Signal Recognition Particle Research Articles

Harnessing Immunoinformatics for Precision Vaccines: Designing Epitope-Based Subunit Vaccines against Hepatitis E Virus

Background/Objectives: Hepatitis E virus (HEV) is an RNA virus recognized to be spread mainly by fecal-contaminated water. Its infection is known to be a serious threat to public health globally, mostly in developing countries, in which Africa is one of the regions sternly affected. An African-based vaccine is necessary to actively prevent HEV infection. Methods: This study developed an in silico epitope-based subunit vaccine, incorporating CTL, HTL, and BL epitopes with suitable linkers and adjuvants. Results: The in silico-designed vaccine construct proved immunogenic, non-allergenic, and non-toxic and displayed appropriate physicochemical properties with high solubility. The 3D structure was modeled and subjected to protein docking with Toll-like receptors 2, 3, 4, 6, 8, and 9, which showed a stable binding efficacy, and the dynamics simulation indicated steady interaction. Furthermore, the immune simulation predicted that the designed vaccine would instigate immune responses when administered to humans. Lastly, using a codon adaptation for the E. coli K12 bacterium produced optimum GC content and a high CAI value, which was followed by in silico integration into a pET28 b (+) cloning vector. Conclusions: Generally, these results propose that the design of an epitope-based subunit vaccine can function as an outstanding preventive vaccine candidate against HEV, although validation techniques via in vitro and in vivo approaches are required to justify this statement.

Quantum Chemistry-Based Protein-Protein Docking without Empirical Parameters.

This study developed a novel protein-protein docking approach based on quantum chemistry. To judge the appropriateness of complex structures, we introduced two criterion values, EV1 and EV2, computed using the fragment molecular orbital method without any empirical parameters. These criterion values enable us to search complex structures in which patterns of the electrostatic potential of the two proteins are optimally aligned at their interface. The performance of our method was validated using 53 complexes in a benchmark set provided for protein-protein docking. When employing bound state structures, docking success rates reached 64% for EV1 and 76% for EV2. On the other hand, when employing unbound state structures, docking success rates reached 13% for EV1 and 17% for EV2.

Intermolecular Electrostatic Interactions in Cytochrome c Protein Monolayer on Montmorillonite Alumosilicate Surface: A Positive Cooperative Effect.

Montmorillonite (MM) crystal nanoplates acquire anticancer properties when coated with the mitochondrial protein cytochrome c (cytC) due to the cancer cells' capability to phagocytize cytC-MM colloid particles. The introduced exogenous cytC initiates apoptosis: an irreversible cascade of biochemical reactions leading to cell death. In the present research, we investigate the organization of the cytC layer on the MM surface by employing physicochemical and computer methods-microelectrophoresis, static, and electric light scattering-to study cytC adsorption on the MM surface, and protein electrostatics and docking to calculate the local electric potential and Gibbs free energy of interacting protein globules. The found protein concentration dependence of the adsorbed cytC quantity is nonlinear, manifesting a positive cooperative effect that emerges when the adsorbed cytC globules occupy more than one-third of the MM surface. Computer analysis reveals that the cooperative effect is caused by the formation of protein associates in which the cytC globules are oriented with oppositely charged surfaces. The formation of dimers and trimers is accompanied by a strong reduction in the electrostatic component of the Gibbs free energy of protein association, while the van der Waals component plays a secondary role.

The RNA Helicase Ded1 from Yeast Is Associated with the Signal Recognition Particle and Is Regulated by SRP21.

The DEAD-box RNA helicase Ded1 is an essential yeast protein involved in translation initiation that belongs to the DDX3 subfamily. The purified Ded1 protein is an ATP-dependent RNA-binding protein and an RNA-dependent ATPase, but it was previously found to lack substrate specificity and enzymatic regulation. Here we demonstrate through yeast genetics, yeast extract pull-down experiments, in situ localization, and in vitro biochemical approaches that Ded1 is associated with, and regulated by, the signal recognition particle (SRP), which is a universally conserved ribonucleoprotein complex required for the co-translational translocation of polypeptides into the endoplasmic reticulum lumen and membrane. Ded1 is physically associated with SRP components in vivo and in vitro. Ded1 is genetically linked with SRP proteins. Finally, the enzymatic activity of Ded1 is inhibited by SRP21 in the presence of SCR1 RNA. We propose a model where Ded1 actively participates in the translocation of proteins during translation. Our results provide a new understanding of the role of Ded1 during translation.

