Organizational Unit: Department of Molecular Biology and Genetics
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Publication Metadata only test(KU yayınevi, 2024-12-30) bir, bir; test, test; Çanak, Tuba Akbaytürk; Department of Molecular Biology and Genetics; College of EngineeringjjlkjlşkkşlkşlşlkşkşlkPublication Metadata only Proteome analysis of the circadian clock protein PERIOD2(Wiley, 2022) Gül, Hüseyin; Selvi, Saba; Yılmaz, Fatma; Özçelik, Gözde; Olfaz-Aslan, Senanur; Yazan, Şeyma; Tiryaki, Büşra; Gül, Şeref; Öztürk, Nuri; N/A; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Yurtseven, Ali; Kavaklı, İbrahim Halil; Master Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; N/A; 40319; 105301Circadian rhythms are a series of endogenous autonomous 24-h oscillations generated by the circadian clock. At the molecular level, the circadian clock is based on a transcription-translation feedback loop, in which BMAL1 and CLOCK transcription factors of the positive arm activate the expression of CRYPTOCHROME (CRY) and PERIOD (PER) genes of the negative arm as well as the circadian clock-regulated genes. There are three PER proteins, of which PER2 shows the strongest oscillation at both stability and cellular localization level. Protein-protein interactions (PPIs) or interactome of the circadian clock proteins have been investigated using classical methods such as two-dimensional gel electrophoresis, immunoprecipitation-coupled mass spectrometry, and yeast-two hybrid assay where the dynamic and weak interactions are difficult to catch. To identify the interactome of PER2 we have adopted proximity-dependent labeling with biotin and mass spectrometry-based identification of labeled proteins (BioID). In addition to known interactions with such as CRY1 and CRY2, we have identified several new PPIs for PER2 and confirmed some of them using co-immunoprecipitation technique. This study characterizes the PER2 protein interactions in depth, and it also implies that using a fast BioID method with miniTurbo or TurboID coupled to other major circadian clock proteins might uncover other interactors in the clock that have yet to be discovered.Publication Metadata only Importance of Ethiopian shade coffee farms for forest bird conservation(Elsevier, 2015) Buechley, Evan R.; Atickem, Anagaw; Gebremichael, Gelaye; Ndungu, James Kuria; Mahamued, Bruktawit Abdu; Beyene, Tifases; Mekonnen, Tariku; Lens, Luc; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 327589Coffee is the most important tropical commodity and is grown in high-priority areas for biological conservation. There is abundant literature on the conservation value of coffee farms internationally, but there has been little research on this topic in Africa. Ethiopia is a diverse and little-studied country with high levels of avian endemism, pressing conservation challenges, and where Coffee arabica originated. We sampled bird communities in shade coffee farms and moist evergreen Afromontane forest in Ethiopia utilizing standard mist netting procedures at seven sites over three years to evaluate bird species richness, diversity and community structure. Although species diversity did not differ between shade coffee and forest, shade coffee farms had over double the species richness of forest sites and all but one of the nine Palearctic migratory species were captured only in shade coffee. There was a greater relative abundance of forest specialists and understory insectivores in forest, demonstrating that little-disturbed forest is critical for sustaining these at-risk groups of birds. Nonetheless, all species recorded in primary forest control sites were also recorded in shade coffee, indicating that Ethiopian shade coffee is perhaps the most "bird-friendly" coffee in the world. This is an important finding for efforts to conserve forest birds in Africa, and for shade coffee farmers that may benefit from avian pest regulation and biodiversity-friendly coffee certifications.Publication Metadata only Avian responses to selective logging shaped by species traits and logging practices(The Royal Society, 2015) Burivalova, Zuzana; Lee, Tien Ming; Giam, Xingli; Wilcove, David S.; Koh, Lian Pin; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 327589Selective logging is one of the most common forms of forest use in the tropics. Although the effects of selective logging on biodiversity have been widely studied, there is little agreement on the relationship between life-history traits and tolerance to logging. In this study, we assessed how species traits and logging practices combine to determine species responses to selective logging, based on over 4000 observations of the responses of nearly 1000 bird species to selective logging