Turkish journal of biology = Turk biyoloji dergisi最新文献

Human growth hormone (GH) is crucial modulator of cellular metabolisms, including cell proliferation and organ development, by stimulating insulin-like growth factor-1 (IGF-1), which has various functions such as cell proliferation, tissue growth, survival, or neuroprotection. Therefore, GH is implicated as a critical player in the cell and can enhance neurogenesis and provide neuroprotection during the treatment of neurological diseases such as Parkinson's disease (PD). In this study, the neuroprotective role of GH was investigated in rotenone-induced PD models for the first time. Both SH-SY5Y and SK-N-AS neuroblastoma cells were exposed to rotenone to mimic PD pathogenesis as stated in previous studies. Our data demonstrated that overexpression of GH led to the resistance of the SH-SY5Y and SK-N-AS cell lines to rotenone treatment. The levels of ER stress markers, CHOP, PERK, XBP-1, and ATF6, were higher in wt cells than GH+ SH-SY5Y cells. However, the level of autophagy markers LC3 increased and the levels of reactive oxygen species (ROS) decreased with the overexpression of GH. Furthermore, while rotenone significantly increased the SubG1 population in the cell cycle of SH-SY5Y wt cells, there was a minor alteration in GH+ cell population. Concomitantly, the levels of the proapoptotic marker, cleaved-PARP, and positive staining of Annexin V in SH-SY5Y wt cells were higher after rotenone treatment. Together, these results revealed that overexpression of GH enhanced the autophagy response by triggering the ER stress of SH-SY5Y cells to rotenone exposure and showed a neuroprotective effect in vitro PD models.

Sequence content is heterogeneous throughout genomes. Therefore, genome-wide next-generation sequencing (NGS) reads biased towards specific nucleotide profiles are affected by the genome-wide heterogeneous nucleotide distribution. Boquila generates sequences that mimic the nucleotide profile of true reads, which can be used to correct the nucleotide-based bias of genome-wide distribution of NGS reads. Boquila can be configured to generate reads from only specified regions of the reference genome. It also allows the use of input DNA sequencing to correct the bias due to the copy number variations in the genome. Boquila uses standard file formats for input and output data, and it can be easily integrated into any workflow for high-throughput sequencing applications.

Clinical observations show that the current spinal fusion with internal fixation has a nonfusion rate of 5%-35%; however, methods to promote spinal fusion are limited. This study aimed to investigate the role of SDF-1-induced directional chemotaxis of BMSCs in bone marrow chimera spinal intervertebral fusion mouse model. BMSCs were isolated from bone marrow and identified by detecting CD44/CD34 positive cells. BMSCs (GFP-BMSCs) were labeled with GFP for tracking in vivo. Mice were inoculated with GFP-BMSCs to construct bone marrow chimera spinal intervertebral fusion model, which were divided into BM-SIF model, BM-SIF+SDF-1, BM-SIF+SDF-1-Anta group. The callus area of intervertebral fusion site was detected by radiology. HE staining was used to detect trabeculae formation. Expressions of osteogenic molecules and fibroblast markers were detected by RT-PCR and Western blotting. GFP-BMSCs showed obvious osteogenic and adipogenic differentiation ability, according to oil-red O and alizarin-red staining. Bone marrow chimera spinal intervertebral fusion mouse model was successfully established, with efficient localization of GFP-BMSCs at intervertebral fusion site. SDF-1 significantly promoted bone trabeculae formation in callus at intervertebral fusion site. SDF-1 significantly increased osteogenic molecules transcription/expression in callus at intervertebral bone graft fusion site of mice; however, SDF-1-Anta (AMD3100) significantly decreased osteogenic molecules transcrition/expression, compared to those of mice from the BM-SIF model group (p < 0.05). SDF-1 markedly induced and SDF-1-Anta significantly decreased fibroblast proliferations in the callus at the intervertebral fusion site of mice, compared to those of mice from the BM-SIF model group (p < 0.05). SDF-1 enhanced expression of Wnt10b and β-catenin in callus at intervertebral fusion site of mice compared to mice of the BM-SIF model group (p < 0.05). In conclusion, SDF-1 induced directional chemotaxis of BMSCs to the intervertebral fusion site and promoted osteogenic differentiation in bone marrow chimera spinal intervertebral fusion mice by regulating Wnt/β-catenin pathway and modulating the proliferation of BMSCs.

Background/aim: Matrix metalloproteinases (MMPs) play an important role in the evaluation of many cancer types; however, the detection usually presents a challenge. Further assays for a better understanding of the fundamental roles of MMPs in pathophysiology are still needed. We aimed to use an activatable probe in scanning acoustic microscopy (SAM) to evaluate acoustically if the probe can aid the visualization of the effects of in vitro MMP activity.

