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1.
Cell ; 186(13): 2748-2764.e22, 2023 06 22.
Article in English | MEDLINE | ID: mdl-37267948

ABSTRACT

Ferroptosis, a cell death process driven by iron-dependent phospholipid peroxidation, has been implicated in various diseases. There are two major surveillance mechanisms to suppress ferroptosis: one mediated by glutathione peroxidase 4 (GPX4) that catalyzes the reduction of phospholipid peroxides and the other mediated by enzymes, such as FSP1, that produce metabolites with free radical-trapping antioxidant activity. In this study, through a whole-genome CRISPR activation screen, followed by mechanistic investigation, we identified phospholipid-modifying enzymes MBOAT1 and MBOAT2 as ferroptosis suppressors. MBOAT1/2 inhibit ferroptosis by remodeling the cellular phospholipid profile, and strikingly, their ferroptosis surveillance function is independent of GPX4 or FSP1. MBOAT1 and MBOAT2 are transcriptionally upregulated by sex hormone receptors, i.e., estrogen receptor (ER) and androgen receptor (AR), respectively. A combination of ER or AR antagonist with ferroptosis induction significantly inhibited the growth of ER+ breast cancer and AR+ prostate cancer, even when tumors were resistant to single-agent hormonal therapies.


Subject(s)
Ferroptosis , Male , Humans , Phospholipid Hydroperoxide Glutathione Peroxidase , Lipid Peroxidation , Peroxides , Phospholipids
2.
Plant Cell ; 2024 May 13.
Article in English | MEDLINE | ID: mdl-38735686

ABSTRACT

Increasing grain yield is a major goal of breeders due to the rising global demand for food. We previously reported that the miR397-LACCASE (OsLAC) module regulates brassinosteroid (BR) signaling and grain yield in rice (Oryza sativa). However, the precise roles of laccase enzymes in the BR pathway remain unclear. Here, we report that OsLAC controls grain yield by preventing the turnover of TRANSTHYRETIN-LIKE (OsTTL), a negative regulator of BR signaling. Overexpressing OsTTL decreased BR sensitivity in rice, while loss-of-function of OsTTL led to enhanced BR signaling and increased grain yield. OsLAC directly binds to OsTTL and regulates its phosphorylation-mediated turnover. The phosphorylation site Ser226 of OsTTL is essential for its ubiquitination and degradation. Overexpressing the dephosphorylation-mimic form of OsTTL (OsTTLS226A) resulted in more severe defects than did overexpressing OsTTL. These findings provide insight into the role of an ancient laccase in BR signaling and suggest that the OsLAC-OsTTL module could serve as a target for improving grain yield.

3.
Genome Res ; 2023 Dec 08.
Article in English | MEDLINE | ID: mdl-37940553

ABSTRACT

DNA methylation and associated regulatory elements play a crucial role in gene expression regulation. Previous studies have focused primarily on the distribution of mean methylation levels. Advances in whole-genome bisulfite sequencing (WGBS) have enabled the characterization of DNA methylation haplotypes (MHAPs), representing CpG sites from the same read fragment on a single chromosome, and the subsequent identification of methylation haplotype blocks (MHBs), in which adjacent CpGs on the same fragment are comethylated. Using our expert-curated WGBS data sets, we report comprehensive landscapes of MHBs in 17 representative normal somatic human tissues and during early human embryonic development. Integrative analysis reveals MHBs as a distinctive type of regulatory element characterized by comethylation patterns rather than mean methylation levels. We show the enrichment of MHBs in open chromatin regions, tissue-specific histone marks, and enhancers, including super-enhancers. Moreover, we find that MHBs tend to localize near tissue-specific genes and show an association with differential gene expression that is independent of mean methylation. Similar findings are observed in the context of human embryonic development, highlighting the dynamic nature of MHBs during early development. Collectively, our comprehensive MHB landscapes provide valuable insights into the tissue specificity and developmental dynamics of DNA methylation.

