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1.
Nat Immunol ; 21(7): 746-755, 2020 07.
Article in English | MEDLINE | ID: mdl-32514064

ABSTRACT

Plasma membranes of animal cells are enriched for cholesterol. Cholesterol-dependent cytolysins (CDCs) are pore-forming toxins secreted by bacteria that target membrane cholesterol for their effector function. Phagocytes are essential for clearance of CDC-producing bacteria; however, the mechanisms by which these cells evade the deleterious effects of CDCs are largely unknown. Here, we report that interferon (IFN) signals convey resistance to CDC-induced pores on macrophages and neutrophils. We traced IFN-mediated resistance to CDCs to the rapid modulation of a specific pool of cholesterol in the plasma membrane of macrophages without changes to total cholesterol levels. Resistance to CDC-induced pore formation requires the production of the oxysterol 25-hydroxycholesterol (25HC), inhibition of cholesterol synthesis and redistribution of cholesterol to an esterified cholesterol pool. Accordingly, blocking the ability of IFN to reprogram cholesterol metabolism abrogates cellular protection and renders mice more susceptible to CDC-induced tissue damage. These studies illuminate targeted regulation of membrane cholesterol content as a host defense strategy.


Subject(s)
Bacterial Infections/immunology , Bacterial Toxins/immunology , Hydroxycholesterols/metabolism , Interferons/isolation & purification , Phagocytes/immunology , Streptolysins/immunology , Animals , Bacteria/immunology , Bacteria/metabolism , Bacterial Proteins/administration & dosage , Bacterial Proteins/immunology , Bacterial Proteins/metabolism , Bacterial Toxins/metabolism , Cell Membrane/metabolism , Cell Membrane Permeability/immunology , Cells, Cultured , Disease Models, Animal , Disease Susceptibility/immunology , Female , Host Microbial Interactions/immunology , Humans , Intravital Microscopy , Male , Mice , Mice, Transgenic , Phagocytes/cytology , Phagocytes/metabolism , Primary Cell Culture , Steroid Hydroxylases/genetics , Steroid Hydroxylases/metabolism , Streptolysins/administration & dosage , Streptolysins/metabolism
2.
Immunity ; 56(1): 180-192.e11, 2023 01 10.
Article in English | MEDLINE | ID: mdl-36563676

ABSTRACT

The reinvigoration of anti-tumor T cells in response to immune checkpoint blockade (ICB) therapy is well established. Whether and how ICB therapy manipulates antibody-mediated immune response in cancer environments, however, remains elusive. Using tandem mass spectrometric analysis of modification of immunoglobulin G (IgG) from hepatoma tissues, we identified a role of ICB therapy in catalyzing IgG sialylation in the Fc region. Effector T cells triggered sialylation of IgG via an interferon (IFN)-γ-ST6Gal-I-dependent pathway. DC-SIGN+ macrophages represented the main target cells of sialylated IgG. Upon interacting with sialylated IgG, DC-SIGN stimulated Raf-1-elicited elevation of ATF3, which inactivated cGAS-STING pathway and eliminated subsequent type-I-IFN-triggered antitumorigenic immunity. Although enhanced IgG sialylation in tumors predicted improved therapeutic outcomes for patients receiving ICB therapy, impeding IgG sialylation augmented antitumorigenic T cell immunity after ICB therapy. Thus, targeting antibody-based negative feedback action of ICB therapy has potential for improving efficacy of cancer immunotherapies.


Subject(s)
Carcinoma, Hepatocellular , Interferon Type I , Liver Neoplasms , Humans , Immunoglobulin G , Carcinoma, Hepatocellular/drug therapy , Liver Neoplasms/drug therapy , Immunotherapy/methods
3.
Cell ; 161(6): 1437-52, 2015 Jun 04.
Article in English | MEDLINE | ID: mdl-26046443

ABSTRACT

Germ cells are vital for transmitting genetic information from one generation to the next and for maintaining the continuation of species. Here, we analyze the transcriptome of human primordial germ cells (PGCs) from the migrating stage to the gonadal stage at single-cell and single-base resolutions. Human PGCs show unique transcription patterns involving the simultaneous expression of both pluripotency genes and germline-specific genes, with a subset of them displaying developmental-stage-specific features. Furthermore, we analyze the DNA methylome of human PGCs and find global demethylation of their genomes. Approximately 10 to 11 weeks after gestation, the PGCs are nearly devoid of any DNA methylation, with only 7.8% and 6.0% of the median methylation levels in male and female PGCs, respectively. Our work paves the way toward deciphering the complex epigenetic reprogramming of the germline with the aim of restoring totipotency in fertilized oocytes.


