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U-Pb Calcite Geochronology, Epr, Geochemistry, And C-O-Sr Isotopes Of Ancient Marbles In The İznik Region (Bursa-Türkiye), Namik Aysal, Özge Karslioğlu, Emre Erdem, Marcel Guillong, Si̇nan Öngen, İbrahi̇m Tonguç Uysal, Ersi̇n Kaygisiz, İpek Deni̇z Yildirim

Turkish Journal of Earth Sciences

The İznik city (ancient Nicaea), located east of Lake İznik (known as -“Bithynia” in ancient times), has been an important political and cultural centre of Asia Minor since the Hellenistic period. Marbles produced in the quarries in the vicinity (Ömerli and İnikli villages, Deliktaş-Sarıtaş hills) were used both in the construction of the walls and in many ancient works in the city. Approximately eighteen ancient marble quarries producing grey and white marbles were investigated in the region. Petrography, EPR, XRD, C-O-Sr isotope and whole rock geochemistry analyses were performed for characterization of the samples collected from the quarries for the …

Tectonic Setting Analysis Of The Early Tortonian Lacustrine Basins In Nw Iran Based On Sedimentological, Paleontological, And Structural Studies, Enayat Haghfarshi, Seyyed Reza Moussavi̇ Harami̇, Mohammad Faridi, Peyman Rezaee

Turkish Journal of Earth Sciences

The Lignite Beds of Tabriz are among the Neogene formations in the northwest region of Iran that were formed as individual basins in the margin of the Tabriz fault and the suburbs of Tabriz City during the Late Miocene. These beds have many similarities in terms of facies and lithology. In this study, two stratigraphic sections of the main Lignite Beds unit, with a total thickness of 203 m, were measured and sampled. Fine- and medium-grained siliciclastics, limestones, lignite, tuff, and calcrete sedimentary facies were identified. The new fossils identified in this study include gastropods (Borysthenia naticina, Hydrobia sp., Lymnaea …

Editorial Note To The Article “Tectonic Geomorphology Of The South-Eastern Section Of The Burdur-Fethiye Shear Zone, Western Taurides: Morphotectonic Framework Of The Eşen Basin” [Turkish Journal Of Earth Sciences 33 (5) 2024 503-529 ], Orhan Tatar

Turkish Journal of Earth Sciences

As part of the journal’s commitment to open scientific dialogue, we are publishing a Letter to the Editor regarding the article “Tectonic geomorphology of the south-eastern section of the Burdur-Fethiye Shear Zone, Western Taurides: morphotectonic framework of the Eşen Basin” along with a reply from the authors, who have provided a clarification in response to the concerns raised. We consider such exchanges to be a normal and healthy part of the scientific process, and we are presenting both perspectives to allow readers to form their own conclusions.The views expressed in the letter and the reply are those of the respective …

A Model Study On Enhancing The Horizontal Gradient Of Potential Fields With The Vertical Derivative, Luan Thanh Pham, Saulo P. Oliveira, Erdi̇nç Öksüm, Jeferson De Souza

Turkish Journal of Earth Sciences

The total horizontal gradient (THG) and its derivatives are commonly used in interpreting potential fields. Because THG is a nonharmonic function, its vertical derivative (VD) can be consistently computed using, e.g., a finite-difference approximation. The calculation of VD in the wavenumber domain is physically meaningful for harmonic functions, but it provides a pseudovertical derivative (PVD) when applied to nonharmonic fields that can be used in some edge detectors, such as THG. Through experiments with synthetic and field datasets, we evaluated the performance of the PVD of THG in the tilt angle of THG (TAHG) and fast sigmoid-based edge detector (FSED). …

On Reference Accuracy: Clarification Of The Original Data, İrem Eli̇tez, Cenk Yaltirak

Turkish Journal of Earth Sciences

Although it is claimed that the same data was correctly attributed to Alçiçek (2007) in Elitez and Yaltırak (2023), no age data from Alçiçek (2007) were actually used in that study. In fact, the stratigraphic interpretation proposed by Alçiçek (2007) exhibits notable discrepancies with the conclusions presented by Elitez and Yaltırak (2023). Alçiçek (2007) defines the geological units overlying the basement as the Eşen Formation (comprising the Çetilidüz, Çaykenarı, and Kocaçay members) and Quaternary units. Based on the fossil Palaeotragus rouenii, the author suggests that the Neogene succession begins with Late Miocene alluvial-fan conglomerates, sandstones, and mudstones, whereas lacustrine sedimentation …