Structure-Based Design, Virtual Screening, and Discovery of Novel Patulin Derivatives as Biogenic Photosystem II Inhibiting Herbicides.

Computer-aided design usually gives inspirations and has become a vital strategy to develop novel pesticides through reconstructing natural lead compounds. Patulin, an unsaturated heterocyclic lactone mycotoxin, is a new natural PSII inhibitor and shows significant herbicidal activity to various weeds. However, some evidence, especially the health concern, prevents it from developing as a bioherbicide. In this work, molecular docking and toxicity risk prediction are combined to construct interaction models between the ligand and acceptor, and design and screen novel derivatives. Based on the analysis of a constructed patulin-Arabidopsis D1 protein docking model, in total, 81 derivatives are designed and ranked according to quantitative estimates of drug-likeness (QED) values and free energies. Among the newly designed derivatives, forty-five derivatives with better affinities than patulin are screened to further evaluate their toxicology. Finally, it is indicated that four patulin derivatives, D3, D6, D34, and D67, with higher binding affinity but lower toxicity than patulin have a great potential to develop as new herbicides with improved potency.

Physiological responses of the nickel hyperaccumulator Bornmuellera emarginata under varying nickel dose levels and pH in hydroponics

Abstract Background and aims The nickel hyperaccumulator Bornmuellera emarginata (Brassicaceae) is a species adapted to thrive on naturally nickel-enriched ultramafic soils in the Balkans and a promising candidate for use in nickel agromining. The main aim of this study was to provide insight into the physiological mechanisms of nickel hyperaccumulation in B. emarginata. Methods Bornmuellera emarginata was cultivated under various nickel exposure concentrations (control, 1, 10, and 100 µM nickel in solution), and different pH levels of the hydroponic solution for four weeks. During this period, the plants underwent assessment for various physiological parameters, including photosynthetic pigments, leaf relative water content, tolerance index, and metal accumulation in plant tissues. Results The results show that the translocation factors and bioconcentration factors were > 1 even at 1 µM nickel in solution. This confirms the ability of B. emarginata to hyperaccumulate nickel (up to 6600 mg kg−1) over a wide range of nickel concentrations in hydroponics. Nickel at 100 µM (a concentration that is an order of magnitude higher than the highest soil solution nickel concentration found in ultramafic soils) induced only mild physiological stress symptoms (e.g. a minor proline response). Alterations in the solution pH did not cause any significant effect on nickel accumulation in the plants. Conclusions Bornmuellera emarginata is a highly adapted nickel-tolerant and nickel hyperaccumulating species that shows very little stress responses even to extreme nickel exposure concentrations in hydroponics. This species shows interesting trade-off responses between nickel and other metals, including non-competitive uptake of zinc. The potential for this species to accumulate zinc should therefore be further explored.

Variety-dependent responses of common tobacco with differential cadmium resistance: Cadmium uptake and distribution, antioxidative activity, and gene expression