Subject(s)
DNA Methylation , Germ Cells/metabolism , Transcriptome , Cell Movement , Chromosomes, Human, X , Cluster Analysis , Embryo, Mammalian/metabolism , Female , Histones/metabolism , Humans , Male , Principal Component Analysis , SOX Transcription Factors/metabolism
4.
Nature ; 627(8004): 628-635, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38383790

ABSTRACT

Interleukin-10 (IL-10) is a key anti-inflammatory cytokine that can limit immune cell activation and cytokine production in innate immune cell types1. Loss of IL-10 signalling results in life-threatening inflammatory bowel disease in humans and mice-however, the exact mechanism by which IL-10 signalling subdues inflammation remains unclear2-5. Here we find that increased saturated very long chain (VLC) ceramides are critical for the heightened inflammatory gene expression that is a hallmark of IL-10 deficiency. Accordingly, genetic deletion of ceramide synthase 2 (encoded by Cers2), the enzyme responsible for VLC ceramide production, limited the exacerbated inflammatory gene expression programme associated with IL-10 deficiency both in vitro and in vivo. The accumulation of saturated VLC ceramides was regulated by a decrease in metabolic flux through the de novo mono-unsaturated fatty acid synthesis pathway. Restoring mono-unsaturated fatty acid availability to cells deficient in IL-10 signalling limited saturated VLC ceramide production and the associated inflammation. Mechanistically, we find that persistent inflammation mediated by VLC ceramides is largely dependent on sustained activity of REL, an immuno-modulatory transcription factor. Together, these data indicate that an IL-10-driven fatty acid desaturation programme rewires VLC ceramide accumulation and aberrant activation of REL. These studies support the idea that fatty acid homeostasis in innate immune cells serves as a key regulatory node to control pathologic inflammation and suggests that 'metabolic correction' of VLC homeostasis could be an important strategy to normalize dysregulated inflammation caused by the absence of IL-10.


Subject(s)
Inflammation , Interleukin-10 , Sphingolipids , Animals , Humans , Mice , Ceramides/chemistry , Ceramides/metabolism , Fatty Acids, Unsaturated/biosynthesis , Fatty Acids, Unsaturated/metabolism , Homeostasis , Immunity, Innate , Inflammation/genetics , Inflammation/metabolism , Inflammation/pathology , Interleukin-10/deficiency , Interleukin-10/genetics , Interleukin-10/metabolism , Proto-Oncogene Proteins c-rel , Sphingolipids/metabolism
5.
Mol Ther ; 32(4): 1110-1124, 2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38341612

ABSTRACT

Whether and how tumor intrinsic signature determines macrophage-elicited metastasis remain elusive. Here, we show, in detailed studies of data regarding 7,477 patients of 20 types of human cancers, that only 13.8% ± 2.6%/27.9% ± 3.03% of patients with high macrophage infiltration index exhibit early recurrence/vascular invasion. In parallel, although macrophages enhance the motility of various hepatoma cells, their enhancement intensity is significantly heterogeneous. We identify that the expression of malignant Dicer, a ribonuclease that cleaves miRNA precursors into mature miRNAs, determines macrophage-elicited metastasis. Mechanistically, the downregulation of Dicer in cancer cells leads to defects in miRNome targeting NF-κB signaling, which in turn enhances the ability of cancer cells to respond to macrophage-related inflammatory signals and ultimately promotes metastasis. Importantly, transporting miR-26b-5p, the most potential miRNA targeting NF-κB signaling in hepatocellular carcinoma, can effectively reverse macrophage-elicited metastasis of hepatoma in vivo. Our results provide insights into the crosstalk between Dicer-elicited miRNome and cancer immune microenvironments and suggest that strategies to remodel malignant cell miRNome may overcome pro-tumorigenic activities of inflammatory cells.


