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Environmental Science and Pollution... Jun 2024Salinity, resulting from various contaminants, is a major concern to global crop cultivation. Soil salinity results in increased osmotic stress, oxidative stress,... (Review)
Review
Salinity, resulting from various contaminants, is a major concern to global crop cultivation. Soil salinity results in increased osmotic stress, oxidative stress, specific ion toxicity, nutrient deficiency in plants, groundwater contamination, and negative impacts on biogeochemical cycles. Leaching, the prevailing remediation method, is expensive, energy-intensive, demands more fresh water, and also causes nutrient loss which leads to infertile cropland and eutrophication of water bodies. Moreover, in soils co-contaminated with persistent organic pollutants, heavy metals, and textile dyes, leaching techniques may not be effective. It promotes the adoption of microbial remediation as an effective and eco-friendly method. Common microbes such as Pseudomonas, Trichoderma, and Bacillus often struggle to survive in high-saline conditions due to osmotic stress, ion imbalance, and protein denaturation. Halophiles, capable of withstanding high-saline conditions, exhibit a remarkable ability to utilize a broad spectrum of organic pollutants as carbon sources and restore the polluted environment. Furthermore, halophiles can enhance plant growth under stress conditions and produce vital bio-enzymes. Halophilic microorganisms can contribute to increasing soil microbial diversity, pollutant degradation, stabilizing soil structure, participating in nutrient dynamics, bio-geochemical cycles, enhancing soil fertility, and crop growth. This review provides an in-depth analysis of pollutant degradation, salt-tolerating mechanisms, and plant-soil-microbe interaction and offers a holistic perspective on their potential for soil restoration.
PubMed: 38877191
DOI: 10.1007/s11356-024-33949-9 -
Food Chemistry Jun 2024This study compared the proteomics of beef patties under high‑oxygen modified atmosphere packaging (HiOx-MAP) and vacuum packaging (VP) during heating. The color and...
This study compared the proteomics of beef patties under high‑oxygen modified atmosphere packaging (HiOx-MAP) and vacuum packaging (VP) during heating. The color and oxidation stability of fresh patties, and myoglobin denaturation of cooked patties were also measured. The results suggested that HiOx-MAP patties contained more oxymyoglobin in fresh meat and had higher myoglobin denaturation during heating than VP patties, resulting in premature browning (PMB) during cooking. Proteomic analysis found that the overabundance of proteasome subunit beta type-2 (PSMB2) and peroxiredoxin-2 (PRDX2) in HiOx-55 °C, which can remove the damaged proteins and inhibit oxidation respectively, are of benefit to meat color stability during storage, however, this was still insufficient to inhibit the occurrence of PMB during cooking. The high abundance of lamin B1 (LMNB1) in VP-55 °C can maintain the stability of meat color. This research provides greater understanding, based on proteomic perspectives, of the molecular mechanism of PMB.
PubMed: 38876067
DOI: 10.1016/j.foodchem.2024.140022 -
PloS One 2024The analysis of nucleic acids is one of the fundamental parts of modern molecular biology and molecular diagnostics. The information collected predominantly depends on...
The analysis of nucleic acids is one of the fundamental parts of modern molecular biology and molecular diagnostics. The information collected predominantly depends on the condition of the genetic material. All potential damage induced by oxidative stress may affect the final results of the analysis of genetic material obtained using commonly used techniques such as polymerase chain reaction or sequencing. The aim of this work was to evaluate the effects of high temperature and pH on DNA structure in the context of the occurrence of oxidative damage, using square-wave voltammetry and two independent research protocols. We resulted in visible oxidation damage registered in acidic conditions after the thermal denaturation process (pH 4.7) with changes in the intensity of guanine and adenine signals. However, using phosphate buffer (pH 7.0) for DNA denaturation negatively affected the DNA structure, but without any oxidized derivatives present. This leads to the conclusion that oxidation occurring in the DNA melting process results in the formation of various derivatives of nucleobases, both electrochemically active and inactive. These derivatives may distort the results of molecular tests due to the possibility of forming complementary bonds with various nucleobases. For example, 8-oxoguanine can form pairs with both cytosine and adenine.
