Biology subjects

Ozdemir, S.

Publications and source records attributed to Ozdemir, S..

4 recordsLinked to original sources

bioRxiv2024

Effects of context changes on memory reactivation

While the influence of context on long-term memory (LTM) is well-documented, its effects on the interaction between working memory (WM) and LTM remain less understood. In this study, we explored these interactions using a delayed match-to-sample task, where participants (6 Male, 16 Female) encountered the same target object across six consecutive trials, facilitating the transition from WM to LTM. During half of these target repetitions, the background color changed. We measured the WM storage of the target using the contralateral delay activity (CDA) in electroencephalography (EEG). Our results reveal that task-irrelevant context changes trigger the reactivation of long-term memories in WM. This reactivation may be attributed to content-context binding in WM and hippocampal pattern separation. Significance StatementUnderstanding the mechanisms of memory updating in response to changing contexts is vital because context plays a pivotal role in shaping long-term memories. This study demonstrates, for the first time, that an irrelevant context change triggers the reactivation of learned memories in visual working memory. This observation underscores the importance of multi-memory interactions during context updating. Challenging traditional memory models that postulate mandatory reactivation of long-term memories upon each use, our results instead reveal a selective reactivation process, especially during transitions to new environments. This finding elucidates the adaptive nature of memories and enhances our understanding of memory storage and retrieval processes.

neuroscience↗

bioRxiv2024

Mutation of the peptide-regulated transcription factor ComR for amidated peptide specificity and heterologous function in Lactiplantibacillus plantarum WCFS1

There is a growing interest in the use of probiotic bacteria as biosensors for the detection of disease. However, there is a lack of bacterial receptors developed for specific disease biomarkers. Here, we have investigated the use of the peptide-regulated transcription factor ComR from Streptococcus spp. for specific peptide biomarker detection. ComR exhibits a number of attractive features that are potentially exploitable to create an exquisitely sensitive biomolecular switch for engineered biosensor circuitry within the probiotic organism Lactiplantibacillus plantarum WCFS1. By screening a library of ComR mutant protein variants, we identified mutations that increased the specificity of ComR toward an amidated version of its cognate extracellular signaling peptide, demonstrating the potential for ComR to detect this important class of biomarker.

synthetic biology↗

bioRxiv2023

Effect of Dual Leucine Zipper Kinase Inhibitor GNE-3511 on Epileptogenesis and Cognitive and Behavioral Changes in a Temporal Lobe Epilepsy Model in Mice

Inflammation and neuronal loss are key factors in the pathophysiology of epilepsy. It is known that activation of Dual Leucine Zipper Kinase (DLK) in chronic neurodegenerative diseases causes neuron death and axon degeneration through apoptotic pathways. Genetic deletion of DLK (dual leucine zipper kinase, MAP3K12) or pharmacological inhibition by GNE-3511 or GNE-8505 was found to have benefits in mouse models of Alzheimers and ALS; however, there is no previous study that uses DLK inhibitors in epilepsy models. Therefore, the aim of our study is to suppress the DLK/JNK pathway with the DLK inhibitor GNE-3511 in the temporal lobe epilepsy model induced by pilocarpine and to determine the effect of this inhibition on cognitive and behavioural defects, as well as epileptogenesis. Open field, elevated plus maze, and Morris water maze tests were used to assess locomotor activity, anxiety and learning and memory, respectively. Following decapitation the hippocampi were removed and, histopathological and biochemical analyses were performed. Both treatment groups had less anxiety and locomotor activity as well as decreased impairment in memory and learning performance compared to SE group (p<0.001). Both doses of GNE-3511 prevented the spontaneous recurrent seizures in a dose dependent manner with respect to the SE group (p<0.01 and p<0.001, respectively). Histological examination of the hippocampus revealed a neuroprotective effect of both doses of treatment in the CA1 area and dentate gyrus (p<0.0001). Thus, DLK inhibitor GNE-3511 was found to be effective in preventing epileptogenesis, neuronal loss and cognitive and behavioural deficits due to pilocarpine induced SE.

neuroscience↗

bioRxiv2016

ULTRAFAST LASER-PROBING SPECTROCOPY FOR STUDYING MOLECULAR STRUCTURE OF POLYMERIC PROTEINS

We report the development of a new technique to screen protein crystallinity quantitatively based on laser-probing spectroscopy with sub-picosecond resolution. First, we show theoretically that the temperature dependence of the refractive index of a polymeric protein is correlated to its crystallinity. Then, we performed time-domain thermo-transmission experiments on purified semi-crystalline proteins, both native and recombinant (i.e., silk and squid ring teeth), and also on intact E. coli cells bearing overexpressed recombinant protein. Our results demonstrate, for the first time, quantification of crystallinity in real time for polymeric proteins. Our approach can potentially be used for screening an ultra-large number of polymeric proteins in vivo.

biophysics↗