Subject(s)
Carcinoma, Hepatocellular , MicroRNAs , Humans , NF-kappa B/genetics , NF-kappa B/metabolism , Carcinoma, Hepatocellular/pathology , Signal Transduction/physiology , MicroRNAs/genetics , MicroRNAs/metabolism , Macrophages/metabolism , Cell Line, Tumor , Tumor Microenvironment/genetics
6.
Nucleic Acids Res ; 51(8): e43, 2023 05 08.
Article in English | MEDLINE | ID: mdl-36919598

ABSTRACT

MINORg is an offline gRNA design tool that generates the smallest possible combination of gRNA capable of covering all desired targets in multiple non-reference genomes. As interest in pangenomic research grows, so does the workload required for large screens in multiple individuals. MINORg aims to lessen this workload by capitalising on sequence homology to favour multi-target gRNA while simultaneously screening multiple genetic backgrounds in order to generate reusable gRNA panels. We demonstrated the practical application of MINORg by knocking out 11 homologous genes tandemly arrayed in a multi-gene cluster in two Arabidopsis thaliana lineages using three gRNA output by MINORg. We also described a new PCR-free modular cloning system for multiplexing gRNA, and used it to knockout three tandemly arrayed genes in another multi-gene cluster with gRNA designed by MINORg. Source code is freely available at https://github.com/rlrq/MINORg.


Subject(s)
RNA, Guide, CRISPR-Cas Systems , Software , Humans , CRISPR-Cas Systems , Gene Knockout Techniques , Polymerase Chain Reaction
7.
Eur Heart J ; 45(24): 2145-2154, 2024 Jun 28.
Article in English | MEDLINE | ID: mdl-38626306

ABSTRACT

BACKGROUND AND AIMS: Emerging evidence has raised an obesity paradox in observational studies of body mass index (BMI) and health among the oldest-old (aged ≥80 years), as an inverse relationship of BMI with mortality was reported. This study was to investigate the causal associations of BMI, waist circumference (WC), or both with mortality in the oldest-old people in China. METHODS: A total of 5306 community-based oldest-old (mean age 90.6 years) were enrolled in the Chinese Longitudinal Healthy Longevity Survey (CLHLS) between 1998 and 2018. Genetic risk scores were constructed from 58 single-nucleotide polymorphisms (SNPs) associated with BMI and 49 SNPs associated with WC to subsequently derive causal estimates for Mendelian randomization (MR) models. One-sample linear MR along with non-linear MR analyses were performed to explore the associations of genetically predicted BMI, WC, and their joint effect with all-cause mortality, cardiovascular disease (CVD) mortality, and non-CVD mortality. RESULTS: During 24 337 person-years of follow-up, 3766 deaths were documented. In observational analyses, higher BMI and WC were both associated with decreased mortality risk [hazard ratio (HR) 0.963, 95% confidence interval (CI) 0.955-0.971 for a 1-kg/m2 increment of BMI and HR 0.971 (95% CI 0.950-0.993) for each 5 cm increase of WC]. Linear MR models indicated that each 1 kg/m2 increase in genetically predicted BMI was monotonically associated with a 4.5% decrease in all-cause mortality risk [HR 0.955 (95% CI 0.928-0.983)]. Non-linear curves showed the lowest mortality risk at the BMI of around 28.0 kg/m2, suggesting that optimal BMI for the oldest-old may be around overweight or mild obesity. Positive monotonic causal associations were observed between WC and all-cause mortality [HR 1.108 (95% CI 1.036-1.185) per 5 cm increase], CVD mortality [HR 1.193 (95% CI 1.064-1.337)], and non-CVD mortality [HR 1.110 (95% CI 1.016-1.212)]. The joint effect analyses indicated that the lowest risk was observed among those with higher BMI and lower WC. CONCLUSIONS: Among the oldest-old, opposite causal associations of BMI and WC with mortality were observed, and a body figure with higher BMI and lower WC could substantially decrease the mortality risk. Guidelines for the weight management should be cautiously designed and implemented among the oldest-old people, considering distinct roles of BMI and WC.


