Ümit Uzun

Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality, underscoring the need to elucidate molecular mechanisms that regulate tumor cell state and behavior. Leucine zipper–like post-translational regulator 1 (LZTR1) regulates RAS/mitogen-activated protein kinase (MAPK) signaling, yet LZTR1-dependent transcriptional alterations in HCC cells remain poorly defined. To address this gap and determine how LZTR1 loss reshapes signaling, transcriptional programs, and cellular phenotypes, we established a LZTR1 knockout (KO) Hep3B model and combined pathway profiling with transcriptomic and functional analyses. Immunoblotting revealed increased phosphorylation across the RAF–MEK–ERK–RSK cascade in LZTR1 KO cells. Transcriptome-wide RNA sequencing (RNA-Seq) identified differentially expressed genes, and selected findings were validated by qRT-PCR. Gene set enrichment analysis indicated that the epithelial–mesenchymal transition (EMT) gene set was enriched in control cells. At the protein level, LZTR1 loss remodeled EMT-associated markers in a hybrid epithelial–mesenchymal pattern consistent with epithelial–mesenchymal plasticity (EMP). Vimentin was suppressed at transcript and protein levels. Functionally, LZTR1 KO cells exhibited impaired wound closure and reduced transwell migration and invasion. Collectively, these findings define an EMP-related molecular and phenotypic state associated with LZTR1 deficiency in Hep3B cells, providing insight into how LZTR1 loss reshapes tumor cell behavior in HCC.

PurposeThe purpose of this ex vivo study was to investigate the effects of 5 distinct irrigant activation systems on bacterial colonization within dentinal tubules utilizing confocal laser scanning microscopy (CLSM).Materials and MethodsSixty extracted human mandibular premolars with single canals were prepared using resiprocal instruments. The teeth were embedded in acrylic resin blocks and the root canals were inoculated with Enterococcus faecalis. Root canals were irrigated using five different irrigant activation methods: standard needle irrigation, IrriFlex, EDDY, Endoactivator, and passive ultrasonic irrigation (PUI). Horizontal sections, 1 ± 0.1 mm in thickness, were obtained at distances of 2, 5 and 8 mm from the apical end of the teeth. Sections were visualized using a CLSM. The penetration depth of dead bacteria was measured to evaluate the antimicrobial efficacy of the irrigant activation systems. Statistical analysis was performed using Kruskal-Wallis and Mann-Whitney U tests with Bonferroni correction.ResultsPUI showed significantly greater penetration depth of dead bacteria in both the coronal and apical thirds compared to the other experimental groups (p<0.05).ConclusionAlthough a statistically significant reduction in bacteria was observed in all experimental groups compared to the control, the canal disinfection was not complete in any of the groups. According to our results, standard needle irrigation had the lowest disinfection efficiency, while PUI demonstrated the highest among the evaluated activation methods.

Considering that most antibiotics originate from actinomycete group bacteria, especially the Streptomyces genus, it is predicted that novel actinomycetes isolated from extreme environments such as caves may bring novel antibiotics to the medical world. The study aimed to screen the antimicrobial activity of actinomycetes isolated from the three karst caves in Türkiye and to identify selected isolates with antimicrobial activity by molecular methods. One hundred seventy-nine actinomycetes isolated from Akçakale, Kırklar (Altıntaş), and Köprübaşı Caves in Gümüşhane province in the Eastern Black Sea Region of Türkiye were included in the study. The antimicrobial activity of isolates was investigated using the modified cross-streak agar method against seven Gram-negative bacteria, three Gram-positive bacteria, and one yeast strain. Fifty-three isolates (29.6%) had antimicrobial activity against at least one of the tested microorganisms. The rate of isolates exhibiting antimicrobial activity against Staphylococcus aureus, Bacillus subtilis, Enterococcus faecalis, Chromobacterium violaceum, Klebsiella pneumoniae, Salmonella Typhimurium, Escherichia coli, Acinetobacter haemolyticus, Pseudomonas aeruginosa, Enterobacter aerogenes, and Candida albicans was 21.2%, 20.0%, 16.8%, 12.8%, 3.4%, 2.8%, 2.2%, 1.1%, 0.6%, 0.6%, and 0.6%, respectively. An actinomycete isolate, TRMS 124, showed antimicrobial activity against ten test microorganisms. The 16S ribosomal RNA (16S rRNA) sequencing was performed for the identification and phylogenetic analysis of 26 isolates randomly selected among actinomycetes that exhibited antimicrobial activity against at least three test microorganisms. As a result, it was determined that 24 isolates showed homology with various Streptomyces species and two isolates with Embleya scabrispora and Couchioplanes caeruleus, respectively. These results showed that karst caves could be good sources for isolating actinomycetes with the potential to produce antimicrobial compounds.

