Scholarly Publications - Molecular Biology and Genetics
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Browsing Scholarly Publications - Molecular Biology and Genetics by Type "Book Chapter"
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Item Open Access Development of CpG ODN based vaccine adjuvant formulations(Humana Press, New York, 2016) Gürsel, M.; Gürsel, İhsan; Thomas, S.Item Open Access In situ hybridization as a method to examine gene regulatory activity in vivo(Humana Press Inc., 2023) Datta, Rhea R.; Onal, Pinar; Simoes-Costa, MarcosTranscription factor-enhancer binding events are among the most well-studied protein-DNA interactions, allowing researchers to determine mechanisms of transcriptional activation or repression during development. While large-scale ChIP-sequence datasets, together with computational predictions and chromatin accessibility data, yield information on potential transcription factor binding activities, reporter gene assays provide measurable information on whether these binding activities are functional in particular cell types during development. Here, we present a detailed protocol to examine enhancer activity in Drosophila embryos using cloning, transgenesis, and in situ hybridization.Item Open Access Inflammatory causes of obesity and metabolic diseases(CRC Press, 2014) Erbay, Ebru; Hotamışlıgil, G. S.; Claude, B.; Bray, G. A.Item Open Access Mammalian target of rapamycin (mTOR), aging, neuroscience, and their association with aging-related diseases(Elsevier Inc., 2016) Celebi-Birand, Ergül Dilan; Karoğlu, Elif Tuğçe; Doldur-Ballı, Füsun; Adams, Michelle M.; Maiese, K.Normal aging is accompanied by cognitive impairment with subtle cellular and molecular changes in the brain, whereas, pathological brain aging manifests as severe behavioral impairments with cellular pathology. Understanding the factors that contribute to both states is undoubtedly important for determining appropriate interventions that alter their progression. Mammalian target of rapamycin (mTOR) signaling has been implicated in affecting lifespan and age-related diseases such as cancer. The relationship of mTOR signaling with pathological brain aging has been more extensively studied, whereas the association with normal brain aging is not well understood. In this chapter we present information about normal and pathological brain aging, the relationship with mTOR signaling and use information from other age-related diseases to suggest that mTOR may have a role in promoting the cellular and molecular changes that underlie age-related cognitive changes. Future work should be directed towards understanding the precise role of mTOR signaling in brain aging. © 2016 Elsevier Inc. All rights reserved.Item Open Access Mesenchymal Stem Cells: Possibilities of New Treatment Options(Humana Press Inc., 2012) Tokcaer-Keskin, Z.; Kocak, H.; Gursel, I.; Akcali, K. C.Stem cell research evolved as a new hope and has gained tremendous interest during the last two decades in developing potential strategies for many debilitating diseases. Mesenchymal stem cells (MSCs) are bone marrow-derived multipotent stem cells capable of self-renewal and of differentiating into multiple lineages, such as osteocytes, adipocytes, chondrocytes, myoblasts, cardiomyocytes, and hepatocytes. MSCs are an important source for cellular therapies. They can easily be obtained and expanded in vitro in large numbers without significantly altering their properties. MSCs not only migrate to the injured site in vivo but also have immunomodulatory effects that make their use attractive for allogeneic grafting. MSCs can also be frozen for preservation; and when thawed, they retain their normal physiological function, allowing future ''off-the-shelf'' therapy approaches. Because of these features, MSCs have high therapeutic value in tissue engineering and regenerative medicine. In this chapter, the contribution of the MSCs to cardiovascular repair and liver regeneration are summarized.Item Open Access Rafting on the plasma membrane: Lipid rafts in signaling and disease(Springer Singapore, 2023-01-18) Işık, Özlem Aybüke; Çizmecioğlu, OnurThe plasma membrane is not a uniform phospholipid bilayer; it has specialized membrane nano- or microdomains called lipid rafts. Lipid rafts are small cholesterol and sphingolipid-rich plasma membrane islands. Although their existence was long debated, their presence in the plasma membrane of living cells is now well accepted with the advent of super-resolution imaging techniques. It is interesting to note that lipid rafts function to compartmentalize receptors and their regulators and substantially modulate cellular signaling. In this review, we will examine the role of lipid rafts and caveolae-lipid raft-like microdomains with a distinct 3D morphology—in cellular signaling. Moreover, we will investigate how raft compartmentalized signaling regulates diverse physiological processes such as proliferation, apoptosis, immune signaling, and development. Also, the deregulation of lipid raft-mediated signaling during tumorigenesis and metastasis will be explored.Item Open Access Suppression subtractive hybridization technology(Elsevier, 2004) Yuluğ, Işık; Atalay, A.; Hayat, M.This chapter describes suppression subtractive hybridization (SSH)—a sophisticated cDNA subtraction method to enrich and isolate differentially expressed genes. SSH accomplishes normalization and subtraction by taking advantage of the different rates of hybridization of cDNA strands for different genes depending on their abundance level and the degree of (differential) expression. SSH may be used for pairwise treatment comparisons and must be replicated with the tester and driver reversed to identify gene expression changes in both directions. It is not a quantitative method for measuring expression differences. SSH is best used for identifying genes that are completely absent, rather than expressed less abundantly, in the driver sample. One of the major problems associated with specific cellular characterization is the low amount of sample. However, problems associated with tissues in small quantities can be solved by a restricted polymerase chain reaction (PCR) amplification step prior to cDNA subtraction. When the amount of starting material is limited, it is possible to start with only a few nanograms of total RNA and produce enough double-stranded cDNA of both tester and driver to subtract two specific cell populations by using PCR technology.Item Open Access Zebrafish aging models and possible interventions(InTechOpen Press, 2018) Birand, Dilan Ç.; Erbaba, Begün; Özdemir, Ahmet T.; Kafalıgönül, Hulusi; Adams, Michelle; Bozkurt, Y.Across the world, the aging population is expanding due to an increasing average life expectancy. The percentage of elderly over the age of 65 is expected to be more than 15% of the total world population by 2025. As the lifespan increases, there will be a need for maintaining a healthy state for these individuals. Our current knowledge on types and durations of potential anti-aging therapies is quite limited. Recently the zebrafish has emerged as a promising model for understanding the cognitive and neurobiological changes during aging, as well as its use with potential anti-aging interventions. Like humans this model organism ages gradually, displays similar behavioral properties and social characteristics, and in addition, there is a wealth of molecular and genetic tools to uncover the cellular mechanism that contribute to age-related cognitive declines. Drug effect and toxicity can be easily tested in the zebrafish. Therefore, this animal model can provide information about potential therapies that could be translated directly into human populations or provide a more focused treatment direction for testing in other mammalian animal models. The zebrafish will be a powerful tool for uncovering the mysteries of the aging brain.