Microenvironment created by Plantago lagopus L. may affect cover and diversity of coexisting species in urban vegetation

Some plant species may exhibit new microenvironments which lead to significant changes in the cover and diversity of the coexisting species. In this investigation, we evaluated the effects of Plantago lagopus L. on the cover and diversity of the associated plant species in the urban vegetation. A total of 70 plots were conducted in sites with- and without this species in urban gardens. Cover of the associated species and different diversity indices including species richness, Shannon-Wiener, evenness, and Simpson indices were measured. The allelopathic potential of P. lagopus was verified using its rhizosphere and non-rhizosphere soils on two target species existing within the same environment. Some soil criteria and seed sizes of the associated species were also determined. Most of the coexisting weeds were reduced in terms of their cover in plots with Plantago. The reduction of plant diversity depended on its cover. Besides, the aboveground biomass was reduced in sites comprising Plantago. The degree of inhibition was not related to the seed size of the species found. This species reduced the incident solar radiation and the local temperature over the soil surface. The locations exhibiting such species contained lower contents of available potassium and zinc. Rhizosphere soil of P. lagopus substantially inhibited germination and growth of Amaranthus viridis, but it didn't do so for Medicago lupulina. Reduction in cover, diversity, and biomass of the urban weeds associated with P. lagopus may be related to the reduction of received solar radiation, soil temperature, and nutrient availability. The allelopathic potential of P. lagopus may have a partial role in this reduction. These results suggest that P. lagopus may create a microenvironment of new conditions not favorable for most of the coexisting species.

Decoding the DSCC1 gene as a pan-cancer biomarker in human cancers via comprehensive multi-omics analyses

OBJECTIVES

While dysregulation of DSCC1 (DNA Replication And Sister Chromatid Cohesion 1) has been established in breast cancer and colorectal cancer, its associations with other tumors remain unclear. Therefore, this study was launched to explore the role of DSCC1 in pan-cancer.

METHODOLOGY

In this study, we investigate the biological functions of DSCC1 across 33 solid tumors, elucidating its role in promoting oncogenesis and progression in various cancers through comprehensive analysis of multi-omics data.

RESULTS

We conducted a comprehensive analysis of DSCC1 expression using RNA-seq data from TCGA and GTEx databases across 30 cancer types. Striking variations were observed, with significant overexpression of DSCC1 identified in numerous cancers. Elevated DSCC1 level was strongly associated with poorer prognosis, shorter survival, and advanced tumor stages in kidney renal papillary cell carcinoma (KIRP), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), as indicated by Kaplan-Meier curves and GEPIA2 analysis. Further investigation into the molecular mechanisms revealed reduced DNA methylation in the DSCC1 promoter region in KIRP, LIHC, and LUAD, supporting enhanced RNA transcription. Protein expression analysis via the Human Protein Atlas (HPA) corroborated mRNA expression findings, showcasing elevated DSCC1 protein in KIRP, LIHC, and LUAD tissues. Mutational analysis using cBioPortal revealed alterations in 0.4% of KIRP, 17% of LIHC, and 5% of LUAD samples, predominantly characterized by amplification. Immune cell infiltration analysis demonstrated robust positive correlations between DSCC1 expression and CD8+ T cells, CD4+ T cells, and B cells, influencing the tumor microenvironment. STRING and gene enrichment analyses unveiled DSCC1's involvement in critical pathways, emphasizing its multifaceted impact. Notably, drug sensitivity analysis highlighted a significant correlation between DSCC1 mRNA expression and responses to 78 anticancer treatments, suggesting its potential as a predictive biomarker and therapeutic target for KIRP, LIHC, and LUAD. Finally, immunohistochemistry staining of clinical samples validated computational results, confirming elevated DSCC1 protein expression.

CONCLUSION

Overall, this study provides comprehensive insights into the pivotal role of DSCC1 in KIRP, LIHC, and LUAD initiation, progression, and therapeutic responsiveness, laying the foundation for further investigations and personalized treatment strategies.

Correction: Biogenic synthesis of silver nanoparticles using Rubus fruticosus extract and their antibacterial efficacy against Erwinia caratovora and Ralstonia solanacearum phytopathogens

[This corrects the article DOI: 10.1039/D3RA06723H.].

