM: to evaluate the effect of arbuscular mycorrhiza on the expression of SWEET genes in M. lupulina L. during key stages of host plant development (stages of leaves rosette, stooling initiation, stooling, lateral branching initiation, lateral branching and flowering). MATERIALS AND METHODS: The study was performed using a highly efficient plant-microbial system “Medicago lupulina + Rhizophagus irregularis” grown under conditions with a high content of available phosphorus in the substrate. RESULTS: Under condition of high phosphorus level in the substrate it was shown for the first time the MlSWEET1b and MlSWEET3c genes in M. lupulina leaves were characterized by specific expression during mycorrhization. CONCLUSIONS: MlSWEET1b and MlSWEET3c and their orthologs can be considered as marker genes of effective symbiosis development, as a tool of biotechnology to increase agricultural productivity with using biostimulants based on arbuscular mycorrhiza fungi.
The intensive application of antimicrobial agents in industrial poultry farming contributes to the formation and maintenance of an extensive resistome – the collection of antibiotic resistance genes within microbial communities. This review synthesizes current data on the structure, diversity, and circulation of antibiotic resistance genes in poultry production systems within the context of the “One Health” concept. It offers a unique, systemic perspective, viewing a poultry farm as an integrated ecosystem for the circulation of resistance genes. Metagenomic studies have revealed over 600 types of resistance genes in the poultry microbiome, conferring resistance to 25 classes of antibiotics. The most prevalent genes confer resistance to tetracyclines (tetA, tetB, tetM), β-lactams (blaTEM, blaCTX-M, blaCMY-2), macrolides (ermB, ermA), fluoroquinolones (qnrS, qnrB), and aminoglycosides. Of particular concern is the detection of carbapenemase genes (blaNDM, blaOXA-48) and genes conferring resistance to last-resort drugs such as tigecycline (tetX4) and colistin (mcr-1). The concentration of resistance genes in poultry litter can reach 10¹⁶ copies per gram, exceeding levels found in other types of livestock waste. The review details key ecological reservoirs, including the gut microbiome, hatcheries, biofilms in water systems, litter, and production surfaces. The primary dissemination mechanisms encompass vertical transmission via hatcheries, horizontal gene transfer mediated by plasmids and transposons, and large-scale dispersion through litter into agro-ecosystems. The role of co-selection with heavy metal and biocide resistance genes in maintaining the resistome in the absence of antibiotic pressure is highlighted. This review emphasizes the necessity for an integrated approach to resistome control. This includes optimizing antimicrobial use, enhancing biosecurity measures, developing alternative prophylactic strategies, and implementing effective waste management protocols to mitigate environmental and epidemiological risks.
BACKGROUND: Experimental data on tissue-specific effects and antigenotoxic potential facilitate more targeted practical applications of antigenotoxicants. AIM: This work aimed to assess the tissue-specific antigenotoxic activity of the natural flavonoids apigenin, naringenin, and hesperetin against the DNA-damaging effects of temozolomide and the cytogenetic effects of genotoxicants with various mechanisms of action. METHODS: The genotoxicants (temozolomide 50 mg/kg, cyclophosphamide 20 mg/kg, methyl methanesulfonate 80 mg/kg, and dioxydin 250 mg/kg) were administered intraperitoneally to mice. Before genotoxicant injections, three oral doses of apigenin (5, 25, and 50 mg/kg) and naringenin and hesperetin (25, 50, and 100 mg/kg) were given. In a separate experiment, apigenin was administered one hour after temozolomide injection. The study used a comet assay in bone marrow, liver, kidney, brain, and rectum cells, as well as chromosome aberration analysis in bone marrow cells. RESULTS: Apigenin decreased temozolomide-induced DNA damage in the bone marrow (52%–66%), liver (31%–65%), kidneys (50%), and rectum (100%), but not in the brain. All apigenin doses reduced kidney levels of atypical DNA comets. Naringenin demonstrated antigenotoxic activity by reducing DNA damage in the bone marrow (48%–62%), brain (26%–44%), and rectum (49%–54%), but not in the liver or kidneys. Hesperetin showed antigenotoxic effects in the bone marrow (23%), kidneys (29%–33%), brain (23%–42%), and rectum (32%–47%). In a cytogenetic assay, apigenin, naringenin, and hesperetin dose-dependently reduced the effects of temozolomide by 49%–73%, 49%–75%, and 39%–55%, respectively. In the post-treatment mode, apigenin 5–50 mg/kg reduced the effects of temozolomide by 47%–51%. Apigenin 5 mg/kg and 25 mg/kg markedly reduced the cytogenetic effects of dioxydin, while apigenin 25 mg/kg decreased those of cyclophosphamide and methyl methanesulfonate. Naringenin 50 mg/kg and 100 mg/kg reduced the effect of cyclophosphamide (43%–71%), but not dioxydin. CONCLUSION: Apigenin, naringenin, and hesperetin show tissue-specific antigenotoxic activity against the effects of temozolomide. Apigenin and naringenin reduce the cytogenetic effects of genotoxicants with various mechanisms of damaging action. The findings highlight the potential of the investigated flavonoids as genome-protecting agents with a possible targeted action.