4.
Brief Bioinform ; 25(3)2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38557677

ABSTRACT

Protein design is central to nearly all protein engineering problems, as it can enable the creation of proteins with new biological functions, such as improving the catalytic efficiency of enzymes. One key facet of protein design, fixed-backbone protein sequence design, seeks to design new sequences that will conform to a prescribed protein backbone structure. Nonetheless, existing sequence design methods present limitations, such as low sequence diversity and shortcomings in experimental validation of the designed functional proteins. These inadequacies obstruct the goal of functional protein design. To improve these limitations, we initially developed the Graphormer-based Protein Design (GPD) model. This model utilizes the Transformer on a graph-based representation of three-dimensional protein structures and incorporates Gaussian noise and a sequence random masks to node features, thereby enhancing sequence recovery and diversity. The performance of the GPD model was significantly better than that of the state-of-the-art ProteinMPNN model on multiple independent tests, especially for sequence diversity. We employed GPD to design CalB hydrolase and generated nine artificially designed CalB proteins. The results show a 1.7-fold increase in catalytic activity compared to that of the wild-type CalB and strong substrate selectivity on p-nitrophenyl acetate with different carbon chain lengths (C2-C16). Thus, the GPD method could be used for the de novo design of industrial enzymes and protein drugs. The code was released at https://github.com/decodermu/GPD.


Subject(s)
Protein Engineering , Proteins , Proteins/chemistry , Amino Acid Sequence , Protein Engineering/methods
5.
Nat Chem Biol ; 20(3): 365-372, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37828400

ABSTRACT

Stimulator of interferon genes (STING) is a dimeric transmembrane adapter protein that plays a key role in the human innate immune response to infection and has been therapeutically exploited for its antitumor activity. The activation of STING requires its high-order oligomerization, which could be induced by binding of the endogenous ligand, cGAMP, to the cytosolic ligand-binding domain. Here we report the discovery through functional screens of a class of compounds, named NVS-STGs, that activate human STING. Our cryo-EM structures show that NVS-STG2 induces the high-order oligomerization of human STING by binding to a pocket between the transmembrane domains of the neighboring STING dimers, effectively acting as a molecular glue. Our functional assays showed that NVS-STG2 could elicit potent STING-mediated immune responses in cells and antitumor activities in animal models.


Subject(s)
Adaptor Proteins, Signal Transducing , Membrane Proteins , Animals , Humans , Adaptor Proteins, Signal Transducing/metabolism , Biological Assay , Cytosol , Immunity, Innate , Ligands , Membrane Proteins/metabolism
6.
Nucleic Acids Res ; 52(D1): D929-D937, 2024 Jan 05.
Article in English | MEDLINE | ID: mdl-37831137

ABSTRACT

DNA methylation acts as a vital epigenetic regulatory mechanism involved in controlling gene expression. Advances in sequencing technologies have enabled characterization of methylation patterns at single-base resolution using bisulfite sequencing approaches. However, existing methylation databases have primarily focused on mean methylation levels, overlooking phased methylation patterns. The methylation status of CpGs on individual sequencing reads represents discrete DNA methylation haplotypes (mHaps). Here, we present mHapBrowser, a comprehensive database for visualizing and analyzing mHaps. We systematically processed data of diverse tissues in human, mouse and rat from public repositories, generating mHap format files for 6366 samples. mHapBrowser enables users to visualize eight mHap metrics across the genome through an integrated WashU Epigenome Browser. It also provides an online server for comparing mHap patterns across samples. Additionally, mHap files for all samples can be downloaded to facilitate local processing using downstream analysis toolkits. The utilities of mHapBrowser were demonstrated through three case studies: (i) mHap patterns are associated with gene expression; (ii) changes in mHap patterns independent of mean methylation correlate with differential expression between lung cancer subtypes; and (iii) the mHap metric MHL outperforms mean methylation for classifying tumor and normal samples from cell-free DNA. The database is freely accessible at http://mhap.sibcb.ac.cn/.


Subject(s)
DNA Methylation , Databases, Genetic , Animals , Humans , Mice , Rats , Epigenesis, Genetic , Haplotypes , Sequence Analysis, DNA
7.
Plant Physiol ; 194(4): 2101-2116, 2024 Mar 29.
Article in English | MEDLINE | ID: mdl-37995372

ABSTRACT

The precise timing of flowering plays a pivotal role in ensuring successful plant reproduction and seed production. This process is intricately governed by complex genetic networks that integrate internal and external signals. This study delved into the regulatory function of microRNA397 (miR397) and its target gene LACCASE-15 (OsLAC15) in modulating flowering traits in rice (Oryza sativa). Overexpression of miR397 led to earlier heading dates, decreased number of leaves on the main stem, and accelerated differentiation of the spikelet meristem. Conversely, overexpression of OsLAC15 resulted in delayed flowering and prolonged vegetative growth. Through biochemical and physiological assays, we uncovered that miR397-OsLAC15 had a profound impact on carbohydrate accumulation and photosynthetic assimilation, consequently enhancing the photosynthetic intensity in miR397-overexpressing rice plants. Notably, we identified that OsLAC15 is at least partially localized within the peroxisome organelle, where it regulates the photorespiration pathway. Moreover, we observed that a high CO2 concentration could rescue the late flowering phenotype in OsLAC15-overexpressing plants. These findings shed valuable insights into the regulatory mechanisms of miR397-OsLAC15 in rice flowering and provided potential strategies for developing crop varieties with early flowering and high-yield traits through genetic breeding.


