Biological Research最新文献

Background: Maintenance of nucleosome-free regions at gene regulatory regions conform a relevant aspect within chromatin dynamics. In the yeast Saccharomyces cerevisiae, Reb1 and Abf1 are among the transcriptions factors that perform this molecular function. These factors are thought to act as a barrier to nucleosome sliding that chromatin remodeling complexes such as ISW1a perform towards this region, being binding affinity a critical feature to act as a barrier. In this regard, sequence variations at positions flanking transcription factor binding sites could affect DNA shape features and, in turn, binding strength. In addition, recent studies have shown that positions of low conservation and/or flanking sequences might vary from gene bodies to gene regulatory regions. Considering these issues, we aimed to analyze whether variations in flanking or less conserved positions of Reb1 and Abf1 target sequences affect their binding affinity, especially dwell time, and their ability to hinder ISW1a's sliding activity.

Results: We found that sequence changes at these positions deeply affect binding strength, particularly dwell time, and the ability to hinder ISW1a's sliding activity. Importantly, even under conditions where a markedly higher transcription factor concentration for a weak binding site was used to compare it to a strong binding site under an equal binding saturation level, the strong site displayed a significantly higher ability to hinder sliding activity. Moreover, genome-wide analyses showed that the sequence variants of Reb1 and Abf1 binding sites conferring this ability to hinder sliding activity to these factors are enriched at promoter regions relative to gene bodies.

Conclusions: Our findings show that dwell time is a key feature to hinder nucleosome sliding activity. For Reb1 and Abf1 factors, sequence variation at less conserved positions of their binding sites strongly affects this feature. The differential frequency at these positions found at promoter regions, relative to gene bodies, highlights the relevance of including this type of comparison in certain strategies used to determine the consensus binding site for transcription factors. To determine the molecular functions that require long dwell times and the transcription factors responsible for these tasks will significantly contribute to untangle the grammar of cis-regulatory elements.

Background: Iron is an essential nutrient for microorganisms, including fungi, which have evolved strategies to acquire it. The most common strategy is the secretion of siderophores, low-molecular-weight compounds with a high affinity for ferric ions, which are involved in cellular iron uptake. Penicillium roqueforti, the fungus responsible for the ripening of blue-veined cheeses, produces coprogen, a hydroxamate-type siderophore. However, to date, the molecular basis for its biosynthesis remains elusive.

Results: In this study, we identified and characterized a biosynthetic gene cluster (BGC) responsible for coprogen biosynthesis in P. roqueforti, named the cop BGC. This BGC contains seven genes, three of which (copA, copB and copE) encode enzymes directly involved in coprogen biosynthesis from precursors molecules. Using CRISPR-Cas9, we targeted these three genes and analyzed the resulting mutants by Liquid Chromatography/High-Resolution Mass Spectrometry (LC/HRMS). Our results confirmed that all three genes are necessary for coprogen biosynthesis. Phenotypically, the mutants displayed growth differences under iron-deficient conditions, which correlated with their ability to either synthesize or fail to synthesize coprogen B and dimerumic acid, intermediates in the coprogen pathway with siderophore activity.

Conclusions: The results obtained in this work provide important insights into the molecular basis of coprogen biosynthesis in P. roqueforti, enhancing the understanding of how siderophores enable this fungus to thrive in iron-deficient environments.

Background: Recent studies have highlighted the critical health implications of environmental exposure to nanoplastics, particularly concerning their effects on human gastrointestinal cells. In this study, we used human colorectal adenocarcinoma (Caco-2) cells to investigate the exposure of polystyrene nanoparticles (PNPs) to cellular processes and DNA repair.

Methods: We exposed Caco-2 cells to various concentrations of PNPs and monitored cytotoxicity, ROS levels, PARP-1-dependent apoptosis, DNA damage, and changes in DNA damage response (DDR) gene expression.

Results: The results indicated that although PNPs did not directly cause SSBs or DSBs, as evidenced by comet assays and γH2AX staining, they induced oxidative stress and significantly altered the expression of genes required for DDR. In particular, critical genes involved in the base excision repair (BER) pathway and DSBs repair were downregulated, suggesting a potential impairment of the cell's ability to repair oxidative DNA damage.

