Volume 48, Issue 6

Nanobiotechnology is a specific field of biotechnology that utilizes nanoscale methods and materials to investigate biological systems and create innovative medical technologies. This review discusses the diverse use of nanobiotechnology in health, focusing on both its superior properties and challenges. The main aims of this report are to present and elaborate on the global market share of this growing field as well as the scientific output, regarding publications and patents in the last decade. Quantitative data is derived from the Statnano database, which includes information related to the articles from the Web of Science (WoS) and approved patents from the European Patent Office and the United States Patent and Trademark Office. The final aim of this review is to provide some suggestions based on these data. Government support is the most important driving force in building up research and publications. Support for advancement in nanotechnology to fabricate products for commercial and public benefit is the top priority of developed nations. Thus, entrepreneurial training of young researchers, and collaborations between scientists, policymakers, investors, and citizens, should be encouraged. To work together globally and set international standards for the creation of consistent methods in characterizing nanoscale products with biological systems is imperative.

This paper discusses the integration of artificial intelligence (AI) tools in education, delineating their potential to transform pedagogical practices alongside the challenges they present. Generative AI models like ChatGPT, had a disruptive impact on teaching and learning, due to their ability to create text, images, and sound, revolutionizing educational content creation and modification. However, nowadays the educational community is polarized, with some embracing AI for its accessibility and efficiency thus advocating it as an indispensable tool, while others cautioning against risks to academic integrity and intellectual development. This document is designed to raise awareness about AI tools and provide some examples of how they can be used to improve education and learning. From an educator’s perspective, AI is an asset for curriculum development, course material preparation, instructional design and student assessment, while reducing bias and workload. For students, AI tools offer personalized learning experiences, timely feedback, and support in various academic activities. The Turkish Biochemical Society (TBS) Academy recommends educators to embrace and utilize AI tools to enhance educational processes, and engage in peer learning for better adaptation while maintaining a critical perspective on their utility and limitations. The transfer of AI knowledge and methods to the teaching experiences should complement and not replace the educator’s creativity and critical thinking. The paper advocates for an informed embrace of AI, AI fluency among educators and students, ethical application of AI in academic settings, and continuous engagement with the evolving AI technologies, ensuring that AI tools are used to augment critical thinking and contribute positively to education and society.

Objectives Autoverification (AV) is releasing laboratory results using predefined rules. AV standardizes the verification of laboratory results, improves turnaround time (TAT), detects errors in the total test process, and enables effective use of laboratory staff. In this study, we aimed to evaluate the outcomes of implementing the AV in a tertiary hospital. Methods The study was performed in Gazi University Health Research and Application Hospital, Core Biochemistry Laboratory, between August 2017 and October 2019. Step by step, AV algorithms were designed and implemented via middleware for 29 clinical biochemistry tests. A comprehensive validation was performed before the AV system was run. Initially, AV system was tested with datasets and simulated patients (dry testing). Next, samples that may violate AV rules were tested anonymously with no-named trial barcodes (wet testing). Finally, validation of the system was performed with real patients, while the AV was running in the background but not active (i.e., while the manual verification was still going on). After all these steps were successful, the system was started. Results In the daytime, AV rates were ≥75 % for 23 of 29 tests. In night-shift, AV rates were ≥70 % for 16 of 25 tests. Report-based performance was found 26 % for daytime. TAT in the daytime decreased after AV implementation. Conclusions Although this is the first time we have implemented the AV, a significant percentage of the tests have been verified. However, approaches that will increase the percentage of report-based verification will enhance the efficiency of autoverification.