Materials and methods: We applied scanning acoustic impedance microscopy to obtain acoustic impedance maps of the cell line models of HT1080, THP-1, and SK-MEL-28 with and without MMPSense 680 probe incubation. We visually validated our results using confocal laser scanning microscopy imaging. We further analyzed the effects of MMPSense 680 probe on cell viabilities to eliminate any artifacts.

Results: This is the first study presenting the applicability of SAM in the acoustical evaluation of MMPSense 680 probe cleavage in a cellular medium through acoustic impedance measurements. We proposed that SAM measurement with the activatable probe can be used as an effective tool for studying the acoustical variations of MMP activities in cell lines. As a result, we detected MMPSense 680 probe cleavage in HT1080 human fibrosarcoma cell line.

Conclusion: We showed that SAM with the smart probe can detect proteolytic activity using MMPSense 680 in in vitro HT1080 cell line by acoustic impedance measurements. SAM could be proposed as an alternative tool leading a novel way for a better understanding of the roles of MMPs in cancer progression before clinical settings.

Shell-sheddable nanoparticles, composed of amphiphilic blockpolymers, have emerged as an attractive vehicle for the site-specific delivery of therapeutic agents. In this study, pH-responsive sheddable copolymers bearing an orthoester linker were synthesized via the ring-opening polymerization between γ-benzyl-L-glutamate N-carboxyanhydride and orthoester-bearing poly (ethylene glycol) macroinitiator (PEG-pH-NH₂). The obtained poly (ethylene glycol)-b-poly(γ-benzyl-L-glutamate) (PEG-PBLG) could form stable nanoparticles in aqueous solutions due to the amphiphilic nature of the block copolymers. The PEG-PBLG-based nanoparticle exhibited good stability in physiological conditions (pH 7.4), whereas the nanoparticle was disassembled under acidic conditions (pH 5.0). The nanoparticles could encapsulate a photosensitizer, protophorphyrin IX (PpIX), and deliver it into acidic environments. According to optical imaging test, it was found that quenched fluorescence signal of PpIX highly recovered under acidic conditions. Acid-responsive sheddable nanoparticles rapidly release the PpIX when they are incubated under acidic conditions (pH 5.0), and the PpIX release was remarkably reduced in physiological buffer (pH 7.4). In vitro cytotoxicity test showed that cells treated with pH-responsive sheddable nanoparticle became highly phototoxic upon irradiation. Microscopic observation demonstrated that PpIX-loaded nanoparticle rapidly degraded at the endosome of SCC7 cancer cells, which enabled PpIX release into the cancer cells. These results suggest that pH-responsive sheddable are a promising carrier for photodynamic agents.

Liver ischemia and reperfusion (IR) injury is the major complication of liver-related operations. Macrophage polarization has an essential effect on the mechanism of liver IR injury. Vitamin D receptor (VDR) has been found to regulate macrophage polarization and alleviate IR injury. Nevertheless, the correlation between VDR and macrophage polarization in liver IR injury has not been clearly elucidated. VDR knockout mice and wild-type littermates underwent partial liver ischemia for 90 min and reperfusion for 6 h. RAW264.7 cells were also used to verify the influence of VDR on macrophage polarization in vitro. VDR activation could promote M2 macrophage polarization and then reduce liver injury. In contrast, VDR deficiency aggravated the liver injury by disturbing M2 macrophage polarization. Moreover, autophagy participated in the effect of VDR on M2 macrophage polarization through mediating suppressor of cytokine signaling. Therefore, VDR plays a vital influence in liver IR injury. The protective role of VDR activation in liver IR injury is related to regulate M2 macrophage polarization by autophagy.