Subject(s)
Oryza , Oryza/metabolism , Flowers/physiology , Plant Breeding , Plant Leaves/genetics , Plant Leaves/metabolism , Reproduction , Plant Proteins/genetics , Plant Proteins/metabolism , Gene Expression Regulation, Plant
8.
Proc Natl Acad Sci U S A ; 119(11): e2118570119, 2022 03 15.
Article in English | MEDLINE | ID: mdl-35263227

ABSTRACT

SignificanceDespite the identification of neural circuits and circulating hormones in olfactory regulation, the peripheral targets for olfactory modulation remain relatively unexplored. Here we show that dopamine D2 receptor (DRD2) is expressed in the cilia and somata of mature olfactory sensory neurons (OSNs), while nasal dopamine (DA) is mainly released from the sympathetic nerve terminals, which innervate the mouse olfactory mucosa (OM). We further demonstrate that DA-DRD2 signaling in the nose plays important roles in regulating olfactory function using genetic and pharmacological approaches. Moreover, the local DA synthesis in mouse OM is reduced during hunger, which contributes to starvation-induced olfactory enhancement. Altogether, we demonstrate that nasal DA and DRD2 receptor can serve as the potential peripheral targets for olfactory modulation.


Subject(s)
Dopamine , Olfactory Receptor Neurons , Receptors, Dopamine D2 , Animals , Dopamine/metabolism , Dopamine D2 Receptor Antagonists/pharmacology , Humans , Mice , Olfactory Receptor Neurons/metabolism , Receptors, Dopamine D2/genetics , Receptors, Dopamine D2/metabolism , Signal Transduction , Smell
9.
BMC Genomics ; 25(1): 130, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38302916

ABSTRACT

BACKGROUND: Circadian rhythm is crucial to the function of the immune system. Disorders of the circadian rhythm can contribute to inflammatory diseases such as Ulcerative colitis (UC). This Mendelian Randomization (MR) analysis applies genetic tools to represent the aggregated statistical results of exposure to circadian rhythm disorders and UC and its comorbidities, allowing for causal inferences. METHODS: Summary statistics of protein, DNA methylation and gene expression quantitative trait loci in individuals of European ancestry (pQTL, mQTL, and eQTL, respectively) were used. Genetic variants located within or near 152 circadian clock-related genes and closely related to circadian rhythm disorders were selected as instrumental variables. Causal relationships with UC and its comorbidities were then estimated through employed Summary data-based Mendelian Randomization (SMR) and Inverse-Variance-Weighted MR (IVW-MR). RESULTS: Through preliminary SMR analysis, we identified a potential causal relationship between circadian clock-related genes and UC along with its comorbidities, which was further confirmed by IVW-MR analysis. Our study identified strong evidence of positive correlation involving seven overlapping genes (CSNK1E, OPRL1, PIWIL2, RORC, MAX, PPP5C, and AANAT) through MWAS and TWAS in UC, four overlapping genes (OPRL1, CHRNB2, FBXL17, and SIRT1) in UC with PSC, and three overlapping genes (ARNTL, USP7, and KRAS) in UC with arthropathy. CONCLUSIONS: This SMR study demonstrates the causal effect of circadian rhythm disorders in UC and its comorbidities. Furthermore, our investigation pinpointed candidate genes that could potentially serve as drug targets.


