Kaan Arslan

Circadian clocks generate daily rhythms of gene expression that influence physiology, disease, and responses to therapeutics, yet how circadian transcription differs between juvenile and adult organisms remains unresolved. Here, we used genome-wide eXcision Repair sequencing (XR-seq) to quantify transcription-coupled repair as an indirect, high-sensitivity measure of transcription. We profiled the brain, liver, kidney, and testis from juvenile and adult C57BL6/J mice across a 24 h cycle and show that XR-seq enables sensitive circadian transcription mapping. In all organs except the testis, rhythmic transcription phases clustered near dawn and dusk. While core clock gene rhythms are largely preserved between juveniles and adults, rhythms of many clock-controlled genes differ markedly by age. Rhythmic genes are strongly organ-specific yet their overlap between ages is limited, indicating substantial developmental changes in circadian control. Together, these data provide a multi-organ map of juvenile versus adult circadian transcription and indicate that adult therapeutic schedules may not translate to juveniles.

Proton channels play a crucial role in many biological functions, as they are responsible for the selective transport of protons across cell membranes. Recently, Otopetrins, a family of eukaryotic proton-selective ion channels, have attracted significant attention due to their diverse physiological roles. Despite the importance of Otopetrins, their structural and functional properties remain relatively unexplored. As a model organism, crayfish have been extensively studied to gain insights into the functioning of the nervous system. These studies cover a wide range of aspects, including the properties of individual neurons and behavioral science. However, studying the physiological systems of crayfish poses challenges for molecular research due to limited molecular sequence information available for these organisms. In the present work was identified an originally cloned mRNA, coding an Otopetrin like proton channel in the crayfish. The coded protein was modeled in silico and possible conduction mechanisms and pathways were revealed. A plasmid of the cloned mRNA was heterologously expressed in HEK293T cells. Functional experiments on transfected cells indicated that the expressed mRNA was coupled to proton conduction across the cell membrane.

Objectives: Voltage-gated calcium channels are essential elements in development of many cellular processes like electrical signaling, contraction secretion and gene expression. There has been a fair amount of information about the functional and structural properties of the calcium channels in mammalian species. Crayfish serves as a model animal for many types of experiments. However, there has been no information related to the molecular and genetic properties of the calcium channels in the crayfish. Methods: Conventional cloning methods, three-dimensional structural calculations, docking experiments have been conducted. Results: An mRNA 7,791 bp in size has been cloned. The coding region has been translated into an alpha peptide with 1,942 residues. The cloned protein sequence has similarity to other L-type voltage-gated calcium channel sequences from the neighboring species. Three-dimensional structure, in reference to human L-type voltage-gated calcium channel, has been calculated. Known calcium channel blockers, nifedipine, verapamil and diltiazem have been successfully docked on the calculated three-dimensional model. Conclusions: Considering the similarity assay in the National Center for Biotechnology Information (NCBI) platform, the three-dimensional structural calculations and the docking experiments it was concluded that the cloned mRNA codes an alpha peptide for a putative voltage-gated calcium channel protein in the crayfish. In the present work by using the conventional molecular biology methods a complete mRNA coding a putative calcium channel has been de novo cloned. Three-dimensional structure of the related protein has been calculated and several pharmacological agents blocking the channel have been docked to the identified receptor sites.

Ion channels gated selectively by mechanical stimulus are the key elements of mechanosensation. Several genes have been associated with putative mechanosensitive ion channels or mechanosensitive channel complexes. Transmembrane channel (TMC)-like protein is one of those candidate proteins that have been explored in mammals and several invertebrates. The presence and possible function of TMC related genes has not been investigated yet in crustaceans. In the present work an mRNA coding TMC-like protein was firstly cloned in Astacus leptodactylus ( Eschscholtz, 1823) (Decapoda: Astacidea: Astacidae) and expressed in HEK293T cells. Three-dimensional structural calculations of the protein predicted a channel. Functional studies, however, indicated that the mechanosensitivity of the transfected HEK293T cells is similar to that in the control cells. It was concluded that a TMC-like protein is present in the crayfish but future studies are necessary to define its function.