Department of Biology, Article

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Recent Submissions

Million-year-old DNA sheds light on the genomic history of mammoths
van der Valk, Tom; et. al. (Springer Science and Business Media LLC, 2021-2-17)
Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into th...
Arid4b alters cell cycle and cell death dynamics during mouse embryonic stem cell differentiation.
Güven, Gözde; Terzi Çizmecioğlu, Nihal (2021-02-09)
Cell division and death play an important role in embryonic development. Cell specialization is accompanied with slow proliferation and quiescence. Cell death is important for morphogenesis. Gene expression changes during ...
Nutrient Loading, Temperature and Heat Wave Effects on Nutrients, Oxygen and Metabolism in Shallow Lake Mesocosms Pre-Adapted for 11 Years
Jeppesen, Erik; Audet, Joachim; Davidson, Thomas A.; Neif, Erika M.; Cao, Yu; Filiz, Nur; Lauridsen, Torben L.; Larsen, Soren E.; Beklioğlu, Meryem; Sh, Tserenpil; Sondergaard, Martin (2021-01-01)
Global changes (e.g., warming and population growth) affect nutrient loadings and temperatures, but global warming also results in more frequent extreme events, such as heat waves. Using data from the world's longest-runni...
Stepwise Reversal of Immune Dysregulation Due to STAT1 Gain-of-Function Mutation Following Ruxolitinib Bridge Therapy and Transplantation
Kayaoğlu, Başak; Kasap, Nurhan; Yilmaz, Naz Surucu; Charbonnier, Louis Marie; Geckin, Busranur; Akcay, Arzu; Eltan, Sevgi Bilgic; Ozturk, Gulyuz; ÖZEN, AHMET OĞUZHAN; Karakoc-Aydiner, Elif; Chatila, Talal A.; Gürsel, Mayda; BARIŞ, SAFA (2021-01-01)
Purpose Patients with heterozygous gain-of-function (GOF) mutations in STAT1 frequently exhibit chronic mucocutaneous candidiasis (CMC), immunodeficiency and autoimmune manifestations. Several treatment options including t...
Human population dynamics and Yersinia pestis in ancient northeast Asia
Kilinc, Gulsah Merve; et. al. (2021-01-01)
We present genome-wide data from 40 individuals dating to c.16,900 to 550 years ago in northeast Asia. We describe hitherto unknown gene flow and admixture events in the region, revealing a complex population history. Whil...
Vitamin E Derivative with Modified Side Chain Induced Apoptosis by Modulating the Cellular Lipids and Membrane Dynamics in MCF7 Cells
Gok, Seher; Kuzmenko, Oleksandr; Babinskyi, Andrii; Severcan, Feride (Springer Science and Business Media LLC, 2021-01-01)
The vitamin E derivative with side chain modification (TC6OAc) has been shown to possess anticancer activity in our earlier in vivo studies. It was hypothesized that, as Vitamin E (VE) and VE derivative are fat soluble lip...
The host musselSinanodonta woodianaalleviates negative effects of a small omnivorous fish (Acheilognathus macropterus) on water quality: A mesocosm experiment
Yu, Jinlei; Xia, Manli; He, Hu; Jeppesen, Erik; Guan, Baohua; Ren, Ze; Elser, James J.; Liu, Zhengwen (University of Chicago Press, 2020-12-01)
Omnivorous fishes are prevalent in warm waters and may have strong impacts on water quality by excreting nutrients and reducing periphyton biomass. However, most studies have focused on large-sized species and overlooked t...
Impact of Nutrients, Temperatures, and a Heat Wave on Zooplankton Community Structure: An Experimental Approach
Iskin, Ugur; Filiz, Nur; Cao, Yu; Neif, Erika M.; Oglu, Burak; Lauridsen, Torben L.; Davidson, Thomas A.; Sondergaard, Martin; Tavsanoglu, Ulku Nihan; Beklioğlu, Meryem; Jeppesen, Erik (MDPI AG, 2020-12-01)
Shallow lakes are globally the most numerous water bodies and are sensitive to external perturbations, including eutrophication and climate change, which threaten their functioning. Extreme events, such as heat waves (HWs)...
Phytoplankton Community Response to Nutrients, Temperatures, and a Heat Wave in Shallow Lakes: An Experimental Approach
Filiz, Nur; Iskin, Ugur; Beklioğlu, Meryem; Oglu, Burak; Cao, Yu; Davidson, Thomas A.; Sondergaard, Martin; Lauridsen, Torben L.; Jeppesen, Erik (MDPI AG, 2020-12-01)
Phytoplankton usually responds directly and fast to environmental fluctuations, making them useful indicators of lake ecosystem changes caused by various stressors. Here, we examined the phytoplankton community composition...
Dual-adjuvant effect of pH-sensitive liposomes loaded with STING and TLR9 agonists regress tumor development by enhancing Th1 immune response
Kocabas, Banu Bayyurt; Almacioglu, Kubra; Bulut, Esin Alpdundar; Gucluler, Gozde; Tincer, Gizem; Bayik, Defne; Gürsel, Mayda; GÜRSEL, İHSAN (Elsevier BV, 2020-12-01)
Nucleic acid-based pattern recognition receptor agonists are effective adjuvants and immunotherapeutic agents. Rather than single applications, ligand combinations could synergistically potentiate immune responses by eleva...
Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub
Culina, Antica; et. al. (Wiley, 2020-12-01)
The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an excep...
A highly substituted and fluorescent aromatic-fused imidazole derivative that shows enhanced antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA)
Bulut, Onur; Öktem, Hüseyin Avni; Yilmaz, M. Deniz (Elsevier BV, 2020-11-01)
A novel highly substituted and fluorescent aromatic-fused imidazole derivative has been synthesized by rational design. This novel fluorescent material acts as an alternative antibacterial agent against Gram positive bacte...
Inorganic Cadmium Detection Using a Fluorescent Whole-Cell Bacterial Bioreporter
Elcin, Evrim; Öktem, Hüseyin Avni (Informa UK Limited, 2020-11-01)
Cadmium pollution has become a serious environmental issue due to its toxicity and frequent entrance into environment components such as soil, water, and air via many anthropogenic sources. Over the last two decades, whole...
Quantifying the effects of climate change on hydrological regime and stream biota in a groundwater-dominated catchment: A modelling approach combining SWAT-MODFLOW with flow-biota empirical models
Liu, Wei; Bailey, Ryan T.; Andersen, Hans Estrup; Jeppesen, Erik; Nielsen, Anders; Peng, Kai; Molina-Navarro, Eugenio; Park, Seonggyu; Thodsen, Hans; Trolle, Dennis (Elsevier BV, 2020-11-01)
Climate change may affect stream ecosystems through flow regime alterations, which can be particularly complex in streams with a significant groundwater contribution. To quantify the impacts of climate change on hydrologic...
Biofilms attached to Myriophyllum spicatum play a dominant role in nitrogen removal in constructed wetland mesocosms with submersed macrophytes: Evidence from N-15 tracking, nitrogen budgets and metagenomics analyses
Mu, Xiaoying; Lv, Xiaoyang; Liu, Wei; Qiu, Changhao; Ma, Yu; Zhang, Songhe; Jeppesen, Erik (Elsevier BV, 2020-11-01)
The mechanisms behind nitrogen removal by the submersed macrophyte-biofilm complex in wetlands remain to be fully elucidated. This study investigated the role of Myriophyllum spicatum and the biofilm on their leaves in nit...
Human Gut Commensal Membrane Vesicles Modulate Inflammation by Generating M2-like Macrophages and Myeloid-Derived Suppressor Cells
Bulut, Esin Alpdundar; Kocabas, Banu Bayyurt; Yazar, Volkan; Aykut, Gamze; GÜLER, ÜLKÜ; SALİH, BEKİR; Yilmaz, Naz Surucu; Ayanoğlu, İhsan Cihan; Polat, Muammer Merve; AKÇALI, KAMİL CAN; GÜRSEL, İHSAN; Gürsel, Mayda (2020-11-01)
Immunomodulatory commensal bacteria modify host immunity through delivery of regulatory microbial-derived products to host cells. Extracellular membrane vesicles (MVs) secreted from symbiont commensals represent one such t...
Nutlet micromorphology and its taxonomic and phylogenetic significance in Salvia (Lamiaceae)
Celep, Ferhat; KAHRAMAN, AHMET; Guerin, Greg R.; KARABACAK, ERSİN; AKAYDIN, GALİP; Doğan, Musa (Informa UK Limited, 2020-11-01)
Salvia (sage) is a species rich and medicinally important genus. Species-level identification is usually very difficult, particularly in closely related species. Here, we investigated nutlet micromorphological characterist...
Arid4b is critical for mouse embryonic stem cell differentiation towards mesoderm and endoderm, linking epigenetics to pluripotency exit.
Terzi Çizmecioğlu, Nihal; Huang, Jialiang; Keskin, Ezgi G; Wang, Xiaofeng; Esen, Idil; Chen, Fei; Orkin, Stuart H (2020-10-15)
Pollination Ecology, Specialization, and Genetic Isolation in Sympatric Bee-PollinatedSalvia(Lamiaceae)
Celep, Ferhat; Atalay, Zeynep; Dikmen, Fatih; Doğan, Musa; Sytsma, Kenneth J.; Classen-Bockhoff, Regine (University of Chicago Press, 2020-10-01)
Premise of research. Previous pollination ecology studies ofSalviahave shown that there is low specialization for certain subgroups of bees and that pollinator number varies with species and locality. We studied 12Salviasp...
Turning up the heat: warming influences plankton biomass and spring phenology in subtropical waters characterized by extensive fish omnivory
He, Hu; Li, Qisheng; Li, Jing; Han, Yanqing; Cao, Yu; Liu, Wei; Yu, Jinlei; Li, Kuanyi; Liu, Zhengwen; Jeppesen, Erik (2020-10-01)
Understanding how biological communities respond to climate change is a major challenge in ecology. The response of ectotherms to changes in temperature depends not only on their species-specific thermal tolerances but als...