BACKGROUND: Guar (Cyamopsis tetragonoloba), an industrially important crop, is valued for the galactomannan gum derived from its seeds. Recent advances in genomic and transcriptomic research have provided valuable resources such as the reference genome and several sets of gene expression profiles. However, these data are currently fragmented and therefore require bioinformatics expertise to access and analyze them. Additionally, several genomic assemblies have been recently published, but there are currently no bioinformatics platforms specifically dedicated to guar genomics and transcriptomics. AIM: To address this challenge, we have developed CTGA, a comprehensive functional genomic web portal for guar. METHODS: Using Flask, as well as popular Python, CSS, and HTML libraries, we have developed a backend and frontend for the genomic platform. RESULTS: We have performed a de novo structural and functional annotation of the guar genome predicting 57,019 protein-coding genes with UTRs. Besides, expression data from 85 public RNA-seq libraries representing various tissues and conditions were collected to create a normalized gene expression atlas. CTGA features an intuitive web interface to provide interactive tools, including a genome browser (IGV), BLAST for homology searching, tools for the Gene Ontology enrichment analysis, for working with guar genomic sequences, as well as a tool for generating heatmaps for more convenient analysis of guar gene expression in various tissues and experimental conditions. It also includes detailed functional annotations from various sources (eggNOG, Mercator4, GO, and KEGG) and instant visualization of gene expression profiles. CONCLUSION: CTGA is available at: https://guar.arriam.ru/
The diamondback moth (Plutella xylostella; Linnaeus, 1758) is a globally significant pest of cruciferous crops, causing substantial economic losses. Resistance to pyrethroid insecticides, which are widely used for its control, has become a major issue. This review explores the molecular and genetic mechanisms underlying pyrethroid resistance in P. xylostella, focusing on mutations in the voltage-gated sodium channel gene (Pxpara), which is the primary target of pyrethroids. The review involved an analysis of P. xylostella populations from various regions, particularly in Asia and Australia, where resistance to pyrethroids is prevalent. Molecular techniques, including KASP assays and PCR analysis followed by sequencing, were employed to identify and characterize resistance-associated mutations in the Pxpara gene. Several key mutations in the Pxpara gene were identified, including T929I, M918I, L1014F, and F1020S, which are associated with pyrethroid resistance. These mutations were found to be widespread in Asian populations, with a high prevalence observed in China. An analysis of publications on resistance mechanisms in other insect species revealed resistance mutations at the same sites in a wide range of species, indicating shared mechanisms. The identified mutations in the Pxpara gene provide valuable markers for resistance detection. The development of diagnostic tools based on these findings is crucial for effective resistance management and sustainable pest control. The review also emphasizes the need for integrated pest management approaches to mitigate the spread of resistance and reduce reliance on chemical insecticides.
Background: Most terrestrial plants form a symbiosis with arbuscular mycorrhizal fungi. Arbuscular mycorrhiza significantly enhances plant growth and their adaptation to biotic and abiotic stress factors. Arbuscular mycorrhizal fungi help plant uptake and improve the water nutrition of host plant. At the same time, the regulation and transport of water in plants is largely determined by the aquaporins activity. The specificity of gene expression of these transporters in different plant species and in different tissues has not been fully studied. Aim: To evaluate the effect of mycorrhization of black medic by arbuscular mycorrhizal fungus on the expression of aquaporin genes in the roots under drought conditions at the early and late stages of symbiosis development. Methods: Medicago lupulina MlS-1 line, characterized by high response to mycorrhization, was selected by the authors and was used in this study. The effective Rhizophagus irregularis RCAM00320 strain was used for mycorrhization. The plants were watered daily by 0.6 volumes of saturated water content. But during one week before the results were recorded, water scarcity conditions were created, 0.4 volumes of saturated water content. The plants were counted on the 24th and 48th days after sowing and inoculation. Total RNA from plant roots was isolated using the trizole method with modifications. Thirty-three aquaporin genes were selected to analyze the expression levels. Changes in gene expression were assessed using the real-time polymerase chain reaction method. Results: It was shown the key genes involved in the mechanism of adaptation of mycorrhizal plants to drought may be NIP and TIP aquaporin genes, namely: MlNIP1;2, MlNIP1;3, MlNIP1;5, MlNIP4;1, MlNIP4;2 genes (mainly at the stage of the second leaf development) and MlTIP1;1, MlTIP1;4, MlTIP2;1, MlTIP2;2, MlTIP2;3, MlTIP3;1, MlTIP4;1, MlTIP5;1 genes (mainly at the flowering stage) in plant-microbial system “M. lupulina + R. irregularis”. The study used previously obtained data on the M. lupulina transcriptome to select target genes. Conclusion: The genes involved in the development of effective symbiosis of plants with arbuscular mycorrhizal fungi in conditions of drought were identified. New information about the mechanisms of effective symbiosis formation is of practical importance for the development of highly productive plant-microbial systems, which will allow the transition from intensive agricultural technologies to biological agriculture with the production of environmentally safe products.