Targeting the NF-κB p65/Bcl-2 signaling pathway in hepatic cellular carcinoma using radiation assisted synthesis of zinc nanoparticles coated with naturally isolated gallic acid

PURPOSE

Oral diethylnitrosamine (DEN) is a known hepatocarcinogen that damages the liver and causes cancer. DEN damages the liver through reactive oxygen species-mediated inflammation and biological process regulation.

MATERIALS AND METHODS

Gallic acid-coated zinc oxide nanoparticles (Zn-GANPs) were made from zinc oxide (ZnO) synthesized by irradiation dose of 50 kGy utilizing a Co-60 γ-ray source chamber with a dose rate of 0.83 kGy/h and gallic acid from pomegranate peel. UV-visible (UV) spectrophotometry verified Zn-GANP synthesis. TEM, DLS, and FTIR were utilized to investigate ZnO-NPs' characteristics. Rats were orally exposed to DEN for 8 weeks at 20 mg/kg five times per week, followed by intraperitoneal injection of Zn-GANPs at 20 mg/kg for 5 weeks. Using oxidative stress, anti-inflammatory, liver function, histologic, apoptotic, and cell cycle parameters for evaluating Zn-GANPs treatment.

RESULTS

DEN exposure elevated inflammatory markers (AFP and NF-κB p65), transaminases (AST, ALT), γ-GT, globulin, and total bilirubin, with reduced protein and albumin levels. It also increased MDA levels, oxidative liver cell damage, and Bcl-2, while decreasing caspase-3 and antioxidants like GSH, and CAT. Zn-GANPs significantly mitigated these effects and lowered lipid peroxidation, AST, ALT, and γ-GT levels, significantly increased CAT and GSH levels (p<0.05). Zn-GANPs caused S and G2/M cell cycle arrest and G0/G1 apoptosis. These results were associated with higher caspase-3 levels and lower Bcl-2 and TGF-β1 levels. Zn-GANPs enhance and restore the histology and ultrastructure of the liver in DEN-induced rats.

CONCLUSION

The data imply that Zn-GANPs may prevent and treat DEN-induced liver damage and carcinogenesis.

Biogenic synthesis of silver nanoparticles using Rubus fruticosus extract and their antibacterial efficacy against Erwinia caratovora and Ralstonia solanacearum phytopathogens

In the current research, we produced green, cost-effective, eco-friendly silver nanoparticles using a single-step approach. Plants are considered highly desirable systems for nanoparticle synthesis because they possess a variety of secondary metabolites with significant reduction potential. In the current research, the dried leaf extract of Rubus fruticosus was utilized as a capping and reducing agent for the fabrication of silver nanoparticles, to prepare reliable biogenic silver nanoparticles and subsequently to investigate their potential against some common phytopathogens. The prepared silver nanoparticles were exploited to quantify the total flavonoid content (TFC), total phenolic content (TPC) and DPPH-based antioxidant activity. Different concentrations of aqueous extracts of plant leaves and silver nitrate (AgNO3) were reacted, and the color change of the reactant mixture confirmed the formation of Rubus fruticosus leaf-mediated silver nanoparticles (RFL-AgNPs). A series of characterization techniques such as UV-vis spectroscopy, transmission electron microscopy, energy dispersive X-ray analysis and X-ray diffraction revealed the successful synthesis of silver nanoparticles. The surface plasmon resonance peak appeared at 449 nm. XRD analysis demonstrated the crystalline nature, EDX confirmed the purity, and TEM demonstrated that the nanoparticles are mostly spherical in form. Furthermore, the biosynthesized nanoparticles were screened for in vitro antibacterial activity, antioxidant activity, and total phenolic and flavonoid content. The nanoparticles were used in different concentrations alone and in combination with plant extracts to inhibit Erwinia caratovora and Ralstonia solanacearum. In high-throughput assays used to inhibit these plant pathogens, the nanoparticles were highly toxic against bacterial pathogens. This study can be exploited for planta assays against phytopathogens utilizing the same formulations for nanoparticle synthesis and to develop potent antibacterial agents to combat plant diseases.