across the tropics. Our analysis shows that species traits, such as feeding group and body mass, and logging practices, such as time since logging and logging intensity, interact to influence a species' response to logging. Frugivores and insectivores were most adversely affected by logging and declined further with increasing logging intensity. Nectarivores and granivores responded positively to selective logging for the first two decades, after which their abundances decrease below pre-logging levels. Larger species of omnivores and granivores responded more positively to selective logging than smaller species from either feeding group, whereas this effect of body size was reversed for carnivores, herbivores, frugivores and insectivores. Most importantly, species most negatively impacted by selective logging had not recovered approximately 40 years after logging cessation. We conclude that selective timber harvest has the potential to cause large and long-lasting changes in avian biodiversity. However, our results suggest that the impacts can be mitigated to a certain extent through specific forest management strategies such as Llengthening the rotation cycle and implementing reduced impact logging.Publication Metadata only Running on empty: Does mitochondrial DNA mutation limit replicative lifespan in yeast? Mutations that increase the division rate of cells lacking mitochondrial DNA also extend replicative lifespan in Saccharomyces cerevisiae(Wiley, 2011) Department of Molecular Biology and Genetics; Dunn, Cory David; Other; Department of Molecular Biology and Genetics; College of Sciences; N/AMitochondrial DNA (mtDNA) mutations escalate with increasing age in higher organisms. However, it has so far been difficult to experimentally determine whether mtDNA mutation merely correlates with age or directly limits lifespan. A recent study shows that budding yeast can also lose functional mtDNA late in life. Interestingly, independent studies of replicative lifespan (RLS) and of mtDNA-deficient cells show that the same mutations can increase both RLS and the division rate of yeast lacking the mitochondrial genome. These exciting, parallel findings imply a potential causal relationship between mtDNA mutation and replicative senescence. Furthermore, these results suggest more efficient methods for discovering genes that determine lifespan.Publication Metadata only Cell scientist to watch - Elif Nur Fırat-Karalar(Company Biologists Ltd, 2019) Breuer, Manuel; N/A; Department of Molecular Biology and Genetics; Karalar, Elif Nur Fırat; N/A; Faculty Member; Department of Molecular Biology and Genetics; N/A; College of Sciences; N/A; 206349N/APublication Metadata only SYBR green dye-based probe-free SNP genotyping: Introduction of T-Plex real-time PCR assay(Elsevier, 2013) Etlik, Ozdal; Koksal, Vedat; Ocak, Zeynep; Baris, Saniye Tugba; Department of Molecular Biology and Genetics; Barış, İbrahim; Teaching Faculty; Department of Molecular Biology and Genetics; College of Sciences; 111629Single-nucleotide polymorphism (SNP) genotyping is widely used in genetic association studies to characterize genetic factors underlying inherited traits. Despite many recent advances in high-throughput SNP genotyping, inexpensive and flexible methods with reasonable throughput levels are still needed. Real-time PCR methods for discovering and genotyping SNPs are becoming increasingly important in various fields of biology. In this study, we introduce a new, single-tube strategy that combines the tetra-primer ARMS PCR assay, SYBR Green I-based real-time PCR, and melting-point analysis with primer design strategies to detect the SNP of interest. This assay, T-Plex real-time PCR, is based on the T. discrimination of the amplified allele-specific amplicons in a single tube. The specificity, sensitivity, and robustness of the assay were evaluated for common mutations in the FV, PII, MTHFR, and FGFR3 genes. We believe that T-Plex real-time PCR would be a useful alternative for either individual genotyping requests or large epidemiological studies.Publication Metadata only Transcriptional regulation of the starch synthases isoforms in the leaf and the stem under long and short photoperiod in lentil(Wiley-Blackwell, 2014) Gercek, Y. C.; Oz, G. Cevahir; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Barış, İbrahim; Kavaklı, İbrahim Halil; Teaching Faculty; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; College of Sciences; College of Engineering; 111629; 40319N/APublication Metadata only 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; 327589Agricultural 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.Publication Metadata only 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/AN/A