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Li, S.

Publications and source records attributed to Li, S..

At least 811 records · Page 45Linked to original sources

Stress-Induced Mucosal Layer Disruption Drives Gut Dysbiosis and Depressive-like Behaviors

Depression is a prevalent psychological condition with limited treatment options. While its etiology is multifactorial, both chronic stress and changes in the microbiome are associated with disease pathology. In depression, stress is known to induce microbiome dysbiosis, defined here as a change in microbial composition associated with a pathological condition. This state of dysbiosis is then known to feedback on depressive symptoms. While studies have demonstrated that targeted restoration of the microbiome can alleviate depressive-like symptoms in mice, translating these findings to human patients has proven challenging due to the complexity of the human microbiome. As such, there is an urgent need to identify factors upstream of microbial dysbiosis. Here we investigate the role of mucin 13 as an upstream mediator of microbiome composition changes. Using a model of chronic stress, we show that the mucosal protein, mucin 13, is selectively reduced after psychological stress exposure. We further demonstrate that the reduction of Muc13 is mediated by the Hnf4 transcription factor family. Finally, we determine that deleting Muc13 is sufficient to drive microbiome shifts and despair behaviors. These findings shed light on the mechanisms behind stress-induced microbial changes and reveal a regulator of mucin 13 expression. SummaryIn this paper, authors identified a pathway by which stress induces microbiome shifts. They found that psychological stress selectively alters a key mucosal protein, mucin 13, which in turn modifies the microbial niche to induce changes in bacterial composition.

microbiology↗

A suberized exodermis is required for tomato drought tolerance

Plant roots integrate environmental signals and developmental programs using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates the entry and exit of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation, but we find that it is absent in the tomato endodermis during normal development. Instead, suberin is present in the exodermis, a cell type that is absent in the model organism Arabidopsis thaliana. Here, we uncover genes driving exodermal suberization and describe its effects on drought responses in tomato, unravelling the similarities and differences with the paradigmatic Arabidopsis endodermis. Cellular resolution imaging, gene expression, and mutant analyses reveal loss of this program from the endodermis, and its co-option in the exodermis. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response. Controlling the degree of exodermal suberization could be a new strategy for breeding climate-resilient plants.

plant biology↗

A novel therapeutic approach of ultrasound stimulation to restore forelimb functions following cervical cord injury in rats

Low-intensity pulsed ultrasound (LIPUS) stimulation has shown promising results in neurorehabilitation following a traumatic injury in brain and peripheral nerves. However, the effects of LIPUS stimulation in the injured neural circuit after spinal cord injury (SCI) are still unknown. We investigated the effects of LIPUS on forelimb functions in chronic cervical cord injured rats with and without a serotonergic agonist drug, Buspirone treatment. Twenty-six rats were trained for forelimb reaching and grasping followed by C4 dorsal funiculi crush injury. To deliver LIPUS, a silicon-coated ultrasound disc was implanted above the cervical cord and EMG electrodes were implanted into forelimb muscles. In two cohorts (LIPUS and LIPUS + Buspirone) rats were tested pre-, with- and post-ultrasound stimulation. In LIPUS group rats, fore-limb reaching and grasping success rates first increased and then dropped after 3 weeks while for combination of drug and LIPUS stimulation the score continued to increase. Furthermore, LIPUS stimulation alone did not result in any significant improvement of grip strength compared to the control and combined groups. The findings of this study indicated the potential of LIPUS in SCI recovery and offer a future research direction of a new neuromodulation method.

neuroscience↗

CiDRE+ M2c macrophages hijacked by SARS-CoV-2 cause COVID-19 severity

Infection of the lungs with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via the angiotensin I converting enzyme 2 (ACE2) receptor induces a type of systemic inflammation known as a cytokine storm. However, the precise mechanisms involved in severe coronavirus disease 2019 (COVID-19) pneumonia are unknown. Here, we show that interleukin-10 (IL-10) changed normal alveolar macrophages into ACE2-expressing M2c-type macrophages that functioned as spreading vectors for SARS-CoV-2 infection. The depletion of alveolar macrophages and blockade of IL-10 attenuated SARS-CoV-2 pathogenicity. Furthermore, genome-wide association and quantitative trait locus analyses identified novel mRNA transcripts in human patients, COVID-19 infectivity enhancing dual receptor (CiDRE), which has unique synergistic effects within the IL-10-ACE2 system in M2c-type macrophages. Our results demonstrate that alveolar macrophages stimulated by IL-10 are key players in severe COVID-19. Collectively, CiDRE expression levels are potential risk factors that predict COVID-19 severity, and CiDRE inhibitors might be useful as COVID-19 therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/510331v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1e96c82org.highwire.dtl.DTLVardef@1d2dc32org.highwire.dtl.DTLVardef@7689d1org.highwire.dtl.DTLVardef@520d17_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