Citing The Citer: A Way To Claim Original Data, Mehmet Ci̇hat Alçi̇çek

Turkish Journal of Earth Sciences

In Elitez and Yaltırak (2024, p. 3), the “Upper Miocene” age data for the Eşen Basin fill is cited from Elitez and Yaltırak (2023). However, in that work, the same data was correctly attributed to Alçiçek (2007), which is the original source. Citing a secondary source instead of the original one is avoided in scientific writing. This letter aims to correct this citation practice.

Effects Of Dietary Supplementation With Codium Fragile And Fennel Essential Oil On Growth, Enzyme Activity, And Hepatopancreas Histology In Juvenile Narrow-Clawed Crayfish (Pontastacus Leptodactylus Eschscholtz, 1823), Yavuz Mazlum, Meti̇n Yazici, Şehri̇ban Çek, Mehmet Naz, Musa Türkmen, Oğuz Yaşar Uzunmehmetoğlu, Kemal Dede

Turkish Journal of Zoology

This study investigated the impact of different levels of Codium fragile macroalgae (CF) dietary supplementation combined with a fixed concentration of 0.05% fennel (Foeniculum vulgare Mill. var. dulce Mill.) essential oil (FO) on the growth performance, enzyme activity, and hepatopancreas histological changes of juvenile narrow-clawed crayfish Pontastacus leptodactylus (initial average weight = 0.25 ± 0.04 g). A 90-day feeding trial was conducted using four experimental groups: CF + FO (control), 1% CF + FO, 2% CF + FO, and 4% CF + FO. The essential oil yield obtained from the fennel seeds was 2.4%. Anethole was the most abundant component …

Monitoring And Control Of Red Palm Weevil Infestation Using Iot Technology, Harun Çi̇men, İbrahi̇m Çakmak, Mustapha Touray, Selçuk Hazir

Turkish Journal of Zoology

Palms are slow-growing arboreal monocots predominantly distributed across warm regions and are frequently incorporated into parks, gardens, and roadsides. The red palm weevil, Rhynchophorus ferrugineus, is a highly destructive invasive insect that threatens palms. This field study investigated the effectiveness of a seismic sensor system to detect R. ferrugineus larvae on palm trees in the İzmir Metropolitan Municipality Culture Park. This park is home to a diverse collection of palm species, including Washingtonia sp. and Phoenix dactylifera. Seismic sensors were attached to the trunks of palm trees to detect the vibrations caused by feeding R. ferrugineus larvae and calibrated to …

The First Documented Case Of Melanism In Sciurus Anomalus, Recorded In Türkiye, Burak Akdağ, Balkan Mega

Turkish Journal of Zoology

This study reports the first documented case of melanism in the Caucasian squirrel (Sciurus anomalus) from Türkiye. While melanism has been documented in 12 other species within the Sciurus genus, it has not previously been recorded in S. anomalus. The observation was made during a herpetological field survey in Erzincan Province, Türkiye, where a melanistic specimen was photographed in a mixed habitat comprising natural vegetation and cultivated land. In mammals, melanism is widely regarded as an adaptive trait, potentially conferring advantages such as improved thermoregulation in colder climates and enhanced crypsis in shaded forest environments. This novel observation not only …

Cover And Contents

Turkish Journal of Zoology

No abstract provided.