Cadmium (Cd), which accumulates in tobacco leaves, enters the human body through inhalation of smoke, causing harmful effects on health. Therefore, identifying the pivotal factors that govern the absorption and resistance of Cd in tobacco is crucial for mitigating the harmful impact of Cd. In the present study, four different Cd-sensitive varieties, namely, ZhongChuan208 (ZC) with resistance, ZhongYan100 (ZY), K326 with moderate resistance, and YunYan87 (YY) with sensitivity, were cultivated in hydroponic with different Cd concentrations (20 µM, 40 µM, 60 µM and 80 µM). The results indicated that plant growth was significantly decreased by Cd. Irrespective of the Cd concentration, ZC exhibited the highest biomass, while YY had the lowest biomass; ZY and K326 showed intermediate levels. Enzymatic (APX, CAT, POD) and nonenzymatic antioxidant (Pro, GSH) systems showed notable variations among varieties. The multifactor analysis suggested that the ZC and ZY varieties, with higher levels of Pro and GSH content, contribute to a decrease in the levels of MDA and ROS. Among all the Cd concentrations, ZC exhibited the lowest Cd accumulation, while YY showed the highest. Additionally, there were significant differences observed in Cd distribution and translocation factors among the four different varieties. In terms of Cd distribution, cell wall Cd accounted for the highest proportion of total Cd, and organelles had the lowest proportion. Among the varieties, ZC showed lower Cd levels in the cell wall, soluble fraction, and organelles. Conversely, YY exhibited the highest Cd accumulation in all tissues; K326 and ZY had intermediate levels. Translocation factors (TF) varied among the varieties under Cd stress, with ZC and ZY showing lower TF compared to YY and K326. This phenomenon mainly attributed to regulation of the NtNramp3 and NtNramp5 genes, which are responsible for the absorption and transport of Cd. This study provides a theoretical foundation for the selection and breeding of tobacco varieties that are resistant to or accumulate less Cd.

Sulfur/zinc co-doped biochar for stabilization remediation of mercury-contaminated soil: Performance, mechanism and ecological risk

In this study, a novel sulfur/zinc co-doped biochar (SZ-BC) stabilizer was successfully developed for the remediation of mercury-contaminated soil. Results from SEM, TEM, FTIR and XRD revealed that biochar (BC) was successfully modified by sulfur and zinc. In the batch adsorption experiments, the sulfur-zinc co-pyrolysis biochar displayed excellent Hg(II) adsorption performance, with the maximum adsorption capacity of SZ-BC (261.074 mg/g) being approximately 16.5 times that of BC (15.855 mg/g). Laboratory-scale static incubation, column leaching, and plant pot experiments were conducted using biochar-based materials. At an additional dosage of 5 % mass ratio, the SZ-BC exhibits the most effective stabilization of mercury in soil, leading to a significant reduction in leaching loss compared to the control group (CK) by 51.30 %. Following 4 weeks of incubation and 2 weeks of leaching with SZ-BC, the residual mercury in the soil increased by 27.84 %. As a result, potential ecological risk index of mercury decreased by 92 % compared to the CK group. In the pot experiment, SZ-BC significantly enhanced the growth of Chinese cabbage, with biomass and root dry weight reaching 3.20 and 2.80 times that of the CK group, respectively. Additionally, the Translocation Factor (TF) and Bioconcentration Factor (BF) were reduced by 44.86 % and 74.43 %, respectively, in the SZ-BC group compared to the CK group. Moreover, SZ-BC can effectively improve enzyme activities and increase microbial communities in mercury-contaminated soils. The mechanisms of adsorption and stabilization were elucidated through electrostatic adsorption, ion exchange, surface complexation, and precipitation. These findings provide a potentially effective material for stabilizing soils contaminated with mercury.

Glycine-doped metal–organic frameworks as intelligent nanocarriers to enhance pesticide delivery and provide micronutrient in plants