Subject(s)
Chronobiology Disorders , Circadian Clocks , Colitis, Ulcerative , Humans , Colitis, Ulcerative/genetics , Circadian Clocks/genetics , Mendelian Randomization Analysis , Comorbidity , Genome-Wide Association Study , Ubiquitin-Specific Peptidase 7 , Argonaute Proteins
10.
Neuroimage ; 296: 120683, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38880308

ABSTRACT

Temporal lobe epilepsy (TLE) stands as the predominant adult focal epilepsy syndrome, characterized by dysfunctional intrinsic brain dynamics. However, the precise mechanisms underlying seizures in these patients remain elusive. Our study encompassed 116 TLE patients compared with 51 healthy controls. Employing microstate analysis, we assessed brain dynamic disparities between TLE patients and healthy controls, as well as between drug-resistant epilepsy (DRE) and drug-sensitive epilepsy (DSE) patients. We constructed dynamic functional connectivity networks based on microstates and quantified their spatial and temporal variability. Utilizing these brain network features, we developed machine learning models to discriminate between TLE patients and healthy controls, and between DRE and DSE patients. Temporal dynamics in TLE patients exhibited significant acceleration compared to healthy controls, along with heightened synchronization and instability in brain networks. Moreover, DRE patients displayed notably lower spatial variability in certain parts of microstate B, E and F dynamic functional connectivity networks, while temporal variability in certain parts of microstate E and G dynamic functional connectivity networks was markedly higher in DRE patients compared to DSE patients. The machine learning model based on these spatiotemporal metrics effectively differentiated TLE patients from healthy controls and discerned DRE from DSE patients. The accelerated microstate dynamics and disrupted microstate sequences observed in TLE patients mirror highly unstable intrinsic brain dynamics, potentially underlying abnormal discharges. Additionally, the presence of highly synchronized and unstable activities in brain networks of DRE patients signifies the establishment of stable epileptogenic networks, contributing to the poor responsiveness to antiseizure medications. The model based on spatiotemporal metrics demonstrated robust predictive performance, accurately distinguishing both TLE patients from healthy controls and DRE patients from DSE patients.


Subject(s)
Epilepsy, Temporal Lobe , Machine Learning , Magnetic Resonance Imaging , Humans , Epilepsy, Temporal Lobe/physiopathology , Epilepsy, Temporal Lobe/diagnostic imaging , Adult , Male , Female , Middle Aged , Magnetic Resonance Imaging/methods , Nerve Net/physiopathology , Nerve Net/diagnostic imaging , Brain/physiopathology , Brain/diagnostic imaging , Young Adult , Drug Resistant Epilepsy/physiopathology , Drug Resistant Epilepsy/diagnostic imaging , Connectome/methods
11.
EMBO J ; 39(10): e103111, 2020 05 18.
Article in English | MEDLINE | ID: mdl-32187724

ABSTRACT

The homeostatic link between oxidative stress and autophagy plays an important role in cellular responses to a wide variety of physiological and pathological conditions. However, the regulatory pathway and outcomes remain incompletely understood. Here, we show that reactive oxygen species (ROS) function as signaling molecules that regulate autophagy through ataxia-telangiectasia mutated (ATM) and cell cycle checkpoint kinase 2 (CHK2), a DNA damage response (DDR) pathway activated during metabolic and hypoxic stress. We report that CHK2 binds to and phosphorylates Beclin 1 at Ser90/Ser93, thereby impairing Beclin 1-Bcl-2 autophagy-regulatory complex formation in a ROS-dependent fashion. We further demonstrate that CHK2-mediated autophagy has an unexpected role in reducing ROS levels via the removal of damaged mitochondria, which is required for cell survival under stress conditions. Finally, CHK2-/- mice display aggravated infarct phenotypes and reduced Beclin 1 p-Ser90/Ser93 in a cerebral stroke model, suggesting an in vivo role of CHK2-induced autophagy in cell survival. Taken together, these results indicate that the ROS-ATM-CHK2-Beclin 1-autophagy axis serves as a physiological adaptation pathway that protects cells exposed to pathological conditions from stress-induced tissue damage.


Subject(s)
Ataxia Telangiectasia Mutated Proteins/metabolism , Beclin-1/metabolism , Checkpoint Kinase 2/metabolism , Ischemic Stroke/metabolism , Reactive Oxygen Species/metabolism , Animals , Autophagy , Cell Line , Disease Models, Animal , HCT116 Cells , HEK293 Cells , HeLa Cells , Humans , Mice , Oxidative Stress , Phosphorylation
12.
Anal Chem ; 96(16): 6381-6389, 2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38593059