Objectives Epstein–Barr virus (EBV) is a member of the herpes virus that causes infectious mononucleosis (IM). Downey cell is the atypical lymphocyte of IM and can be seen in various conditions. Peripheral blood smear (PBS) microscopic evaluation is used to identify Downey cells. A lack of experienced professionals or professional errors may obstruct early and accurate diagnostics for the microscopic evaluation. The main objective of this study is to create a decision support system by digitizing the PBS samples. A general tool providing an inexpensive and measurable solution is envisioned to analyze the PBS samples in detail to give alerting flags to prevent missing Downey cells in manual analysis. Methods The PBS dataset collected was split into Downey positives and negatives. The negative set consisted of 5 leucocyte subtypes. Mantiscope, a cloud-based slide scanner system, was used to collect images from the physical PBS samples. Clinically and laboratory-confirmed 35 IM patients and 124 healthy PBS slides were selected for this procedure. A number of cell counts were obtained after the application of annotation and augmentation methods, and a partially balanced dataset was created for the artificial intelligence (AI) network training. The verification steps included the calculation of sensitivity, specificity, and Cohen’s kappa metrics from the partitioned testing set that was not used during training. A validation process was also performed over the manually identified PBS samples to measure whether the algorithm noticed the samples or not. Results After testing this setup, we have observed 98 % sensitivity and 99 % specificity for Downey cells. According to the validation procedure of Downey positive and negative samples that were carried out by the physicians, a sensitivity of 57 %, specificity of 100 %, and Cohen’s kappa value of 0 . 5 were observed. Besides, the accuracy was found to be 66 % according to the physicians’ evaluations employing the digital images which were identified by Mantiscope, Conclusions Decision support systems can alert the physician for Downey cells and increase the rate of true diagnosis in PBS evaluation. A higher sensitivity and specificity for the detection of Downey cells would be achieved. However, the variance over the dataset is a constraint for effective diagnosis. As the annotation and AI development process continues to collect more data from patients, the model can be updated for future releases.

Objectives Determining low-density lipoprotein (LDL) is a costly and time-consuming operation, but triglyceride value above 400 (TG>400) always requires LDL measurement. Obtaining a fast LDL forecast by accurate prediction can be valuable to experts. However, if a high error margin exists, LDL prediction can be critical and unusable. Our objective is LDL value and level prediction with an error less than low total acceptable error rate (% TEa). Methods Our present work used 6392 lab records to predict the patient LDL value using state-of-the-art Artificial Intelligence methods. The designed model, p-LDL-M, predicts LDL value and class with an overall average test score of 98.70 %, using custom, hyper-parameter-tuned Ensemble Machine Learning algorithm. Results The results show that using our innovative p-LDL-M is advisable for subjects with critical TG>400. Analysis proved that our model is positively affected by the Hopkins and Friedewald equations normally used for (TG≤400). The conclusion follows that the test score performance of p-LDL-M using only (TG>400) is 7.72 % inferior to the same p-LDL-M, using Hopkins and Friedewald supported data. In addition, the test score performance of the NIH-Equ-2 for (TG>400) is much inferior to p-LDL-M prediction results. Conclusions In conclusion, obtaining an accurate and fast LDL value and level forecast for people with (TG>400) using our innovative p-LDL-M is highly recommendable.

Objectives Human immunodeficiency virus (HIV) is a significant infection that attacks immune system cells and integrates its genetic material into host cells. Left untreated, it leads to acquired immunodeficiency syndrome (AIDS). Antiretroviral therapy (ART) is used to control HIV infection. Etravirine (ETR) is an important non-nucleoside reverse transcriptase inhibitor (NNRTI) utilized in the treatment of HIV. Low-level viremia (LLW) is a serious clinical condition, and the underlying mechanisms remain incompletely understood. The aim of our study is to analyze and elucidate the resistance status of Lys104Gln, Lys102Gln, Lys101Arg-Lys104Arg, Ser191Phe, Ile94Leu-Lys104Arg, Lys104Glu-His235Leu, Ala98Ser and Val179Ile mutations using in-silico methods, which are identified as low-level viremic strains, because their resistance status to ETR is unknown. Methods Homology modeling was performed using the Swiss Model program. Molecular docking of ETR with the reverse transcriptase (RT) enzyme was conducted using the CB-Dock program developed by AutoDock Vina. Protein-ligand interaction analysis was carried out using the protein-ligand interaction profiler (PLIP). Results A98S and V179I mutations altered the physicochemical properties of the region, resulting in changes to the conformational structure of the NNRTI hydrophobic pocket compared to the wild-type and consequently decreased docking scores. Conclusions Based on the evaluation of literature data and in-silico analyses, it is believed that A98S and V179I mutations may alter the conformational structure of the hydrophobic pocket where ETR binds, potentially resulting in low-level resistance against ETR.

