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    Bud14 function is crucial for spindle pole body size maintenance
    (TUBITAK, 2024) Department of Molecular Biology and Genetics; Girgin, Sevilay Münire; Çaydaşı, Ayşe Koca; Department of Molecular Biology and Genetics; College of Sciences; Graduate School of Sciences and Engineering
    Background/aim: Spindle pole bodies (SPB), the functional equivalent of centrosomes in yeast, duplicate through generation of a new SPB next to the old one. However, SPBs are dynamic structures that can grow and exchange, and mechanisms that regulate SPB size remain largely unknown. This study aims to elucidate the role of Bud14 in SPB size maintenance in Saccharomyces cerevisiae. Materials and methods: We employed quantitative fluorescence microscopy to assess the relative and absolute amounts of SPB structural proteins at SPBs of wildtype cells and in cells lacking BUD14 (bud14∆). Quantifications were performed using asynchronous cell cultures, as well as cultures synchronously progressing through the cell cycle and upon different cell cycle arrests. We also utilized mutants that allow the separation of Bud14 functions. Results: Our results indicate that higher levels of SPB inner, outer, and central plaque proteins are present at the SPBs of bud14∆ cells compared to wildtype cells during anaphase, as well as during nocodazole-induced M-phase arrest. However, during α-factor mediated G1 arrest, inner and outer plaque proteins responded differently to the absence of BUD14. A Bud14 mutant that cannot interact with the Protein Phosphatase 1 (Glc7) phenocopied bud14∆ in terms of SPB-bound levels of the inner plaque protein Spc110, whereas disruption of Bud14-Kel1-Kel2 complex did not alter Spc110 levels at SPBs. In cells synchronously released from α-factor arrest, lack of Bud14-Glc7 caused increase of Spc110 at the SPBs at early stages of the cell cycle. Conclusion: We identified Bud14 as a critical protein for SPB size maintenance. The interaction of Bud14 with Glc7, but not with the Kelch proteins, is indispensable for restricting levels of Spc110 incorporated into the SPBs. © TÜBİTAK.
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    PublicationOpen Access
    Comparative RNA-seq analysis of the drought-sensitive lentil (Lens culinaris) root and leaf under short- and long-term water deficits
    (Springer, 2019) Morgil, Hande; Cevahir, Gül; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; N/A; Kavaklı, İbrahim Halil; Tardu, Mehmet; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; 40319; N/A
    Drought stress is one of the main environmental factors that affects growth and productivity of crop plants, including lentil. To gain insights into the genome-wide transcriptional regulation in lentil root and leaf under short- and long-term drought conditions, we performed RNA-seq on a drought-sensitive lentil cultivar (Lens culinaris Medik. cv. Sultan). After establishing drought conditions, lentil samples were subjected to de novo RNA-seq-based transcriptome analysis. The 207,076 gene transcripts were successfully constructed by de novo assembly from the sequences obtained from root, leaf, and stems. Differentially expressed gene (DEG) analysis on these transcripts indicated that period of drought stress had a greater impact on the transcriptional regulation in lentil root. The numbers of DEGs were 2915 under short-term drought stress while the numbers of DEGs were increased to 18,327 under long-term drought stress condition in the root. Further, Gene Ontology analysis revealed that the following biological processes were differentially regulated in response to long-term drought stress: protein phosphorylation, embryo development seed dormancy, DNA replication, and maintenance of root meristem identity. Additionally, DEGs, which play a role in circadian rhythm and photoreception, were downregulated suggesting that drought stress has a negative effect on the internal oscillators which may have detrimental consequences on plant growth and survival. Collectively, this study provides a detailed comparative transcriptome response of drought-sensitive lentil strain under short- and long-term drought conditions in root and leaf. Our finding suggests that not only the regulation of genes in leaves is important but also genes regulated in roots are important and need to be considered for improving drought tolerance in lentil.
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    Conservation of ecosystem services does not secure the conservation of birds in a Peruvian shade coffee landscape
    (Cambridge Univ Press, 2017) Aerts, Raf; Spranghers, Sarah; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 327589
    Agricultural intensification in shade coffee farms has strong impacts on the structure and diversity of the agroforest, with negative consequences for forest specialist birds, understorey insectivores and their associated ecosystem services. Utilising variable distance transect counts, we sampled the bird community in a multiple-certified yet changing shade coffee landscape in the Peruvian East Andean foothills, to evaluate bird functional diversity and to assess potential impacts of coffee production on avian ecosystem services. To account for incomplete detection, we also calculated expected species richness per functional group, and to evaluate the effect of future species losses, we derived reduced bird communities by subsampling our data using a Monte Carlo procedure. We compared the relative abundances of functional groups based on preferred diets in the observed, expected and reduced bird communities to global functional signatures of tropical bird assemblages of forest, agroforests and agriculture. The birds in the shade coffee landscape were predominantly birds of secondary and disturbed forest habitats, indicating, as expected, strong human impact on the forest structure. Yet, the diet signatures of the observed, expected and simulated bird communities were not significantly different from global diet signatures of forest and agroforest bird communities of mixed tropical landscapes. Our results suggest that avian ecological function can be conserved at bird community level despite intensive human ecosystem use and associated losses of forest specialist and other less resilient bird species. These results underscore that forest management strategies or certification audits focused solely at ecosystem services may be insufficient to support conservation of rare or threatened bird species and that shade coffee systems can in no way replace the role of protected natural forests.
