Browsing by Author "Karakus, F."

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Estimation of Marketing Live Weight of Lambs by Different Machine Learning Algorithms
(Agricultural Research Communication Centre, 2025) Karakus, F.
Background: Further research is needed to estimate the marketable live weight of lambs with high accuracy and reliability while minimizing contact and measurement. This study aimed to estimate the 120th-day marketing weight of Morkaraman lambs by different machine learning algorithms, considering the variables of dam age, sex, birth type, birth weight, as well as 30th day, 60th day and 90th day live weights. Methods: Artificial neural networks (ANN), classification and regression trees (CART), support vector machines with radial basis function kernel (SVMR) and Random Forest (RF) algorithms for estimation of the marketing weight were performed for training (75%) and testing (25%) datasets. Models used in this study were compared based on mean absolute error (MAE), root mean squared error (RMSE) and mean absolute per cent error (MAPE) performance metrics. The most significant predictor of the marketing live weight in all models was the 90th day live weight, whereas the birth weight, birth type and dam age were the least important predictors. The correlation coefficients between live weight values estimated by the SVMR, CART, RF and ANN models and the actual marketing live weight were determined as 0.82, 0.82, 0.82 and 0.84, respectively. Result: The best prediction for the marketing live weight of Morkaraman lambs in the 4 th month was obtained from the ANN model. Using artificial neural networks to determine the marketing weight of lambs can save time and labor because of the reduced number of weighings. It may improve decisions made in flock management.
Exploring Natural Compounds Targeting Pd-L1 and Stat3: Toxicogenomic Analysis, Virtual Screening, Molecular Docking, Admet Evaluation, and Biological Activity Prediction
(Bentham Science Publ Ltd, 2025) Karakus, F.; Kuzu, B.; Kostekci, S.; Tuluce, Y.
BACKGROUND: One of the most important targets in cancer immunotherapy is programmed cell death ligand 1 (PD-L1). Monoclonal antibodies developed for this target have disadvantages due to their low bioavailability and some immune-related adverse effects. Additionally, small molecules targeting PD-L1 are still in the experimental stage. At this point, discovering non-toxic natural compounds that directly or indirectly target PD-L1 is essential. In this in silico study, a comprehensive literature search was conducted to identify publications reporting the master regulator of PD-L1, which was suggested as a Signal Transducer and Activator of Transcription 3 (STAT3). The relationship between STAT3 and PD-L1 was further investigated through bioinformatic analysis. METHODS: Subsequently, natural compounds targeting PD-L1 and STAT3 were screened, and compounds with suitable toxicity profiles were docked against both PD-L1 and STAT3. Following molecular docking, the selected molecules underwent DNA docking, ADMET profile analysis, and in silico assessment of biological activities. The relationship between PD-L1 and STAT3 was determined in 52 out of the 453 articles, and it was further demonstrated in genegene interactions. Following the virtual screening, 76 natural compounds were identified, and after pre-filtering based on physicochemical properties, drug-likeness, and ADMET profiles, 29 compounds remained. RESULTS: Subsequent docking revealed that two compounds, 6-Prenylapigenin, and Gelomulide J, persisted. ADMET and biological activity prediction results suggested that 6-Prenylapigenin is non-toxic and has the potential to inhibit PD-L1 and STAT3 in silico. The present study highlights that STAT3 serves as the master regulator of PD-L1, and it further suggests that 6- Prenylapigenin exhibits the potential to modulate PD-L1 and/or STAT3. CONCLUSION: This finding could pave the way for the development of small molecules designed to block the PD-1/PD-L1 interaction by silencing the PD-L1 and/or STAT3 genes or reducing protein levels. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.
Isoimperatorin-Mediated Anticancer Activity: Role of Mitochondrial Dysfunction in Hepg2 Cells
(University of Ankara, 2023) Ergüç, A.; Arzuk, E.; Albayrak, G.; Karakus, F.; Okur, H.; Baykan, S.
Objective: The first goal of the present study is to investigate the role of mitochondria due to the Crabtree effect in HepG2 cells exposed to ISO in either glucose-or galactose-conditioned media. The second aim is to predict the interactions between electron transport chain (ETC) complexes and ISO, which might be the possible reason for mitochondrial dysfunction. Material and Method: Cell viability and membrane damage for HepG2 cells exposed to ISO (12.5, 25, 50, 100, and 250 uM) were assessed by MTT and LDH leakage assays in either glucose-or galactose-conditioned media. The affinity of ISO to ETC complexes was also determined by a molecular docking study. Result and Discussion: MTT assay showed that 250 uM ISO leads to cytotoxic activity in glucose-conditioned media, while 25 uM and higher concentrations of ISO decrease cell viability in galactose-conditioned media. A membrane damage assay conducted in a glucose-conditioned media assay revealed that 250 uM ISO disrupts the cell membrane. 100 and 250 uM ISO increased membrane damage in galactose-conditioned media. According to docking simulations, binding affinities of ISO to ETC complexes are in descending order: Complex IV Complex I Complex III Complex II. Inhibition of complex IV by ISO inhibits the transfer of electrons from cytochrome c to oxygen, and the proton gradient collapses. The present study proposed that ISO leads to mitochondrial dysfunction via inhibition of the ETC. © 2023 University of Ankara. All rights reserved.
Lhrh Fusion Protein Immunization Alters Testicular Development, Ultrasonographic and Histological Appearance of Ram Testis
(Wiley-blackwell Publishing, inc, 2009) Ulker, H.; Yilmaz, A.; Karakus, F.; Yoruk, M.; Budag, C.; deAvila, D. M.; Reeves, J. J.