Objectives Owing to its avascular nature, cartilage tissue has a restricted capacity for regeneration. These structural features make it difficult for a fully functional tissue to regenerate after damage. Therefore, studies aiming at cartilage tissue regeneration are getting quite interesting. In this study, we employed a novel approach to induce chondrogenic differentiation using a collagen mimetic peptide amphihile (PA) nanofiber. The nanofiber comprised a specific peptide sequence – glycine-phenylalanine-hydroxyproline-glycine-glutamate-arginine (GFOGER), corresponding to the α1 (I) collagen chain. This sequence was selected for its ability to mimic the structure and function of natural collagen in the extracellular matrix (ECM). This specific peptide sequence is expected to enhance the chondrogenic differentiation process by providing a more efficient and effective method for tissue engineering applications. Methods ATDC5 cells were cultured on the synthetic scaffold of collagen-mimicking PA nanofibers, facilitating adhesion, division, and chondrogenic cell differentiation. Results In our study, ATDC5 cells cultured on collagen mimetic peptide nanofiber expressed chondrogenic marker proteins, namely Collagen II and Sox9, significantly high at the 5th and 10th days compared to cells cultured on TCP in the absence of insulin as inducer. Conclusions According to our results, the collagen mimetic peptide-based scaffold supports cell growth and differentiation by mimicking the natural cell matrix.

Objectives Alzheimer’s disease (AD) is an irreversible and progressive neurogenerative disorder, which affects the learning part of brain. It mainly affects the aged population and becoming a global health issue, expecting to increase more in near future. Late diagnosis of AD worsens the situation and difficult to treat the patient. Various biosensing techniques with suitable biomarkers have been developed by researchers to diagnose the earlier stages of AD. Methods This research was focused to develop a highly sensitive zeolite-dual probe-modified impedance biosensor for identifying AD biomarker, Aβ Oligomer (AβO). The sensing surface was initially modified with zeolite through the chemical linker and then a dual probe of anti-AβO aptamer and anti-AβO antibody were attached to the surface of the zeolite. Results On these dual probe-modified surfaces, AβO was quantified to diagnose AD. Further, AβO spiked artificial CSF was identified by dual probes without any interference, indicating the selective identification of AβO. In addition, control experiments with non-immune, complementary, and control proteins failed to show the increment of responses, confirming the specific detection of AβO. Conclusions This zeolite-dual probe-modified biosensor helps to lower the limit of detection to 0.1 pM and diagnose AD at the earlier stages.

Objectives Voltage-gated calcium channels are essential elements in development of many cellular processes like electrical signaling, contraction secretion and gene expression. There has been a fair amount of information about the functional and structural properties of the calcium channels in mammalian species. Crayfish serves as a model animal for many types of experiments. However, there has been no information related to the molecular and genetic properties of the calcium channels in the crayfish. Methods Conventional cloning methods, three-dimensional structural calculations, docking experiments have been conducted. Results An mRNA 7,791 bp in size has been cloned. The coding region has been translated into an alpha peptide with 1,942 residues. The cloned protein sequence has similarity to other L-type voltage-gated calcium channel sequences from the neighboring species. Three-dimensional structure, in reference to human L-type voltage-gated calcium channel, has been calculated. Known calcium channel blockers, nifedipine, verapamil and diltiazem have been successfully docked on the calculated three-dimensional model. Conclusions Considering the similarity assay in the National Center for Biotechnology Information (NCBI) platform, the three-dimensional structural calculations and the docking experiments it was concluded that the cloned mRNA codes an alpha peptide for a putative voltage-gated calcium channel protein in the crayfish. In the present work by using the conventional molecular biology methods a complete mRNA coding a putative calcium channel has been de novo cloned. Three-dimensional structure of the related protein has been calculated and several pharmacological agents blocking the channel have been docked to the identified receptor sites.