Recent clinical developments in tissue bioengineering have applications in acute cardiac ischemia and infarction and include the use of stem cells that combine injectable scaffold material. This study aimed to evaluate the effects of adipose-derived stem cells (ADSCs) that combine the Matrigel scaffold on cardiac morphology/functions. The autologous ADSCs myocardial infarction (MI) model was induced by the permanent ligation method of the left anterior descending coronary artery (LAD). MI-operated rats were randomly divided into PBS group, Matrigel group, PBS plus ADSCs group (PBS+ADSCs), and Matrigel plus ADSCs group (Matrigel+ADSCs). Matrigel was used as an injectable scaffold. Rats with a 1-week-old myocardial infarction were injected with 2 × 10⁶ labeled ADSCs in the border area of the ischemic heart. Heart function was determined by echocardiography. The hemodynamics, cardiac structure, and graft characteristics were evaluated. The ADSCs were successfully isolated and identified, demonstrating a good proliferative status and cell retention in the Matrigel. ADSCs+Matrigel exhibited the most improved heart functions (LVESD, LVEDD, LVFS, LVEF) compared to those of other groups (p < 0.05). ADSCs+Matrigel significantly reduced infarct size compared to other groups (p < 0.05). Cotransplantation of ADSCs and Matrigel showed the best effect on maintaining the thickness of the ventricular wall compared to the other groups (p < 0.05). Engrafted ADSCs played a role in the formation of the neovasculature in myocardial infarction. ADSCs+Matrigel triggered the greatest enhancement in arteriole density than other groups (p < 0.05). Cotransplanting with ADSCs and Matrigel showed significantly higher levels of cardiac troponin T (cTnT), NK2-transcription factor related locus-5 (Nkx2.5), von Willebrand factor (vWF) than the other groups (p < 0.05). In conclusion, this study demonstrated that cotransplanting ADSCs with Matrigel resulted in improved cardiac morphology and cardiac function in the rat model of myocardial infarction.

X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, İstanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis.

Breast cancer is the most common cancer in women. The human epidermal growth factor receptor 2 (HER2) overexpressing subtype is related to poor prognosis with an aggressive phenotype and is reported as one of the most commonly seen subtypes. Trastuzumab is prevalently used as a treatment method for HER2+ breast cancer however, resistance to the drug frequently occurs following the treatment. MicroRNAs (miRNAs) are 19-23 nucleotide long small RNAs, which regulate gene expression at post-transcriptional level and studies show that there are differentially expressed miRNAs between drug sensitive and resistant groups, indicating that they might have some key roles in drug effectiveness. In this study, the aim is to find out the role of miR-216b-5p in trastuzumab resistance. SK-BR-3 cells developed resistance to trastuzumab after continuous treatment with increasing concentrations of the drug for 6 months. To investigate the effect of miR-216b-5p on cancer cell behavior in resistance state, proliferation, motility, and invasion capacities of these resistant cells were analyzed by xCELLigence real-time cell analyzer. To further understand the molecular mechanisms underlying the regulation of resistant SK-BR-3 cells by miR-216b-5p, microarray analysis was performed. Apoptosis analysis was also performed since the pathway enrichment analysis pointed out cell death related pathways. The proliferation, motility, and invasion capacities of the miR-216b-5p transfected resistant cells were diminished compared to sensitive cells. We identified the necroptosis signaling pathway as the result of microarray and pathway enrichment analyses. STAT1, IRF9, and PKR were validated as the significant elements of the pathway, which are also the putative targets of miR-216b-5p. Our apoptosis analysis showed that a significant amount of trastuzumab resistant SK-BR-3 cells entered to late apoptosis/necrosis stage upon miR-216b-5p overexpression, it could be concluded that reexpression of miR-216b-5p sensitizes trastuzumab resistance through necroptosis in breast cancer.

Background/aim: Serum and growth factor deprivation, a common cellular stressor in solid tumors, arises upon irradiation, chemotherapy, and antiangiogenesis. Spheroid body culture aims to enrich cancer stem cells by using low attachment conditions and some growth factors, such as basic fibroblast growth factor and epidermal growth factor to support the spheroid formation in serum-free spheroid culture. However, spheroid culture without any growth factors can imitate the tumor environment more realistically.In this study, we aimed to identify the effect of growth factor deprivation on the MKN-45 gastric cancer cell line in terms of stemness characteristics.

Materials and methods: The spheroids were obtained by culturing MKN-45 gastric cancer cells in low attachment conditions, and then spheroids were dissociated to obtain cells for further analyses. Self-renewal, multipotency, cellular transformation, invasiveness, chemoresistance, and the expression of stemness-related genes were analyzed using tumor spheroid formation assay, soft agar colony formation assay, transwell invasion assay, chemosensitivity assay, and quantitative RT-PCR assay, respectively.

Results: Fetal bovine serum and growth factor deprivation caused an increase in stemness markers of OCT4, NANOG, SOX2, MUC1, CD24 and CD90. Increasing functional aggressiveness-related properties, such as self-renewal, chemoresistance, and invasive ability, have also been observed in fetal bovine serum-growth factor-free conditions.

Conclusion: Growth factors may not be essential for spheroid culture to enrich cancer stem cells. The deprivation of both fetal bovine serum and growth factors also induces a more aggressive phenotype in MKN-45 cells; thus, it provides an opportunity for further studies targeting tumor cells.