Subject(s)
Body Mass Index , Mendelian Randomization Analysis , Waist Circumference , Humans , Female , Male , Aged, 80 and over , China/epidemiology , Cardiovascular Diseases/mortality , Cardiovascular Diseases/genetics , Polymorphism, Single Nucleotide , Obesity/genetics , Obesity/mortality , Cause of Death , Risk Factors , Mortality
8.
Am J Physiol Renal Physiol ; 326(2): F265-F277, 2024 02 01.
Article in English | MEDLINE | ID: mdl-38153852

ABSTRACT

Dyslipidemia, with changes in plasma membrane (PM) composition, is associated with hypertension, while rising PM cholesterol induces Na+ channel activity. We hypothesize that ablation of renal tubular ABCA1, a cholesterol efflux protein, leads to cholesterol- and Na+-dependent changes in blood pressure (BP). Transgenic mice (TgPAX8rtTA;tetO-Cre/+) expressing a doxycycline (dox)-inducible CRE recombinase were bred with mice expressing floxed ABCA1 to generate renal tubules deficient in ABCA1 (ABCA1FF). Tail-cuff systolic BP (SBP) was measured in mice on specific diets. Immunoblotting was performed on whole and PM protein lysates of kidney from mice completing experimental diets. Cortical PM of ABCA1FF showed reduced ABCA1 (60 ± 28%; n = 10, P < 0.05) compared with wild-type littermates (WT; n = 9). Tail-cuff SBP of ABCA1FF (n = 11) was not only greater post dox, but also during cholesterol or high Na+ feeding (P < 0.05) compared with WT mice (n = 15). A Na+-deficient diet abolished the difference, while 6 wk of cholesterol diet raised SBP in ABCA1FF compared with mice before cholesterol feeding (P < 0.05). No difference in α-ENaC protein abundance was noted in kidney lysate; however, γ-ENaC increased in ABCA1FF mice versus WT mice. In kidney membranes, NKCC2 abundance was greater in ABCA1FF versus WT mice. Cortical lysates of ABCA1FF mouse kidneys expressed less renin and angiotensin I receptor than WT mouse kidneys. Furosemide injection induced a greater diuretic effect in ABCA1FF (n = 7; 45.2 ± 8.7 µL/g body wt) versus WT (n = 7; 33.1 ± 6.9 µL/g body wt; P < 0.05) but amiloride did not. Tubular ABCA1 deficiency induces cholesterol-dependent rise in SBP and modest Na+ sensitivity of SBP, which we speculate is partly related to Na+ transporters and channels.NEW & NOTEWORTHY Cholesterol has been linked to greater Na+ channel activity in kidney cells, which may predispose to systemic hypertension. We showed that when ABCA1, a protein that removes cholesterol from tissues, is ablated from mouse kidneys, systemic blood pressure is greater than normal mice. Dietary cholesterol further increases blood pressure in transgenic mice, whereas low dietary salt intake reduced blood pressure to that of normal mice. Thus, we speculate that diseases and pharmaceuticals that reduce renal ABCA1 expression, like diabetes and calcineurin inhibitors, respectively, contribute to the prominence of hypertension in their clinical presentation.


Subject(s)
Hypertension , Sodium , Animals , Male , Mice , Blood Pressure , Cholesterol/pharmacology , Epithelial Sodium Channels/metabolism , Mice, Knockout , Mice, Transgenic , Sodium/metabolism
9.
BMC Plant Biol ; 24(1): 133, 2024 Feb 23.
Article in English | MEDLINE | ID: mdl-38395770

ABSTRACT

BACKGROUND: 1-Deoxynojirimycin (DNJ), the main active ingredient in mulberry leaves, with wide applications in the medicine and food industries due to its significant functions in lowering blood sugar, and lipids, and combating viral infections. Cytochrome P450 is a key enzyme for DNJ biosynthesis, its activity depends on the electron supply of NADPH-cytochrome P450 reductases (CPRs). However, the gene for MaCPRs in mulberry leaves remains unknown. RESULTS: In this study, we successfully cloned and functionally characterized two key genes, MaCPR1 and MaCPR2, based on the transcriptional profile of mulberry leaves. The MaCPR1 gene comprised 2064 bp, with its open reading frame (ORF) encoding 687 amino acids. The MaCPR2 gene comprised 2148 bp, and its ORF encoding 715 amino acids. The phylogenetic tree indicates that MaCPR1 and MaCPR2 belong to Class I and Class II, respectively. In vitro, we found that the recombinant enzymes MaCPR2 protein could reduce cytochrome c and ferricyanide using NADPH as an electron donor, while MaCPR1 did not. In yeast, heterologous co-expression indicates that MaCPR2 delivers electrons to MaC3'H hydroxylase, a key enzyme catalyzing the production of chlorogenic acid from 3-O-p-coumaroylquinic acid. CONCLUSIONS: These findings highlight the orchestration of hydroxylation process mediated by MaCPR2 during the biosynthesis of secondary metabolite biosynthesis in mulberry leaves. These results provided a foundational understanding for fully elucidating the DNJ biosynthetic pathway within mulberry leaves.