Staphylococci are pathogens that cause serious infections in humans and animals. Nosocomial infections caused by staphylococci, particularly methicillin-resistant Staphylococcus aureus (MRSA) strains, are mostly transmitted through healthcare workers, patients, or contaminated materials and food. In recent years, studies have been carried out to develop alternative antimicrobial strategies due to the inadequacy of existing antibiotics in the prevention of systemic, skin and implant-related biofilm infections caused by these multi-antibiotic resistant strains. One of these new approaches is the development of products containing the bacteriophage endolysin, which is particularly effective against multi-antibiotic-resistant bacteria. In this study, endolysin genes of bacteriophages (prophages) integrated into the chromosomes of Staphylococcus strains were amplified by polymerase chain reaction (PCR) and cloned into pET SUMO and pET-30b(+) vectors and produced recombinantly in E. coli. Anti-staphylococcal and antibiofilm activity of recombinant endolysins against S. aureus, S. epidermidis, and S. haemolyticus strains isolated from clinical specimens, were demonstrated using turbidity reduction, biofilm removal in microwell plates by crystal violet method, and capacity of endolysins to kill biofilm-forming bacteria by confocal microscopy imaging by live-dead staining. The combination of endolysin was shown to reduce bacterial culture turbidity by at least 50% at 60 minutes and biofilms by approximately 70% at 12 hours. These results show that endolysins have the potential to be used in the prevention of staphylococcal infections.

Background: Aim of the study was to produce α-amylase cheaply from Rhizoctonia solani AG-4 strain ZB-34 by solid-state fermentation and investigate its suitability for some industries. Methods: Rhizoctonia solani AG-4 strain ZB-34 α-amylase was purified with starch affinity method. Results: The best production of enzyme was achieved by using corn bran. Optimum pH and temperature were 5.5 and 50°C, respectively. V _max and K _0.5 were determined as 238.8 U/mg protein and 0.03% from substrate-activity curve. Activity was maintained about 100% in the tested pHs after 1 day incubation. The enzyme conserved full of its activity at 4 and 28°C for 120 min. Mn ²⁺ , Ca ²⁺ , Tween 20, Triton X-100 and Triton X-114 activated the enzyme. The enzyme was highly active in the presence of some commercial detergents. The chocolate stains on the cotton fabrics were more effectively cleaned with the combination of a commercial detergent and purified enzyme. The purified enzyme also clarified the raw apple juice and desized the cotton fabrics. Conclusion: The results showed that Rhizoctonia solani AG-4 strain ZB-34 α-amylase might have potential application as a detergent additive. In addition, its activity between pH 4.0 and 7.0 may facilitate its use in the food and fruit processing industries.

Purpose: The purpose of this paper is to study the fertility potential of the iron- and steel-making process waste granulated blast furnace slag to recover it as a beneficial product. Design/methodology/approach: This slag fertilizer was mixed with organic fertilizer to enrich and dung the vegetable sets are pepper, lettuce and cucumbers. Findings: In this study, 100 per cent granulated slag, 75 per cent granulated slag + 25 per cent fermented manure, 50 per cent granulated slag + 50 per cent fermented manure and 25 per cent granulated slag + 75 per cent fermented manure compositions were mixed with water and added to seeding pots. The growth rate of vegetable sets and also the level of contamination of heavy metals such as lead, copper, aluminum, mercury and cadmium were analyzed. The analyses results showed that contamination rates of lead, copper, aluminum, mercury and cadmium in lettuce and cucumber samples were in the range of acceptable levels for human health. Slag fertilizer enforced the set of growth rate and productivity, too. Originality/value: By the recovery of the waste slag storage, transport and annihilation economical load on the industry would be eliminated, waste recovery contributes to the economical gaining and beneficial recovered products replace the need of fertility products.