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    PublicationOpen Access
    Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level
    (Springer, 2019) Korkmaz, Tuba; Özturk, Nuri; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Department of Computer Engineering; N/A; Kavaklı, İbrahim Halil; Keskin, Özlem; Cavga, Ayşe Derya; Gürsoy, Attila; Tardu, Mehmet; Faculty Member; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; 40319; 26605; N/A; 8745; N/A
    Previous studies have demonstrated that deletion of cryptochrome (Cry) genes protects p53(-/-) mutant mice from the early onset of cancer and extends their median life-span by about 1.5-fold. Subsequent in vitro studies had revealed that deletion of Crys enhances apoptosis in response to UV damage through activation of p73 and inactivation of GSK3 beta. However, it was not known at the transcriptome-wide level how deletion of Crys delays the onset of cancer in p53(-/-) mutant mice. In this study, the RNA-seq approach was taken to uncover the differentially expressed genes (DEGs) and pathways following UV-induced DNA damage in p53(-/-) and p53(-/-)Cry1(-/-)Cry2(-/-) mouse skin fibroblasts. Gene set enrichment analysis with the DEGs demonstrated enrichment in immune surveillance-associated genes regulated by IFN-gamma and genes involved in TNF alpha signaling via NF-kappa B. Furthermore, protein network analysis enabled identification of DEGs p21, Sirt1, and Jun as key players, along with their interacting partners. It was also observed that the DEGs contained a high ratio of non-coding transcripts. Collectively, the present study suggests new genes in NF-kappa B regulation and IFN-gamma response, as well as non-coding RNAs, may contribute to delaying the onset of cancer in p53(-/-)Cry1(-/-)Cry2(-/-) mice and increasing the life-span of these animals compared to p53(-/-) mice.
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    Deep mutational scanning reveals characteristics important for mitochondrial targeting of a tail-anchored protein.
    (The American Society for Cell Biology, 2017) N/A; N/A; N/A; Department of Molecular Biology and Genetics; Keskin, Abdurrahman; Akdoğan, Emel; Dunn, Cory David; Master Student; Master Student; Other; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A
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    Dynamic recruitment of the retinal degeneration gene product CCDC66 to the centrosome/cilium complex is regulated by satellites and nnicrotubules
    (Amer Soc Cell Biology, 2018) N/A; Department of Molecular Biology and Genetics; N/A; Karalar, Elif Nur Fırat; Çonkar, Deniz; Faculty Member; PhD Student; Department of Molecular Biology and Genetics; College of Sciences; Graduate School of Sciences and Engineering; 206349; N/A
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    EDA2R-NIK signaling in cancer cachexia
    (Lippincott Williams and Wilkins, 2024) Department of Molecular Biology and Genetics; Ağca, Samet; Kır, Serkan; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Sciences
    Purpose of review Cachexia is a debilitating condition causing weight loss and skeletal muscle wasting that negatively influences treatment and survival of cancer patients. The objective of this review is to describe recent discoveries on the role of a novel signaling pathway involving ectodysplasin A2 receptor (EDA2R) and nuclear factor kappa B (NF kappa B)-inducing kinase (NIK) in muscle atrophy.Recent findingsStudies identified tumor-induced upregulation of EDA2R expression in muscle tissues in pre-clinical cachexia models and patients with various cancers. Activation of EDA2R by its ligand promoted atrophy in cultured myotubes and muscle tissue, which depended on NIK activity. The non-canonical NF kappa B pathway via NIK also stimulated muscle atrophy. Mice lacking EDA2R or NIK were protected from muscle loss due to tumors. Tumor-induced cytokine oncostatin M (OSM) upregulated EDA2R expression in muscles whereas OSM receptor-deficient mice were resistant to muscle wasting.SummaryRecent discoveries revealed a mechanism involving EDA2R-NIK signaling and OSM that drives cancer-associated muscle loss, opening up new directions for designing anti-cachexia treatments. The therapeutic potential of targeting this mechanism to prevent muscle loss should be further investigated. Future research should also explore broader implications of the EDA2R-NIK pathway in other muscle wasting diseases and overall muscle health.
