Biology subjects

Baran, B.

Publications and source records attributed to Baran, B..

9 recordsLinked to original sources

bioRxiv2026

NREM sleep microarchitecture is associated with internalizing symptoms and emotional functioning in early adolescence

Study Objectives: Sleep disturbances are common in youth with anxiety disorders, yet most prior work relies on subjective measures and does not capture underlying neural processes. We examined whether alterations in non-rapid eye movement (NREM) sleep oscillations are present in children with anxiety disorders and whether these features relate to internalizing symptoms and emotional functioning. Methods: Children aged 9-13 years with diagnosed anxiety disorders (ANX; n = 17) and typically developing non-psychiatric comparison participants (NC; n = 26) completed overnight polysomnography. Slow oscillations (SO) and slow and fast sleep spindles were characterized using validated automated detection algorithms. Participants also completed a pre-sleep emotional processing task, and parents provided standardized measures of youth mental health. Group differences and dimensional associations between NREM oscillations, internalizing symptoms, and behavioral indices of emotional processing were examined. Results: Sleep architecture did not differ between groups. Slow spindle duration was shorter in the ANX group. Across the full sample, shorter slow spindle duration was associated with greater internalizing symptoms, whereas higher SO density was positively associated with internalizing symptoms. Children in the ANX group exhibited greater facial emotional arousal and more frequent look-away behavior during the emotional processing task. Across participants, greater emotional arousal and look-away behavior were associated with shorter spindle duration during subsequent sleep. Conclusions: Specific features of NREM microarchitecture were associated with individual differences in internalizing symptoms and emotional functioning during early adolescence. These findings highlight the potential relevance of NREM oscillations for understanding developmental links between sleep and youth psychopathology.

neuroscience↗

bioRxiv2026

When Time Online Tells Us Little: Duration of Social Media Use does not Influence Sleep Disruption or Psychopathology in Adolescents

Background: Adolescent mental health problems have risen alongside increasing sleep disruption and widespread social media use (SMU). However, the mechanisms linking these factors remain unclear. This study concurrently examined objectively measured sleep and SMU in relation to psychopathology to test whether SMU moderates the sleep-mental health association and to characterize day-to-day bidirectional relations among sleep, affect, mood, and SMU during the school year. Methods: Eighty-five adolescents (ages 12-18) completed 14 days of wrist actigraphy, smartphone-based ecological momentary assessments of mood and affect, and objective SMU duration tracking. Cross-sectional models tested whether SMU moderated associations between sleep and psychopathology, and multilevel daily models examined within-person lagged associations among sleep, SMU, and affect, controlling for age and sex. False discovery rate correction was applied. Results: Shorter average sleep duration and greater variability in sleep duration between weekdays and weekends were associated with higher psychopathology symptoms, primarily externalizing problems. SMU duration neither moderated nor directly predicted psychopathology or sleep. Within-person analyses showed that longer-than-usual sleep predicted more positive and less negative affect and lower next-day SMU, though these associations did not survive correction for multiple comparisons. Conclusions: Sleep disruption showed consistent associations with adolescent psychopathology, whereas the amount of time spent on social media did not. These findings suggest that duration-based measures of SMU may incompletely capture adolescents digital experiences and highlight the need for more granular, context-sensitive indicators of online behavior in understanding youth mental health.

neuroscience↗

bioRxiv2024

Harnessing CRISPR/Cas12a Technology to Combat Wheat Dwarf Virus Without Genetic Modification

Wheat (Triticum aestivum L.) is a staple crop globally, but its yield and quality are significantly affected by viral diseases, particularly the Wheat Dwarf Virus (WDV). Developing antiviral strategies is crucial for enhancing wheat productivity. This study aims to investigate the use of CRISPR/Cas12a as an antiviral agent against WDV without the need for genetic modification of the host plants. WDV genomic DNAs were isolated from wheat and barley samples collected from various regions in Turkey and other countries. Guide RNAs (gRNAs) targeting conserved regions in the coat protein (CP) gene of WDV were designed and synthesized. The CRISPR/Cas12a ribonucleoprotein (RNP) complex was tested for its ability to induce DNA cleavage in WDV genomes through in vitro assays, and results were analysed using agarose gel electrophoresis. The designed gRNAs effectively induced DNA cleavage in WDV genomes, with gRNA1 showing consistent performance across all tested isolates. gRNA2 exhibited variability, successfully targeting seven out of ten isolates. No off-target effects were observed in control assays, confirming the specificity of the gRNAs. The CRISPR/Cas12a system, guided by specifically designed gRNAs, can effectively target and cleave WDV genomes, providing a potent, non-GMO antiviral strategy. This approach has potential applications for managing WDV infections in wheat and barley, highlighting its versatility and effectiveness.

