Biology subjects

Feng, Z.

Publications and source records attributed to Feng, Z..

4 recordsLinked to original sources

bioRxiv2018

Identification of genome-wide nucleotide sites associated with mammalian virulence in influenza A viruses

MotivationThe virulence of influenza viruses is a complex multigenic trait. Previous studies about the virulence determinants of influenza viruses mainly focused on amino acid sites, ignoring the influence of nucleotide mutations.\n\nResultsWe collected more than 200 viral strains from 21 subtypes of influenza A viruses with virulence in mammals and obtained over 100 mammalian virulence-related nucleotide sites across the genome by computational analysis. Interestingly, 50 of these nucleotide sites only experienced synonymous mutations. Further experiments showed that synonymous mutations in the top two of these nucleotide sites, i.e., PB1-2031 and PB1-633, enhanced the pathogenicity of the viruses in mice. Finally, machine-learning models with accepted accuracy for predicting mammalian virulence of influenza A viruses were built. Overall, this study highlighted the importance of nucleotide mutations, especially synonymous mutations in viral virulence, and provided rapid methods for evaluating the virulence of influenza A viruses. It could be helpful for early warning of newly emerging influenza A viruses.

microbiology↗

bioRxiv2018

A robust image registration interface for large volume brain atlas

Mapping the brain structures in three-dimensional accurately is critical for an in-depth understanding of the brain functions. By using the brain atlas as a hub, mapping detected datasets into a standard brain space enables efficiently use of various datasets. However, because of the heterogeneous and non-uniform characteristics of the brain structures at cellular level brought with the recently developed high-resolution whole-brain microscopes, traditional registration methods are difficult to apply to the robust mapping of various large volume datasets. Here, we proposed a robust Brain Spatial Mapping Interface (BrainsMapi) to address the registration of large volume datasets at cellular level by introducing the extract regional features of the anatomically invariant method and a strategy of parameter acquisition and large volume transformation. By performing validation on model data and biological images, BrainsMapi can not only achieve robust registration on sample tearing and streak image datasets, different individual and modality datasets accurately, but also are able to complete the registration of large volume dataset at cellular level which dataset size reaches 20 TB. Besides, it can also complete the registration of historical vectorized dataset. BrainsMapi would facilitate the comparison, reuse and integration of a variety of brain datasets.

neuroscience↗

bioRxiv2018

Mechanical Properties of a Primary Cilium from the Stochastic Motions of the Cilium Tip

The stochastic tip dynamics of a primary cilium held within an optical trap is quantified by combining experimental, analytical and computational tools. Primary cilia are cellular organelles, present on most vertebrate cells, hypothesized to function as a fluid flow sensor. The mechanical properties of a cilium remain incompletely characterized. We measured the fluctuating position of an optically trapped cilium tip under untreated, Taxol-treated, and HIF-stabilized conditions. We applied analytical modeling to derive the mean-squared displacement of the trapped tip of a cilium and compared the results with experimental measurements. We provide, for the first time, evidence that the effective flexural rigidity of a ciliary axoneme is length-dependent, and longer cilia are stiffer than shorter cilia. We then provide a rational explanation for both effects. We demonstrate that the apparent length-dependent flexural rigidity can be understood by a combination of modeling axonemal microtubules orthotropic elastic shells and including (actin-driven) active stochastic basal body motion. It is hoped that our improved characterization of cilia will result in deeper understanding of the biological function of cellular flow sensing by this organelle. Our model could be profitably applied to motile cilia and our results also demonstrate the possibility of using easily observable ciliary dynamics to probe interior cytoskeletal dynamics.

biophysics↗

bioRxiv2017

A plant receptor-like kinase promotes cell-to-cell spread of RNAi and is targeted by a virus

RNA interference (RNAi) in plants can move from cell to cell, allowing for systemic spread of an anti-viral immune response. How this cell-to-cell spread of silencing is regulated is currently unknown. Here, we describe that the C4 protein from Tomato yellow leaf curl virus has the ability to inhibit the intercellular spread of RNAi. Using this viral protein as a probe, we have identified the receptor-like kinase (RLK) BARELY ANY MERISTEM 1 (BAM1) as a positive regulator of the cell-to-cell movement of RNAi, and determined that BAM1 and its closest homologue, BAM2, play a redundant role in this process. C4 interacts with the intracellular domain of BAM1 and BAM2 at the plasma membrane and plasmodesmata, the cytoplasmic connections between plant cells, interfering with the function of these RLKs in the cell-to-cell spread of RNAi. Our results identify BAM1 as an element required for the cell-to-cell spread of RNAi and highlight that signalling components have been co-opted to play multiple functions in plants.

plant biology↗