Turkish journal of biology = Turk biyoloji dergisi最新文献

Background/aim: Delayed wound healing in diabetic patients is a significant complication that reduces quality of life, prompting the continuous investigation of new therapeutic agents. This study designed to explore the dose-dependent effects of different parts of Chelidonium majus L. (CM), a medicinal plant traditionally used for skin disorders, on diabetic skin wounds.

Materials and methods: In diabetic rats, full-thickness excisional wounds were formed. CM-containing gels (aerial parts at 3%, 6%, 9% and root at 0.5%, 1%, 1.5%) were developed and applied to the wounds. After the treatment period, the rats were sacrificed, and wound healing activity was assessed macroscopically, histopathologically, and biochemically.

Results: The CM-containing gels (aerial parts or root) accelerated wound closure and increased collagen, glutathione (GSH), and ascorbic acid (AA) content. Additionally, these gels reduced oxidative stress markers, and interleukin-1β (IL-1β) and IL-13 levels, while modulating the activities of matrix metalloproteinase-2 (MMP-2) and MMP-9.

Conclusion: CM accelerates the healing process by increasing antioxidant capacity and modulating MMP activity, and it may have dose-dependent effectiveness in diabetic wound management.

Background/aim: Boron is an essential micronutrient for plants and certain bacteria, where it plays critical roles in cellular processes at low concentrations. However, elevated levels of boron-containing compounds, such as boric acid, exhibit antimicrobial toxicity. Although the physiological effects of boric acid on bacteria have been partially characterized, its proteome-wide impacts remain poorly elucidated. This study employs a 2D-PAGE-based proteomic approach to investigate how sublethal boric acid stress alters the cytoplasmic proteome of Escherichia coli BW25113.

Materials and methods: E. coli BW25113 cultures were grown to mid-log phase in tryptic soy broth (TSB) and exposed to 70 mM boric acid (a sublethal concentration) or left untreated as a control. Cytoplasmic protein extracts were subjected to 2D-PAGE analysis to identify differentially expressed proteins. Selected protein spots were excised, identified via MALDI-TOF mass spectrometry, and validated by RT-PCR to assess corresponding mRNA expression levels.

Results: Proteomic analysis revealed 12 differentially regulated cytoplasmic proteins under boric acid stress. Upregulated proteins included SodA, KduD, KduI, DeoB, Icd, AceE, RpsM, TdcE, Tuf1, LexA, and LamB, while GatY was downregulated. Functional annotation linked these proteins to oxidative stress defense (SodA), carbohydrate metabolism (KduD, KduI, DeoB), energy production (Icd, AceE), translation (RpsM, Tuf1), and membrane integrity (LamB). RT-PCR validation confirmed transcriptional upregulation of sodA, kduD, and kduI, corroborating proteomic findings. These results suggest that boric acid disrupts metabolic homeostasis, induces oxidative stress, and modulates structural and translational processes in E. coli.

Conclusion: This study provides the first proteomic evidence of E. coli's cytoplasmic response to boric acid stress, highlighting its multifaceted effects on metabolic, oxidative, and translational pathways. The upregulation of KduI and KduD, enzymes involved in carbohydrate utilization, points to potential adaptive mechanisms for boron detoxification. Further investigation into these targets could elucidate molecular strategies for bacterial boron tolerance and inform the development of boron-based antimicrobials.

Background/aim: The Kelch-like-ECH associated protein 1 (Keap1) is an integral component of the E3-ubiquitin ligase complex, which binds to Nuclear factor erythroid 2-related factor 2 (Nrf2) and facilitates its degradation by the 26S proteasome. The Kelch domain of Keap1, composed of six repeated structural motifs, plays a key role in this interaction. This study aims to investigate the dimeric structure of the Keap1 Kelch domain at ambient temperature and to examine its implications for conformational dynamics, particularly in relation to the DMF and Nrf2 binding sites.