plant biology↗

bioRxiv2024

In Vitro Generation and Characterization of The Wu Syndrome Model That Causes Mental Retardation in Neural Cell Lines

Wu Syndrome, also known as X-Linked Wu Type Intellectual Developmental Disorder, is caused by a mutation in the GRIA3 (Glutamate Ionotropic Receptor AMPA Type Subunit 3) gene located at position 25 on the X chromosome. GRIA3 encodes iGluR3, a subunit of the AMPA (-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, which plays a critical role in rapid excitatory synaptic transmission in the central nervous system. This receptor is essential for learning, memory, and the processes of long-term depression (LTD) and long-term potentiation (LTP). Despite its significance, Wu Syndrome remains under-researched and lacks effective treatments. Notably, some genetic variants have been identified, but many, including the W637S variant, are still unstudied. This study pioneers the development of a Wu Syndrome model in neural cell lines using genetic modification techniques to identify and characterize new GRIA3 variants. By focusing on variants such as G833R and W637S, this research provides novel insights into their effects on GRIA3 function, paving the way for potential therapeutic strategies. This is the first study to explore the responses of neural cells to these mutations in vitro, thereby contributing valuable knowledge toward understanding and treating Wu Syndrome.

molecular biology↗

bioRxiv2023

NREM sleep oscillations and their relations with sleep-dependent memory consolidation in early course psychosis and first-degree relatives

Sleep spindles are believed to mediate sleep-dependent memory consolidation, particularly when coupled to neocortical slow oscillations. Schizophrenia is characterized by a deficit in sleep spindles that correlates with reduced overnight memory consolidation. Here, we examined sleep spindle activity, slow oscillation-spindle coupling, and both motor procedural and verbal declarative memory consolidation in early course, minimally medicated psychosis patients and non-psychotic first-degree relatives. Using a four-night experimental procedure, we observed significant deficits in spindle density and amplitude in patients relative to controls that were driven by individuals with schizophrenia. Schizophrenia patients also showed reduced sleep-dependent consolidation of motor procedural memory, which correlated with spindle density. Contrary to expectations, there were no group differences in the consolidation of declarative memory on a word pairs task. Nor did the relatives of patients differ in spindle activity or memory consolidation compared with controls, however increased consistency in the timing of SO-spindle coupling were seen in both patient and relatives. Our results extend prior work by demonstrating correlated deficits in sleep spindles and sleep-dependent motor procedural memory consolidation in early course, minimally medicated patients with schizophrenia, but not in first-degree relatives. This is consistent with other work in suggesting that impaired sleep-dependent memory consolidation has some specificity for schizophrenia and is a core feature rather than reflecting the effects of medication or chronicity. Statement of significanceWe investigated sleep neurophysiology and memory consolidation in minimally-medicated, early course psychosis patients and unaffected first-degree relatives of patients in a four-night study. Early-course schizophrenia patients had a sleep spindle deficit that correlated with reduced procedural memory consolidation. Although first-degree relatives did not show any deficit in spindles or memory consolidation, the spindles of both relatives and patients showed increased consistency of the temporal coupling of spindles with slow oscillations compared with controls. These results suggest that sleep spindle and memory consolidation deficits are a core feature of schizophrenia. Spindle deficits may be a biomarker of schizophrenia modifiable by treatment, and motivate the development of targeted novel interventions.

neuroscience↗

bioRxiv2022

Autonomous Remotely Controlled Closed System Transgenic Cell Technologies Robot: CRISPR.BOT