An Integrated Physiological, Cytology and Proteomics Reveals Network of Sugarcane Protoplasts Responses to Enzymolysis

The protoplast experimental system has been becoming a powerful tool for functional genomics and cell fusion breeding. However, the physiology and molecular mechanism during enzymolysis is not completely understood and has become a major obstacle to protoplast regeneration. Our study used physiological, cytology, iTRAQ (Isobaric Tags for Relative and Absolute Quantification) -based proteomic and RT-PCR analyses to compare the young leaves of sugarcane (ROC22) and protoplasts of more than 90% viability. We found that oxidation product MDA content increased in the protoplasts after enzymolysis and several antioxidant enzymes such as POD, CAT, APX, and O2- content significantly decreased. The cytology results showed that after enzymolysis, the cell membranes were perforated to different degrees, the nuclear activity was weakened, the nucleolus structure was not obvious, and the microtubules depolymerized and formed many short rod-like structures in protoplasts. The proteomic results showed that 1,477 differential proteins were down-regulated and 810 were up-regulated after enzymolysis of sugarcane young leaves. The GO terms, KEGG and KOG enrichment analysis revealed that differentially abundant proteins were mainly involved in bioenergetic metabolism, cellular processes, osmotic stress, and redox homeostasis of protoplasts, which would allow protein biosynthesis or / degradation. The RT-PCR analysis revealed the expression of osmotic stress resistance genes such as DREB, WRKY, MAPK4, and NAC were up-regulated. Meanwhile, the expression of key regeneration genes such as CyclinD3, CyclinA, CyclinB, Cdc2, PSK, CESA and GAUT were significantly down-regulated in the protoplasts. Hierarchical clustering, identification of redox proteins and oxidation products showed that these proteins were involved in dynamic networks in response to oxidative stress after enzymolysis. We used a variety of methods to figure out how young sugarcane leaves react to enzymes.

cell biology↗

Global transmission of Salmonella enterica serovars associated with historical pork trade via Euramerica centralized sourcing

Past decades have witnessed swine as the common sources of Salmonella enterica infections. Nevertheless, how Salmonella enterica entered food supply chains and caused foodborne outbreaks remains to be excluded. By analysis of 718 publicly Salmonella enterica isolates, we demonstrated that Euramerica act as the centralized sourcing for the global spread of Salmonella enterica which origins at the pinnacle of pork production. Specifically, the lineage of Salmonella Choleraesuis lend geographic support for their dispersal from Euramerica centralized origins. We used the generalized linear model to quantify the relative contributions of potential explanatory variables to the global transmission of Salmonella enterica. The global pork trade may act as the key driver for the geographic dispersal of Salmonella enterica over the world. In addition, the application of antimicrobials over the past 80 years may also exert a large impact on the evolution of Salmonella enterica genomics. Taken together, our findings provided the global lineage evolution of Salmonella enterica. Further investigation and potential intervention are needed to identify the global spread of Salmonella enterica over the world.

microbiology↗

Vascular-water-exchange MRI (VEXI) enables the detection of subtle BBB breakdown in Alzheimer's disease without MRI contrast agent

Blood-brain barrier (BBB) impairment is an important pathophysiological process in Alzheimers disease (AD) and a potential biomarker for early diagnosis of AD. However, most current neuroimaging methods assessing BBB function need the injection of exogenous contrast agents (or tracers), which limits the application of these methods in a large population. In this study, we aim to explore the feasibility of vascular water exchange MRI (VEXI), a diffusion-MRI-based method to assess the BBB permeability to water molecules without using a contrast agent, in the detection of the BBB breakdown in AD. We tested VEXI on a 3T MRI scanner on three groups: AD patients (AD group), mild cognitive impairment (MCI) patients due to AD (MCI group), and the age-matched normal cognition subjects (NC group). Interestingly, we find that VEXI can detect the BBB permeability to water molecules increase in MCI and this BBB breakdown happens specifically in the hippocampus. This BBB breakdown gets worse and extends to more brain regions (orbital frontal cortex and thalamus) from MCI group to the AD group. Furthermore, we find that the BBB breakdown of these three regions detected by VEXI is correlated significantly with impairment of respective cognitive domains independent of age, sex and education. These results suggest VEXI is a promising method to assess the BBB breakdown in AD. HighlightsO_LIThe vascular water exchange MRI (VEXI) is a contrast-agent-free method to assess BBB permeability C_LIO_LIBBB breakdown happens specifically in the hippocampus, orbital frontal cortex, and thalamus in AD C_LIO_LIBBB breakdown detected by VEXI is significantly correlated with cognitive dysfunction C_LI

neuroscience↗

Generation and functional analysis of defective viral genomes during SARS-CoV-2 infection

Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from RNA-seq datasets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hotspots were identified for DVG recombination and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single cell RNA-seq analysis indicated the IFN stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the NGS dataset from a published cohort study and observed significantly higher DVG amount and frequency in symptomatic patients than that in asymptomatic patients. Finally, we observed unusually high DVG frequency in one immunosuppressive patient up to 140 days after admitted to hospital due to COVID-19, first-time suggesting an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection. ImportanceDefective viral genomes (DVGs) are ubiquitously generated in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide them the potential for novel antiviral therapies and vaccine development. SARS-CoV-2 DVGs are generated through the recombination of two discontinuous genomic fragments by viral polymerase complex and the recombination is also one of the major mechanisms for the emergence of new coronaviruses. Focusing on the generation and function of SARS-CoV-2 DVGs, these studies identify new hotspots for non-homologous recombination and strongly suggest that the secondary structures within viral genomes mediate the recombination. Furthermore, these studies provide the first evidence for IFN stimulation activity of de novo DVGs during natural SARS-CoV-2 infection. These findings set up the foundation for further mechanism studies of SARS-CoV-2 recombination and provide the evidence to harness DVGs immunostimulatory potential in the development of vaccine and antivirals for SARS-CoV-2.

microbiology↗

Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products

Toll/interleukin-1 receptor (TIR) domain proteins function in cell death and immunity. In plants and bacteria, TIR domains are enzymes that produce isomers of cyclic ADPR (cADPR) as putative immune signaling molecules. The identity and functional conservation of cADPR isomer signals is unclear. A previous report found that a plant TIR could cross-activate the prokaryotic Thoeris TIR-immune system, suggesting the conservation of plant and prokaryotic TIR-immune signals. Here, we generate auto-active Thoeris TIRs and test the converse hypothesis: do prokaryotic Thoeris TIRs also cross-activate plant TIR-immunity? Using in planta and in vitro assays, we find that Thoeris and plant TIRs generate overlapping sets of cADPR isomers, and further clarify how plant and Thoeris TIRs activate the Thoeris system via producing 3cADPR. This study demonstrates that the TIR-signaling requirements for plant and prokaryotic immune systems are distinct and that TIRs across kingdoms generate a diversity of small molecule products.

plant biology↗

Evolutionary conservation of sequence motifs at sites of protein modification

Gene duplications are common in biology and are likely to be an important source of functional diversification and specialization. The yeast Saccharomyces cerevisiae underwent a whole genome duplication event early in evolution, and a substantial number of duplicated genes have been retained. We identified more than 3,500 instances where only one of two paralogous proteins undergoes post-translational modification despite having retained the same amino acid residue in both. We also developed a web-based search algorithm (CoSMoS.c.) that scores conservation of amino acid sequences based on 1011 wild and domesticated yeast isolates and used it to compare differentially-modified pairs of paralogous proteins. We found that the most common modifications - phosphorylation, ubiquitylation and acylation but not N-glycosylation - occur in regions of high sequence conservation. Such conservation is evident even for ubiquitylation and succinylation, where there is no established consensus site for modification. Differences in phosphorylation were not associated with predicted secondary structure or solvent accessibility, but did mirror known differences in kinase-substrate interactions. By integrating data from large scale proteomics and genomics analysis, in a system with such substantial genetic diversity, we obtained a more comprehensive understanding of the functional basis for genetic redundancies that have persisted for 100 million years.

systems biology↗

HOPE-SIM, a cryo-structured illumination fluorescence microscopy system for accurately targeted cryo-electron tomography

