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HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations Donthu, Ravikiran; et. al. (2024-12-01) Background: Honey bees are the principal commercial pollinators. Along with other arthropods, they are increasingly under threat from anthropogenic factors such as the incursion of invasive honey bee subspecies, pathogens ...
Harnessing plant-mediated RNAi for effective management of Phthorimaea absoluta by targeting AChE1 and SEC23 genes Hashmi, Muneeb Hassan; Tariq, Haneef; Saeed, Faisal; Demirel, Ufuk; Gökçe, Ayhan; Merzendorfer, Hans; Aksoy, Emre; Bakhsh, Allah (2024-12-01) Tomato production on a global scale is under persistent pressure due to the devastating impact of Phthorimaea absoluta Meyrick (Lepidoptera: Gelechiidae), the South American tomato leaf miner. To combat this devastating pe...
Eurasian watermilfoil (Myriophyllum spicatum) alters its root topology but conserves its root branching in response to freshwater cultural eutrophication Huang, Xiaolong; Lu, Jing; He, Hu; Guan, Baohua; Luo, Jing; Yu, Jinlei; Mao, Zhigang; Li, Kuanyi; Jeppesen, Erik (2024-11-01) Cultural eutrophication is the main cause of the decline of submerged plants in freshwater ecosystems. While many studies have focused on the nutrient uptake by the roots of these plants, less attention has been given to t...
Cascading effects of human activities and ENSO on the water quality of Poyang Lake in China Ge, Yili; Wu, Zhouhang; Chen, Yaoqi; Guo, Peiqin; Wu, Aiping; Liu, Huanyao; Yuan, Guixiang; Li, Youzhi; Fu, Hui; Jeppesen, Erik (2024-11-01) The aquatic environment in lake ecosystems is greatly affected by human activities and global climate change, while studies on the cascading effects on water environments using a holistic approach are scarce. We employed g...
Glutamine withdrawal leads to the preferential activation of lipid metabolism in metastatic colorectal cancer Güleç Taşkıran, Aliye Ezgi; Karaoğlu, Diren Arda; EYLEM, CEMİL CAN; Ermiş, Çağdaş; Güderer, İsmail; NEMUTLU, EMİRHAN; DEMİRKOL CANLI, SEÇİL; Banerjee, Sreeparna (2024-10-01) Introduction: Glutamine is a non-essential amino acid that is critical for cell growth. However, the differential metabolism of L-glutamine in metastatic versus primary colorectal cancer (CRC) has not been evaluated adequa...
An explanation for the sister repulsion phenomenon in Patterson's f-statistics Atag, Gozde; Waldman, Shamam; Carmi, Shai; Somel, Mehmet (2024-09-18) Patterson's f-statistics are among the most heavily utilized tools for analyzing genome-wide allele frequency data for demographic inference. Beyond studying admixture, f3- and f4-statistics are also used for clustering po...
SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes Boulton, William; Fidan, Fatma Rabia; Denise, Hubert; De Maio, Nicola; Goldman, Nick (2024-09-01) Motivation: Tracking SARS-CoV-2 variants through genomic sequencing has been an important part of the global response to the pandemic and remains a useful tool for surveillance of the virus. As well as whole-genome sequenc...
Tirbanibulin (KX2-391) analog KX2-361 inhibits botulinum neurotoxin serotype A mediated SNAP-25 cleavage in pre- and post-intoxication models in cells Koc, Dilara; Ibis, Kubra; Besarat, Peri; BANOĞLU, ERDEN; Kiriş, Erkan (2024-09-01) Botulinum neurotoxins (BoNT) inhibit neuroexocytosis, leading to the potentially lethal disease botulism. BoNT serotype A is responsible for most human botulism cases, and there are no approved therapeutics to treat alread...
Post-Transcriptional Regulation of Rab7a in Lysosomal Positioning and Drug Resistance in Nutrient-Limited Cancer Cells Güleç Taşkıran, Aliye Ezgi; Hüsnügil, Hepşen Hazal; Soltani, Zahra E.; Oral, Göksu; Menemenli, Nazlı S.; Hampel, Chuanpit; Huebner, Kerstin; Erlenbach-Wuensch, Katharina; Sheraj, Ilır; Schneider-Stock, Regine; Akyol, Aytekin; Liv, Nalan; Banerjee, Sreeparna (2024-09-01) Limited nutrient availability in the tumor microenvironment can cause the rewiring of signaling and metabolic networks to confer cancer cells with survival advantages. We show here that the limitation of glucose, glutamine...
Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise Çokoğlu, Sevim Seda; Koptekin, Dilek; Fidan, Fatma Rabia; Somel, Mehmet (2024-07-01) The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epige...
The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus) Özkan, Mustafa; et. al. (2024-07-01) We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6–6.4×. Mitochondrial DNA haplotypes of the Anatolian individuals clustered w...
Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region Larsson, Martin N. A; Morell Miranda, Pedro; Pan, Li; Başak Vural, Klvllclm; Kaptan, Damla; Rodrigues Soares, André Elias; Kivikero, Hanna; Kantanen, Juha; Somel, Mehmet; ÖZER, FÜSUN; Johansson, Anna M; Storå, Jan; Günther, Torsten (2024-06-01) Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centu...
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...
Barley preferentially activates strategy-II iron uptake mechanism under iron deficiency Aksoy, Emre (2024-06-01) Plants utilize two main strategies for iron (Fe) uptake from the rhizosphere. Strategy-I is based on the reduction of ferric (Fe3+) to ferrous (Fe2+) iron by ferric chelate reductase (FCR) and is mainly observed in dicots....
Hyperlipidemia does not suppress mitophagy in the hippocampus. Science Communications World Wide. Mengi, Naz; Seker, Busranur; Kızıldag, Fulya; Onat, Umut Inci; Yanık, Tülin; Adams, Michelle (2024-06-01) Hyperlipidemia is a risk factor for developing atherosclerosis and neurodegenerative disorders, however, the underlying molecular mechanisms are not well understood. Protein Kinase R-like Endoplasmic Reticulum Kinase...
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...
Optimizing cancer therapy: a review of the multifaceted effects of metronomic chemotherapy Basar, Oyku Yagmur; Mohammed, Sawsan; Qoronfleh, M. Walid; Acar, Ahmet (2024-05-01)
Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages Atag, Gözde; et. al. (2024-05-01) Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered...
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...
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...

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