Comparative Mitogenomics Of Clitellata Reveals Mitogenome Organization Can Affect The Mode Of Phylogeny, Deni̇z Mercan, Austin Horenkamp, Merve Nur Aydemi̇r, Habeş Bi̇lal Aydemi̇r, Kurt Neubig, Nai̇me Arslan, Frank E. Anderson

Turkish Journal of Zoology

Clitellata is a major clade of Annelida that includes almost all freshwater and terrestrial annelids as well as many marine species. Aquatic oligochaetes include the union of the two multispecies families: Naididae and Tubificidae. There has been much debate regarding the phylogeny and classification of the cosmopolitan and diverse Naididae. In this study, the total mitogenome sequences of Potamothrix hammoniensis (Naididae: Tubificinae), Stylaria fossularis, Stylaria lacustris, Chaetogaster diaphanus, Chaetogaster diaphanus sp. B, and Slavina appendiculata (Naididae: Naidinae) were sequenced and characterized and can be accessed from NCBI under accession numbers OQ654101, PP909790, PP909791, PP909792, PP909793, and PP893275, respectively. For comparative …

Reproductive Dynamics Of Diplostraca In The Black Sea: Insights From Hamsilos Bay, Sinop, Türkiye, Funda Üstün

Turkish Journal of Zoology

In the coastal marine ecosystem of the Black Sea, Diplostraca is the second most dominant mesozooplankton after Copepoda. Its parthenogenetic reproductive strategy enables significant population growth from spring (March) to fall (December), contributing substantially to mesozooplankton abundance. This study investigated the fecundity, embryonic development stages, and population structure of four of Diplostraca species in Hamsilos Bay: Evadne spinifera, Pleopis polyphemoides, Penilia avirostris, and Pseudevadne tergestina. Samples were taken every month from three stations between July 2015 and June 2016. Population analysis showed that parthenogenetic females were dominant, reaching up to 100% of the population. Gamogenetic females, females without embryos, and …

Winter Breeding Of The Long-Eared Owl (Asio Otus) In Türkiye, Alaz Uslu, Gencer Yaprak, Sali̇h Tora Benzeyen, Alper Tüydeş, İbrahi̇m Kaan Özgenci̇l

Turkish Journal of Zoology

The long-eared owl (Asio otus) is a widespread nocturnal raptor found across the Holarctic, inhabiting a variety of wooded habitats with adjacent open areas. While the species is not globally threatened, its population is declining, which is primarily attributed to threats such as habitat degradation, pesticide use, hunting, and disturbance. Although winter breeding has been documented in several European countries, no such records have been reported from Türkiye up to date. In this study, we compiled 11 records of winter breeding long-eared owls from northwest and central Türkiye, based on our field observations and data from rehabilitation centers. The estimated …

Insights Into Therapeutic Discovery Through The Kelch Domain Structure Of Keap1 At Ambient Temperature, Merve Yilmaz, Belgi̇n Sever, Yi̇ği̇t Kutlu, Mehmet Gül, Ceren Okuducu, Serra Tavli, Masami Otsuka, Mikako Fujita, Turkan Hali̇loğlu, Hali̇li̇brahi̇m Çi̇ftçi̇, Hasan Demi̇rci̇

Turkish Journal of Biology

Background/aim: The Kelch-like-ECH associated protein 1 (Keap1) is an integral component of the E3-ubiquitin ligase complex, which binds to Nuclear factor erythroid 2-related factor 2 (Nrf2) and facilitates its degradation by the 26S proteasome. The Kelch domain of Keap1, composed of six repeated structural motifs, plays a key role in this interaction. This study aims to investigate the dimeric structure of the Keap1 Kelch domain at ambient temperature and to examine its implications for conformational dynamics, particularly in relation to the DMF and Nrf2 binding sites.Materials and methods: The dimeric crystal structure of the Keap1 Kelch domain was determined at …

Antiinflammatory Effects Of Cucurbitacins And Sorafenib In Hepg2 Cells By Modulating The Iκb/Nf-Κb/Cox-2 Pathway Through Akt Signaling, Muhammed Mehdi̇ Üremi̇ş, Yusuf Türköz, Nuray Üremi̇ş

Turkish Journal of Biology

Aim: Cucurbitacins possess antitumor, antiproliferative, and antiinflammatory properties. This study aims to examine the antiinflammatory effects of CuD, CuI, and CuE on NF-κB, iNOS, COX-2, and Akt and compare their cytotoxic and antiinflammatory effects on HepG2 cells with sorafenib, the primary chemotherapeutic agent used in HCC treatment. Methods: Cytotoxic effects of cucurbitacins and sorafenib on HepG2 cells were evaluated using MTT and LDH assays, along with Annexin V, MMP, and comet assays. Levels of proteins related to the Akt/NF-κB pathway and COX-2, iNOS, and NO were also measured. Results: Our study showed that CuD, CuI, CuE, and sorafenib have antiproliferative …

Cover And Contents

Turkish Journal of Biology

No abstract provided.