Interfacial coupling of CuFe2O4 induced hotspots over self-assembled g-C3N4 nanosheets as an efficient photocatalytic bacterial disinfectant

Most bacterial disinfectants contain high levels of extremely toxic and environmental hazardous chemicals, which pose a significant threat to the ecosystem. Semiconductor photocatalysis exhibits attractive prospects as an emerging greener technology for waste water disinfection. However, the fast recombination of charge carriers limits its practical application. Herein, self-assembled polymeric feather-like g-C3N4 (GCN) nanosheets modified with ferromagnetic CuFe2O4 (CFO) nanospheres were successfully applied as a reusable visible light photocatalytic disinfectant. As expected, the g-C3N4/CuFe2O4 (GCF) nanohybrid displayed superior photocatalytic inactivation efficiency of 0.157log within 120 min towards Escherichia coli DH5α (E. coli) compared with pristine GCN and CFO. The characterization results revealed the synergistic heterostructure interfaces, high surface area, and the transformative self-assembly of GCN to feather-like structure providing a rich active site for improved charge separation efficiency, and wide spectral response, therefore the superior performance of GCF. The radical trapping assay proclaimed that both O2•- and •OH radical played major role in the photocatalytic inactivation among the other reactive oxygen species (ROS). Furthermore, the chemical oxygen demand (COD), protein estimation, and DNA estimation assay results validated the cell damage caused by the photocatalyst. Besides that, GCN showed applicability in real-time wastewater samples with improved efficiency than in the saline solution. The excellent magnetic characteristics facilitated the recycling of the catalyst with insignificant leaching, magnetic induction, and distinguished separation. The results of this work signify the well-designed GCF as a high-performance and reusable photocatalyst for real-world pathogenic bacterial disinfection operations.

Decolorization of Textile Azo Dye via Solid-State Fermented Wheat Bran by Lasiodiplodia sp. YZH1

Textile dyes are one of the major water pollutants released into water in various ways, posing serious hazards for both aquatic organisms and human beings. Bioremediation is a significantly promising technique for dye decolorization. In the present study, the fungal strain Lasiodiplodia sp. was isolated from the fruiting bodies of Schizophyllum for the first time. The isolated fungal strain was examined for laccase enzyme production under solid-state fermentation conditions with wheat bran (WB) using ABTS and 2,6-Dimethoxyphenol (DMP) as substrates, then the fermented wheat bran (FWB) was evaluated as a biosorbent for Congo red dye adsorption from aqueous solutions in comparison with unfermented wheat bran. A Box-Behnken design was used to optimize the dye removal by FWB and to analyze the interaction effects between three factors: fermentation duration, pH, and dye concentration. Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and scanning electron microscopy (SEM) were applied to study the changes in the physical and chemical characteristics of wheat bran before and after fermentation. An additional experiment was conducted to investigate the ability of the Lasiodiplodia sp. YZH1 to remove Congo red in the dye-containing liquid culture. The results showed that laccase was produced throughout the cultivation, reaching peak activities of ∼6.2 and 22.3 U/mL for ABTS and DMP, respectively, on the fourth day of cultivation. FWB removed 89.8% of the dye (100 mg L-1) from the aqueous solution after 12 h of contact, whereas WB removed only 77.5%. Based on the Box-Behnken design results, FWB achieved 93.08% dye removal percentage under the conditions of 6 days of fermentation, pH 8.5, and 150 mg L-1 of the dye concentration after 24 h. The fungal strain removed 95.3% of 150 mg L-1 of the dye concentration after 8 days of inoculation in the dye-containing liquid culture. These findings indicate that this strain is a worthy candidate for dye removal from environmental effluents.