The development of multifunctional pesticide-delivery system is of practical significance for realizing efficient utilization of pesticides and minimizing environmental risks. In this work, methoxyfenozide (Met)-loaded glycine-doped zeolitic imidazolate framework-8 composites (Met@Gly@ZIF-8) for intelligent-release of Met and effective pest management were facilely constructed. The physical properties of Met@Gly@ZIF-8, including ultraviolet (UV) resistance, deposition and release profiles were evaluated. Compared with Met, the residual content after UV irradiation and retention content on cabbage leaves of Met@Gly@ZIF-8 increased by 121.2% and 98.2%, respectively, and the contact angle on foliar decreased by 26.5% compared with Met suspension concentrate (SC), demonstrating better photolysis resistance, deposition and wetting ability. Release experiments indicated that Met@Gly@ZIF-8 possessed significant stimuli-responsive release characteristics which were negatively correlated with pH, due to the acidic degradation of ZIF-8. The biological activity experiments showed that Met@Gly@ZIF-8 possessed elevated control efficacy on Plutella xylostella compared with Met and reduced the LC50 value by 53.2%. The application performance experiments indicated that the penetration amount of Met@Gly@ZIF-8 in cabbage leaves increased by 194.7% and the translocation factor (TFleaf) increased by 63.3%, respectively, as compared with those of Met. Compared with the blank control, Gly@ZIF-8 and Met@Gly@ZIF-8 increased the total biomass of cabbage by 37.8% and 25.7%, respectively, exhibiting nutritional functions for plants. Toxicity test showed that Met@Gly@ZIF-8 was relatively safe for zebrafish compared with Met. The present approach could be strategically promising for constructing functional and environmentally friendly smart-nanopesticide.

The potential of Phragmites australis to bioaccumulation and translocate heavy metals from landfill leachate

Constructed wetlands serve as an eco-friendly solution for treating landfill leachate, leading to reduced energy use, economic savings, and less environmental harm. A novel study in the cold climate of western Iran has examined the effectiveness of Phragmites australis, also known as common reed, in a pilot-scale project. The study focused on the reed's capacity to bioaccumulate and translocate heavy metals within a horizontal subsurface flow constructed wetland. The findings revealed significant removal rates for heavy metals such as Fe, Mn, Cd, Cr, Ni, and Pb, with efficiencies of 81.23 %, 76.02 %, 26.92 %, 44.73 %, 20.13 %, and 28.24 % respectively. The bioaccumulation factor for these metals was above 1.0, signifying effective uptake by the plant. However, the translocation factor for all metals, except for Mn, did not exceed 1.0. This indicates that although Phragmites australis is an effective phytostabilizer, effectively sequestering heavy metals in its root system, it is not adept at moving these metals to its aboveground tissues. Rather, it tends to concentrate them within its roots and rhizomes.

Native desert plants have the potential for phytoremediation of phytotoxic metals in urban cities: implications for cities sustainability in arid environments

Arid regions can benefit from using native desert plants, which require minimal freshwater and can aid in remediating soil phytotoxic metals (PTMs) from traffic emissions. In this study, we assessed the ability of three native desert plants—Pennisetum divisum, Tetraena qatarensis, and Brassica tournefortii—to accumulate phytotoxic metals (PTMs) in their different plant organs, including leaves, stems, and roots/rhizomes. The PTMs were analyzed in soil and plant samples collected from Dubai, United Arab Emirates (UAE). The results indicated significantly higher levels of PTMs on the soil surface than the subsurface layer. Brassica exhibited the highest concentrations of Fe and Zn, measuring 566.7 and 262.8 mg kg−1, respectively, while Tetraena accumulated the highest concentration of Sr (1676.9 mg kg−1) in their stems. In contrast, Pennisetum recorded the lowest concentration of Sr (21.0 mg kg−1), while Tetraena exhibited the lowest concentrations of Fe and Zn (22.5 and 30.1 mg kg−1) in their leaves. The roots of Pennisetum, Brassica, and Tetraena demonstrated the potential to accumulate Zn from the soil, with concentration factors (CF) of 1.75, 1.09, and 1.09, respectively. Moreover, Brassica exhibited the highest CF for Sr, measuring 2.34. Pennisetum, however, could not translocate PTMs from its rhizomes to other plant organs, as indicated by a translocation factor (TF) of 1. In contrast, Brassica effectively translocated the studied PTMs from its roots to the stem and leaves (except for Sr in the leaves). Furthermore, Pennisetum exclusively absorbed Zn from the soil into its leaves and stems, with an enrichment factor (EF) greater than 1. Brassica showed the ability to uptake the studied PTMs in its stem and leaves (except for Fe), while Tetraena primarily absorbed Sr and Zn into its stems. Based on the CF and TF results, Pennisetum appears to be a suitable species for phytostabilization of both Fe and Zn, while Brassica is well-suited for Sr and Zn polluted soils. Tetraena shows potential for Zn phytoremediation. These findings suggest that these plants are suitable for PTMs phytoextraction. Furthermore, based on the EF results, these plants can efficiently sequester PTMs.