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    Elevational changes in the avian community of a mesoamerican cloud forest park
    (Wiley, 2018) Neate-Clegg, Montague H. C.; Jones, Samuel E. I.; Burdekin, Oliver; Jocque, Merlijn; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 327589
    Harboring many range-restricted and specialized species, high elevation tropical cloud forests are diverse habitats represented in many protected areas. Despite this, many such areas receive little practical protection from deforestation and land conversion. Moreover, montane species may be more sensitive to climate change owing to various factors affecting community assembly across elevational gradients. Few studies have used annual monitoring to assess how biological communities in cloud forests may be shifting in response to habitat or climate change or assessed the efficacy of protected areas in buffering these effects. We analyzed avifaunal community trends in a 10-yr dataset of constant-effort bird point-count data in a cloud forest national park in Honduras, Central America. We found that species richness and diversity increased at higher elevations, but decreased at lower elevations. Abundances of most dietary and forest-dependency groups exhibited similar trends, and many key cloud forest species shifted upslope and/or increased in abundance. Taken together, our results suggest that the avian community is moving upslope and species composition is changing. Results for species richness and diversity were similar when only nondegraded transects were considered, suggesting the role of climate change as an important driver. At lower elevations, however, many species may be negatively affected by increased habitat degradation, favoring species with low forest dependency. Continued habitat conversion and climate change could push the cloud forest bird community further upslope, potentially resulting in increased competition, mortality, and even extirpation of some species. Increased protection is unlikely to mitigate the effects of climate change.
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    PublicationOpen Access
    Endangered Basra Reed-warbler (Acrocephalus griseldis) recorded for the first time in Turkey (Aves: Acrocephalidae)
    (TÜBİTAK, 2019) Neate-Clegg, Montague H. C.; Ramirez Roman, Juan; Demir, Berkay; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences
    The Basra Reed-warbler (Acrocephalus griseldis) is an endangered songbird that breeds in the reed beds of southern Mesopotamia. Hydrological projects, war, and drought have greatly reduced the breeding habitat of this species, making its future uncertain. The first Basra Reed-warbler for Turkey was caught in a mist net on 22 May 2018 at the Aras River Ornithological Research Station, between the provinces of Kars and Igdir. This represents one of only a few vagrant records in the eastern Mediterranean, and the northernmost record to date. It is likely that this bird was an overshooting spring migrant, but the existence of other small breeding populations elsewhere in the Middle East could lead to more migrants, or even breeding pairs, occurring in eastern Turkey in the future. Riparian oases such as the Aras River Bird Paradise are vital habitats for millions of migrating birds of hundreds of species and if more individuals of Turkey's first endangered songbird are discovered, it would raise the conservation priority of the region's wetlands even further.
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    Expression analyses of soluble starch synthase and starch branching enzyme isoforms in stem and leaf tissues under different photoperiods in lentil (Lens culinaris Medik.)
    (Springer, 2022) Gerçek, Yusuf Can; Boztaş, Kadir; Aydın, Cihan; Morgil, Hande; Öz, Gül Cevahir; Tulum, Işıl; Department of Molecular Biology and Genetics; Barış, İbrahim; Teaching Faculty; Department of Molecular Biology and Genetics; College of Sciences; 111629
    The metabolism of starch is sensitive to changes in light and plants respond to different light regimes by adjusting their carbon metabolism and regulating enzymes that participate in starch biosynthesis. Although there are several studies showing the influence of the circadian clock mechanism on starch biosynthesis on model plants, there is still limited information on how the circadian regulation of carbon assimilation and utilization works on crop plants and long-day plants. In our previous study, we examined lentil (Lens culinaris Medik.), a long-day crop plant, and determined the influence of circadian control on starch metabolism by investigating the transcriptional regulation of large (LS) and small (SS) subunits of ADP glucose pyrophosphorylase (AGPase). However, the regulation mechanism of the enzymes responsible for the formation of the starch granule remains unclear. In this study, the transcriptional regulation of soluble starch synthase isoforms I and III (SSSI and SSSIII) and starch branching enzyme isoforms I and II (SBEI and SBEII) were examined in sink and source tissues under different photoperiods in lentils by quantitative real time PCR (qPCR). The results showed that the temporal distribution of gene expression was altered when isoforms for both enzymes from the stem and leaf tissues were compared for different photoperiod regimes, exhibiting a rhythmic period of 4-6 h with maximal expression times and levels altered due to the shifting photoperiod. These results were in agreement with our previous observations on lentil AGPase supporting the circadian control of carbohydrate metabolism.