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With Biophysics Reports, we will provide a resource on novel theories, methods, protocols and improvements on basic research techniques in the biological and biomedical sciences.
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Tubulin posttranslational modifications (PTMs) add “tubulin code” to generate functional diversities of microtubules. Several types of tubulin PTMs accumulate on axonemes and basal bodies of cilia, including acetylation, glutamylation, glycylation and detyrosination. Among them, glutamylation, glycylation and detyrosination are mostly enriched in the B-tubules, whereas acetylation occurs on both Aand B-tubule of the microtubule doublets in a similar level. Recent studies indicate that tubulin PTMs are critical for the fine tuning of assembly/disassembly, maintenance, motility, and signaling of cilia. Dysregulated tubulin PTMs are strongly implicated in human disorders including ciliopathies and neuron degeneration. Here, we review the current understanding how tubulin PTMs regulate cilia formation and function, and their relevance to human health.
In eukaryotic cells, the endoplasmic reticulum (ER) forms a continuous network of tubules and sheets. ER membranes are inter-connected by a class of dynamin-like GTPases termed atlastins (ATLs). Deletion or mutation of ATLs results in long and unbranched ER tubules in cells. Mutations in ATL1 in humans have been linked to the neurodegenerative disease hereditary spastic paraplegia. The basis of ATL-mediated membrane fusion has been studied extensively, but specific functions of ATL remain unclear. In this review, we summarize ER-related cellular processes that directly or indirectly involve ATL, including membrane trafficking, lipid metabolism, autophagy, microtubule dynamics, pathogen infections, calcium signaling, and protein homeostasis. These findings provide important clues for deciphering the physiological roles of the tubular ER network.
Hepatitis B is caused by hepatitis B virus (HBV), and persistent HBV infection is a global public health problem, with 257 million people as HBV chronic carriers. Viral covalently closed circular DNA (cccDNA) is a key factor to establish persistent infection in infected hepatocytes. Current antiviral therapies have no direct impact on pre-existing cccDNA reservoir, which can be assembled into minichromosome by hijacking host factors. Understanding the mechanisms of epigenetic regulation in cccDNA minichromosome is crucial to develop new therapy on cccDNA, an attractive target for HBV cure. This review summarizes the current advances in epigenetic regulation of cccDNA minichromosome, which might provide clues to novel druggable targets to cure hepatitis B by either silencing or eliminating cccDNA reservoir.
The development of multi-photon microscopic technique has made it possible to image submicron structures deep in biological tissues. This technique is widely used for imaging of cortical structures in developing and adult animals, and there have been detail descriptions of in vivo imaging of synaptic structures in normal animals through a thinned-skull or open-skull cranial window. However, several challenges should be considered carefully for high-resolution imaging of cortical structures under pathological conditions. Here we describe a protocol for in vivo imaging of dendritic structures following ischemic stroke through thinned skull. This protocol can also be applied for acute or chronic imaging of neuronal structural plasticity, glial activation, cerebral microcirculation, or synaptic functions in other pathological conditions.
Mechanical properties of brain tissue can provide vital information for understanding the mechanism of traumatic brain injury (TBI). As mouse models were commonly adopted for TBI studies, a method to produce injury to the brain and characterize the injured tissue is desired. In this paper, a complete workflow of TBI induction, sample preparation, and biomechanical characterization is presented for measurement of the injured brain tissue. A controlled cortical impact device was used to induce injury to the brain. By setting the angle, speed, and position of the impact, the level of brain injuries could be controlled. Viscoelastic properties of both injured and non-injured brain tissues were measured using a ramp-hold indentation test. Regions of interests (ROIs) were tested and compared to contralateral corresponding counterparts. Methods introduced in this paper could be easily extended to produce and test a variety of other injured soft biological tissues.
Noncoding RNAs play important roles in cell and their secondary structures are vital for understanding their tertiary structures and functions. Many prediction methods of RNA secondary structures have been proposed but it is still challenging to reach high accuracy, especially for those with pseudoknots. Here we present a coupled deep learning model, called 2dRNA, to predict RNA secondary structure. It combines two famous neural network architectures bidirectional LSTM and U-net and only needs the sequence of a target RNA as input. Benchmark shows that our method can achieve state-of-the-art performance compared to current methods on a testing dataset. Our analysis also shows that 2dRNA can learn structural information from similar RNA sequences without aligning them.