Molecular docking and toxicity analysis of ribosome-inactivating protein and natural chemical compounds as promising antiretroviral candidates against HIV-1

Background: HIV (human immunodeficiency virus) uses HIV-1 reverse transcriptase as the receptor to convert RNA into viral DNA. In addition, the CD4 receptor is also used by the virus to enter CD4+ T cells and subsequently replicate. Objective: To screen several proteins in Indonesian plants for the potential to bind to the CD4 receptor. Method: Molecular docking was carried out on Cluspro 2.0 specifically for protein to protein and MOE for protein to ligand. Results: The protein ligands were Cinnamomin III, Agglutinin, PAP, PAP-S, Momordin I, MAP30, Beta-luffin, Luffaculin I, Cucurmosin, DAP, Dianthin-30, Bouganin, Maize, Ricin, Abrin, Balsamin, and the bond energy values (Joules/kg.mol) were -602.8, -973.5, -511.3, -439.1, -532.2, -661.9, -487.0, -472.8, -530.9, -413.6, 444.1, -504.5, -617.2, -855.6, -883.9, -558.6, respectively. The best binding energy with CD4 was selected to identify the compound's molecule. These compounds were abrusin, abrusogenin, eicosadienoic acid, heneicosane, precatorine, and trigonelline, and the bond energy values (Joules/kg.mol) were -19.2158, -16.7057, -15.5155, -13.9632, -15.6119, and -9.2620, respectively. The toxicity test of abrusin was carried out against 18 targets, and two targets showed toxic activities. Conclusion: The content of RIP and natural chemical compounds in Abrus precatorius seeds make them the best candidate for antiretroviral therapy against HIV-1.

Dendroremediation of soil contaminated by mining sludge: A three-year study on the potential of Tilia cordata and Quercus robur in remediation of multi-element pollution

The vast amounts of mining and metallurgical wastes containing unimaginable quantities of toxic metal(loid)s require searching for managed ways. The study aimed to long-term assess the growth, elements accumulation (As, Cd, Hg, In, Mn, Mo, Pb, Sb, Sn, Ti, Tl, Zn) and proline content in 2-year-old Tilia cordata Mill. and Quercus robur L. seedlings growing under 1 and 3% extremely polluted mining sludge (MS) after 1, 2 and 3 years.Both species were able to grow efficiently without significant differences resulting from the impact of MS. The overall rise was higher for T. cordata than for Q. robur. The accumulation ability for As, Hg, In, Mn, Mo, Pb, Ti, and Zn in the whole plant was significantly higher for T. cordata, while Cd, Sb, Sn and Tl did not differ considerably between species. The highest content was found for As, Mn and Zn (68.7, 158, and 157 mg per plant, respectively) for T. cordata after 3 years of growth. The calculated Bioconcentration Factors were the highest for Cu (1.23), In (6.86), and Zn (38.4) for Q. robur, as well as for As (1.55), Hg (3.24), Mn (32.8), Mo (1.64) and Ti (18.0) for T. cordata after 3 years. The highest Translocation Factors were observed for In (1.35) and Sn (1.25) after 3 years, as well as for Mn (2.72, 3.38, and 3.03 after 1, 2, and 3 years) for Q. robur seedlings. The proline content was higher for Q. robur, regardless of which organ was examined, and the differences increased with the time of the experiment and the amount of MS addition (possibly more sensitive to stress).Young T. cordata seedlings show much greater potential than Q. robur. This is the first time that a demonstration of the high potential of long-living trees in multi-element MS remediation has been described.