Subject(s)
1-Deoxynojirimycin , Morus , 1-Deoxynojirimycin/analysis , 1-Deoxynojirimycin/metabolism , Morus/genetics , NADP/metabolism , Biosynthetic Pathways , Phylogeny , Recombinant Proteins/metabolism , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism , Amino Acids/metabolism , Plant Leaves/metabolism
10.
Expert Rev Mol Med ; 26: e15, 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38621674

ABSTRACT

In mammals, the skin acts as a barrier to prevent harmful environmental stimuli from entering the circulation. CYP450s are involved in drug biotransformation, exogenous and endogenous substrate metabolism, and maintaining the normal physiological function of the skin, as well as facilitating homeostasis of the internal environment. The expression pattern of CYP450s in the skin is tissue-specific and thus differs from the liver and other organs. The development of skin topical medications, and knowledge of the toxicity and side effects of these medications require a detailed understanding of the expression and function of skin-specific CYP450s. Thus, we summarized the expression of CYP450s in the skin, their function in endogenous metabolic physiology, aberrant CYP450 expression in skin diseases and the influence of environmental variables and medications. This information will serve as a crucial foundation for future studies on the skin, as well as for the design and development of new drugs for skin diseases including topical medications.


Subject(s)
Cytochrome P-450 Enzyme System , Skin , Humans , Skin/metabolism , Cytochrome P-450 Enzyme System/metabolism , Cytochrome P-450 Enzyme System/genetics , Animals , Skin Diseases/metabolism
11.
Planta ; 260(1): 3, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38767800

ABSTRACT

MAIN CONCLUSION: Transcription factors MhMYB1 and MhMYB2 correlate with monoterpenoid biosynthesis pathway in l-menthol chemotype of Mentha haplocalyx Briq, which could affect the contents of ( -)-menthol and ( -)-menthone. Mentha haplocalyx Briq., a plant with traditional medicinal and edible uses, is renowned for its rich essential oil content. The distinct functional activities and aromatic flavors of mint essential oils arise from various chemotypes. While the biosynthetic pathways of the main monoterpenes in mint are well understood, the regulatory mechanisms governing different chemotypes remain inadequately explored. In this investigation, we identified and cloned two transcription factor genes from the M. haplocalyx MYB family, namely MhMYB1 (PP236792) and MhMYB2 (PP236793), previously identified by our research group. Bioinformatics analysis revealed that MhMYB1 possesses two conserved MYB domains, while MhMYB2 contains a conserved SANT domain. Yeast one-hybrid (Y1H) analysis results demonstrated that both MhMYB1 and MhMYB2 interacted with the promoter regions of MhMD and MhPR, critical enzymes in the monoterpenoid biosynthesis pathway of M. haplocalyx. Subsequent virus-induced gene silencing (VIGS) of MhMYB1 and MhMYB2 led to a significant reduction (P < 0.01) in the relative expression levels of MhMD and MhPR genes in the VIGS groups of M. haplocalyx. In addition, there was a noteworthy decrease (P < 0.05) in the contents of ( -)-menthol and ( -)-menthone in the essential oil of M. haplocalyx. These findings suggest that MhMYB1 and MhMYB2 transcription factors play a positive regulatory role in ( -)-menthol biosynthesis, consequently influencing the essential oil composition in the l-menthol chemotype of M. haplocalyx. This study serves as a pivotal foundation for unraveling the regulatory mechanisms governing monoterpenoid biosynthesis in different chemotypes of M. haplocalyx.


