Department of Biology, Article

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Recent Submissions

GATA transcription factor in common bean: A comprehensive genome-wide functional characterization, identification, and abiotic stress response evaluation
Abdulla, Mohamed Farah; Mostafa, Karam; Aydin, Abdullah; Kavas, Musa; Aksoy, Emre (2024-06-01)
The GATA transcription factors (TFs) have been extensively studied for its regulatory role in various biological processes in many plant species. The functional and molecular mechanism of GATA TFs in regulating tolerance t...
Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples
Yaka, Reyhan; Maja Krzewińska, Krzewinska; Lagerholm, Vendela Kempe; Linderholm, Anna; ÖZER, FÜSUN; Somel, Mehmet; Götherström, Anders (2024-05-01)
Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction an...
Genome-wide characterization and expression analysis of GATA transcription factors under combination of light wavelengths and drought stress in potato
Aksoy, Emre; Yavuz, Caner; Yagiz, Ayten Kübra; Unel, Necdet Mehmet; Baloğlu, Mehmet Cengiz (2024-04-01)
GATA is one of the prominent transcription factor families conserved among many organisms in eukaryotes and has different biological roles in many pathways, particularly in light regulation in plants. Although GATA transcr...
Genome-wide association studies identifies genetic loci related to fatty acid and branched-chain amino acid metabolism and histone modifications under varying nitrogen treatments in safflower (Carthamus tinctorius)
Ali, Fawad; Arif, Mian A R; Ali, Arif; Nadeem, Muhammad A.; Aksoy, Emre; Bakhsh, Allah; Khan, Shahid U.; KURT, CEMAL; Tekdal, Dilek; Ilyas, Muhammad K.; Hameed, Amjad; Chung, Yong S.; Baloch, Faheem S. (2024-04-01)
Effective identification and usage of genetic variation are prerequisites for developing nutrient-efficient cultivars. A collection of 94 safflower (Carthamus tinctorius ) genotypes (G) was investigated for important morph...
A partial epithelial-mesenchymal transition signature for highly aggressive colorectal cancer cells that survive under nutrient restriction
Pastorino, Gil A; Sheraj, Ilır; Huebner, Kerstin; Ferrero, Giulio; Kunze, Philipp; Hartmann, Arndt; Hampel, Chuanpit; Hüsnügil, Hepşen Hazal; Maiuthed, Arnatchai; Gebhart, Florian; Schlattmann, Fynn; Gulec Taskiran, Aliye Ezgi; Oral, Goksu; Palmisano, Ralph; Pardini, Barbara; Naccarati, Alessio; Erlenbach-Wuensch, Katharina; Banerjee, Sreeparna; Schneider-Stock, Regine (2024-03-01)
Partial epithelial-mesenchymal transition (p-EMT) has recently been identified as a hybrid state consisting of cells with both epithelial and mesenchymal characteristics and is associated with the migration, metastasis, an...
Lysosomal alkalinization in nutrient restricted cancer cells activates cytoskeletal rearrangement to enhance partial epithelial to mesenchymal transition
Hüsnügil, Hepşen Hazal; Güleç Taşkıran, Aliye Ezgi; Güderer, İsmail; Nehri, Leman Nur; Oral, Göksu; Menemenli, Nazlı Şevval; Özcan, Özün; Noghreh, Ariana; AKYOL, AYTEKİN; Banerjee, Sreeparna (2024-03-01)
Introduction: Nutrient restriction in cancer cells can activate a number of stress response pathways for cell survival. We aimed to determine mechanistically how nutrient depletion in colorectal cancer (CRC) cells leads to...
SETD3 regulates endoderm differentiation of mouse embryonic stem cells through canonical Wnt signaling pathway.
Alganatay, Ceren; Balbasi, Emre; Tuncbag, Nurcan; Sezginmert, Dersu; Terzi Çizmecioğlu, Nihal (2024-02-29)
With self- renewal and pluripotency features, embryonic stem cells (ESCs) provide an invaluable tool to investigate early cell fate decisions. Pluripotency exit and lin-eage commitment depend on precise regulation of...
Dynamic proximity interaction profiling suggests that YPEL2 is involved in cellular stress surveillance
Turan, Gizem; Olgun, Çağla Ece; Ayten, Hazal; Toker, Pelin; Ashyralyyev, Annageldi; Savaş, Büşra; KARACA EREK, EZGİ; Muyan, Mesut (2024-02-01)
YPEL2 is a member of the evolutionarily conserved YPEL family involved in cellular proliferation, mobility, differentiation, senescence, and death. However, the mechanism by which YPEL2, or YPEL proteins, mediates its effe...
Roles and Regulation of H3K4 Methylation During Mammalian Early Embryogenesis and Embryonic Stem Cell Differentiation.
