Biology subjects

WANG, L.

Publications and source records attributed to WANG, L..

7 recordsLinked to original sources

bioRxiv2024

Degradation of indole-3-acetic acid by plant-associated microbes

Plant-associated microbiota affect pant growth and development by regulating plant hormones homeostasis. Indole-3-acetic acid (IAA), a well-known plant hormone, can be produced by various plant-associated bacteria. However, the prevalence of microbes with the capacity to degrade IAA in the rhizosphere has not been systematically studied. In this study, we analyzed the IAA degradation capabilities of bacterial isolates from the roots of Arabidopsis and rice. Using genomics analysis and in vitro assays, we found that 21 out of 189 taxonomically diverse bacterial isolates possess the ability to degrade IAA. Through comparative genomics and transcriptomic assays, we identified iac-like or iad-like operon in the genomes of these IAA degraders. Additionally, the regulator of the operon was found to be highly conserved among these strains through protein structure similarity analysis. Some of the IAA degraders could utilize IAA as their sole carbon and energy source. In planta, most of the IAA degrading strains mitigated Arabidopsis seedling root growth inhibition (RGI) triggered by exogenous IAA. Importantly, we observed increased colonization preference of IAA degraders from soil to root according to the frequency of the biomarker genes in metagenome-assembled genomes (MAGs) collected from different habitats, suggesting that there is a close association between IAA degraders and IAA-producers. In summary, our findings further the understanding of the functional diversity and roles of plant-associated microbes.

microbiology↗

bioRxiv2022

Analysis of Phylogeny of Agrocybe Genus Based on Nucleotide Database in NCBI

The study of the phylogeny of species is a basic discipline for the effective protection, development, and utilization of their germplasm resources. Since this century, the fungi of the Agrocybe genus have become the most successful class of medium and high-grade edible and medicinal fungi that have been artificially domesticated and grown on a large scale, and have high commercial value. However, there are few reports on its germplasm resources. To clarify the genetic and developmental relationship at the genus level of the Agrocybe in the world. In this paper, based on the NCBI Nucleotide database(National Center for Biotechnology Information), taking the single gene ITS sequence as the research object, the T92 (Tamura 3-parameters) parameter model was used to calculate the genetic distance, and the neighbor joining method was used to construct the genus-level phylogenetic tree of the Agrocybe. The results showed that the phylogenetic tree constructed by 192 ITS single gene sequences of 43 species of the Agrocybe (including 31 known species and 12 undetermined species) in the NCBI Nucleotide database was roughly divided into 6 branches and belonged to different groups, and 17 undetermined species of the Agrocybe sp. was preliminarily identified. This study has a certain reference value for the genetic relationship among different species of Agrocybe all over the world, as well as the selection of the parent bank and the protection of germplasm resources of each species of the genus.

bioinformatics↗

bioRxiv2021

An awareness-dependent saliency map in the human visual system

The bottom-up contribution to the allocation of exogenous attention is a saliency map. However, how the saliency map is distributed when multiple salient stimuli are presented simultaneously and how this distribution interacts with awareness remain unclear. These questions were addressed here using visible and invisible stimuli that consisting of two salient foregrounds: the high one served as the target and the low one served as the distractor, which did or did not interfere the target saliency, indicating a gradient or winner-take-all manner, respectively. By combining psychophysics, fMRI, and effective connectivity analysis, we found that the saliency map was distributed as a gradient or winner-take-all manner with and without awareness, respectively. Crucially, we further revealed that the gradient manner was derived by feedback from pIPS, whereas the winner-take-all manner was constructed in V1. Together, our findings indicate an awareness-dependent saliency map and reconcile previous, seemingly contradictory findings on the saliency map.

neuroscience↗

bioRxiv2020

Evaluation of Fecal Immunoassays for Canine Echinococcus Infection in China

Human echinococcosis is present worldwide but it is in China that prevalence is the highest. Western China and in particular the Tibetan plateau is the region where the burden of echinococcosis is the most important. Dogs are a major carrier of echinococcosis and monitoring the presence of Echinococcus worms in dogs is therefore essential for efficiently controlling the disease. Detection kits based on three different technologies, i.e. sandwich ELISA, ELISA and gold immunodiffusion are currently marketed and used in China. The objective of this work was to assess the efficacy of these kits, in particular with respect to sensitivity and specificity. Four fecal antigen detection kits for canine echinococcosis covering the three technologies were obtained from companies and tested in parallel on 220 fecal samples. The results indicate that the performance is lower than expected, in particular in terms of sensitivity. The best results were obtained with the sandwich ELISA technology. The gold immunofiltration yielded the poorest results. In all cases, further development is needed to improve the performance of these kits, which represent a key element for the control of echinococcosis. Author summaryAlthough present worldwide, human echinococcosis is at its highest prevalence in Western China and particularly on the Tibetan plateau. Controlling echinococcosis is a national priority and routine monitoring must be established. Dogs are the main carriers of echinococcosis and surveying Echinococcus worms in dogs is therefore a key issue. Commercial detection kits are currently in use in China for monitoring the presence of Echinococcosis in dogs. These kits are based on three different technologies, i.e. sandwich ELISA with two monoclonal antibodies, ELISA, and gold immunodiffusion. National survey programs are essential for the control of echinococcosis and it is thus very important to assess the efficacy of these kits, planned to be used for the national survey programs. The work was thus undertaken to assess this efficacy, in particular with respect to sensitivity and specificity. Four fecal antigen detection kits for canine echinococcosis covering the three technologies were obtained from companies and tested in parallel on 220 fecal samples. The performance was lower than expected, in particular for their sensitivity, which ranged from 51.5% to 83.9% with only two samples displaying a worm burden lower than 100. Three out of four kits showed non-specific cross-reactions with other parasites. The best results were obtained with the sandwich ELISA technology, whereas gold immunofiltration yielded the poorest results. However, in all cases, further development is strongly needed to improve the performance of these kits, which represent a key element for the control of echinococcosis.