Fda-Approved Drugs As Potential Covalent Inhibitors Of Key Sars-Cov-2 Proteins: An In Silico Approach, Murat Seri̇lmez, Anwar Abuelrub, İsmai̇l Erol, Serdar Durdaği

Turkish Journal of Biology

Background/aim: The COVID-19 pandemic caused by SARS-CoV-2 necessitated rapid development of effective therapeutics, prompting this study to identify potential inhibitors targeting key viral and host proteins: RNA-dependent RNA polymerase (RdRp), main protease (Mpro), transmembrane serine protease 2 (TMPRSS2), and angiotensin-converting enzyme 2 (ACE2). Methods: We used covalent docking and molecular dynamics (MD) simulations to screen FDA-approved compounds against these targets using diverse covalent reaction mechanisms. Top-ranking compounds underwent further evaluation through MD simulations to assess binding stability and conformational dynamics. Results: Several promising drug repurposing candidates were identified: bremelanotide, lanreotide, histrelin, and leuprolide as potential RdRp inhibitors; azlocillin, cefiderocol, and …

Screening Of Ccdc43 Molecular Partners By Bioid2-Based Proximity Labeling, Merve Tuzlakoğlu Öztürk

Turkish Journal of Biology

Background/aim: CCDC43 (coiled-coil domain containing protein 43) is a eukaryotic protein that contains alpha-helical domains in its structure, consistent with the family to which it belongs. It is predominantly located in the cytosol of the cell. CCDC43 protein has been shown to play a role in cell proliferation, invasion, metastasis, and epithelial–mesenchymal transition in gastric and colorectal cancer types. The fundamental function and cellular interaction network of this protein, which is known to have varying expression levels in various cancer types, has not yet been fully elucidated. Here, we conducted a proximity-dependent biotin identification (BioID2) screening approach for CCDC43 to …

Butyrylcholinesterase (Bche) Downregulation In Taxane Resistance: Implications For Prostate Cancer, Buse Cevatemre, Arda Işiklar, İpek Bulut, Ezgi̇ Karyemez, Hamzah Syed, Ceyda Açilan

Turkish Journal of Biology

Background/aim: Despite advancements in chemotherapeutic strategies, drug resistance remains a major barrier to effective cancer treatment. While primary prostate cancers (PC) can be treated with surgery and radiotherapy, treatment options for recurrent PC are limited. Upon progression to the castration-resistant (CR) phase, therapies rely on taxanes (chemotherapeutic drugs) like docetaxel (Dtx) and cabazitaxel (Cbz); however, resistance to taxanes is common in CRPC, highlighting the importance of identifying underlying molecular mechanisms or targets in resistant cells.Materials and methods: In transcriptome (RNA sequencing) analyses comparing taxane-resistant PC cells (resistant to both Dtx and Cbz) with parental (nonresistant, sensitive) cells, butyrylcholinesterase (BChE) was …

Proteomic Profiling Of Escherichia Coli Cytoplasmic Proteins Under Sublethal Boric Acid Stress, Beki̇r Çöl, Begüm Hazar Çi̇ftçi̇, Merve Sezer Kürkçü, Esra Di̇bek

Turkish Journal of Biology

Background/aim: Boron is an essential micronutrient for plants and certain bacteria, where it plays critical roles in cellular processes at low concentrations. However, elevated levels of boron-containing compounds, such as boric acid, exhibit antimicrobial toxicity. Although the physiological effects of boric acid on bacteria have been partially characterized, its proteome-wide impacts remain poorly elucidated. This study employs a 2D-PAGE-based proteomic approach to investigate how sublethal boric acid stress alters the cytoplasmic proteome of Escherichia coli BW25113. Materials and methods: E. coli BW25113 cultures were grown to mid-log phase in tryptic soy broth (TSB) and exposed to 70 mM boric acid …

Novel Mrsa-Targeting Phage Metb16: Genomic Features, Structural Insights, And Therapeutic Applications, Berna Erdoğdu, Senanur Dokuz, Görkem Güngör, Wei Lin, Yigang Tong, Tüli̇n Özbek