ABSTRACT

Pyroptosis is closely related to the development and treatment of various cancers; thus, comprehensive studies of the correlations between pyroptosis and its inductive or inhibitive factors can provide new ideas for the intervention and diagnosis of tumors. The dysfunction of mitochondria may induce pyroptosis in cancer cells, which can be reflected by the fluctuations of the microenvironmental parameters in mitochondria as well as the changes of mitochondrial DNA level and morphology, etc. To precisely track and assess the mitochondria-associated pyroptosis process, simultaneous visualization of changes in multiphysiological parameters in mitochondria is highly desirable. In this work, we reported a nonreaction-based, multifunctional small-molecule fluorescent probe Mito-DK with the capability of crosstalk-free response to polarity and mtDNA as well as mitochondrial morphology. Accurate assessment of mitochondria-associated pyroptosis induced by palmitic acid/H2O2 was achieved through monitoring changes in mitochondrial multiple parameters with the help of Mito-DK. In particular, the pyroptosis-inducing ability of an antibiotic doxorubicin and the pyroptosis-inhibiting capacity of an anticancer agent puerarin were evaluated by Mito-DK. These results provide new perspectives for visualizing mitochondria-associated pyroptosis and offer new approaches for screening pyroptosis-related anticancer agents.


Subject(s)
Fluorescent Dyes , Mitochondria , Pyroptosis , Pyroptosis/drug effects , Fluorescent Dyes/chemistry , Fluorescent Dyes/chemical synthesis , Humans , Mitochondria/metabolism , Mitochondria/drug effects , Small Molecule Libraries/chemistry , Small Molecule Libraries/pharmacology , Doxorubicin/pharmacology , Doxorubicin/chemistry
13.
Anal Chem ; 96(10): 4232-4241, 2024 Mar 12.
Article in English | MEDLINE | ID: mdl-38421725

ABSTRACT

Myocardial fibrosis is frequently accompanied by elevated levels of oxidative stress. Mitochondrial glutathione (mGSH), an essential biomolecule for maintaining redox homeostasis in mitochondria, could serve as an effective indicator for investigating the oxidative stress associated with myocardial fibrosis. In this study, a ratiometric fluorescent probe named Mito-NS6, capable of being anchored in mitochondria and reversibly responding to GSH with an appropriate dissociation equilibrium constant, was rationally designed and utilized to visualize and evaluate the changes of mGSH levels caused by oxidative stress in myocardial fibrosis. Benefiting from the good performance of Mito-NS6, we successfully achieved the quantification of mGSH in cardiac fibroblasts using a confocal laser-scanning microscope, revealing that salvianolic acid B (SalB) can act as an effective drug to alleviate myocardial fibrosis through depressing oxidative stress. Moreover, we employed ratio fluorescence imaging to track the fluctuation in GSH levels within a mice model of myocardial fibrosis induced by isoproterenol and found that myocardial fibrosis caused a higher oxidative stress level in myocardial tissue as well as heart organs. These results provide a novel point of view for the diagnosis and treatment of myocardial fibrosis.


Subject(s)
Mitochondria , Oxidative Stress , Mice , Animals , Mitochondria/metabolism , Glutathione/metabolism , Myocardium/metabolism , Fibrosis
14.
Genome Res ; 31(4): 622-634, 2021 04.
Article in English | MEDLINE | ID: mdl-33722936

ABSTRACT

Heterosis or hybrid vigor is a common phenomenon in plants and animals; however, the molecular mechanisms underlying heterosis remain elusive, despite extensive studies on the phenomenon for more than a century. Here we constructed a large collection of F1 hybrids of Saccharomyces cerevisiae by spore-to-spore mating between homozygous wild strains of the species with different genetic distances and compared growth performance of the F1 hybrids with their parents. We found that heterosis was prevalent in the F1 hybrids at 40°C. A hump-shaped relationship between heterosis and parental genetic distance was observed. We then analyzed transcriptomes of selected heterotic and depressed F1 hybrids and their parents growing at 40°C and found that genes associated with one-carbon metabolism and related pathways were generally up-regulated in the heterotic F1 hybrids, leading to improved cellular redox homeostasis at high temperature. Consistently, genes related with DNA repair, stress responses, and ion homeostasis were generally down-regulated in the heterotic F1 hybrids. Furthermore, genes associated with protein quality control systems were also generally down-regulated in the heterotic F1 hybrids, suggesting a lower level of protein turnover and thus higher energy use efficiency in these strains. In contrast, the depressed F1 hybrids, which were limited in number and mostly shared a common aneuploid parental strain, showed a largely opposite gene expression pattern to the heterotic F1 hybrids. We provide new insights into molecular mechanisms underlying heterosis and thermotolerance of yeast and new clues for a better understanding of the molecular basis of heterosis in plants and animals.