A novel biogenic Allium cepa leaf mediated silver nanoparticles for antimicrobial, antioxidant, and anticancer effects on MCF-7 cell line

In the present study, Allium cepa leaf extract was utilized to reduce the silver nitrate into the nanoscale range of silver ions (Ag NPs). The biosynthesized Ag NPs were extensively characterized by X-ray diffraction analysis (XRD), Dynamic light scattering analysis (DLS), UV-Visible spectroscopy (UV-vis), Transmission electron microscopy (TEM), Energy dispersive X-ray analysis (EDX) and Fourier transform infrared spectroscopy (FTIR). The antioxidant activity of synthesized Ag NPs was verified by DPPH assay. From the results obtained from XRD and DLS studies, the size of Ag NPs was determined to be around 54.3 nm. The measured zeta potential value of -19.1 mV confirms the excellent stability of biosynthesized Ag NPs. TEM analyses reveal that the biosynthesized Ag NPs have a spherical structure of 13 nm in size. The presence of various functional groups was confirmed through FTIR studies and EDAX verifies the weight percentage of silver content in biosynthesized nanoparticles to be 30.33%. In the present study, anti-cancer activity was carried out by using breast cancer cell line MCF-7. Further, silver nanoparticles exhibited antimicrobial effectiveness against gram-positive Bacillus cereus and gram-negative Escherichia coli. The MTT assay also showed better cytotoxic activity against the MCF- 7 cell line.

Stabilization and improved properties of Salipaludibacillus agaradhaerens alkaline protease by immobilization onto double mesoporous core-shell nanospheres

In this study, serine alkaline protease from halotolerant alkaliphilic Salipaludibacillus agaradhaerens strain AK-R was purified and immobilized onto double mesoporous core-shell silica (DMCSS) nanospheres. Covalent immobilization of AK-R protease onto activated DMCSS-NH₂ nanospheres was more efficient than physical adsorption and was applied in further studies. DMCSS-NH₂ nanospheres showed high loading capacity of 103.8 μg protein/mg nanospheres. Relative to free AK-R protease, the immobilized enzyme exhibited shifts in the optimal temperature and pH from 60 to 65 °C and pH 10.0 to 10.5, respectively. While the soluble enzyme retained 47.2% and 9.1% of its activity after treatment for 1 h at 50 and 60 °C, the immobilized protease maintained 87.7% and 48.3%, respectively. After treatment for 2 h at pH 5 and 13, the immobilized protease maintained 73.6% and 53.4% of its activity, whereas the soluble enzyme retained 32.9% and 1.4%, respectively. Furthermore, the immobilized AK-R protease showed significant improvement of enzyme stability in high concentration of NaCl, organic solvents, surfactants, and commercial detergents. In addition, the immobilized protease exhibited a very good operational stability, retaining 79.8% of its activity after ten cycles. The results clearly suggest that the developed immobilized protease system is a promising nanobiocatalyst for various protease applications.

Alkaline serine protease from the new halotolerant alkaliphilic Salipaludibacillus agaradhaerens strain AK-R: purification and properties

Herein, we report the purification and characterization of an alkaline protease from the alkaliphilic Salipaludibacillus agaradhaerens (formerly Bacillus agaradhaerens) strain AK-R, which was previously isolated from Egyptian soda lakes. The purification procedures resulted in enzyme purification up to 13.3-fold, with a recovery yield of 16.3% and a specific activity of 3488 U/mg protein. AK-R protease was a monomeric protein with an estimated molecular weight of 33.0 kDa. The optimum pH and temperature for AK-R protease were pH 10 and 60 °C, respectively. The enzyme thermostability was significantly enhanced in the presence of CaCl₂ by approximately 1.3-fold. Moreover, under optimal conditions, the K _m and V _max values of the enzyme were 2.63 mg/ml and 4166.7 U/mg, respectively. PMSF caused complete inhibition of the enzyme activity, suggesting that AK-R belongs to the serine protease family. In addition, the enzyme was completely inhibited by EDTA, revealing the requirement of metal ions for AK-R protease activity; hence, it can be classified as a metalloprotease. AK-R protease is a mostly thiol-independent enzyme, since thiol reductants such as β-mercaptoethanol and dithiothreitol had no effect on the enzyme activity. AK-R protease exhibited high stability in several organic solvents, including butanol, amyl alcohol, dimethyl ether, toluene, diethyl ether and methanol. Moreover, AK-R protease showed significant stability to a variety of surfactants and commercial detergents. The features and properties of AK-R alkaline protease are favourable and suggest its potential applications in various industries, particularly in the laundry detergent industry.