Turkish Journal of Biology

Background/aim: Recent reports have indicated that multidrug-resistant strains of S. aureus, including methicillin-resistant strains, may pose a significant threat to public health and global economic stability. Materials and methods: In this study, we present the isolation and comprehensive characterization of a novel phage, derived from clinically isolated MRSA strains. Results: MetB16 exhibited an incubation period of approximately 20 min, a lysis period of around 45 min, and a burst size of 127 Plaque Forming Units (PFU)/cell. The phage demonstrated remarkable biological stability across a pH spectrum of 4.0–9.0 and maintained integrity within a temperature range of 37 and –80 °C. …

Discovery And Characterization Of Selective Lipase-Inhibiting Polyheterocyclic Derivatives: A Combined In Silico And In Vitro Study, Madjda Benguechoua, Mebarka Imane Benguechoua, Khedidja Benarous, Houssem Boulebd, Ibtissem Kadi, Ari̇f Mermer, Yakup Şi̇ri̇n, Alaeddine Kaouka, Mohamed Yousfi

Turkish Journal of Biology

Background/aim: Obesity has become a global health crisis with an increasing prevalence, necessitating the search for effective therapies. Schiff base derivatives, known for their broad pharmacological activities, have gained attention as potential antiobesity agents. This study aimed to investigate the lipase inhibitory potential of novel Schiff base derivatives and assess their drug-like properties through in vitro assays and in silico methods. Materials and methods: The lipase inhibitory activity of synthesized Schiff base derivatives was evaluated using in vitro assays, with IC50 values determined for each compound. Additionally, in silico ADMET predictions (absorption, distribution, metabolism, excretion, and toxicity), molecular docking studies, …

The Effects Of Hsa-Mir-26a-5p On Cell Proliferation, Migration, And Pi3k Inhibitor Sensitivity In Metformin-Resistant Triple Negative Breast Cancer Cells, Şahi̇ka Cingir Köker, Senem Noyan, Banu Yalçin, İrem Doğan Turaçli

Turkish Journal of Biology

Background/aim: Metformin is commonly used to manage type 2 diabetes (T2D) and is being investigated for its potential antiproliferative effects in cancer, particularly in patients with both T2D and malignancies. Drug resistance can develop with any therapeutic agent, and metformin is no exception. As we showed in our previous study, metformin-resistant MDA-MB-468 (MET-R) cells exhibited an EMT-like phenotype. Many transcription factors, as well as miRNAs, can contribute to this altered phenotype. Our current study identifies the contribution of hsa-miR-26a-5p expression to the previously observed phenotype. Materials and methods: By utilizing bioinformatic tools, we identified hsa-miR-26a-5p, whose expression was significantly altered …

Expression Of Concern: Characterization Of Tfiie-Regulated Genes By Transcriptomeanalysis, Serdar Baysal

Turkish Journal of Biology

Update: This Expression of Concern has been superseded by a Retraction Notice. The Expression of Concern remains part of the permanent publication record. Please see the Retraction Notice and the original article.

The Editors of Turkish Journal of Biology wish to issue an Expression of Concern regarding the article entitled: “Characterization of TFIIE-regulated genes by transcriptome analysis” by Serdar Baysal published on 20.12.2024. Following the publication of this article, concerns have been raised regarding• Potential violations of academic ethical standards in the published study• Potential intellectual property infringement, including plagiarism• An academic sanction reportedly imposed on the author by …

In Vitro Regeneration Potential Of Pistacia Integerrima And Pistacia Khinjuk Rootstocks: A Modeling Approach For Optimal Medium Formulation, Heydem Eki̇nci̇, Beki̇r Erol Ak

Turkish Journal of Agriculture and Forestry

Micropropagation involves the development of whole plants from small meristematic tissues by culturing them in vitro under aseptic conditions on a nutrient medium. However, identifying a single nutrient medium suitable for propagating Pistacia, a recalcitrant species, remains challenging. While some species exhibit good growth on Murashige and Skoog (MS) medium, Pistacia species generally yield insufficient results. To address this, a five-dimensional experimental design was developed using Design- Expert software (Stat-Ease Inc., Minneapolis, MN, USA). Thirty-three experimental databases were generated by the software using the modified I-optimal criterion. MS medium served as the control treatment. A response surface model (RSM) employing …