Topics: DNA; Oxidative Stress; Nucleic Acid Denaturation; Temperature; Oxidation-Reduction; DNA Damage; Hydrogen-Ion Concentration; Guanine; Electrochemical Techniques; Adenine
PubMed: 38875261
DOI: 10.1371/journal.pone.0305590 -
Molecular Biology Reports Jun 2024Human Amniotic Membrane (hAM) is endowed with several biological activities and might be considered an optimal tool in surgical treatment for different ophthalmic...
BACKGROUND
Human Amniotic Membrane (hAM) is endowed with several biological activities and might be considered an optimal tool in surgical treatment for different ophthalmic pathologies. We pioneered the surgical use of hAM to treat retinal pathologies such as macular holes, tears, and retinal detachments, and to overcome photoreceptor damage in age-related macular degeneration. Although hAM contributed to improved outcomes, the mechanisms of its effects are not yet fully understood. The characterization and explanation of the effects of hAM would allow the adoption of this new natural product in different retinal pathologies, operative contexts, and hAM formulations. At this end, we studied the properties of a hAM extract (hAME) on the ARPE-19 cells.
METHODS AND RESULTS
A non-denaturing sonication-based technique was developed to obtain a suitable hAME. Viability, proliferation, apoptosis, oxidative stress, and epithelial-mesenchymal transition (EMT) were studied in hAME-treated ARPE-19 cells. The hAME was able to increase ARPE-19 cell viability even in the presence of oxidative stress (HO, TBHP). Moreover, hAME prevented the expression of EMT features, such as EMT-related proteins, fibrotic foci formation, and migration induced by different cytokines.
CONCLUSIONS
Our results demonstrate that the hAME retains most of the properties observed in the whole tissue by others. The hAME, other than providing a manageable research tool, could represent a cost-effective and abundant drug to treat retinal pathologies in the future.
Topics: Humans; Amnion; Cell Line; Retinal Pigment Epithelium; Cell Survival; Apoptosis; Oxidative Stress; Cell Proliferation; Epithelial-Mesenchymal Transition; Tissue Extracts
PubMed: 38874663
DOI: 10.1007/s11033-024-09647-7 -
Annals of Laboratory Medicine Jun 2024Droplet digital (dd)PCR is a new-generation PCR technique with high precision and sensitivity; however, the positive and negative droplets are not always effectively...
BACKGROUND
Droplet digital (dd)PCR is a new-generation PCR technique with high precision and sensitivity; however, the positive and negative droplets are not always effectively separated because of the "rain" phenomenon. We aimed to develop a practical optimization and evaluation process for the ddPCR assay and to apply it to the detection of V600E in fine-needle aspiration (FNA) specimens of thyroid nodules, as an example.
METHODS
We optimized seven ddPCR parameters that can affect "rain." Analytical and clinical performance were analyzed based on histological diagnosis after thyroidectomy using a consecutive prospective series of 242 FNA specimens.
RESULTS
The annealing time and temperature, number of PCR cycles, and primer and probe concentrations were found to be more important considerations for assay optimization than the denaturation time and ramp rate. The limit of blank and 95% limit of detection were 0% and 0.027%, respectively. The sensitivity of ddPCR for histological papillary thyroid carcinoma (PTC) was 82.4% (95% confidence interval [CI], 73.6%-89.2%). The pooled sensitivity of V600E in FNA specimens for histological PTC was 78.6% (95% CI, 75.9%-81.2%, I=60.6%).
CONCLUSIONS
We present a practical approach for optimizing ddPCR parameters that affect the separation of positive and negative droplets to reduce rain. Our approach to optimizing ddPCR parameters can be expanded to general ddPCR assays for specific mutations in clinical laboratories. The highly sensitive ddPCR can compensate for uncertainty in cytological diagnosis by detecting low levels of V600E.