Objectives The key component of neuroprotection after cerebral ischemia–reperfusion (I–R) injury is mitochondrial improvement. By focusing on the function of mitochondrial biogenesis and ATP-sensitive potassium (mK–ATP) channels and inflammatory responses, the current study assessed the neuroprotective potentials of lemon essential oil, D-limonene (LIM), in rats with cerebral I–R injury. Methods In order to simulate cerebral I–R injury, Sprague Dawley rats (n=72) were subjected to a two h local ischemia induced by middle cerebral artery blockage, followed by a 24 h reperfusion period. Five minutes before starting reperfusion, rats were intraperitoneally given LIM at doses of 10 or 100 mg/kg. Cerebral infarct volume was assessed by triphenyl-tetrazolium chloride staining, brain activity by behavioral tests and mitochondrial function/biogenesis, as well as proinflammatory cytokines by fluorometry, immunoblotting and other related techniques. Results When compared to the untreated control group, the administration of LIM substantially and dose-dependently decreased cerebral infarct volumes and neurological deficits (p<0.01). I–R injury-induced alterations in mitochondrial membrane depolarization, mitochondrial reactive oxygen species (mitoROS), and superoxide dismutase (mnSOD), as well as inflammatory cytokines TNF-α, IL-6 and IL-1β, were all significantly reversed after treatment with LIM 100 mg/kg (p<0.01). Additionally, this dose of LIM increased the expression of mitochondrial biogenesis proteins PGC-1α, TFAM, and NRF1. Interestingly, blockage of mK–ATP channels by 5-hydoxydecanoate diminished the effects of LIM on cerebral positive endpoints, cytokines production, and mitochondrial function/biogenesis. Conclusions Thus, the strong neuroprotective effects of LIM-postconditioning were mediated by an increase in mK–ATP channel activity, which improved mitochondrial biogenesis and suppressed inflammatory responses.

Objectives Colon cancer is the most common gastrointestinal cancer worldwide with high morbidity and mortality rates. The main purpose of our study is to elucidate the interaction mechanism of the H + ion concentration effect in the CO 2 /HCO 3 − buffer system of tumor-associated carbonic anhydrase IX (CA IX) enzyme inhibition in the HT-29 colon cancer cell line on cell epigenetic modifications. Methods Cell culture was performed using the human colon cancer cell line HT-29. CA IX enzyme inhibitor Acetazolamide (AZA) was administered. The results of the cell viability test and inhibition were evaluated. Extracellular pH measurements were performed. Total histone protein isolation was performed and Histone H3 modifications were analyzed by ELISA method. After RNA isolation, complementary DNA (cDNA) synthesis was carried out. RT-PCR was performed to determine the gene expression levels of hypoxia-inducible factor 1A ( HIF1A ), enhancer of zeste homolog 2 ( EZH2 ) and CA IX. Results CA IX enzyme inhibition in the HT-29 cell line decreased the expression of CA IX (p<0.05) and HIF1A (p<0.01) genes and increased the expression of the EZH2 (p<0.05). There was a significant decrease in the expression of CA IX (p<0.05) and HIF1A genes as a result of inhibition with AZA performed under hypoxic conditions. It was observed that CA IX enzyme inhibition increases the expression of the EZH2 gene by more than 3 times (p<0.01). As a result of AZA inhibition, methylation levels were observed to increase in normoxic conditions, while methylation levels were observed to decrease in hypoxic conditions. Conclusions Observing the changes in the H3 modifications and changes in the expression of CA IX, HIF1A and EZH2 genes in this study supports that CA IX enzyme inhibition plays an active role in epigenetic modifications.