In manually advancing experimental processes, the stages may be long-term and need to be repeated. Human errors with the repetition of the steps turn into a time-consuming and high-cost for the experiment processes. For this reason, autonomous liquid processing systems are promising technologies. However, in addition to the high cost of fully automatic systems, their maintenance is also quite expensive. Furthermore, conventional systems usually require system-specific protocols and laboratory equipment. Here, we aimed to show that the autonomous robotic systems may provide a closed and error-free molecular biology bench to perform genetic engineering automatically, quickly, and practically 7-24. In this way, researchers can save time from repetitive experiment processes and perform BSL3 experiments including pathogens without human contact. In this study, we built CRISPR.BOT robotic systems to perform Green Fluorescent Protein (GFP) encoding plasmid DNA transfer into bacteria, lentiviral transduction of the gene-of-interests including GFP encoding gene and CRISPR-Cas9 with gRNAs genetic editing system to a human cell line. Furthermore, we showed that CRISPR.BOT system achieved to accomplish single-cell subcloning of GFP+ CRISPR-gRNA+ cells with 90-100% purity. This study suggests that CRISPR.BOT-like approaches may reduce manpower in a safely closed bench in which molecular biology and genetic engineering can be done by robots in a closed system without touching pathogenic microorganisms (virus or bacteria, for example, SARS CoV-2 virus). Furthermore, LEGO Mindstorms robots showed to have the potential to be used in daily laboratory routines with their cost-effectiveness reduced by up to 50 times compared to normal commercial robots.

molecular biology↗

bioRxiv2022

Motivational trade-offs in bumblebees

Mammals can supress their nociceptive responses to prioritise other important responses via endogenous modulation from the brain. It is well established that insects display nociception, but not whether the insect brain can modulate nociceptive processing. To address this question, we investigated whether bumblebees (Bombus terrestris) attraction to higher sucrose solution concentrations reduces their avoidance of noxious heat. Bees were given the choice between either unheated or noxiously-heated (55{degrees}C) feeders with different sucrose concentrations. The feeders were associated with colour stimuli to act as conditioned cues. Bees fed more from higher sucrose concentration heated feeders than lower sucrose concentration unheated feeders. Further, bees "testing out" of feeders (landing but not feeding) reduced as the experiment progressed, demonstrating that conditioned colour cues informed the bees behaviour. Therefore, bees trade off competing conditioned motivational stimuli to modulate nocifensive behaviour, suggesting a form of pain perception.

animal behavior and cognition↗

bioRxiv2021

The exocyst complex and intracellular vesicles mediate soluble protein trafficking to the primary cilium

The efficient transport of proteins into the primary cilium is a crucial step for many signaling pathways. Dysfunction of this process can lead to the disruption of signaling cascades or cilium assembly, resulting in developmental disorders and cancer. Previous studies on the protein delivery to the cilium were mostly focused on the membrane-embedded receptors. In contrast, how soluble proteins are delivered into the cilium is poorly understood. In our work, we identify the exocyst complex as a key player in the ciliary trafficking of soluble Gli transcription factors. In line with the known function of the exocyst in intracellular vesicle transport, we demonstrate that soluble proteins, including Gli2/3 and Lkb1, can use the endosome recycling machinery for their delivery to the primary cilium. Finally, we identify GTPases: Rab14, Rab18, Rab23, and Arf4 that are involved in vesicle-mediated Gli protein ciliary trafficking. Our data pave the way for a better understanding of ciliary transport and uncover novel transport mechanisms inside the cell.

cell biology↗

bioRxiv2019

Learning to find the center of symmetric and asymmetric spatial layouts by the house cricket, Acheta domesticus

The capacity to navigate by layout geometry has been widely recognized as a robust navigational strategy. It was reported in various species, albeit most studies were performed with vision-based paradigms. In the presented study, we aimed to investigate layout symmetry-based navigation in the house cricket, Acheta domesticus, in the absence of visual cues. For this purpose, we used a non-visual paradigm modeled on the Tennessee Williams setup. We also verified the inaccessibility of visual cues for tested insects using antennal positioning reflex towards looming stimulus and by testing the performance of blinded crickets. In the main experiment, we tested the crickets capacity to learn to find a cool spot positioned centrally in heated arenas of different shapes (i.e., circular, square, triangular, and asymmetric quadrilateral). We found that the symmetry of the arena significantly facilitates crickets learning to find the cool spot, indicated by the increase of time spent on the cool spot and decrease of the latency of locating it in subsequent trials. To investigate possible mechanisms utilized by crickets during the experiment, we analyzed insects approach paths to the spot. The trajectories were grouped in four distinct clusters corresponding to both heuristic and directed strategies of approaching the target, with the dominance of a semi-directed strategy (thigmotactic phase preceding direct navigation to the target). Against these results, we discuss the possibility of insects navigation by using a non-visual space representation and possible limitations of navigation capacities in such conditions in relation to multimodally-guided navigation.

animal behavior and cognition↗