Author: Halil Kavaklı

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Just Published Paper

Our paper titled “Transcriptomic and fatty acid analyses of Neochloris aquatica grown under different nitrogen concentration” is published in Functional & Integrative Genomics. This work is done with collaboration with Profs Füsun Akgül and Rıza Akgül

figure 1
Light and scanning electron micrographs of N. aquatica. A General view with 10X and B with 40X. CColony, scale bar: 10 µm; D A cell scale bar: 4 µm

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Just Published Paper

Our paper titled “Structure-based design and classifications of small molecules regulating the circadian rhythm period” is published in Scientific Reports. This work is done with collaboration with Prof Metin Türkay.

Figure 1
Crystal structure of Cryptochrome 1(CRY1). There are two functionally important pockets, called primary and secondary pockets. Regions in primary and secondary pockets on CRY1 are shown in red color.

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Just Published Paper

Şeref’s paper titled “The Arg293 of Cryptochrome 1 is responsible for the allosteric regulation of CLOCK-CRY1 binding in circadian rhythm” is accepted to be published in Journal of Biological Chemistry.

This picture describes allosteric pathway between Arg293 and Ser-loop for binding of CLOCK/BMAL1.

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Just Published Paper

Şeref’s paper titled “In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials” is accepted to be published in Journal of Biomolecular Structure and Dynamics.

The paper describes identification of well-tolerated and widely used drugs that have potential to be used against SARS-CoV-2

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Circadian Clock

Our laboratory is interested in understanding how clock works at cellular level. For more information please visit our research interest section. 

Almost every day, we wake up, get hungry, feel ourselves energetic or tired or succumb to sleep at the same hours. Although people may have different cycles, at certain hours of the day our bodies show the same responses. The circadian clock regulates the timing of sleep and wakefulness and, therefore, all dependent behavioural and physiological processes. In humans, a defect in the clock gene PER2 produces familial advanced sleep phase syndrome (FASPS); an analogous mutation causes the same phenotype in mice. People with a causal mutation in casein kinase CSNK1D and an associated variant in CSNK1E display ASPS and delayed sleep phase syndrome (DSPS), respectively. Finally, a human CLOCK variant is associated with diurnal sleep preference. Circadian clock genes are also associated with a host of neurological disorders including schizophrenia, unipolar major depression, and bipolar disorder.  Although it was widely believed that circadian clock disruption predisposes humans to cancer based largely on epidemiologic data, studies with Cry mutant mice revealed a more complex pattern of interactions among the clock, apoptosis, and oncogenic transformation.