Subject(s)
Carbon/metabolism , Homeostasis , Hot Temperature , Hybrid Vigor , Saccharomyces cerevisiae , Homeostasis/genetics , Hybrid Vigor/genetics , Hybridization, Genetic , Oxidation-Reduction , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Up-Regulation
15.
Small ; : e2403002, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38923293

ABSTRACT

Van der Waals (vdW) magnetic materials have broad application prospects in next-generation spintronics. Inserting magnetic elements into nonmagnetic vdW materials can introduce magnetism and enhance various transport properties. Herein, the unconventional magnetic and magneto-transport phenomena is reported in Ni0.28TaSeS crystal by intercalating Ni atoms into nonmagnetic 2H-TaSeS matrix. Magnetic characterization reveals a canted magnetic structure in Ni0.28TaSeS, which results in an antiferromagnetic (AFM) order along the c-axis and a ferromagnetic (FM) moment in the ab-plane. The presence of spin-flop (SF) behavior can also be attributed to the canted magnetic structure. Temperature-dependent resistivity exhibits a metallic behavior with an abrupt decrease corresponding to the magnetic transition. Magneto-transport measurements demonstrate a positive magnetoresistance (MR) with a plateau that is different from conventional magnetic materials. The field-dependent Hall signal exhibits nonlinear field dependence when the material is in magnetically ordered state. These unconventional magneto-transport behaviors are attributed to the field-induced formation of a complex spin texture in Ni0.28TaSeS. In addition, it further investigated the angle dependence of MR and observed an unusual fourfold anisotropic magnetoresistance (AMR) effect. This work inspires future research on spintronic devices utilizing magnetic atom-intercalated quasi-2D materials.

16.
Appl Environ Microbiol ; 90(5): e0004624, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38563787

ABSTRACT

Dietary fiber metabolism by gut microorganisms plays important roles in host physiology and health. Alginate, the major dietary fiber of daily diet seaweeds, is drawing more attention because of multiple biological activities. To advance the understanding of alginate assimilation mechanism in the gut, we show the presence of unsaturated alginate oligosaccharides (uAOS)-specific alginate utilization loci (AUL) in human gut microbiome. As a representative example, a working model of the AUL from the gut microorganism Bacteroides clarus was reconstructed from biochemistry and transcriptome data. The fermentation of resulting monosaccharides through Entner-Doudoroff pathway tunes the metabolism of short-chain fatty acids and amino acids. Furthermore, we show that uAOS feeding protects the mice against dextran sulfate sodium-induced acute colitis probably by remodeling gut microbiota and metabolome. IMPORTANCE: Alginate has been included in traditional Chinese medicine and daily diet for centuries. Recently discovered biological activities suggested that alginate-derived alginate oligosaccharides (AOS) might be an active ingredient in traditional Chinese medicine, but how these AOS are metabolized in the gut and how it affects health need more information. The study on the working mechanism of alginate utilization loci (AUL) by the gut microorganism uncovers the role of unsaturated alginate oligosaccharides (uAOS) assimilation in tuning short-chain fatty acids and amino acids metabolism and demonstrates that uAOS metabolism by gut microorganisms results in a variation of cell metabolites, which potentially contributes to the physiology and health of gut.


Subject(s)
Alginates , Gastrointestinal Microbiome , Oligosaccharides , Alginates/metabolism , Oligosaccharides/metabolism , Mice , Animals , Humans , Colitis/microbiology , Colitis/chemically induced , Mice, Inbred C57BL , Fatty Acids, Volatile/metabolism , Inflammation/metabolism , Dextran Sulfate , Dietary Fiber/metabolism
17.
Opt Express ; 32(8): 14713-14718, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38859408

ABSTRACT

High power 509 nm continuous-wave (CW) lasers have important applications in science and communication. Here we demonstrate a robust high-power single-frequency 509 nm laser system based on nonlinear phase demodulation technique and single-pass second harmonic generation (SHG) configuration. In experiments, the single-frequency fundamental wave at 1018 nm was linewidth-broadened by an electro-optical modulator and then amplified to 207 W in a ytterbium-doped fiber amplifier. In subsequent single-pass SHG stage, over 20 W CW single-frequency 509 nm laser was generated in a LiB3O5 crystal with a SHG efficiency of 9.7%. To the best of our knowledge, this is the highest reported power for CW single-frequency 509 nm laser, which could be used for advanced underwater optical communication and preparation of cesium Rydberg state.

