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Cell & Bioscience Jun 2024Histone ubiquitination modification is emerging as a critical epigenetic mechanism involved in a range of biological processes. In vitro reconstitution of ubiquitinated...
BACKGROUND
Histone ubiquitination modification is emerging as a critical epigenetic mechanism involved in a range of biological processes. In vitro reconstitution of ubiquitinated nucleosomes is pivotal for elucidating the influence of histone ubiquitination on chromatin dynamics.
RESULTS
In this study, we introduce a Non-Denatured Histone Octamer Ubiquitylation (NDHOU) approach for generating ubiquitin or ubiquitin-like modified histone octamers. The method entails the co-expression and purification of histone octamers, followed by their chemical cross-linking to ubiquitin using 1,3-dibromoacetone. We demonstrate that nucleosomes reconstituted with these octamers display a high degree of homogeneity, rendering them highly compatible with in vitro biochemical assays. These ubiquitinated nucleosomes mimic physiological substrates in function and structure. Additionally, we have extended this method to cross-linking various histone octamers and three types of ubiquitin-like proteins.
CONCLUSIONS
Overall, our findings offer an efficient strategy for producing ubiquitinated nucleosomes, advancing biochemical and biophysical studies in the field of chromatin biology.
PubMed: 38886783
DOI: 10.1186/s13578-024-01265-x -
The Biochemical Journal Jun 2024Catalase is a major antioxidant enzyme located in plant peroxisomes that catalyzes the decomposition of H2O2. Based on our previous transcriptomic (RNA-Seq) and...
Catalase is a major antioxidant enzyme located in plant peroxisomes that catalyzes the decomposition of H2O2. Based on our previous transcriptomic (RNA-Seq) and proteomic (iTRAQ) data at different stages of pepper fruit ripening and after exposure to NO enriched atmosphere, a broad analysis has allowed to characterize the functioning of this enzyme. Three genes were identified, and their expression was differentially modulated during ripening and by NO gas treatment. A dissimilar behavior was observed in the protein expression of the encoded protein catalases (CaCat1-CaCat3). Total catalase activity was downregulated by 50% in ripe fruits concerning immature green fruits. This was corroborated by non-denaturing polyacrylamide gel electrophoresis, where only a single catalase isozyme was identified. In vitro analyses of the recombinant CaCat3 protein exposed to peroxynitrite confirmed, by immunoblot assay, that catalase underwent a nitration process. Mass spectrometric analysis identified that Tyr348 and Tyr360 were nitrated by peroxynitrite, occurring near the catalase active center. The data indicate the complex regulation at gene and protein levels of catalase during the ripening of fruits, with activity significantly downregulated in ripe fruits. Nitration plays a key role in this downregulation, favoring an increase in H2O2 during ripening. This pattern can be reversed by the exogenous NO application. While plant catalases are generally reported to be tetrameric, the analysis of the protein structure supports that pepper catalase has a favored quaternary homodimer nature. Taken together, data show that pepper catalase is downregulated during fruit ripening, becoming a target of tyrosine nitration, which provokes its inhibition.
PubMed: 38884605
DOI: 10.1042/BCJ20240247 -
Journal of Pharmacy & Bioallied Sciences Apr 2024Considerable focus has been directed toward green synthesis as a dependable, sustainable, and environmentally friendly approach for synthesizing various nanomaterials. ,...
BACKGROUND
Considerable focus has been directed toward green synthesis as a dependable, sustainable, and environmentally friendly approach for synthesizing various nanomaterials. , a quickly grown pantropical weed, has been used widely for its anti-inflammatory and antimicrobial activity in traditional medicine. The development of strontium-based nanoparticles and nanoparticles linked with strontium has garnered attention in recent years due to their established utility in diverse domains such as effective drug distribution, bioimaging, cancer treatment, and advancements in bone engineering.
AIMS AND OBJECTIVES
To examine the green synthesise of strontium nanoparticles using Mimosa pudica and its anti-inflammatory activity.
MATERIAL AND METHODS
-mediated strontium nanoparticles' anti-inflammatory activity was tested using bovine serum albumin denaturation assay, egg albumin denaturation assay, and membrane stabilization assay with diclofenac sodium as the standard. Result: In all three assays, increasing concentration of -mediated strontium nanoparticles exhibited an increasing anti-inflammatory effect, which was similar to the standard diclofenac sodium.
CONCLUSION
Consequently, this holds promise as a new potential anti-inflammatory agent in forthcoming applications.
