Biology subjects

Kilic, A.

Publications and source records attributed to Kilic, A..

3 recordsLinked to original sources

bioRxiv2023

Predictive Uncertainty in State-Estimation Drives Active Sensing in Weakly Electric Fish

Animals use active sensing movements to shape the spatiotemporal characteristics of sensory signals to better perceive their environment under varying conditions. However, the underlying mechanisms governing the generation of active sensing movements are not known. To address this, we investigated the role of active sensing movements in the refuge tracking behavior of Eigenmannia virescens, a species of weakly electric fish. These fish track the longitudinal movements of a refuge in which they hide by swimming back and forth in a single linear dimension. During refuge tracking, Eigenmannia exhibits stereotyped whole-body oscillations when the quality of the sensory signals degrades. We developed a feedback control model to examine the role of these ancillary movements on the task performance. Here, we show that the proposed model generates fish trajectories that are statistically indistinguishable from the actual fish, implying that active sensing movements are regulated to minimize the predictive uncertainty in state estimation.

animal behavior and cognition↗

bioRxiv2023

Tenascin-C activation of lung fibroblasts in a 3D synthetic lung extracellular matrix mimic

The lung extracellular matrix (ECM) maintains the structural integrity of the tissue and regulates the phenotype and functions of resident fibroblasts. Lung-metastatic breast cancer alters these cell-ECM interactions, promoting fibroblast activation. There is a need for bio-instructive ECM models that contain the ECM composition and biomechanics of the lung to study these cell-matrix interactions in vitro. Here, we developed a synthetic, bioactive hydrogel that mimics the native lung modulus, and includes a representative distribution of the most abundant ECM peptide motifs responsible for integrin binding and matrix metalloproteinase (MMP)-mediated degradation in the lung, which promotes quiescence of human lung fibroblasts (HLFs). Stimulation with transforming growth factor {beta}1 (TGF-{beta}1), metastatic breast cancer conditioned media (CM), or tenascin-C activated these hydrogel-encapsulated HLFs in a manner reflective of their native in vivo responses. We propose this lung hydrogel platform as a tunable, synthetic approach to study the independent and combinatorial effects of ECM in regulating fibroblast quiescence and activation.

bioengineering↗

bioRxiv2022

Parkinson mutations in DNAJC6 cause lipid defects and neurodegeneration that are rescued by Synj1

Recent evidence links dysfunctional lipid metabolism to the pathogenesis of Parkinsons disease, but the mechanisms are not resolved. Here, we created a new Drosophila knock-in model of DNAJC6/Auxilin and find that the pathogenic mutation causes synaptic dysfunction, neurological defects and neurodegeneration, as well as specific lipid metabolism alterations. In these mutants membrane lipids containing long-chain polyunsaturated fatty acids, including phosphatidylinositol lipid species that are key for synaptic vesicle recycling and organelle function are reduced. Overexpression of another protein mutated in Parkinsons disease, Synaptojanin-1, known to bind and synthesize specific phosphoinositides, strongly rescues the DNAJC6/Auxilin neuronal defects and neurodegeneration. Our work reveals a functional relation between two proteins mutated in Parkinsons disease and implicates deregulated phosphoinositide metabolism in the maintenance of neuronal integrity and neuronal survival in Parkinsonism.

cell biology↗