Biology subjects

Wen, Q.

Publications and source records attributed to Wen, Q..

41 records · Page 3Linked to original sources

bioRxiv2019

Pathway Commons: 2019 Update

Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g., metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (1) tools to search this comprehensive resource, (2) a download site offering integrated bulk sets of pathway data (e.g., tables of interactions and gene sets), (3) reusable software libraries for working with pathway information in several programming languages (Java, R, Python, and Javascript), and (4) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4,794 detailed human biochemical processes (i.e., pathways) and [~]2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.

bioinformatics↗

bioRxiv2019

DECODING THE MECHANOCHEMISTRY OF NEURITE PLASTICITY

The formation and disruption of synaptic connections during development is a fundamental step in neural circuit formation. Subneuronal structures such as neurites are known to be sensitive to the level of spontaneous neuronal activity but the specifics of how neurotransmitter-induced calcium activity regulates neurite homeostasis are not yet fully understood. In response to stimulation by neurotransmitters such as acetylcholine, calcium responses in cells are mediated the Gq/phospholipase C{beta} (PLC{beta})/ phosphatidylinositol 4,5 bisphosphate (PI(4, 5)P2) signaling pathway. Here, we show that prolonged Gq stimulation results in the retraction of neurites in PC12 cells and rupture of neuronal synapses by modulating membrane tension. To understand the underlying cause, we dissected the behavior of individual components of the Gq/PLC{beta}/PI(4, 5)P2 pathway during retraction, and correlated these to the retraction of the membrane and cytoskeletal elements impacted by calcium signaling. We developed a mathematical model that combines biochemical signaling with membrane tension and cytoskeletal mechanics, to show how signaling events are coupled to retraction velocity, membrane tension and actin dynamics. The coupling between calcium and neurite retraction is shown to be operative in the C. elegans nervous system. This study uncovers a novel mechanochemical connection between the Gq/PLC{beta}/(PI(4, 5)P2 pathway that couples calcium responses with neural plasticity.

biophysics↗

bioRxiv2018

Visual intensity ratio modulates operant learning responses in larval zebrafish

Larval zebrafish is a promising vertebrate model for understanding neural mechanisms underlying learning and memory. Here, we report on a high-throughput operant learning system for zebrafish larvae and demonstrate that lower visual intensity ratio of the conditioned stimulus to the background can enhance learning ability, highlighted by several behavioral metrics. We further characterize the learning curves as well as memory extinction for each conditioned pattern. Finally, we show how this learning process developed from 7 days old to 10 days old zebrafish.\n\nHighlightsO_LIConditioned visual patterns with lower intensity ratio to the background elicited stronger operant learning responses\nC_LIO_LIMemory extinction was modulated by the visual intensity ratio of the conditioned stimulus to the background\nC_LIO_LIA high-throughput automated system for acquiring and analyzing behavioral data\nC_LI

animal behavior and cognition↗

bioRxiv2017

A descending pathway through electrical coupling facilitates undulatory wave propagation in C. elegans

Descending signals from the brain play critical roles in controlling and modulating locomotion kinematics. In the Caenorhabditis elegans nervous system, descending AVB premotor interneurons exclusively form gap junctions with B-type motor neurons that drive forward locomotion. We combined genetic analysis, optogenetic manipulation, and computational modeling to elucidate the function of AVB-B gap junctions during forward locomotion. First, we found that some B-type motor neurons generated intrinsic rhythmic activity, constituting distributed central pattern generators. Second, AVB premotor interneurons drove bifurcation of B-type motor neuron dynamics, triggering their transition from stationary to oscillatory activity. Third, proprioceptive couplings between neighboring B-type motor neurons entrained the frequency of body oscillators, forcing coherent propagation of bending waves. Despite substantial anatomical differences between the worm motor circuit and those in higher model organisms, we uncovered converging principles that govern coordinated locomotion.\n\nSignificance StatementA deep understanding of the neural basis of motor behavior must integrate neuromuscular dynamics, mechanosensory feedback, as well as global command signals, to predict behavioral dynamics. Here, we report on an integrative approach to defining the circuit logic underlying coordinated locomotion in C. elegans. Our combined experimental and computational analysis revealed that (1) motor neurons in C. elegans could function as intrinsic oscillators; (2) Descending inputs and proprioceptive couplings work synergistically to facilitate the sequential activation of motor neuron activities, allowing bending waves to propagate efficiently along the body. Our work thus represents a key step towards an integrative view of animal locomotion.

neuroscience↗

bioRxiv2017

Rapid Whole Brain Imaging Of Neural Activities In Freely Behaving Larval Zebrafish

The internal brain dynamics that link sensation and action are arguably better studied during natural animal behaviors. Here we report on a novel volume imaging and 3D tracking technique that monitors whole brain neural activity in freely swimming larval zebrafish (Danio rerio). We demonstrated the capability of our system through functional imaging of neural activity during visually evoked and prey capture behaviors in larval zebrafish.

neuroscience↗