18.
Opt Express ; 32(7): 11271-11280, 2024 Mar 25.
Article in English | MEDLINE | ID: mdl-38570978

ABSTRACT

The advent of optical metrology applications has necessitated the development of compact, reliable, and cost-effective picosecond lasers operating around 900 nm, specifically catering to the requirements of precise ranging. In response to this demand, our work introduces an innovative solution-an all-fiber, all-polarization-maintaining (PM) figure-9 mode-locked laser operating at 915 nm. The proposed figure-9 Nd-doped fiber laser has a 69.2 m long cavity length, strategically designed and optimized to yield pulses with a combination of high pulse energy and low repetition rate. The laser can generate 915 nm laser pulses with a pulse energy of 4.65 nJ, a pulse duration of 15.2 ps under the repetition rate of 3.05 MHz. The 1064 nm amplified spontaneous emission (ASE) is deliberately filtered out, in order to prevent parasitic lasing and increase the spectral proportion of the 915 nm laser. The all-PM fiber configuration of this laser imparts exceptional mode-locking performance and environmental robustness, which is confirmed by long-term output power and spectral stability test. This compact and long-term reliable fiber laser could be a promising light source for applications like inter-satellite ranging.

19.
Opt Express ; 32(11): 18562-18571, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38859009

ABSTRACT

The relative intensity noise (RIN) characteristics of a continuous-wave diamond Raman laser are investigated for the first time. The results reveal the parasitic stimulated Brillouin scattering (SBS) that usually occurred with higher-order spatial modes in the diamond Raman resonator is a pivotal factor impacting the Raman longitudinal modes and deteriorating the RIN level. The diamond Raman laser automatically switches to single-longitudinal-mode operation and the RIN level is significantly decreased in the frequency range of 200 Hz to 1 MHz after the parasitic SBS is effectively suppressed through inserting a spatial aperture or a χ(2) nonlinear crystal into the cavity. Due to the introduction of additional nonlinear loss to the high intensity Raman fluctuations and the non-lasing spontaneous Raman modes, the χ(2) nonlinear crystal enables better performance in the RIN-level reduction compared to the spatial aperture which can only achieve SBS inhibition. The RIN reduction routes are well suited for various crystalline Raman media to achieve high power and low intensity noise laser at different wavelengths.

20.
NMR Biomed ; : e5166, 2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38654579

ABSTRACT

Arterial spin labeling (ASL) and dynamic susceptibility contrast (DSC) magnetic resonance imaging (MRI) have shown potential for differentiating tumor progression from pseudoprogression. For pseudocontinuous ASL with a single postlabeling delay, the presence of delayed arterial transit times (ATTs) could affect the evaluation of ASL-MRI perfusion data. In this study, the influence of ATT artifacts on the perfusion assessment and differentiation between tumor progression and pseudoprogression were studied. This study comprised 66 adult patients (mean age 60 ± 13 years; 40 males) with a histologically confirmed glioblastoma who received postoperative radio (chemo)therapy. ASL-MRI and DSC-MRI scans were acquired at 3 months postradiotherapy as part of the standard clinical routine. These scans were visually scored regarding (i) the severity of ATT artifacts (%) on the ASL-MRI scans only, scored by two neuroradiologists; (ii) perfusion of the enhancing tumor lesion; and (iii) radiological evaluation of tumor progression versus pseudoprogression by one neuroradiologist. The final outcome was based on combined clinical and radiological follow-up until 9 months postradiotherapy. ATT artifacts were identified in all patients based on the mean scores of two raters. A significant difference between the radiological evaluation of ASL-MRI and DSC-MRI was observed only for ASL images with moderate ATT severity (30%-65%). The perfusion assessment showed ASL-MRI tending more towards hyperperfusion than DSC-MRI in the case of moderate ATT artifacts. In addition, there was a significant difference between the prediction of tumor progression with ASL-MRI and the final outcome in the case of severe ATT artifacts (McNemar test, p = 0.041). Despite using ASL imaging parameters close to the recommended settings, ATT artifacts frequently occur in patients with treated brain tumors. Those artifacts could hinder the radiological evaluation of ASL-MRI data and the detection of true disease progression, potentially affecting treatment decisions for patients with glioblastoma.

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