Optimizing biochar, vermicompost, and duckweed amendments to mitigate arsenic uptake and accumulation in rice (Oryza sativa L.) cultivated on arsenic-contaminated soil

The accumulation of arsenic (As) in rice (Oryza sativa L.) grain poses a significant health concern in Bangladesh. To address this, we investigated the efficacy of various organic amendments and phytoremediation techniques in reducing As buildup in O. sativa. We evaluated the impact of five doses of biochar (BC; BC0.1: 0.1%, BC0.28: 0.28%, BC0.55: 0.55%, BC0.82: 0.82% and BC1.0: 1.0%, w/w), vermicompost (VC; VC1.0: 1.0%, VC1.8: 1.8%, VC3.0: 3.0%, VC4.2: 4.2% and VC5.0: 5.0%, w/w), and floating duckweed (DW; DW100: 100, DW160: 160, DW250: 250, DW340: 340 and DW400: 400 g m− 2) on O. sativa cultivated in As-contaminated soil. Employing a three-factor five-level central composite design and response surface methodology (RSM), we optimized the application rates of BC-VC-DW. Our findings revealed that As contamination in the soil negatively impacted O. sativa growth. However, the addition of BC, VC, and DW significantly enhanced plant morphological parameters, SPAD value, and grain yield per pot. Notably, a combination of moderate BC-DW and high VC (BC0.55VC5DW250) increased grain yield by 44.4% compared to the control (BC0VC0DW0). As contamination increased root, straw, and grain As levels, and oxidative stress in O. sativa leaves. However, treatment BC0.82VC4.2DW340 significantly reduced grain As (G-As) by 56%, leaf hydrogen peroxide by 71%, and malondialdehyde by 50% compared to the control. Lower doses of BC-VC-DW (BC0.28VC1.8DW160) increased antioxidant enzyme activities, while moderate to high doses resulted in a decline in these activities. Bioconcentration and translocation factors below 1 indicated limited As uptake and translocation in plant tissues. Through RSM optimization, we determined that optimal doses of BC (0.76%), VC (4.62%), and DW (290.0 g m− 2) could maximize grain yield (32.96 g pot− 1, 44% higher than control) and minimize G-As content (0.189 mg kg− 1, 54% lower than control). These findings underscore effective strategies for enhancing yield and reducing As accumulation in grains from contaminated areas, thereby ensuring agricultural productivity, human health, and long-term sustainability. Overall, our study contributes to safer food production and improved public health in As-affected regions.

Citrullinating enzyme PADI4 and transcriptional repressor RING1B bind in cancer cells

Polycomb groups (PcGs) are transcriptional repressors, formed by a complex of several proteins, involved in multicellular development and cancer epigenetics. One of these proteins is the E3 ubiquitin-protein ligase RING1 (or RING1B), associated with the regulation of transcriptional repression and responsible for monoubiquitylation of the histone H2A. On the other hand, PADI4 is one of the human isoforms of a family of enzymes implicated in the conversion of arginine to citrulline, and it is also involved in the development of glioblastoma, among other types of cancers. In this work, we showed the association of PADI4 and RING1B in the nucleus and cytosol in several cancer cell lines by using immunofluorescence and proximity ligation assays. Furthermore, we demonstrated that binding was hampered in the presence of GSK484, an enzymatic PADI4 inhibitor, suggesting that RING1B could bind to the active site of PADI4, as confirmed by protein-protein docking simulations. In vitro and in silico findings showed that binding to PADI4 occurred for the isolated fragments corresponding to both the N-terminal (residues 1–221) and C-terminal (residues 228–336) regions of RING1B. Binding to PADI4 was also hampered by GSK484, as shown by isothermal titration calorimetry (ITC) experiments for the sole N-terminal region, and by both NMR and ITC for the C-terminal one. The dissociation constants between PADI4 and any of the two isolated RING1B fragments were in the low micromolar range (~2–10 μM), as measured by fluorescence and ITC. The interaction between RING1B and PADI4 might imply citrullination of the former, leading to several biological consequences, as well as being of potential therapeutic relevance for improving cancer treatment with the generation of new antigens.

