Biology subjects

Dong, X.

Publications and source records attributed to Dong, X..

328 records · Page 19Linked to original sources

bioRxiv2017

In vivo calcium imaging visualizes peripheral neuron sensitization in murine osteoarthritis

ObjectiveThe purpose of this study was to develop a method for analyzing sensory neuron responses to mechanical stimuli in vivo, and to evaluate whether these neuronal responses change after destabilization of the medial meniscus (DMM).\n\nMethodsDMM or sham surgery was performed in 10-week old male C57BL/6 wild-type or Pirt-GCaMP3+/- mice. All experiments were performed eight weeks after surgery. Knee and hind paw hyperalgesia were assessed in wild-type mice. The retrograde label DiI was injected into the ipsilateral knee to quantify the number of knee-innervating neurons in the L4 dorsal root ganglion (DRG) in wild-type mice. In vivo calcium imaging was performed on the ipsilateral L4 DRG of Pirt-GCaMP3+/- mice as mechanical stimuli (paw pinch, knee pinch, knee twist) were applied to the ipsilateral hind limb.\n\nResultsEight weeks after surgery, DMM mice had more hyperalgesia in the knee and hind paw compared to sham mice. Intra-articular injection of DiI labeled similar numbers of neurons in the L4 DRG of sham and DMM mice. Increased numbers of sensory neurons responded to all three mechanical stimuli in DMM mice, as assessed by in vivo calcium imaging. The majority of responses in sham and DMM mice were in small-to-medium-sized neurons, consistent with the size of nociceptors. The magnitude of responses was similar between sham and DMM mice.\n\nConclusionsWe demonstrated that increased numbers of small-to-medium sized DRG neurons respond to mechanical stimuli 8 weeks after DMM surgery, suggesting that nociceptors have become sensitized by lowering the response threshold.

neuroscience↗

bioRxiv2017

Insm1a regulates motor neuron development in zebrafish

Insulinoma-associated1a (Insm1a) is a zinc-finger transcription factor playing a series of functions in cell formation and differentiation of vertebrate central and peripheral nervous systems and neuroendocrine system. However, its roles on the development of motor neuron have still remained uncovered. Here, we provided evidences that insmla was a vital regulator of motor neuron development and provide a mechanistic understanding of how it contributes to this process. Firstly, we showed the localization of insmla in spinal cord and primary motor neurons (PMNs) of zebrafish embryos by in situ hybridization and imaging analysis of transgenic reporter line Tg(insmla: mCherry) ntu805. Then we demonstrated that the deficiency of insmla in zebrafish larvae lead to the defects of PMNs development, including the reduction of caudal primary motor neurons (CaP) and middle primary motor neurons (MiP), the excessive branching of motor axons, and the disorganized distance between adjacent CaPs. Additionally, knockout of insm1 impaired motor neuron differentiation in the spinal cord. Locomotion analysis showed that insmla-null zebrafish significantly reduced the swimming activity. Furthermore, we proved that the insmla loss of function significantly decreased the transcripts levels of both olig2 and nkx6.1. Microinjection of olig2 and nkx6.1 mRNA rescued the motor neuron defects in insmla deficient embryos. Taken together, these data indicate that insmla regulates the motor neuron development, at least in part, through modulation of the expressions of olig2 and nkx6.1.

developmental biology↗

bioRxiv2017

Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp

Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present the MetaAmp pipeline for processing of SSU rRNA gene and other non-coding or protein-coding amplicon sequencing data by investigators that are inexperienced with bioinformatics procedures. It accepts single-end or paired-end sequences in fasta or fastq format from various sequencing platforms. It includes read quality control, and merging of forward and reverse reads of paired-end reads. It makes use of UPARSE, Mothur, and the SILVA database for clustering, removal of chimeric reads, taxonomic classification and generation of diversity metrics. The pipeline has been validated with a mock community of known composition. MetaAmp provides a convenient web interface as well as command line interface. It is freely available at: http://ebg.ucalgary.ca/metaamp. Since its launch two years ago, MetaAmp has been used >2,800 times, by many users worldwide.

bioinformatics↗

bioRxiv2017

Assessing species biomass contributions in microbial communities via metaproteomics

Assessment of microbial community composition is the cornerstone of microbial ecology. Microbial community composition can be analyzed by quantifying cell numbers or by quantifying biomass for individual populations. However, as cell volumes can differ by orders of magnitude, these two approaches yield vastly different results. Methods for quantifying cell numbers are already available (e.g. fluorescence in situ hybridization, 16S rRNA gene amplicon sequencing), yet methods for assessing community composition in terms of biomass are lacking.\n\nWe developed metaproteomics based methods for assessing microbial community composition using protein abundance as a measure for biomass contributions of individual populations. We optimized the accuracy and sensitivity of the method using artificially assembled microbial communities and found that it is less prone to some of the biases found in sequencing-based methods. We applied the method using communities from two different environments, microbial mats from two alkaline soda lakes and saliva from multiple individuals.

microbiology↗