Subject(s)
Gene Expression Regulation, Plant , Mentha , Menthol , Monoterpenes , Plant Proteins , Transcription Factors , Transcription Factors/genetics , Transcription Factors/metabolism , Mentha/genetics , Mentha/metabolism , Monoterpenes/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Menthol/metabolism , Oils, Volatile/metabolism , Biosynthetic Pathways/genetics , Promoter Regions, Genetic/genetics
12.
Mod Pathol ; 37(6): 100486, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38588882

ABSTRACT

The role of artificial intelligence (AI) in pathology offers many exciting new possibilities for improving patient care. This study contributes to this development by identifying the viability of the AICyte assistive system for cervical screening, and investigating the utility of the system in assisting with workflow and diagnostic capability. In this study, a novel scanner was developed using a Ruiqian WSI-2400, trademarked AICyte assistive system, to create an AI-generated gallery of the most diagnostically relevant images, objects of interest (OOI), and provide categorical assessment, according to Bethesda category, for cervical ThinPrep Pap slides. For validation purposes, 2 pathologists reviewed OOIs from 32,451 cases of ThinPrep Paps independently, and their interpretations were correlated with the original ThinPrep interpretations (OTPI). The analysis was focused on the comparison of reporting rates, correlation between cytological results and histologic follow-up findings, and the assessment of independent AICyte screening utility. Pathologists using the AICyte system had a mean reading time of 55.14 seconds for the first 3000 cases trending down to 12.90 seconds in the last 6000 cases. Overall average reading time was 22.23 seconds per case compared with a manual reading time approximation of 180 seconds. Usage of AICyte compared with OTPI had similar sensitivity (97.89% vs 97.89%) and a statistically significant increase in specificity (16.19% vs 6.77%) for the detection of cervical intraepithelial neoplsia 2 and above lesions. When AICyte was run alone at a 50% negative cutoff value, it was able to read slides with a sensitivity of 99.30% and a specificity of 9.87%. When AICyte was run independently at this cutoff value, no sole case of high-grade squamous intraepithelial lesions/squamous cell carcinoma squamous lesion was missed. AICyte can provide a potential tool to help pathologists in both diagnostic capability and efficiency, which remained reliable compared with the baseline standard. Also unique for AICyte is the development of a negative cutoff value for which AICyte can categorize cases as "not needed for review" to triage cases and lower pathologist workload. This is the largest case number study that pathologists reviewed OOI with an AI-assistive system. The study demonstrates that AI-assistive system can be broadly applied for cervical cancer screening.


Subject(s)
Artificial Intelligence , Uterine Cervical Neoplasms , Vaginal Smears , Humans , Female , Uterine Cervical Neoplasms/diagnosis , Uterine Cervical Neoplasms/pathology , Vaginal Smears/methods , Early Detection of Cancer/methods , Papanicolaou Test/methods , Image Interpretation, Computer-Assisted/methods , Reproducibility of Results , Uterine Cervical Dysplasia/diagnosis , Uterine Cervical Dysplasia/pathology , Cytology
13.
Bioinformatics ; 39(6)2023 06 01.
Article in English | MEDLINE | ID: mdl-37166451

ABSTRACT

MOTIVATION: Due to the rapid growth of the genetic database size, genealogical search, a process of inferring familial relatedness by identifying DNA matches, has become a viable approach to help individuals finding missing family members or law enforcement agencies locating suspects. A fast and accurate method is needed to search an out-of-database individual against millions of individuals. Most existing approaches only offer all-versus-all within panel match. Some prototype algorithms offer one-versus-all query from out-of-panel individual, but they do not tolerate errors. RESULTS: A new method, random projection-based identity-by-descent (IBD) detection (RaPID) query, is introduced to make fast genealogical search possible. RaPID-Query identifies IBD segments between a query haplotype and a panel of haplotypes. By integrating matches over multiple PBWT indexes, RaPID-Query manages to locate IBD segments quickly with a given cutoff length while allowing mismatched sites. A single query against all UK biobank autosomal chromosomes was completed within 2.76 seconds on average, with the minimum length 7 cM and 700 markers. RaPID-Query achieved a 0.016 false negative rate and a 0.012 false positive rate simultaneously on a chromosome 20 sequencing panel having 86 265 sites. This is comparable to the state-of-the-art IBD detection method TPBWT(out-of-sample) and Hap-IBD. The high-quality IBD segments yielded by RaPID-Query were able to distinguish up to fourth degree of the familial relatedness for a given individual pair, and the area under the receiver operating characteristic curve values are at least 97.28%. AVAILABILITY AND IMPLEMENTATION: The RaPID-Query program is available at https://github.com/ucfcbb/RaPID-Query.