PubMed: 38872331
DOI: 10.3343/alm.2023.0405 -
Food Chemistry Jun 2024This study aimed to explore how pulsed electric field (PEF) treatment affects the structural, physicochemical, and emulsification properties of porcine-derived...
Mechanisms underlying the changes in the structural, physicochemical, and emulsification properties of porcine myofibrillar proteins induced by prolonged pulsed electric field treatment.
This study aimed to explore how pulsed electric field (PEF) treatment affects the structural, physicochemical, and emulsification properties of porcine-derived myofibrillar proteins (MPs). Increasing PEF treatment induced partial polarization and protein unfolding, resulting in notable denaturation that affected both the secondary and tertiary structures. PEF treatment also improved the solubility and emulsification ability of MPs by reducing their pH and surface hydrophobicity. Confocal laser scanning microscopy confirmed the effective adsorption of MPs and PEF-treated MPs at the oil/water interface, resulting in well-fabricated Pickering emulsions. A weak particle network increased the apparent viscosity in short-term PEF-treated Pickering emulsions. Conversely, in emulsions with long-term PEF-treated MP, rheological variables decreased, and dispersion stability increased. These results endorse the potential application of PEF-treated porcine-derived MPs as efficient Pickering stabilizers, offering valuable insights into the creative use of PEF for enhancing high-quality meat products, meeting the increasing demand for clean-label choices.
PubMed: 38870818
DOI: 10.1016/j.foodchem.2024.140024 -
Lab on a Chip Jun 2024Physical properties of blood plasma, such as viscosity, serve as crucial indicators of disease. The inherent capillary effect of paper microchannels, coupled with...
Physical properties of blood plasma, such as viscosity, serve as crucial indicators of disease. The inherent capillary effect of paper microchannels, coupled with minimal sample requirement, stimulated the advancement of paper-based viscometers. This study presents a precise, non-contact optoelectronic system using a microfluidic platform for the measurement of blood plasma viscosity. Microchannels were defined onto the filter paper using an available and inexpensive wax crayon, without the need for conventional wax printing equipment. The time required for the 5 μL sample to pass a specific distance was measured using two pairs of infrared sensors. Subsequently, this data was sent to the microcontroller, which automatically calculated the viscosity. Throughout the measurements, sample temperature was maintained at a constant 37 °C through an integrated heater with automated control. The microfluidic platform successfully processed real samples, yielding viscosity measurements in under three minutes. Evaluation with fetal bovine serum, spiked with varying protein concentrations in both native and denatured states, demonstrated a precision exceeding 96% compared to conventional Ostwald viscometer readings. For human subjects exhibiting pathologies affecting serum and plasma viscosity compared to physiological norms, strong correlations were observed between resultant values and clinical diagnoses. The proposed device aims to replace expensive and complex optical equipment, offering a safer alternative for measuring plasma viscosity. Unlike similar devices, it eliminates the risk of component deformation due to chemical contact or unsafe irradiation.
Topics: Blood Viscosity; Humans; Lab-On-A-Chip Devices; Microfluidic Analytical Techniques; Cattle; Animals; Point-of-Care Systems; Equipment Design
PubMed: 38869225
DOI: 10.1039/d4lc00211c -
Biometals : An International Journal on... Jun 2024Schiff bases of existing antimicrobial drugs are an area, which is still to be comprehensively explored to improve drug efficiency against consistently resisting...