Materials and methods: The dimeric crystal structure of the Keap1 Kelch domain was determined at 3.0 Å resolution using data collected at the Turkish Light Source 'Turkish DeLight.' To analyze structural dynamics, Gaussian Network Model (GNM) analysis was applied, and molecular docking studies were performed using the ambient temperature structure to evaluate the binding of compounds acting as inhibitors of the Keap1/Nrf2 complex.

Results: The study reveals significant potential conformational changes in Keap1 residues, especially at the DMF and Nrf2 binding sites, driven by temperature-induced shifts. GNM analysis suggests that the allosteric behavior of DMF binding residues is fully realized in the ambient temperature structure. Molecular docking of various compounds, including CNN (a hybrid of L-carnosine and L-histidyl hydrazide), ZINC 12433145, and ZINC 105508677, demonstrated favorable binding interactions with key Keap1 residues, highlighting their potential as inhibitors.

Conclusion: Our in silico and crystallo results suggest that CNN is a promising lead compound for Keap1 inhibition. Understanding the dimeric form of the Keap1 Kelch domain and its conformational changes at ambient temperature is crucial for elucidating the dynamics of the Keap1-Nrf2 interaction.

Background/aim: The COVID-19 pandemic caused by SARS-CoV-2 necessitated rapid development of effective therapeutics, prompting this study to identify potential inhibitors targeting key viral and host proteins: RNA-dependent RNA polymerase (RdRp), main protease (Mpro), transmembrane serine protease 2 (TMPRSS2), and angiotensin-converting enzyme 2 (ACE2).

Methods: We used covalent docking and molecular dynamics (MD) simulations to screen FDA-approved compounds against these targets using diverse covalent reaction mechanisms. Top-ranking compounds underwent further evaluation through MD simulations to assess binding stability and conformational dynamics.

Results: Several promising drug repurposing candidates were identified: bremelanotide, lanreotide, histrelin, and leuprolide as potential RdRp inhibitors; azlocillin, cefiderocol, and sultamicillin for Mpro inhibition; tenapanor, isavuconazonium, and ivosidenib targeting TMPRSS2; and cefiderocol, cefoperazone, and ceftolozane as potential ACE2 inhibitors.

Conclusion: This study provides valuable insights into repurposing existing drugs as potential COVID-19 therapeutics by targeting crucial viral proteins. However, further experimental validation and preclinical studies are necessary to confirm the efficacy and safety of these compounds before consideration for clinical application.

Background/aim: Despite advancements in chemotherapeutic strategies, drug resistance remains a major barrier to effective cancer treatment. While primary prostate cancers (PC) can be treated with surgery and radiotherapy, treatment options for recurrent PC are limited. Upon progression to the castration-resistant (CR) phase, therapies rely on taxanes (chemotherapeutic drugs) like docetaxel (Dtx) and cabazitaxel (Cbz); however, resistance to taxanes is common in CRPC, highlighting the importance of identifying underlying molecular mechanisms or targets in resistant cells.

Materials and methods: In transcriptome (RNA sequencing) analyses comparing taxane-resistant PC cells (resistant to both Dtx and Cbz) with parental (nonresistant, sensitive) cells, butyrylcholinesterase (BChE) was identified as the most significantly downregulated gene. Although low serum BChE levels have been documented in various cancers, its role in chemotherapy resistance remains unclear. To address this gap, we validated its expression in taxane-resistant CRPC lines and manipulated BChE levels in both parental and resistant cells via lentiviral overexpression or depletion using shRNA and gRNA (CRISPR-Cas9), to assess its impact on taxane resistance.

Results: BChE suppression in parental CRPC cells conferred resistance, whereas its overexpression in taxane-resistant cells was insufficient to resensitize them. Analysis of publicly available databases showed reduced BChE mRNA levels in patient samples across various cancers, including PC. Additionally, The Cancer Genome Atlas (TCGA) analyses identified BChE as a significant posttreatment neoplasm marker in PC.

