Biology subjects

li, c.

Publications and source records attributed to li, c..

4 recordsLinked to original sources

bioRxiv2021

Exosomal miR-106b-5p promotes Mtb survival via targeting CREB5 followed by SOAT1-CIDEC and CASP9-CASP3 pathway

Tuberculosis(TB) is one of the top ten fatal diseases, but the research on the mechanism of TB is still not perfect. Exosome, as an important intercellular signal transmission signal vehicle and the mechanism of exosomes in the interaction between macrophages and Mycobacterium tuberculosis(Mtb), is crucial for TB treatment. In the study, we found that exosomes, derived from Mtb-infected macrophage, exhibited differential enrichment in different organs in mice, causing inflammatory cell infiltration in lungs. Further experiments in vitro showed that exosomes resulted in increased lipid synthesis and inhibition of apoptosis in normal macrophages. In order to further explore its molecular mechanism, bioinformatics analysis showed that miR-106b-5p was up-regulated in exosomes. Subsequently, we verified miR-106b-5p was increased through a large number of blood samples from TB patients. In addition, we demonstrated that miR-106b-5p was upregulated in exosomes from Mtb-infected macrophages, which can be engulfed by uninfected macrophages and further result in miR-106b-5p increase. We next found that miR-106b-5p mediated the same effect as the exosomes derived from infected macrophage. Through further research, we indicated that miR-106b-5p promoted lipid droplet accumulation through regulation of Creb5-SOAT1-CIDEC and suppressed macrophage apoptosis via Creb5-CASP9-CASP3 pathway, which ultimately led to Mtb survival. These findings provide a certain theoretical basis and ideas for the diagnosis and treatment of TB as well as the selection of biomarkers.

microbiology↗

bioRxiv2020

Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III

BackgroundThe relationship between transcription and the 3D genome organization is one of the most important questions in molecular biology, but the roles of transcription in 3D chromatin remain controversial. Multiple groups showed that transcription affects global Cohesin binding and genome 3D structures. At the same time, several studies have indicated that transcription inhibition does not affect global chromatin interactions. ResultsHere, we provide the most comprehensive evidence to date to demonstrate that transcription plays a marginal role in organizing the 3D genome in mammalian cells: 1) degraded Pol I, Pol II and Pol III proteins in mESCs, and showed their loss results in little or no changes of global 3D chromatin structures for the first time; 2) selected RNA polymerases high abundance binding sites-associated interactions and found they still persist after the degradation; 3) generated higher resolution chromatin interaction maps and revealed that transcription inhibition mildly alters small loop domains; 4) identified Pol II bound but CTCF and Cohesin unbound loops and disclosed that they are largely resistant to transcription inhibition. Interestingly, Pol II depletion for a longer time significantly affects the chromatin accessibility and Cohesin occupancy, suggesting RNA polymerases are capable of affecting the 3D genome indirectly. So, the direct and indirect effects of transcription inhibition explain the previous confusing effects on the 3D genome. ConclusionsWe conclude that Pol I, Pol II, and Pol III loss only mildly alter chromatin interactions in mammalian cells, suggesting the 3D chromatin structures are pre-established and relatively stable.

genomics↗

bioRxiv2019

Experimental and simulated CO2 responses of photosynthesis in leaves of Hippophae rhamnoides L. under different soil water conditions

CO2 concentrations and soil moisture conditions seriously affect tree growth and physiological mechanisms. CO2 responses of photosynthesis are an important part of plant physiology and ecology research. This study investigated the photosynthetic CO2 responses in the leaves of two-year-old Hippophae rhamnoides L. under eight soil water conditions in a semi-arid loess hilly region, and discussed the quantitative relationship between CO2 responses and soil moisture. CO2 response curves and parameters were fitted using a rectangular hyperbola model, non-rectangular hyperbola model, exponential equation, and modified rectangular hyperbola model. Results revealed that the relative soil water content (RWC) required to maintain a high photosynthetic rate (Pn) and carboxylation efficiency (CE) ranged from 42.8% to 83.2%. When RWC fell outside these ranges, the photosynthetic capacity (Pnmax), CE, and CO2 saturation point (CSP) decreased. CO2 response curves and three parameters, CE, CO2 compensation point ({Gamma}), and photorespiration rate (Rp), were well fitted by the four models when RWC was appropriate. When RWC exceeded the optimal range, only the modified rectangular hyperbola model fitted the CO2 response curves and photosynthetic parameters better.

plant biology↗

bioRxiv2018

Response of soil microbial communities to alpine meadow degradation severity levels in the Qinghai-Tibet Plateau

Soil microbial community structure is an effective indicator to reflect changes in soil quality. Little is known about the effect of alpine meadow degradation on the soil bacterial and fungal community. In this study, we used the Illumina MiSeq sequencing method to analyze the microbial community structure of alpine meadow soil in five different degradation levels (i.e., non-degraded (ND), slightly degraded (LD), moderately degraded (MD), severely degraded (SD), and very severely degraded (VD)) in the Qinghai-Tibet Plateau. Proteobacteria, Actinobacteria, and Acidobacteria were the mainly bacterial phyla in meadow soil across all five degradation levels investigated. Basidiomycota was the mainly fungal phylum in ND; however, we found a shift from Basidiomycota to Ascomycota with an increase (severity) in degradation level. The overall proportion of Cortinariaceae exhibited high fungal variability, and reads were highest in ND (62.80%). Heatmaps of bacterial genera and fungal families showed a two-cluster sample division on a genus/family level: (1) an ND and LD group and (2) an SD, VD, and MD group. Redundancy analysis (RDA) showed that 79.7%and 71.3% of the variance in bacterial and fungal composition, respectively, could be explained by soil nutrient conditions (soil organic carbon, total nitrogen, and moisture) and plant properties (below-ground biomass). Our results indicate that meadow degradation affects both plant and soil properties and consequently drives changes in soil microbial community structure.

microbiology↗