Subject(s)
Algorithms , Chromosomes , Humans , Haplotypes , Sequence Analysis
14.
J Transl Med ; 22(1): 570, 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38879538

ABSTRACT

BACKGROUND: Gut microbiota (GM) have been implicated as important regulators of gastrointestinal symptom which is commonly occurred along with respiratory influenza A virus (IAV) infection, suggesting the involvement of the gut-to-lung axis in a host's response to IAV. IAV primarily destroys airway epithelium tight junctions (TJs) and consequently causes acute respiratory disease syndrome. It is known that GM and their metabolism produce an anti-influenza effect, but their role in IAV-induced airway epithelial integrity remains unknown. METHODS: A mouse model of IAV infection was established. GM were analyzed using 16S rRNA gene sequencing, and short-chain fatty acids (SCFAs) levels were measured. GM depletion and fecal microbiota transplantation (FMT) were conducted to validate the role of GM in IAV infection. A pair-feeding experiment was conducted to reveal whether IAV-induced GM dysbiosis is attributed to impaired food intake. Furthermore, human bronchial epithelial (HBE) cells were cocultured with IAV in the presence or absence of acetate. TJs function was analyzed by paracellular permeability and transepithelial electronic resistance (TEER). The mechanism of how acetate affects TJs integrity was evaluated in HBE cells transfected with G protein-coupled receptor 43 (GPR43) short hairpin RNA (shRNA). RESULTS: IAV-infected mice exhibited lower relative abundance of acetate-producing bacteria (Bacteroides, Bifidobacterium, and Akkermansia) and decreased acetate levels in gut and serum. These changes were partly caused by a decrease in food consumption (due to anorexia). GM depletion exacerbated and FMT restored IAV-induced lung inflammatory injury. IAV infection suppressed expressions of TJs (occludin, ZO-1) leading to disrupted airway epithelial barrier function as evidenced by decreased TEER and increased permeability. Acetate pretreatment activated GPR43, partially restored IAV-induced airway epithelial barrier function, and reduced inflammatory cytokines levels (TNF-α, IL-6, and IL-1ß). Such protective effects of acetate were absent in HBE cells transfected with GPR43 shRNA. Acetate and GPR43 improved TJs in an AMP-activated protein kinase (AMPK)-dependent manner. CONCLUSION: Collectively, our results demonstrated that GM protected airway TJs by modulating GPR43-AMPK signaling in IAV-induced lung injury. Therefore, improving GM dysbiosis may be a potential therapeutic target for patients with IAV infection.


Subject(s)
Acetates , Gastrointestinal Microbiome , Lung Injury , Orthomyxoviridae Infections , Tight Junctions , Animals , Tight Junctions/metabolism , Gastrointestinal Microbiome/drug effects , Acetates/metabolism , Humans , Orthomyxoviridae Infections/complications , Mice, Inbred C57BL , Influenza A virus , Fecal Microbiota Transplantation , Receptors, G-Protein-Coupled/metabolism , Mice , Epithelial Cells/metabolism , Dysbiosis , Fatty Acids, Volatile/metabolism
15.
Ann Surg Oncol ; 31(8): 5240-5251, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38739239