Evidence of heavy metal in soil, irrigation water and vegetable cultivated in peri‑urban area of Yaoundé-Cameroon

Environmental pollution from anthropogenic activities is of global concern. The levels of heavy metal contamination were evaluated in the soil and irrigation water, and their transferability to the cultivated plant was appraised in the locality of Nkolbisson, Yaoundé-Cameroun. The levels of Zn, Cu, Cd, Ni, Pb, Cr, and Mn contamination were evaluated to determine the current status, possible source(s), bio-accumulation in food crops, the suitability of the water for irrigation purposes, and hence the probable health risk. The analysis of soils, waters, and crops (Corchorus olitorius and Lactuca sativa) samples has shown high levels of heavy metal contamination. Cd, Ni, and Cr concentrations in water samples (0.98, 2.230, and 2.635 mg/l) were above the threshold set by FAO for irrigation water. In agricultural soils, only the level of Mn (1013.090 mg/kg) contained in soil samples was above the European Union (EU) and the Canadian Council of Ministers for Environment (CCME) thresholds of toxicity. Except for Pb (0.361; 0.394 and 0.043; 0.041 mg/kg DM) and Mn (113.457; 123.341 and 173.667; 180.321 mg/kg DM), the concentration of heavy metals analysed in plant samples were above the standard values in the edible parts. Market gardening in this city presents risks due to the presence of heavy metals in soils and irrigation waters. Thus, market gardeners must be taking appropriate measures to avoid crop contamination. The bioconcentration and translocation factors have shown that Lactuca sativa can be used for phytoextraction of Zn, Cu and Cd whereas Corchorus olitorius can be used for phytomobilization of the same elements.

Strengthen sunflowers resilience to cadmium in saline-alkali soil by PGPR-augmented biochar

In the center of the Nile Delta in Egypt, the Kitchener drain as the primary drainage discharges about 1.9 billion m3 per year of water, which comprises agricultural drainage (75 %), domestic water (23 %), and industrial water (2 %), to the Mediterranean Sea. Cadmium (Cd) stands out as a significant contaminant in this drain; therefore, this study aimed to assess the integration of biochar (0, 5, and 10 ton ha−1) and three PGPRs (PGPR-1, PGPR-2, and PGPR-3) to alleviate the negative impacts of Cd on sunflowers (Helianthus annuus L.) in saline-alkali soil. The treatment of biochar (10 ton ha−1) and PGPR-3 enhanced the soil respiration, dehydrogenase, nitrogenase, and phosphatase activities by 137 %, 129 %, 326 %, and 127 %, while it declined soil electrical conductivity and available Cd content by 31.7 % and 61.3 %. Also, it decreased Cd content in root, shoot, and seed by 55.3 %, 50.7 %, and 92.5 %, and biological concentration and translocation factors by 55 % and 5 %. It also declined the proline, lipid peroxidation, H2O2, and electrolyte leakage contents by 48 %, 94 %, 80 %, and 76 %, whereas increased the catalase, peroxidase, superoxide dismutase, and polyphenol oxidase activities by 80 %, 79 %, 61 %, and 116 %. Same treatment increased seed and oil yields increased by 76.1 % and 76.2 %. The unique aspect of this research is its investigation into the utilization of biochar in saline-alkali soil conditions, coupled with the combined application of biochar and PGPR to mitigate the adverse effects of Cd contamination on sunflower cultivation in saline-alkali soil.

Molecular mechanism of Saikosaponin-d in the treatment of gastric cancer based on network pharmacology and in vitro experimental verification.