Prevalence, serotyping and antimicrobials resistance mechanism of Salmonella enterica isolated from clinical and environmental samples in Saudi Arabia

Salmonella is recognized as a common foodborne pathogen, causing major health problems in Saudi Arabia. Herein, we report epidemiology, antimicrobial susceptibility and the genetic basis of resistance among S. enterica strains isolated in Saudi Arabia. Isolation of Salmonella spp. from clinical and environmental samples resulted in isolation of 33 strains identified as S. enterica based on their biochemical characteristics and 16S-rDNA sequences. S. enterica serovar Enteritidis showed highest prevalence (39.4%), followed by S. Paratyphi (21.2%), S. Typhimurium (15.2%), S. Typhi and S. Arizona (12.1%), respectively. Most isolates were resistant to 1st and 2nd generation cephalosporin; and aminoglycosides. Moreover, several S. enterica isolates exhibited resistance to the first-line antibiotics used for Salmonellosis treatment including ampicillin, trimethoprim–sulfamethoxazole and chloramphenicol. In addition, the results revealed the emergence of two S. enterica isolates showing resistance to third-generation cephalosporin. Analysis of resistance determinants in S. enterica strains (n = 33) revealed that the resistance to β-lactam antibiotics, trimethoprim–sulfamethoxazole, chloramphenicol, and tetracycline, was attributed to the presence of carb-like, dfrA1, floR, tetA gene, respectively. On the other hand, fluoroquinolone resistance was related to the presence of mutations in gyrA and parC genes. These findings improve the information about foodborne Salmonella in Saudi Arabia, alarming the emergence of multi-drug resistant S. enterica strains, and provide useful data about the resistance mechanisms.

Enhancement of Alkaline Protease Activity and Stability via Covalent Immobilization onto Hollow Core-Mesoporous Shell Silica Nanospheres

The stability and reusability of soluble enzymes are of major concerns, which limit their industrial applications. Herein, alkaline protease from Bacillus sp. NPST-AK15 was immobilized onto hollow core-mesoporous shell silica (HCMSS) nanospheres. Subsequently, the properties of immobilized proteases were evaluated. Non-, ethane- and amino-functionalized HCMSS nanospheres were synthesized and characterized. NPST-AK15 was immobilized onto the synthesized nano-supports by physical and covalent immobilization approaches. However, protease immobilization by covalent attachment onto the activated HCMSS–NH₂ nanospheres showed highest immobilization yield (75.6%) and loading capacity (88.1 μg protein/mg carrier) and was applied in the further studies. In comparison to free enzyme, the covalently immobilized protease exhibited a slight shift in the optimal pH from 10.5 to 11.0, respectively. The optimum temperature for catalytic activity of both free and immobilized enzyme was seen at 60 °C. However, while the free enzyme was completely inactivated when treated at 60 °C for 1 h the immobilized enzyme still retained 63.6% of its initial activity. The immobilized protease showed higher V_max, k_cat and k_cat/K_m, than soluble enzyme by 1.6-, 1.6- and 2.4-fold, respectively. In addition, the immobilized protease affinity to the substrate increased by about 1.5-fold. Furthermore, the enzyme stability in various organic solvents was significantly enhanced upon immobilization. Interestingly, the immobilized enzyme exhibited much higher stability in several commercial detergents including OMO, Tide, Ariel, Bonux and Xra by up to 5.2-fold. Finally, the immobilized protease maintained significant catalytic efficiency for twelve consecutive reaction cycles. These results suggest the effectiveness of the developed nanobiocatalyst as a candidate for detergent formulation and peptide synthesis in non-aqueous media.

A novel cyclodextrin glycosyltransferase from Alkaliphilic Amphibacillus sp. NPST-10: purification and properties