zoology↗

bioRxiv2020

Hybrid diffuse optical monitoring of hemodynamic changes following acute cerebral ischemia in a porcine model

Rapid screening for stroke in pre-hospital settings may improve patient outcomes by allowing early deployment of thrombolytic therapies. Near-infrared hybrid diffuse optical screening devices may fill this need. This study seeks to determine whether hybrid diffuse optical measurements can measure hemodynamic changes associated with cerebral ischemia within the first few hours of the onset of acute ischemia in a large animal model. A hybrid diffuse optical device combining of near-infrared spectroscopy (NIRS) and diffuse correlation spectroscopy (DCS) was fabricated to measure total hemoglobin concentration (HbT), tissue oxygen saturation (StO2) and blood flow index (BFI). Cerebral ischemia was induced by ligation of the bilateral common carotid arteries (CCA) in five miniature pigs. Additionally, a fatal stroke was induced in two pigs by injecting 5ml air emboli into both CCA. Cerebral hemodynamic parameters were monitored continuously throughout the study with the hybrid optical device. Relative changes BFI showed the good repeatability both of the ligation and fatal stroke experiments. During bilateral CCA ligation, the BFI decreased by up to about 66% of baseline values; during the fatal stroke experiment, the BFI decreased by up to about 95%, with a temporal resolution of 20 seconds. To the best of our knowledge, there are not existing methods which can measure the cerebral ischemia within the first few hours of the onset noninvasively. The MRI scanning was conducted at 24 h post injury. However, the images showed no abnormality. The results show the hybrid diffuse optical method can immediately measure the hemodynamic changes of miniature pigs in the first few hours of each single cerebral ischemia onset, and the BFI may be the promising biomarker to distinguish the cerebral ischemia and cerebral death.

neuroscience↗

bioRxiv2019

A general strategy to develop cell permeable and fluorogenic probes for multi-colour nanoscopy

Live-cell fluorescence nanoscopy is a powerful tool to study cellular biology on a molecular scale, yet its use is held back by the paucity of suitable fluorescent probes. Fluorescent probes based on regular fluorophores usually suffer from low cell permeability and unspecific background signal. We report a general strategy to transform regular fluorophores into fluorogenic probes with excellent cell permeability and low unspecific background signal. The strategy is based on the conversion of a carboxyl group found in rhodamines and related fluorophores into an electron-deficient amide. This conversion does not affect the spectroscopic properties of the fluorophore but permits it to exist in a dynamic equilibrium between two different forms: a fluorescent zwitterion and a non-fluorescent, cell permeable spirolactam. Probes based on such fluorophores generally are fluorogenic as the equilibrium shifts towards the fluorescent form when the probe binds to its cellular targets. The resulting increase in fluorescence can be up to 1000-fold. Using this simple design principle we created fluorogenic probes in various colours for different cellular targets for wash-free, multicolour, live-cell nanoscopy. The work establishes a general strategy to develop fluorogenic probes for live-cell bioimaging.

biochemistry↗

bioRxiv2017

A simple and powerful analysis of lateral subdiffusion using single particle tracking

In biological membranes many factors such as cytoskeleton, lipid composition, crowding and molecular interactions deviate lateral diffusion from the expected random walks. These factors have different effects on diffusion but act simultaneously so the observed diffusion is a complex mixture of diffusive behaviors (directed, >Brownian, anomalous or confined). Therefore commonly used approaches to quantify diffusion based on averaging of the displacements, such as the mean square displacement, are not adapted to the analysis of this heterogeneity. We introduce a new parameter, the packing coefficient Pc, which gives an estimate of the degree of free movement that a molecule displays in a period of time independently of its global diffusivity. Applying this approach to two different situations (diffusion of a lipid probe and trapping of receptors at synapses), we show that Pc detected and localized temporary changes of diffusive behavior both in time and in space. More importantly, it allowed the detection of periods with very high confinement (~immobility), their frequency and duration, and thus it can be used to calculate the effective kon and koff of scaffolding interactions such those that immobilize receptors at synapses.

biophysics↗