Cryo-focused ion beam (cryo-FIB) milling technology has been developed for the fabrication of cryo-lamella of frozen native specimens for study by in situ cryo-electron tomography (cryo-ET). However, the precision of the target of interest is still one of the major bottlenecks limiting application. Here, we developed a new cryo-correlative light and electron microscopy (cryo-CLEM) system named HOPE-SIM by incorporating a 3D structured illumination fluorescence microscopy (SIM) system and an upgraded high-vacuum stage to achieve efficiently targeted cryo-FIB. With the 3D super resolution of cryo-SIM as well as our cryo-CLEM software, 3D-View, the correlation precision of targeting region of interest can reach to 150 nm enough for the subsequent cryo-lamella fabrication. We successfully utilized the HOPE-SIM system to prepare cryo-lamellae targeting mitochondria, centrosomes of HeLa cells and herpesvirus assembly compartment of infected BHK-21 cells, which suggests the high potency of the HOPE-SIM system for future in situ cryo-ET workflows.

biophysics↗

Novel Small Molecular Compound AE-848 Showed Potent Inhibitory Activity Against Human Hepatoblastoma Cells

PurposeAE-848/33345007, is a novel small molecular compound that was independently synthesized by our laboratory. The aim of the current study was to investigate potential therapeutic effects of the small molecule compound AE-848 on human hepatoblastoma cells. MethodsHuman hepatoblastoma cell line HepG2 was cultured under different concentrations of AE-848. MTT assay was used to detect the inhibitory ability of AE-848 on the activity of this cell line, while flow cytometry was applied to quantify apoptosis. Western-blot technique was used to determine expression levels of signaling pathway-associated molecules. The antitumor in vivo activity of AE-848 against hepatoblastoma was evaluated using hepatoblastoma-bearing nude mice randomly divided into AE-848 (experimental) and saline (control) groups respectively. Changes in survival and tumor sizes were compared between these two groups. ResultsAE-848 significantly inhibited proliferation and induced apoptosis of HepG2 cells, and induced activation of PI3K/Akt/mTOR signaling pathways. More importantly, AE-848 administration significantly inhibited tumor growth and prolonged survival of hepatoblastoma-bearing mice. ConclusionAE-848 had a strong anti-hepatoblastoma activity both in vitro and in vivo, indicating the importance of developing AE-848 as a potential drug for hepatoblastoma treatment.

cancer biology↗

Cuproptosis is correlated with clinical status, tumor immune microenvironment and immunotherapy in colorectal cancer: a multi-omic analysis

Copper, like double-edged sword, either too little or too much can lead to cell death. Cuproptosis, a novel identified cell death form induced by copper, is characterized by aggregation of lipoylated mitochondrial enzymes and the destabilization of Fe-S cluster proteins. However, the function and potential clinical value of cuproptosis in colorectal cancer remains largely unknown. In this study, 16 cuproptosis-related molecules (CPRMs) were identified and analyzed by transcriptomics, genomics, and single-cell transcriptome profiling from multiple databases. We established two cuproptosis-related molecular phenotypes (CMP1 and 2) to distinguish CRC individuals, in which there were significantly differences in prognosis, biological function, somatic mutation frequency, immune cell infiltration in CRC individuals. A novel cuproptosis-related scoring system (CuproScore) was also constructed to predict the prognosis of CRC individuals, TME and the response to immunotherapy. Of notion, the value of CuproScore was also confirmed in our transcriptome cohort, demonstrating that CRC individuals in the high CuproScore group tended to have higher immune cell infiltrations and higher immune checkpoint expression. We also checked and analyzed the expression and clinical significance of 16 CPRMs in CRC cell lines and CRC tissues. This study indicated that cuproptosis and CPRMs played significant role in CRC progression and in modeling the TME. Inducing cuproptosis may be a useful tool for tumor therapy in the future.

cancer biology↗

Reactivation-induced memory integration prevents proactive interference in perceptual learning

We acquire perceptual skills through experience to adapt ourself to the changing environment. Accomplishing an effective skill acquisition is a main purpose of perceptual learning research. Given the often observed learning effect specificity, multiple perceptual learnings with shared parameters could serve to improve the generalization of the learning effect. However, the interference between the overlapping memory traces of different learnings may impede this effort. Here, we trained human participants on an orientation discrimination task. We observed a proactive interference effect that the first training blocked the second training at its untrained location. This was a more pronounced effect than the well-known location specificity in perceptual learning. We introduced a short reactivation of the first training before the second training and successfully eliminated the proactive interference when the second training was inside the reconsolidation time window of the reactivated first training. Interestingly, we found that practicing an irrelevant task at the location of the second training immediately after the reactivation of the first training could also restore the effect of the second training but in a smaller magnitude, even if the second training was conducted outside of the reconsolidation window. We proposed a two-level mechanism of reactivation-induced memory integration to account for these results. The reactivation-based procedure could integrate either the previously trained and untrained locations or the two trainings at these locations, depending on the activated representations during the reconsolidation process. The findings provide us with new insight into the roles of long-term memory mechanisms in perceptual learning.