Conclusions: This study highlights the sublethal effects of nanoplastics on intestinal barrier cells. It underscores the possible risks of exposure to these environmental contaminants, which can lead to genome instability and other long-term health consequences.

Background: Rheumatoid arthritis (RA) is a chronic and multifactorial inflammatory disease inducing damages in joints and extra-articular organs. Our previous study has revealed that Huayu-Qiangshen-Tongbi decoction (HQT) ameliorates RA through upregulating microRNA (miRNA) miR-125b-5p to suppress inflammation in rheumatoid fibroblast-like synoviocytes (FLSs). However, the mechanism of HQT increasing miR-125b-5p level in FLSs remains unclear. It has been reported that exosomal miR-125b-5p derived from adipose-derived stem cells (ADSCs) could ameliorate various diseases, yet the effect of exosomal miR-125b-5p derived from ADSCs on FLSs in RA under HQT treatment is largely unknown. The aim is to investigate whether HQT upregulated miR-125b-5p in FLSs through modifying exosomal miR-125b-5p derived from ASCs.

Methods: Here, HQT-containing serum was prepared, co-culture of human FLS MH7A cells with ADSCs was performed, gene knockdown in ADSCs was assessed by short hairpin RNA (shRNA), protein degradation was identified after cycloheximide (CHX) treatment and ADSC-derived exosomes were collected to incubate MH7A cells and inject into RA rat model.

Results: HQT elevates lipopolysaccharide (LPS)-reduced miR-125b-5p level in FLSs by enhancing the secretion of exosomal miR-125b-5p derived from ADSCs. Besides, HQT attenuates inflammation of FLSs in RA by exosomal miR-125b-5p derived from ADSCs in vitro and in vivo. Mechanistically, HQT suppresses CD63 degradation in ADSCs to facilitate the release of exosomal miR-125b-5p derived from ADSCs.

Conclusion: In summary, these findings reveal the mechanism of HQT elevating miR-125b-5p expression in FLSs and provide novel therapeutic strategy for RA treatment.

Background: Pain serves as a vital protective mechanism triggered by tissue damage. While NSAIDs and opioids offer relief, their prolonged usage is hindered by adverse effects. Developing analgesics with fewer side effects is crucial for effective pain treatment. The TRPV1 channel is a key target for pain relief, with its inhibitors effectively reducing hyperalgesia in animals. This research utilized virtual screening to identify TRPV1-selective natural compounds for potent analgesic properties.

Results: The physcion exhibited the notable affinity for TRPV1 compared to the compounds examined. After conducting molecular dynamics simulations, physcion emerged as the compound demonstrating the highest binding affinity towards TRPV1, a finding corroborated by calcium imaging, which validated its inhibitory impact. Furthermore, physcion mitigated the stretch number in the acetic acid-induced stretching model, prolonged the latency period in the hot water tail-flick and hot plate assays, and heightened the pain withdrawal threshold lowered by complete Freund's adjuvant (CFA). Notably, physcion exerted a marked effect in ameliorating bone cancer-induced pain in the hot plate and von Frey tests. Additionally, physcion diminished the levels of inflammatory cytokines and the mRNA expression of both inflammatory and calcium-related genes in the CFA-induced murine model. Furthermore, physcion downregulated the expression of inflammatory genes induced by tumor necrosis factor-α (TNF-α) in RAW264.7 cells. The underlying mechanism potentially involves the suppression of the NF-κB and MAPK signaling cascades.

Conclusions: Our investigation underscores the potential of physcion as a promising candidate for analgesic therapy.

Background: Endothelial progenitor cells (EPCs) play a critical role in vasculogenesis and vascular repair, but their clinical application is hindered by challenges such as cell purity, quantity, and reliance on fetal bovine serum (FBS). This study developed an animal-free system for isolating, induction, and expanding EPCs from the human placenta, evaluating their potential for wound repair.