Screening for cyclodextrin glycosyltransferase (CGTase)-producing alkaliphilic bacteria from samples collected from hyper saline soda lakes (Wadi Natrun Valley, Egypt), resulted in isolation of potent CGTase producing alkaliphilic bacterium, termed NPST-10. 16S rDNA sequence analysis identified the isolate as Amphibacillus sp. CGTase was purified to homogeneity up to 22.1 fold by starch adsorption and anion exchange chromatography with a yield of 44.7%. The purified enzyme was a monomeric protein with an estimated molecular weight of 92 kDa using SDS-PAGE. Catalytic activities of the enzyme were found to be 88.8 U mg⁻¹ protein, 20.0 U mg⁻¹ protein and 11.0 U mg⁻¹ protein for cyclization, coupling and hydrolytic activities, respectively. The enzyme was stable over a wide pH range from pH 5.0 to 11.0, with a maximal activity at pH 8.0. CGTase exhibited activity over a wide temperature range from 45 °C to 70 °C, with maximal activity at 50 °C and was stable at 30 °C to 55 °C for at least 1 h. Thermal stability of the purified enzyme could be significantly improved in the presence of CaCl₂. K_m and V_max values were estimated using soluble starch as a substrate to be 1.7 ± 0.15 mg/mL and 100 ± 2.0 μmol/min, respectively. CGTase was significantly inhibited in the presence of Co²⁺, Zn²⁺, Cu²⁺, Hg²⁺, Ba²⁺, Cd²⁺, and 2-mercaptoethanol. To the best of our knowledge, this is the first report of CGTase production by Amphibacillus sp. The achieved high conversion of insoluble raw corn starch into cyclodextrins (67.2%) with production of mainly β-CD (86.4%), makes Amphibacillus sp. NPST-10 desirable for the cyclodextrin production industry.

Hexavalent chromate reduction by alkaliphilic Amphibacillus sp. KSUCr3 is mediated by copper-dependent membrane-associated Cr(VI) reductase

The present study was aimed to localize and characterize hexavalent chromate [Cr(VI)] reductase activity of the extreme alkaliphilic Amphibacillus sp. KSUCr3 (optimal growth pH 10.5). The resting cells were able to reduce about 62 % of the toxic heavy metal Cr(VI) at initial concentration of 200 μM within 30 min. Cell permeabilization resulted in decrease of Cr(VI) reduction in comparison to untreated cells. Enzymatic assays of different sub-cellular fractions of Amphibacillus sp. KSUCr3 demonstrated that the Cr(VI) reductase was mainly associated with the membranous fraction and expressed constitutively. In vitro studies of the crude enzyme indicated that copper ion was essential for Cr(VI) reductase activity. In addition, Ca²⁺ and Mn²⁺ slightly stimulated the chromate reductase activity. Glucose was the best external electron donor, showing enhancement of the enzyme activity by about 3.5-fold. The K (m) and V (max) determined for chromate reductase activity in the membranous fraction were 23.8 μM Cr(VI) and 72 μmol/min/mg of protein, respectively. Cr(VI) reductase activity was maximum at 40 °C and pH 7.0 and it was significantly inhibited in the presence of disulfide reducers (2-mercaptoethanol), ion chelating agent (EDTA), and respiratory inhibitors (CN and Azide). Complete reduction of 100 and 200 μM of Cr(VI) by membrane associated enzyme were observed within 40 and 180 min, respectively. However, it should be noted that biochemical characterization has been done with crude enzyme only, and that final conclusion can only be drawn with the purified enzyme.

Changes in the water status and osmotic solute contents in response to drought and salicylic acid treatments in four different cultivars of wheat (Triticum aestivum)

Salicylic acid (SA) controls growth and stress responses in plants. It also induces drought tolerance in plants. In this paper, four wheat (Triticum aestivum L.) cultivars with different drought responses were treated with SA in three levels of drain (90, 60, 30% of maximum field capacity) to examine its interactive effects on drought responses and contents of osmotic solutes that may be involved in growth and osmotic adjustment. Under drought condition, the cultivars Geza 164 and Sakha 69 had the plant biomass and leaf relative water content (LRWC) greater than the cultivars Gemaza 1 and Gemaza 3. In all cultivars, drought stress decreased the biomass, LRWC, and the contents of inorganic solutes (Ca, K, Mg) and largely increased the contents of organic solutes (soluble sugars and proline). By contrast, SA increased the biomass, LRWC and the inorganic and organic solute contents, except proline. Correlation analysis revealed that the LRWC correlated positively with the inorganic solute contents but negatively with proline in all cultivars. SA caused maximum accumulations of soluble sugars in roots under drought. These results indicated that SA-enhanced tolerance might involve solute accumulations but independently of proline biosynthesis. Drought-sensitive cultivars had a trait lowering Ca and K levels especially in shoots. Possible functions of the ions and different traits of cultivars were discussed.