This study was designed to evaluate the effectiveness of a luteinizing hormone releasing hormone (LHRH) fusion protein immunization on reproductive traits in ram lambs including the changes in histology and ultrasonographic appearance of testis. Thirty native ram lambs at 19 weeks of age were divided into control (C, n = 10), immunization (I, n = 10) and castration (E, n = 10) groups. Animals in immunization group were immunized against LHRH using ovalbumin-LHRH-7 (OL) protein generated by recombinant DNA technology as a primary and a booster injection at 19 and 23 weeks of age respectively. Animals were bled via jugular venepuncture at 2-week intervals to determine LHRH antibody and testosterone concentrations. Bi-weekly ultrasonographic examination of the testes was performed to determine the changes in ultrasonographic appearance as the age increased. Biopsied testicular tissues taken at 19, 29 and 41 weeks age were also evaluated. At 41 weeks of age, animals were slaughtered. Semen and epididymis were evaluated for the presence of sperm cells. Testicular development and sperm production were suppressed in the immunized animals. Semineferous tubule diameters decreased, basal membrane of the tubule was thickened and hyalinized in immunized ram lambs. While testes of control animals gained their normal ultrasonographic appearance as the age increased, immunized animals had uniform hypoechogenic testicular structure as observed at 19 weeks of age until slaughter. Simultaneous histological and ultrasonographic evaluations indicated that the changes in testicular histology could partly be monitored via ultrasonographic imaging. Nevertheless, it is difficult to claim that ultrasonographic image reflects the exact changes in such instances. In conclusion, these results indicate that recombinant OL fusion protein is effective in immunocastration in ram lambs and has a potential to be used as an alternative to physical castration. Further research studies should be conducted to help assess reproductive status of testes from ultrasound images.
Performance of Electronic and Visual Ear Tags in Lambs Under Extensive Conditions in Turkey
(Archiv Fur Tierzucht, 2015) Karakus, F.; Demir, A. O.; Akkol, S.; Duzgun, A.; Karakus, M.
The objective of this study was to evaluate the effectiveness of electronic and visual ear tags in animal traceability, and to investigate the effect of placement site on ear-tag retention in Akkaraman lambs under rural conditions. A total of 380 lambs were identified with electronic and visual ear tags. Electronic and visual ear tags displayed 98.9 and 98.7% readability at the end of 7 months, and 98.0 and 98.0% readability at the end of the first year after tagging, respectively. Regarding the placement site, it was observed that there was more loss in ear tags placed on the mid-point part of the ear than the first-quarter part from the head side, but the difference was not statistically significant (P > 0 : 05). Breakages and electronic failures were not recorded during this study. In conclusion, electronic and visual ear tags demonstrated similar on-farm efficiency for the identification of Akkaraman lambs and fulfilled the minimum efficiency of 98% required by the International Committee for Animal Recording (ICAR) for an official animal identification device at the end of the first year after tagging. Based on the findings of the study, placement of the ear tag in a cranial position and near the base of the ear would be advised.
Phenotypic Correlations Among Fleece Traits in Norduz and Karakas Sheep
(2011) Kor, A.; Karakus, F.; Tuncer, S.; Yilmaz, A.; Bingol, M.; Cengiz, F.
In this research, it was aimed to determine the phenotypic correlations among some physical traits of Norduz and Karakas sheep. Animal material was consisted from 2-6 years of age of breeding flocks of 50 Norduz and 50 Karakas ewes. Traits measured were greasy fleece weight, fiber diameter, clean fleece percentage, staple length, single fiber actual length, single fiber natural length, breaking strength, elasticity and the number of crimp in 2.54 cm. There was a positive correlation between clean fleece percentage and fiber diameter, it was insignificant for both genotypes. The estimated phenotypic correlations between staple length and greasy fleece weight was 0.403 (p<0.01) and 0.445 (p<0.01) in Norduz and Karakas sheep, respectively. It was understood that traits like fiber diameter, length, fleece weight and the number of crimp should be evaluated together in breeding studies on fleece yield in Norduz and Karakas sheep. © Medwell Journals, 2011.
The Role of Dgat1-Alui and Cast-Mspi Polymorphisms in Early Growth Traits of Morkaraman Lambs
(John Wiley and Sons Inc, 2025) Daldaban, F.; Karakus, F.; Arslan, K.; Cinar, M.U.; Akyuz, B.
Farm animals’ birth weight and postnatal live weight gain (LWG) are essential for offspring survival and meat yield. This study investigated the relationship between DGAT1-AluI and CAST-MspI polymorphisms, DGAT1-AluI and CAST-MspI genotypic interaction and LWG in Morkaraman lambs. A total of 514 Morkaraman lambs were genotyped for DGAT1-AluI and CAST-MspI polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) methods. The TT genotype in the DGAT1-AluI polymorphism consistently exhibited higher birth weight and weights at 30th, 60th and 90th days compared to the other genotypes. At the MM genotype, CAST-MspI showed an association between the 30th and 60th and weaning weights. In this study, we found that the M allele for the CAST-MspI polymorphism positively influenced growth performance in sheep. However, the TT genotype in the DGAT1-AluI was associated with even better growth performance. On the other hand, we determined for the first time that the TTMN genotype interaction in the DGAT1 × CAST genes serves as a robust genetic marker for weight gain at birth and on the 30th, 60th and 90th days. In conclusion, it is suggested that the DGAT1 × CAST gene TTMN genotype interaction, identified for the first time in this study, may serve as a novel and effective marker for body weight gain in the Morkaraman sheep breed. © 2025 The Author(s). Veterinary Medicine and Science published by John Wiley & Sons Ltd.