Biology subjects

sun, l.

Publications and source records attributed to sun, l..

4 recordsLinked to original sources

bioRxiv2024

Mass spectrometry-based top-down proteomics in nanomedicine: proteoform-specific measurement of protein corona

Conventional mass spectrometry (MS)-based bottom-up proteomics (BUP) analysis of protein corona [i.e., an evolving layer of biomolecules, mostly proteins, formed on the surface of nanoparticles (NPs) during their interactions with biomolecular fluids] enabled nanomedicine community to partly identify the biological identity of NPs. Such an approach, however, fails pinpoint the specific proteoforms--distinct molecular variants of proteins, which is essential for prediction of the biological fate and pharmacokinetics of nanomedicines. Recognizing this limitation, this study pioneers a robust and reproducible MS-based top-down proteomics (TDP) technique for precisely characterizing proteoforms in the protein corona. Our TDP approach has successfully identified hundreds of proteoforms in the protein corona of polystyrene NPs, ranging from 3-70 kDa, revealing over 20 protein biomarkers with combinations of post-translational modifications, signal peptide cleavages, and/or truncations--details that BUP could not fully discern. This advancement in MS-based TDP offers a more comprehensive and exact characterization of NP protein coronas, deepening our understanding of NPs biological identities and potentially revolutionizing the field of nanomedicine.

systems biology↗

bioRxiv2022

Gut microbiota assemblages of generalist predators are driven by local- and landscape-scale factors

The gut microbiomes of arthropods are reported to have significant impact on key physiological functions such as nutrition, reproduction, behavior, and health. Spiders are diverse and numerically dominant predators in crop fields where they are potentially important regulators of pests. The taxonomic structure of spider gut microbiomes, and environmental drivers of composition are unknown. Harnessing spiders to support agricultural productivity is likely to be supported by an understanding of the gut microbiomes of these predators. This study aimed to deciphering the gut microbiome assembly of predators as well as elucidating the potential implications of key environmental constraints in this process. Here, we used high-throughput sequencing to examine for the first time how the assemblages of bacteria in the gut of spiders are shaped by diverse environmental variables. A total of 27 bacterial phyla were detected with Proteobacteria and Firmicutes dominant. The core bacterial communities included the families Enterobacteriaceae, Chloroplast, Lactobacillaceae, Pseudomonadaceae, Lachnospiraceae, Leuconostocaceae and Ruminococcaceae. Local drivers of microbiome composition were the globally-relevant input use system (organic production versus conventional practice), and crop identity (Chinese cabbage versus cauliflower). Landscape-scale factors, proportion of forest and grassland, compositional diversity, and habitat edge density, also strongly affected gut microbiota. Specific bacterial taxa were enriched in the gut of spiders sampled from different settings and seasons. These findings provide a comprehensive insight into the composition and plasticity of spider gut microbiota. Understanding the temporal responses of specific microbiota could lead to innovative strategies development for boosting biological control services of predators.

ecology↗

bioRxiv2022

DNA metabarcoding of gut contents reveals key habitat and seasonal drivers of trophic networks involving generalist predators in agricultural landscapes

BACKGROUNDUnderstanding the networks of trophic interactions into which generalist predators are embedded is key to assessing their ecological role of in trophic networks and the biological control services they provide. The advent of affordable DNA metabarcoding approaches greatly facilitates quantitative understanding of trophic networks and their response to environmental drivers. Here, we examine how key environmental gradients interact to shape predation by Lycosidae in highly dynamic vegetable growing systems in China. RESULTSFor the sampled Lycosidae, crop identity, pesticide use, and seasons shape the abundance of preydetected in spider guts. For the taxonomic richness of prey, local- and landscape-scale factors gradients were more influential. Multivariate ordinations confirm that these crop-abundant spiders dynamically adjust their diet to reflect environmental constraints and seasonal availability to prey. CONCLUSIONThe plasticity in the diet composition is likely to account for the persistence of spiders in relatively ephemeral brassica crops. Our findings provide further insights into the optimization of habitat management for predator-based biological control practices.

ecology↗

bioRxiv2021

Nrf2 mediated ER-phagy protects against oxidative damage in intervertebral disc degeneration

Intervertebral disc degeneration (IDD) increases the risk of low back pain (LBP). Oxidative stress may induce cellular damage and contribute to various diseases including IDD. Endoplasmic reticulum autophagy (ER-phagy) is a specific type of autophagy, its role in oxidative stress induced damage as well as in IDD is unknown. This study explores the role of ER-phagy in oxidative damage in intervertebral disc nucleus pulposus cells (NPCs), as well as the Nrf2/FAM134B axis in ER-phagy regulation and IDD therapy. We found ER-phagy was decreased in NPCs during oxidative stress; while FAM134B may promote ER-phagy and alleviate oxidative stress induced ER-stress and apoptosis. In addition, the nuclear transcription factor Nrf2 may promote the expression of FAM134B as well as ER-phagy, and suppress ER-stress and apoptosis in NPCs. Furthermore, overexpression of FAM134B and Nrf2 could effectively attenuate the progression of IDD in rats in vivo. These results suggest Nrf2/FAM134B mediated ER-phagy may combat oxidative damage in cells; meanwhile, ER-phagy as well as Nrf2 could be potential therapeutic targets for IDD. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/469451v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@188b390org.highwire.dtl.DTLVardef@1c4e4f6org.highwire.dtl.DTLVardef@193fe77org.highwire.dtl.DTLVardef@12770e2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