PubMed: 38882793
DOI: 10.4103/jpbs.jpbs_586_23 -
Journal of Pharmacy & Bioallied Sciences Apr 2024contains andrograpanin, which is both anti-inflammatory and anti-infective. comprises over 150-200 species from the family . exerts various properties, including...
contains andrograpanin, which is both anti-inflammatory and anti-infective. comprises over 150-200 species from the family . exerts various properties, including anti-inflammatory property. Herbal mouthwash was made using and extract. The anti-inflammatory effect was evaluated using an albumin denaturation assay and egg albumin denaturation. The percentage of protein denaturation that is inhibited by the formulation of and indicates that it has strong anti-inflammatory effect. According to the findings, as concentration is raised, the formulation's anti-inflammatory activity rises. The formulation's percentage inhibition values are also equivalent to those of a typical anti-inflammatory medicine, indicating that it may be effective as a natural anti-inflammatory agent.
PubMed: 38882775
DOI: 10.4103/jpbs.jpbs_581_23 -
Peptide Science (Hoboken, N.J.) Mar 2024Coiled coils are one of most common protein quaternary structures and represent the best understood relationship between amino acid sequence and protein conformation....
Coiled coils are one of most common protein quaternary structures and represent the best understood relationship between amino acid sequence and protein conformation. Whereas the roles of residues at the canonical heptad positions the , , , and are understood in precise detail, conventional approaches often assume that the solvent-exposed -, -, and -positions can be varied broadly for application-specific purposes with minimal consequences. However, a growing body of evidence suggests that interactions among these , , and residues can contribute substantially to coiled-coil conformational stability. In the trimeric coiled coil described here, we find that -position Glu10 engages in a stabilizing long-range synergistic interaction with -position Lys18 (ΔΔΔG = -0.65 ± 0.02 kcal/mol). This favorable interaction depends strongly on the presence of two nearby -position residues: Lys 7 and Tyr14. Extensive mutational analysis of these residues in the presence of added salt vs. denaturant suggests that this long-range synergistic interaction is primarily electrostatic in origin, but also depends on the precise location and acidity of a side-chain hydrogen-bond donor within -position Tyr14.
PubMed: 38882551
DOI: 10.1002/pep2.24336 -
GeroScience Jun 2024Ageing is a complex biological process with variations among individuals, leading to the development of ageing clocks to estimate biological age. Glycans, particularly...
Ageing is a complex biological process with variations among individuals, leading to the development of ageing clocks to estimate biological age. Glycans, particularly in immunoglobulin G (IgG), have emerged as potential biomarkers of ageing, with changes in glycosylation patterns correlating with chronological age.For precision analysis, three different plasma pools were analysed over 26 days in tetraplicates, 312 samples in total. In short-term variability analysis, two cohorts were analysed: AstraZeneca MFO cohort of 26 healthy individuals (median age 20) and a cohort of 70 premenopausal Chinese women (median age 22.5) cohort monitored over 3 months. Long-term variability analysis involved two adult men aged 47 and 57, monitored for 5 and 10 years, respectively. Samples were collected every 3 months and 3 weeks, respectively. IgG N-glycan analysis followed a standardized approach by isolating IgG, its subsequent denaturation and deglycosylation followed by glycan cleanup and labelling. Capillary gel electrophoresis with laser-induced fluorescence (CGE-LIF) and ultra-performance liquid chromatography analyses were employed for glycan profiling. Statistical analysis involved normalization, batch correction, and linear mixed models to assess time effects on derived glycan traits.The intermediate precision results consistently exhibited very low coefficient of variation values across all three test samples. This consistent pattern underscores the high level of precision inherent in the CGE method for analysing the glycan clock of ageing. The AstraZeneca MFO cohort did not show any statistically significant trends, whereas the menstrual cycle cohort exhibited statistically significant trends in digalactosylated (G2), agalactosylated (G0) and fucosylation (F). These trends were attributed to the effects of the menstrual cycle. Long-term stability analysis identified enduring age-related trends in both subjects, showing a positive time effect in G0 and bisected N-acetylglucosamine, as well as a negative time effect in G2 and sialylation, aligning with earlier findings. Time effects measured for monogalactosylation, and F remained substantially lower than ones observed for other traits.The study found that IgG N-glycome analysis using CGE-LIF exhibited remarkably high intermediate precision. Moreover, the study highlights the short- and long-term stability of IgG glycome composition, coupled with a notable capacity to adapt and respond to physiological changes and environmental influences such as hormonal changes, disease, and interventions. The discoveries from this study propel personalized medicine forward by deepening our understanding of how IgG glycome relates to age-related health concerns. This study underscores the reliability of glycans as a biomarker for tracking age-related changes and individual health paths.
PubMed: 38877341
DOI: 10.1007/s11357-024-01239-4 -
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