neuroscience↗

ApoE4 causes severe COVID-19 outcomes via downregulation of ACE2

The coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); host cell entry by this virus relies on the interaction between the receptor-binding domain (RBD) of its spike glycoprotein and the angiotensin-converting enzyme 2 (ACE2) receptor on cell membranes. In addition to serving as a receptor for SARS-CoV-2, ACE2 was originally discovered as a protective factor in the renin-angiotensin system (RAS) that catalyses the degradation of angiotensin II (Ang II) to Ang 1-7, which is involved in multiple organ pathology. Recent genetic and clinical studies reported that ApoE4 expression is associated with increased susceptibility to SARS-CoV-2 infection and the development of severe COVID-19, but the underlying mechanism is currently unclear. In the present study, by using immunofluorescence staining, molecular dynamics simulations, proximity ligation assay (PLA) and coimmunoprecipitation (Co-IP) combined with a biolayer interferometry (BLI) assay, we found that ApoE interacts with both the spike protein and ACE2 but does not show obvious isoform-dependent binding effects. These data suggest that ApoE4 increases SARS-CoV-2 infectivity in a manner that may not depend on differential interactions with the spike protein or ACE2. Importantly, further immunoblotting and immunofluorescence staining results showed that ApoE4 significantly downregulates ACE2 protein expression in vitro and in vivo and subsequently decreases the conversion of Ang II to Ang 1-7, which could worsen tissue lesions; these findings provide a possible explain by which ApoE4 exacerbates COVID-19 disease.

neuroscience↗

Host mixotrophy, habitat stability and recombination may all decrease geographic differentiation between symbiont populations in Western Pacific deep-sea mussels

The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetics, environmental and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains, it is unknown whether these patterns are universal and how differences in ecological characteristics among host-symbiont associations influence the genomic structure of symbiont populations. To address this question, we sequenced metagenomes of different populations of the deep-sea mussel Bathymodiolus septemdierum, which are common at Western Pacific deep-sea hydrothermal vents and show characteristic patterns of niche partitioning with sympatric gastropod symbioses. Bathymodiolus septemdierum lives in close symbiotic relationship with sulfur-oxidizing chemosynthetic bacteria but supplements its symbiotrophic diet through filter-feeding, enabling it to occupy ecological niches with less exposure to geochemical reductants. Our analyses indicate that symbiont populations associated with B. septemdierum show structuring by geographic location, but that the dominant symbiont strain is uncorrelated with vent site. These patterns are in contrast to co-occurring Alviniconcha and Ifremeria symbioses that exhibit greater symbiont nutritional dependence and occupy habitats with higher spatial variability in environmental conditions. Our results suggest that relative habitat homogeneity combined with sufficient symbiont dispersal and genomic mixing might promote persistence of similar symbiont strains across geographic locations, while mixotrophy might decrease selective pressures on the host to affiliate with locally adapted symbiont strains. Overall, these data contribute to our understanding of the potential mechanisms influencing symbiont population structure across a spectrum of marine microbial symbioses that vary in ecological niche and relative host dependency.

evolutionary biology↗

Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility

Nucleosomes containing the histone variant H2A.Z are important for gene transcription initiation and termination, chromosome segregation and DNA double-strand break repair, among other functions. However, the underlying mechanism of how H2A.Z influences nucleosome stability, dynamics and DNA accessibility remains elusive as experimental and computational evidence are inconclusive. Our modeling efforts of nucleosome stability and dynamics, along with comparisons with experimental data show that the incorporation of H2A.Z results in a substantial decrease of the energy barrier for DNA unwrapping. This leads to spontaneous DNA unwrapping of about forty base pairs in total, enhanced DNA accessibility, nucleosome gapping and histone plasticity, which otherwise is not observed for canonical nucleosomes. We demonstrate that both N- and C-terminal tails of H2A.Z play major roles in these events, whereas H3.3 variant exerts a negligible impact in modulating the DNA end unwrapping. In summary, our results indicate that H2A.Z deposition makes nucleosomes more mobile and DNA more accessible to transcriptional machinery and other chromatin components.

biophysics↗

TMEM100, a Lung-Specific Endothelium Gene

The heterogeneity of endothelium across different organs was recently explored using single-cell RNA-sequencing analysis. Compared to other organs, the lung exhibits a distinct structure composed of a thin layer of capillary for efficient gas exchange. In this study, we demonstrate that Tmem100 is a lung-specific endothelium gene.

physiology↗