Conclusion: Our study confirmed the downregulation of BChE in taxane-resistant CRPC cell models and established its role in conferring resistance when depleted in parental CRPC cells, highlighting its association with taxane resistance. Additionally, the identification of BChE as a posttreatment neoplasm marker, derived from data mining analyses, suggests it might serve as a biomarker for tracking disease progression in PC.

Background/aim: CCDC43 (coiled-coil domain containing protein 43) is a eukaryotic protein that contains alpha-helical domains in its structure, consistent with the family to which it belongs. It is predominantly located in the cytosol of the cell. CCDC43 protein has been shown to play a role in cell proliferation, invasion, metastasis, and epithelial-mesenchymal transition in gastric and colorectal cancer types. The fundamental function and cellular interaction network of this protein, which is known to have varying expression levels in various cancer types, has not yet been fully elucidated. Here, we conducted a proximity-dependent biotin identification (BioID2) screening approach for CCDC43 to uncover proximity interactors.

Materials and methods: Using mass spectrometry of streptavidin pull-down of biotinylated proteins with filtering approaches, we identified candidate protein interactors for CCDC43.

Results: We suggest an association between CCDC43 and RNA-binding proteins based on all our biological replicates. The strongest candidate for the interactome is YBX1, a highly conserved cold shock domain and nucleic acid-binding protein that has multiple essential functions in the cell.

Conclusion: These findings suggest that CCDC43 may play a role in critical pathways within the cell.

Background/aim: Metformin is commonly used to manage type 2 diabetes (T2D) and is being investigated for its potential antiproliferative effects in cancer, particularly in patients with both T2D and malignancies. Drug resistance can develop with any therapeutic agent, and metformin is no exception. As we showed in our previous study, metformin-resistant MDA-MB-468 (MET-R) cells exhibited an EMT-like phenotype. Many transcription factors, as well as miRNAs, can contribute to this altered phenotype. Our current study identifies the contribution of hsa-miR-26a-5p expression to the previously observed phenotype.

Materials and methods: By utilizing bioinformatic tools, we identified hsa-miR-26a-5p, whose expression was significantly altered with increasing concentrations of metformin in MET-R cells. We rescued hsa-miR-26a-5p expression and examined the EMT phenotype and apoptotic markers via Western blot analysis.

Results: We observed a reduction in hsa-miR-26a-5p expression in response to increasing concentrations of metformin in MET-R cells. Upon successful restoration of hsa-miR-26a-5p expression, a subsequent decrease in the proliferation rate was noted. Moreover, when combined with a PI3K inhibitor, we observed increased sensitivity to the PI3K inhibitor. The EMT and apoptotic markers also tended to decrease upon combinatorial treatment.

Conclusion: In this study, we rescued the diminished expression of hsa-miR-26a-5p in MET-R cells to increase the sensitivity to PI3K inhibitor. The combination of a PI3K inhibitor and rescued hsa-miR-26-5p expression resulted in the restoration of the EMT phenotype and proliferation in these cells.

Background/aim: Recent reports have indicated that multidrug-resistant strains of S. aureus, including methicillin-resistant strains, may pose a significant threat to public health and global economic stability.

Materials and methods: In this study, we present the isolation and comprehensive characterization of a novel phage, derived from clinically isolated MRSA strains.

Results: MetB16 exhibited an incubation period of approximately 20 min, a lysis period of around 45 min, and a burst size of 127 Plaque Forming Units (PFU)/cell. The phage demonstrated remarkable biological stability across a pH spectrum of 4.0-9.0 and maintained integrity within a temperature range of 37 and -80 °C. Scanning transmission electron microscopy and phylogenetic analyzes classified MetB16 as belonging to the Triavirus genus, representing a novel species within the Triaviruses. Whole-genome sequencing revealed a 45,295 bp-long genome size with a G + C content of 33.34%. Notably, bioinformatic analyses identified random integration sites within the MRSA genome. Functional annotation of the genome uncovered 72 open reading frames (ORFs), of which 34 encoded hypothetical proteins of unknown function, and these ORFs were associated with phage structure, packaging, host lysis, DNA metabolism, and additional functions. To elucidate the therapeutic potential of temperate phages, detailed structural analyses were conducted on key proteins, including holin, endolysin, and minor tail proteins of MetB16.