Terzi Çizmecioğlu, Nihal (2024-01-18)
From generation of germ cells, fertilization, and throughout early mammalian embryonic development, the chromatin undergoes significant alterations to enable precise regulation of gene expression and genome use. Methylatio...
Characterization of dabrafenib-induced drug insensitivity via cellular barcoding and collateral sensitivity to second-line therapeutics
Baygin, Rana Can; Yilmaz, Kubra Celikbas; Acar, Ahmet (2024-01-02)
Current Technologies and Future Perspectives in Immunotherapy towards a Clinical Oncology Approach.
Adhikary, Subhamay; Pathak, Surajit; Palani, Vignesh; Acar, Ahmet; Banerjee, Antara; Al-Dewik, Nader I; Essa, Musthafa Mohamed; Mohammed, Sawsan G A A; Qoronfleh, M Walid (2024-01-01)
Immunotherapy is now established as a potent therapeutic paradigm engendering antitumor immune response against a wide range of malignancies and other diseases by modulating the immune system either through the stimulation...
Editorial: Metal transport in plants, volume II
Clemens, Stephan; Eroğlu, Seçkin; Grillet, Louis; Nozoye, Tomoko (2024-01-01)
Heterogeneity is key to supporting forest-dweller butterflies
Ambarlı, Didem (2024-01-01)
Heterogeneity is key to supporting forest-dweller butterflies. Worldwide, forests are considered biodiversity hotspots. Butterflies are among the surrogate species for forest biodiversity yet in many parts of the world, li...
Modulation of Caco-2 Colon Cancer Cell Viability and CYP2W1 Gene Expression by Hesperidin-treated Lacticaseibacillus rhamnosus GG (LGG) Cell-free Supernatants.
Akkulak, Merve; Evin, Emre; Durukan, Ozlem; Celebioglu, Hasan Ufuk; Adali, Orhan (2023-12-06)
Insect decline in forests depends on species’ traits and may be mitigated by management
Staab, Michael; Gossner, Martin M.; Simons, Nadja K.; Achury, Rafael; Ambarlı, Didem; Bae, Soyeon; Schall, Peter; Weisser, Wolfgang W.; Blüthgen, Nico (2023-12-01)
Insects are declining, but the underlying drivers and differences in responses between species are still largely unclear. Despite the importance of forests, insect trends therein have received little attention. Using 10 ye...
Effects of lithium on locomotor activity and circadian rhythm of honey bees
ERDEM, BABÜR; Arslan, Okan Can; SEVİN, SEDAT; Gözen, Ayşe Gül; Agosto-Rivera, Jose L.; Giray, Tugrul; Alemdar, Hande (2023-12-01)
Lithium has been considered a potential acaricidal agent against the honey bee (Apis mellifera) parasite Varroa. It is known that lithium suppresses elevated activity and regulates circadian rhythms and light response when...
Single hybrid population but multiple parental individuals at the origin of parthenogenetic rock lizards Darevskia sapphirina and D. bendimahiensis Schmidtler, & Eiselt Darevsky (1994) endemic to the area of Lake Van in East Turkey
Erdolu, Meriç; ŞAHİN, MEHMET KÜRŞAT; Somel, Mehmet; Yanchukov, Alexey (2023-12-01)
Among vertebrates, obligate parthenogenesis is only found in Squamata, where it always has a hybrid origin and a few lizard genera contain most of the known hybridogenous parthenogenetic taxa. Parthenogenesis thus seems to...
The time and place of origin of South Caucasian languages: insights into past human societies, ecosystems and human population genetics
Gavashelishvili, Alexander; Chukhua, Merab; Sakhltkhutsishvili, Kakhi; Koptekin, Dilek; Somel, Mehmet (2023-12-01)
This study re-examines the linguistic phylogeny of the South Caucasian linguistic family (aka the Kartvelian linguistic family) and attempts to identify its Urheimat. We apply Bayesian phylogenetics to infer a dated phylog...
Generation and characterization of human induced pluripotent stem cell line METUi002-A from a patient with primary familial brain calcification (PFBC) carrying a heterozygous mutation (c.687dupT (p.Val230CysfsTer28)) in the SLC20A2 gene.
Begentas, Onur Can; Koc, Dilara; Sendur, Nuriye Kayali; Besarat, Peri; Ezgin, Sena; Temel, Musa; Bora, Hatice Ayse Tokcaer; Kiriş, Erkan (2023-10-18)
Designing of rapid assay for the detection of RdRp/Orf1ab specific to SARS-CoV-2
Derin, Dilek Çam; Gültekin, Enes; Taşkın, Irmak İçen; OTLU, BARIŞ; Öktem, Hüseyin Avni (2023-10-01)
SARS-CoV-2 is still threat and mostly used detection method is real time reverse transcriptase polymerase chain reaction (rRT-PCR) for the open reading frame (Orf1ab), RNA-dependent RNA polymerase (RdRp), nucleocapsid (N) ...
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