Methods: Mononuclear cells (MNCs) were isolated from full-term placenta and induced into EPCs using an animal-free medium supplemented with bFGF, IGF, and VEGF. EPCs were characterized by flow cytometry for markers CD133, CD34, and VEGFR2, while CD31 and CD45 served as negative markers. Functional assays, including Ac-LDL uptake, migration, and tube formation, confirmed EPC properties. The wound-repair potential was assessed in a mouse model.

Results: The induced EPCs exhibited high purity (> 95%) and expressed CD133, CD34, and VEGFR2 while being negative for CD31 and CD45. The system yielded 1 × 10⁸ EPCs from 10 g of placental tissue, demonstrating high proliferative capacity. Functional assays confirmed robust tube formation, migration, and Ac-LDL uptake in vitro. In vivo, EPCs significantly enhanced wound repair.

Conclusions: In conclusion, human placenta-derived EPCs cultured in an animal-free system displayed high purity, self-renewal capacity, and functional efficacy, making them a promising cell source for therapeutic applications, particularly in wound repair.

Granulosa cells (GCs) are the main supporting cells for follicles, and histone acetylation has been reported to regulate follicular development. However, the mechanism of histone acetylation regulating follicular development is still unclear in GCs. In this study, we found that FGA, fibrinogen alpha chain, mediated the survival and fate of GCs. Knockdowns of HDAC1 and HDAC3 significantly inhibited the mRNA level of FGA, while knockdown of HDAC2 notably decreased the protein level of FGA. Moreover, knockdown of HDAC2 repressed the chromatin accessibility and the enrichment level of H3K9ac at -1350/-1454 bp of FGA. In addition, FGA promoted GCs proliferation and cycle progression by up-regulating the expressions of PCNA and CCNE1, whereas it inhibited apoptosis by suppressing the expression of Caspase3. In vitro, FGA was likely to promote follicular development of pigs. In mice, FGA inhibited the apoptosis of GCs and increased the number of corpora lutea, as a result, elevating estradiol levels and advancing the day of pubertal initiation. Both in vitro and in vivo experiments, FGA promoted follicular development by up-regulating PCNA and CCNE1, while inhibited follicular apoptosis by down-regulating Caspase3 and Caspase9. Overall, knockdown of HDAC2 repressed transcription by reducing chromatin accessibility and decreasing H3K9ac binding at the FGA promoter. FGA inhibited apoptosis of GCs by suppressing the expression of Caspase3 and promoted follicular development. This study showed that FGA is a novel target for histone acetylation to regulate follicular development in mammals.

Background: Cephalopods are widely distributed in oceans worldwide and are important fishery resources. Most species have a lifespan of approximately one year and die after reproduction. In cephalopods, gonadal development may be influenced by seawater temperature; however, the endocrine mechanisms underlying reproductive maturity remain unclear. In recent years, gonadotropin-releasing hormone (GnRH)-like peptide has been identified in invertebrates, including cephalopods, as a possible endocrine regulator, similar to their role in vertebrates. Nevertheless, knowledge of its specific functions in cephalopod reproduction remains limited. This study aimed to clarify the involvement of the endogenous peptide in gonadal development in cephalopods in the bigfin reef squid (Sepioteuthis lessoniana). We performed histological observations of gonadal maturation and analyzed brain expression levels and localization of the peptide throughout sexual maturation. Additionally, we examined the relationship between annual gonadal maturation and the seawater temperature cycle.

Results: We identified coding sequences for peptides with conserved functional regions similar to those of other mollusks. Quantitative analysis revealed that brain expression significantly increased during the spermatid stage of testicular development, whereas no association with ovarian development was observed. Immunoreactivity was primarily localized in the optic lobe and around the optic gland, a central site of reproductive regulation in cephalopods. Although ovarian development progressed with increasing seawater temperature, testicular development showed no clear association with the temperature cycle.

Conclusions: These findings suggest that GnRH-like peptides may contribute to early testicular development in S. lessoniana through optic gland signaling or direct neural pathways. In contrast, ovarian maturation appears to be strongly influenced by seawater temperature. This study provides foundational insight into the reproductive physiology of cephalopods and highlights regulatory mechanisms governing male and female gonadal development.