Conclusion: This study provides for the first time, the preliminary studies on the biological properties of MetB16 and comprehensive data facilitating an in-depth analysis of the mechanism underlying phage-host interactions, serving as a valuable reference for the evaluation of temperate phages in phage therapy.

Background: Cadherin-based biomaterials play a pivotal role in influencing the fate of mesenchymal stem cells (MSC). Enhancing the adhesion of adipose tissue-derived MSCs has been shown to augment their paracrine effects while N-cadherin biomaterials have been suggested to regulate the paracrine effects of MSCs via specific growth factors although the precise mechanisms underlying this regulation remain insufficiently understood. This study aims to compare the effects of a 3D N-cadherin mimetic environment on cell viability, apoptosis, extracellular matrix regulation, and growth factor expression with those observed in traditional 2D and 3D spheroid cultures. Additionally, the study seeks to evaluate the effects of conditioned media derived from the N-cadherin mimetic environment on the viability and migration of endothelial cells.

Materials and methods: Peptide hydrogels, including HAVDI and SCRAM, were used as N-cadherin mimetics at a concentration of 1 mM, and four experimental groups were established: 2D classical culture, 3D spheroid culture, 3D HAVDI, and 3D SCRAM. Cell viability was assessed using the MTT assay, while gene expression analysis (BCL-XL, BCL-2, BAX, MMP-9, TIMP1, MMP-2, PLAU, HGF, FGF, and VEGFR2) was performed via qRT-PCR. Secretion levels of growth factors (PDGF-BB, FGF-2, and VEGF-A) were quantified using ELISA. The effects of conditioned media on the proliferation and migration of human umbilical vein endothelial cells were evaluated through MTT assays, calcein staining, and wound healing assays.

Results: In the 3D HAVDI group, where MSCs were cultured in an N-cadherin mimetic peptide environment, cell viability increased, and apoptosis decreased. Moreover, this environment upregulated genes associated with tissue remodeling and increased the expression and secretion of growth factors, compared to the classical 2D culture. Additionally, treatment with conditioned media at 1:2 and 1:5 dilutions significantly improved the viability and migration potential of endothelial cells.

Conclusion: The N-cadherin mimetic peptide hydrogel represents a more effective culturing strategy than traditional 2D for enhancing the paracrine and regenerative properties of MSCs.

Background/aim: The root gall nematode Meloidogyne incognita constitute the most damaging species that infects many crops in Algeria. The intense use of harmful agricultural chemical products has incited research to develop alternative methods with natural and ecological advantages like essential oils extracted from plants. The objective of this study was to evaluate the efficacy of Origanum vulgare subsp. glandulosum Desf. (Lamiaceae) essential oil on the development of the root-knot nematode M. incognita in potted tomatoes.

Materials and methods: In pot trials, we assessed the activity of O. vulgare subsp. glandulosum essential oil at two concentrations of 0.75 and 0.37 mg/L against M. incognita. These dilutions were applied in two treatments to soil: the preventive treatment (pretomato planting), and the curative treatment (posttomato planting), using an artificially inoculated tomato under controlled conditions.

Results: The application of O. vulgare subsp. glandulosum essential oil was very effective at the pretomato planting treatment compared to the chemical treatments, and the inoculated control. We noted a reduction in number of roots and soil juveniles, galling index, and an increase in the tomato root and stem weights. The phytochemical screening of O. vulgare subsp. glandulosum revealed the presence of five classes of bioactive compounds (glycosides, saponins, flavonoids, tannins, and gallic tannins).

Conclusion: This study showed a potential nematicidal effect of O. vulgare subsp. glandulosum essential oil on root-knot nematode.