The study aimed to utilize network pharmacology combined withcell experiments to research the mechanism of action of Saikosaponin-d in the treatment of gastric cancer. Drug target genes were obtained from the PubChem database and the Swiss Target Prediction database. Additionally, target genes for gastric cancer were obtained from the GEO database and the Gene Cards database. The core targets were then identified and further analyzed through gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and GESA enrichment. The clinical relevance of the core targets was assessed using the GEPIA and HPA databases. Molecular docking of drug monomers and core target proteins was performed using Auto Duck Tools and Pymol software. Finally, in vitro cellular experiments including cell viability, apoptosis, cell scratch, transwell invasion, transwell migration, qRT-PCR, and Western blot were conducted to verify these findings of network pharmacology. The network pharmacology analysis predicted that the drug monomers interacted with 54 disease targets. Based on clinical relevance analysis, six core targets were selected: VEGFA, IL2, CASP3, BCL2L1, MMP2, and MMP1. Molecular docking results showed binding activity between the Saikosaponin-d monomer and these core targets. Saikosaponin-d could inhibit gastric cancer cell proliferation, induce apoptosis, and inhibit cell migration and invasion.

Arsenic uptake by Agrostis capillaris, as related to its genotypic diversity in the area of historical ore mining and processing

Common bentgrass Agrostis capillaris L. is known as tolerant to toxic elements. A hypothesis was examined that its ecotypes growing in historically polluted sites show a limited arsenic uptake and have genetic features that distinguish them from commercially available cultivars. The study was conducted in Złoty Stok, a historical area of arsenic mining. Additionally, two commercial cultivars were grown in pots with arsenic-rich soils. Based on arsenic concentrations in plant roots and shoots, bioconcentration and translocation factors BCF and TF were calculated. Commercial cultivars indicated many times higher BCF shoots and TF values compared to field plants. DNA analysis of leaf blades showed a clear distinction between the plants growing in some sites and patches in the field, and also a gene overlap between the plants in the field and commercial forms. The research did not allow for identification of ecotypes with exceptionally limited arsenic uptake. Moreover, there were no significant differences between the genotypic characteristics of plants growing in polluted sites and those poorly tolerant grown from commercially available seeds. Apparently, other factors, and not genetically determined features, are responsible for A. capillaris tolerance to arsenic in Złoty Stok.

Salicylic acid and jasmonic acid-mediated different fate of nickel phytoremediation in two populations of Alyssum inflatum Nyár.

This study investigates Ni phytoremediation and accumulation potential in the presence of salicylic acid (SA) (0, 50 and 200 μM) and jasmonic acid (JA) (0, 5 and 10 μM) in two populations of Alyssum inflatum under various nickel (Ni) doses (0, 100 and 400 μM). By measuring Ni levels in the shoots and roots, values of bioaccumulation coefficient (BAC), biological concentration factor (BCF) and translocation factor (TF) were calculated to quantify Ni accumulation and translocation between plant organs. Additionally, the amounts of histidine (His), citric acid (CA) and malic acid (MA) were explored. The results showed that plant dry weight (DW) [in shoot (29.8%, 8.74%) and in root (21.6%, 24.4%)] and chlorophyll [a (17.1%, 32.5%), b (10.1%, 30.9%)] declined in M and NM populations respectively, when exposed to Ni (400 μM). Conversely, the levels of MA [in shoot (37.0%, 32.0%) and in root (25.5%, 21.2%)], CA [in shoot (17.0%, 10.0%) and in root (47.9%, 37.2%)] and His [in shoot (by 1.59- and 1.34-fold) and in root (by 1.24- and 1.18-fold)] increased. Also, in the presence 400 μM Ni, the highest accumulation of Ni was observed in shoots of M (1392 μg/g DW) and NM (1382 μg/g DW). However, the application of SA and JA (especially in Ni 400 μM + SA 200 μM + JA 5 and 10 μM treatments) mitigated the harmful impact of Ni on physiological parameters. Also, a decreasing trend was observed in the contents of MA, CA, and His. The reduction of these compounds as important chelators of Ni caused a decrease in root-to-shoot Ni transfer and reducing accumulation in the shoots of both populations. The values of phytoremediation indices in both populations exposed to Ni (400 μM) were above one. In presence of the SA and JA, these indices showed a decreasing trend, although the values remained above one (BAC, BCF and TF > 1). Overall, the results indicated that SA and JA can reduce phytoremediation potential of the two populations through different mechanisms.