Deep Reinforcement Learning-Driven Decision Support System Design For Precision Agriculture: Optimizing Farming And Resource Use, Qingshan Bai

Turkish Journal of Agriculture and Forestry

This study focuses on enhancing the efficiency of agricultural decision support systems by integrating deep reinforcement learning techniques to optimize the path planning of agricultural vehicles. By decomposing the system into dynamics, action, strategy, reward, and discount factor components, a robust framework is established. A value-based reinforcement learning algorithm is introduced, enriched with policy gradient (PG) methodology to enable continuous and adaptive state-to-action decision-making process. A deep neural network (DNN) was used to approximate the state-action value function, resulting in the innovative DNN-PG-Q-learning algorithm. This algorithm leverages an empirical playback pool to enable efficient and intelligent path planning for agricultural …

Accurate Crop Yield Prediction Via Temporal Convolutional Network And Variational Autoencoder, Lei Liu, Xiaoling Song

Turkish Journal of Agriculture and Forestry

With the advancement of technology, smart agriculture assumes a pivotal role in enhancing the efficiency and sustainability of agricultural production. Nevertheless, accurately forecasting crop yields and understanding their determining factors often faces limitations inherent in conventional data processing techniques. To address this challenge, this study proposes a TCN-VAE framework, amalgamating temporal convolutional networks (TCNs) and variational autoencoders (VAEs), to tackle the crop yield prediction task in smart agricultural systems. The framework intricately models four principal categories of features—meteorological conditions, soil conditions, agricultural management, and environmental conditions—via TCN and compensates for missing data using VAE, thereby achieving a comprehensive analysis and …

Comprehensive Characterization Of Purified Naringinase: Effect On Naringin Content, Antioxidant Activity, Phenolic Profile, And Grapefruit Juice Quality, Arzu İmece, Memnune Şengül, Bülent Çeti̇n, Ömer İrfan Küfrevi̇oğlu, Arzu Öztürk Kesebi̇r

Turkish Journal of Agriculture and Forestry

Bitterness arising from naringin is a problem in citrus juices, especially grapefruit juice, in terms of consumer preference. Naringinase enzyme is used to eliminate the bitterness. In this study, naringinase was extracellularly extracted, isolated, and characterized from an Aspergillus niger strain in different media. The extracted enzyme was added to grapefruit juice at different concentrations (0.1%, 0.5%, 1%) (0.078, 0.39 and 0.78 EU) and stored at different temperatures (25, 35, and 45 °C) for 5 h. At the end of the first and fifth h, the amount of naringin, physicochemical properties, phenolic profiles, and antioxidant activities of the grapefruit juice …

Human Settlement Environment And Architectural Ecological Design Based On Artificial Intelligence Technology, Mingxing Xu, Xiongjun Tao

Turkish Journal of Agriculture and Forestry

The main purpose of this paper was to use artificial intelligence (AI) technology to improve the coordination between architectural design and the natural environment, so as to optimize resource utilization and reduce negative environmental impacts and improve the quality of human settlements. To do this, multiple types of data covering the environment, buildings, and user feedback were first collected and preprocessed. Based on these data, the long short-term memory model was used to predict future environmental changes, and the particle swarm optimization algorithm was used for multiobjective optimization of architectural design. The experimental results showed that the AI-driven design scheme …

Circular Motion And Thermodynamic Characteristics Of Particles Around A Quintessential Nonrotating Black Hole, Indrajit Halder, Kamal Lochan Mahanta, Rakesh Ranjan Sahoo

Turkish Journal of Physics

This paper investigates the geodesics of the Schwarzschild black hole modified with the quintessence field and modeled as a barotropic fluid with a constant equation of state derived in Boyer Lindquist coordinates with natural units G = c = 1. Hamilton–Jacobi formalization is applied to investigate the geodesics in both static and nonstatic black hole spacetime. It specifically examines the formation of bound orbits of test particles around the black hole, highlighting that these orbits result from the interplay between the gravitational pull of the black hole and a repulsive force associated with quintessence. The thermodynamic properties of a black …