Objectives This study aimed to investigate whether a growth factor and a cytokine midkine (MK) can be a new biomarker for the diagnosis and treatment of unexplained female infertility (UFI) cases. Methods Serum (S), follicle fluid (FF), and cumulus cells (CCs) of the patients aged 20–42 years, diagnosed with male factor (MF) and UFI were used. Patients underwent Intracytoplasmic Sperm Injection (ICSI). The anti-Müllerian hormone (AMH) and MK levels with other hormone levels (FSH, LH, E2, PRL, INHB, TSH), the oocyte and embryo qualities, the fertilization and pregnancy rates, and cumulus cells (Cell number and ultrastructure, apoptosis rate) were evaluated. Student-T-test was performed and p<0.05 was considered statistically significant. Results The lowest numbers of CCs were found at UFI (p<0.05). The lowest apoptosis rate with the highest CC viability rate was evaluated at MF (p<0.05). The lowest AMH and MK levels (S, FF) were detected at UFI in comparison to MF (p<0.05). MK and AMH levels of non-pregnant subjects were much lower than pregnant subjects (p<0.05). In addition, these levels were lower in the subjects above 35 age (p<0.05). Structural analysis of CCs showed that the number of lytic cells with cell remnants and apoptotic bodies was higher in non-pregnant subjects. It seems that MK did not show any resistance to both AMH and apoptosis. Conclusions MK can not be accepted as a new biomarker for the diagnosis and treatment monitoring of UFI cases.

Objectives Cholangiocarcinoma (CCA) is usually diagnosed at a late stage due to resistance to chemotherapeutic drugs. Epithelial mesenchymal transition (EMT) is a biological process in cancer that allows multiple biochemical changes that enable epithelial cells to acquire a mesenchymal phenotype. In the present study, we focused on the EMT process which is an important in carcinogenesis and metastatic progression, and also investigate the effect of silibinin on cell proliferation, colony formation, migration, apoptosis, cell cycle and EMT. Methods Cell viability, apoptosis and cell cycle were measured by Muse Cell Analyzer. All the protein levels were determined by ELISA method. Results We found that silibinin significantly reduced cell proliferation in a dose-dependent manner and the IC 50 value was 200 μM. Silibinin, significantly inhibited colony formation, inhibited cell migration of cancer cells induced total apoptosis due to the induction of early and late apoptosis, arrest cancer cells in the G0/G1 phase of the cell cycle compared to the control group. We found that E-cadherin, N-cadherin, Vimentin and α-SMA protein levels were significantly decreased in the silibinin group compared to the control group. Conclusions Our results showed that silibinin could significantly prevent tumor proliferation, reduce colony formation, prevent migration, increase the arrest of the G0/G1 phase and induce apoptosis progress in human extracellular cholangiocarcinoma cell line. Another important data is that silibinin inhibits EMT in the cholangiocarcinoma cell line (TFK-1). Our study shows significant effects of silibinin in the TFK-1 cell line, which may be exciting to explore its implications in future animal studies.

Objectives The aim of this study is to investigate the diagnostic and prognostic characteristics of fetuin A and fetuin B in chronic hepatitis B (CHB) and HBe Ag-negative chronic infection (HCI) and the relationship between the levels of these proteins and fibrosis in CHB. Methods In this study, we examined 98 patients with CHB, 58 with HCI and 42 control groups. Fetuin A and B levels were determined via ELISA. Results Serum fetuin A and B levels were significantly higher in the control group than the hepatitis B cases (p=0.001). No significant difference in fetuin A and B levels between patients in the CHB and HCI. In the CHB, fetuin A level was significantly lower in patients with significant fibrosis than those with mild fibrosis (p=0.007). Fetuin B was lower in patients with significant fibrosis than in with mild fibrosis; however, this difference was not significant. In predicting the absence of significant fibrosis, the area under the curve was estimated as 0.855 for fetuin A and 0.866 for fetuin B using the ROC curve. Conclusions Fetuin A and B were lower in CHB and HCI compared to the control group and there was no difference between the two groups suggests that these proteins may be effective in the pathogenesis of hepatitis B-induced liver damage. Fetuin A and B, which are found to be lower in patients with significant fibrosis in CHB, can be used as non-invasive markers in the early detection of fibrosis and in the follow-up of progression to significant fibrosis.