Browsing by Author "Arvas, Yunus Emre"

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Antiprotozoal Effects of Pediococcus Acidilactici-Derived Postbiotic on Blastocystis Subtypes ST1/ST3
(MDPI, 2025) Aydemir, Selahattin; Arvas, Yunus Emre; Aydemir, Mehmet Emin; Barlik, Fethi; Gurbuz, Esra; Yazgan, Yener; Ekici, Abdurrahman
Blastocystis, a common intestinal protozoan in humans, is associated with gastrointestinal disorders, irritable bowel syndrome, urticaria, and colorectal cancer. Its genetic diversity and potential for treatment resistance make it a focus of ongoing research. This study evaluated the in vitro antiprotozoal activity of a postbiotic derived from Pediococcus acidilactici as a natural alternative treatment. P. acidilactici cultures were grown in MRS broth under anaerobic conditions, and the postbiotic was collected and characterized for pH, yield, organic acid composition, and phenolic compound content. Human isolates of Blastocystis subtypes ST1 and ST3 were cultured in Jones' medium and exposed to varying postbiotic concentrations for 72 h. Viability was assessed microscopically. The cytotoxic effect of the postbiotic-derived P. acidilactici was evaluated by investigating its impact on the viability of HT-29 cells using the Cell Counting Kit 8. The postbiotic showed a 7% yield and a pH of 4.52 +/- 0.11. It contained seven different organic acids, predominantly lactic acid, and eleven phenolic compounds, with naringin as the most abundant. At 4.38 mg/mL, the postbiotic achieved over 94% inhibition and 100% inhibition at 8.75 mg/mL and above. A pH analysis confirmed that the inhibition was independent of the culture medium acidity. Cell viability was not affected at the postbiotic concentration showing 100% antiprotozoal activity (8.75 mg/mL). These findings suggest that the P. acidilactici postbiotic is effective on a mixed culture of ST1 and ST3 subtypes and holds promise as a safe, natural antiprotozoal agent. Further in vivo studies are needed to confirm this.
Investigation the Effect of Drought Stress on Tolerant and Resistant Rice (Oryza Sativa L.) Varieties in Terms of Morphologic and Genetic Characters
(Springer, 2023) Arvas, Yunus Emre; Yolci, Muhammed Said; Marakli, Sevgi
Drought associated with global warming is a major limiting factor for crop production. This abiotic stress affects the quality and yield of rice (Oryza sativa L.) which is a model organism and also one of the major consumed products all over the world. In this study, we aimed to analyse morphologic (root length, shoot length, root wet weight, shoot wet weight, root dry weight and shoot dry weight) of rice varieties (Dhan 65, Dhan 71, Kiziltan and Karacadag local rice) grown under drought stress during 21 days. For genetic properties, Hopi and Osr30 retrotransposon movements were investigated by using IRAP marker technique. Depending on the decreasing in the amount of water, we observed that all growth parameters showed variable results in four varieties. Moreover, IRAP-PCR indicated different polymorphism ratios among samples. These rates were 0-75% for Hopi and 0-50% for Osr30. As far as we know, this is the first detailed report on dhan 65, dhan 71, kiziltan and Karacadag local rice varieties grown under drought stress.
LC-MS/MS-based Phenolic Profiling and IRAP-PCR Analysis Reveal Biochemical and Genomic Responses of Flax (Linum Usitatissimum L.) to Salt Stress
(Springer, 2025) Arvas, Yunus Emre
Background Salinity is a major abiotic stress factor that affects plant growth, secondary metabolism, and genomic stability. Phenolic compounds and antioxidant capacity are key biochemical indicators of plant stress responses, while retrotransposon activity reflects molecular-level genomic plasticity. This study investigated the physiological and molecular responses of Linum usitatissimum L. (flax) to different salt concentrations, aiming to better understand the mechanisms underlying salinity tolerance. Methods and results Flax plantlets were grown in vitro on Murashige and Skoog (MS) medium supplemented with 15, 30, or 60 mM NaCl for 15 days. Total phenolic content (TPC) was quantified using the Folin-Ciocalteu method, while antioxidant activity was assessed via DPPH and ABTS radical scavenging assays. LC-MS/MS was employed to identify and quantify individual phenolic compounds, and IRAP-PCR was used to evaluate retrotransposon mobility. Salinity resulted in a significant reduction in biochemical parameters. TPC decreased from 1.13 mu g GAE/100 mu g extract in the control to 0.85, 1.06, and 0.69 mu g GAE under 15, 30, and 60 mM NaCl, respectively. Antioxidant activity showed a similar decline: DPPH inhibition dropped from 25% (control) to approximately 12% under 60 mM stress, while ABTS inhibition decreased from over 90% to approximately 72% at 0.03 mg/mL. LC-MS/MS profiling revealed salt-sensitive reductions in chlorogenic acid, caffeic acid, trans-ferulic acid, and naringenin, with chlorogenic acid particularly diminished at 60 mM NaCl. At the molecular level, IRAP-PCR yielded high polymorphism rates, ranging from 50% to 100% (primer 1845), 60% to 100% (1846), 54% to 100% (1875), and 36% to 100% (1899), indicating enhanced retrotransposon activity under increasing salinity. Conclusion Overall, rising salt concentrations reduced phenolic accumulation and antioxidant potential while increasing retrotransposon-mediated genomic variability in flax. These results suggest that both biochemical markers (phenolics, antioxidant activity) and molecular indicators (IRAP polymorphism) are valuable tools for assessing salinity stress responses and can support the development of salt-tolerant cultivars in flax breeding programs.
Revealing Molecular Diagnosis With Whole Exome Sequencing in Patients With Inherited Retinal Disorders
(Wiley, 2025) Yavas, Cuneyd; Arvas, Yunus Emre; Dogan, Mustafa; Gezdirici, Alper; Aslan, Elif Sibel; Karapapak, Murat; Eroz, Recep
Inherited retinal diseases (IRDs) constitute a heterogeneous group of clinically and genetically diverse conditions, standing as a primary cause of visual impairment among individuals aged 15-45, with an estimated incidence of 1:2000. Our study aimed to comprehensively evaluate the genetic variants underlying IRDs in the Turkish population. This study included 50 unrelated Turkish IRD patients and their families. Genomic DNA was extracted from each participant, and candidate variants were identified via next-generation sequencing to determine their pathogenicity. We detected variants in 58% of the patients, of which six novel variants were identified. Among these, 16 cases exhibited variants associated with retinitis pigmentosa and Stargardt disease, while 13 presented variants linked to other retinal diseases. The spectrum of identified variants included 21 homozygous cases and five compound heterozygous variants, both indicative of autosomal recessive inheritance. Three cases revealed heterozygous variants suggestive of autosomal dominant inheritance, and two cases featured hemizygous variants suggestive of X-linked inheritance. Importantly, no matches with copy number variants were detected in our analysis. This study comprehensively portrays clinical and genetic profiles within the Turkish population affected by IRDs. Identifying novel variants and delineating inheritance patterns contribute to a deeper understanding of the genetic diagnosis of IRDs, paving the way for more precise diagnostic and therapeutic interventions.