Schiff bases of existing antimicrobial drugs are an area, which is still to be comprehensively explored to improve drug efficiency against consistently resisting bacterial species. In this study, we have targeted a new and eco-friendly method of condensation reaction that allows the "green synthesis" as well as improved biological efficacy. The transition metal complexes of cefpodoxime with well-enhanced biological activities were synthesized. The condensation reaction product of cefpodoxime and vanillin was further reacted with suitable metal salts of [Mn (II), Cu (II), Fe (II), Zn (II), and Ni (II)] with 1:2 molar ratio (metal: ligand). The characterization of all the products were carried out by using UV-Visible, elemental analyzer, FTIR, H-NMR, ICP-OES, and LC-MS. Electronic data obtained by UV-Visible proved the octahedral geometry of metal complexes. The biological activities Schiff base ligand and its transition metal complexes were tested by using in-vitro anti-bacterial analysis against various Gram-negative, as well as Gram-positive bacterial strains. Proteinase and protein denaturation inhibition assays were utilized to evaluate the products in-vitro anti-inflammatory activities. The in vitro antioxidant activity of the ligand and its complexes was evaluated by utilizing the 2,2-diphenyl-1-picrylhydrazyl (DPPH) in-vitro method. The final results proved metal complexes to be more effective against bacterial microorganisms as compared to respective parent drug as well as their free ligands. Patch Dock, a molecular docking tool, was used to dock complexes 1a-5e with the crystal structure of GlcN-6-P synthase (ID: 1MOQ). According to the docking results, complex 2b exhibited a highest score (8,882; ACE = -580.43 kcal/mol) that is well correlated with a high inhibition as compared to other complexes which corresponds to the antibacterial screening outcomes.
PubMed: 38864936
DOI: 10.1007/s10534-024-00601-5 -
International Journal of Biological... Jun 2024Given the severe protein denaturation and self-aggregation during the high-temperature desolubilization, denatured soy meal (DSM) is limited by its low reactivity, high...
Given the severe protein denaturation and self-aggregation during the high-temperature desolubilization, denatured soy meal (DSM) is limited by its low reactivity, high viscosity, and poor water solubility. Preparing low-cost and high-performance adhesives with DSM as the key feedstock is still challenging. Herein, this study reveals a double-enzyme co-activation method targeting DSM with the glycosidic bonds in protein-carbohydrate complexes and partial amide bonds in protein, increasing the protein dispersion index from 10.2 % to 75.1 % improves the reactivity of DSM. The green crosslinker transglutaminase (TGase) constructs a robust adhesive isopeptide bond network with high water-resistant bonding strength comparable to chemical crosslinkers. The adhesive has demonstrated high dry/wet shear strength (2.56 and 0.93 MPa) for plywood. After molecular recombination by enzyme strategy, the adhesive had the proper viscosity, high reactivity, and strong water resistance. This research showcases a novel perspective on developing a DSM-based adhesive and blazes new avenues for changes in protein structural function and adhesive performance.
PubMed: 38862054
DOI: 10.1016/j.ijbiomac.2024.133054 -
Chemistry & Biodiversity Jun 2024Any pathogenic attack, infection, or disease can initiate inflammation. It results in significant adverse consequences like inflammatory bowel disease, rheumatoid...
A Structure-Based Design Strategy with Pyrazole-Pyridine Derivatives Targeting TNFα as Anti-inflammatory Agents: E-pharmacophore, Dynamic Simulation, Synthesis and In Vitro Evaluation.
Any pathogenic attack, infection, or disease can initiate inflammation. It results in significant adverse consequences like inflammatory bowel disease, rheumatoid arthritis, etc. TNFα is one of the major pro-inflammatory cytokines for the progression of inflammation-the present study designed a series of hybrid compounds consisting of the pyrazole-pyridine moiety. Virtual screening was performed utilizing the e-pharmacophore hypothesis with the co-ligand of TNFα, screening, docking, and ADMET study. Induced fit docking, DFT analysis, and molecular dynamic simulation showed that the four best molecules - Dh1- Dh4 - showed crucial interaction with Tyrosine, higher dock scores, and better stability than Diclofenac. Following the synthesis of hit molecules, an in vitro albumin denaturation IC50 of Dh1 was found to be 118.01μM. Further in-depth in vitro and in vivo analyses of these pyrazole-pyridine small compounds may serve as potential space for creating new anti-inflammatory leads.
PubMed: 38861376
DOI: 10.1002/cbdv.202400778