ABSTRACT

BACKGROUND: Enhanced recovery after surgery (ERAS) for radical distal gastrectomy needs to be improved urgently. We investigated the effects of probiotic compounds (including Lactobacillus plantarum, L. rhamnosus, L. acidophilus, and Bifidobacterium animalis subsp.lactis) on enhance recovery after gastrectomy. METHODS: The patients in this prospective study were divided into probiotic group (PG group, n = 36) and placebo group (CG group, n = 38), taking corresponding capsule according to the protocol during the perioperative period. We compared the trends in perioperative hematologic findings and the postoperative outcomes. Patients' feces were collected for bacterial 16S rRNA sequencing. Patients were followed up at 1 month postoperatively. RESULTS: After the application of probiotics, the patients' postoperative inflammatory response level was reduced, and the trend of postoperative NLR decrease was significantly faster in the patients of the PG group than in the CG group (P = 0.047, partial η2 = 0.054). The trend of postoperative increase in serum albumin concentration in the patients of the PG group was significantly better than that in the CG group (P = 0.016, partial η2 = 0.078). In addition, patients in the PG group met discharge criteria earlier postoperatively and had fewer medical expenses. The quality of life of PG group was improved postoperatively. Postoperative inflammation-related markers, including the ratio of Firmicutes/Bacteroidetes, were increasing in untreated patients. In addition, the postoperative microbial diversity and abundance in the PG group remained stable. CONCLUSIONS: Probiotic compounds can reduce the inflammatory response after gastrectomy and enhance the recovery of the DGC patients by maintaining the stability of the gut microbiota.


Subject(s)
Enhanced Recovery After Surgery , Gastrectomy , Probiotics , Stomach Neoplasms , Humans , Stomach Neoplasms/surgery , Male , Female , Probiotics/therapeutic use , Prospective Studies , Middle Aged , Aged , Follow-Up Studies , Quality of Life , Postoperative Complications , Gastrointestinal Microbiome/drug effects , Prognosis
16.
Opt Express ; 32(4): 6309-6328, 2024 Feb 12.
Article in English | MEDLINE | ID: mdl-38439337

ABSTRACT

Visible light communication (VLC) benefits from the underwater blue-green window and holds immense potential for underwater wireless communication. In order to address the limitations of various equipment and harsh channel conditions in the underwater visible light communication (UVLC) system, the researchers proposed to use the method of autoencoder (AE) to tap the potential of the system. However, traditional AE schemes involve replacing the transmitting and receiving components of a communication system with a large multilayer perceptron (MLP) network, and they have significant drawbacks due to their reliance on a single network structure. In this paper, a novel 2D adaptive optimization autoencoder (2D-AOAE) framework is proposed to realize adaptive modulation and demodulation of two-dimensional signals. By implementing this scheme, we experimentally achieved a transmission rate of 2.85 Gbps over a 1.2-meter underwater VLC link. Compared to the traditional 32QAM UVLC system, the 2D-AOAE scheme demonstrated a 15.4% data rate increase. Moreover, the 2D-AOAE scheme exhibited a remarkable 73% improvement when compared to the UVLC system utilizing the traditional AE scheme. This significant enhancement highlights the superior performance and capabilities of the 2D-AOAE scheme in terms of transmission rate.

17.
Opt Express ; 32(8): 13095-13110, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38859288

ABSTRACT

Modulation format recognition (MFR) is a key technology for adaptive optical systems, but it faces significant challenges in underwater visible light communication (UVLC) due to the complex channel environment. Recent advances in deep learning have enabled remarkable achievements in image recognition, owing to the powerful feature extraction of neural networks (NN). However, the high computational complexity of NN limits their practicality in UVLC systems. This paper proposes a communication-informed knowledge distillation (CIKD) method that achieves high-precision and low-latency MFR with an ultra-lightweight student model. The student model consists of only one linear dense layer under a communication-informed auxiliary system and is trained under the guidance of a high-complexity and high-precision teacher model. The MFR task involves eight modulation formats: PAM4, QPSK, 8QAM-CIR, 8QAM-DIA, 16QAM, 16APSK, 32QAM, and 32APSK. Experimental results show that the student model based on CIKD can achieve comparable accuracy to the teacher model. After knowledge transfer, the prediction accuracy of the student model can be increased by up to 87%. Besides, it is worth noting that CIKD's inference accuracy can reach up to 100%. Moreover, the parameters constituting the student model in CIKD correspond to merely 18% of the parameters found in the teacher model, which facilitates the hardware deployment and online data processing of MFR algorithms in UVLC systems.

18.
Respir Res ; 25(1): 186, 2024 Apr 27.
Article in English | MEDLINE | ID: mdl-38678295

ABSTRACT

BACKGROUND: Influenza A viruses (IAV) are extremely common respiratory viruses for the acute exacerbation of chronic obstructive pulmonary disease (AECOPD), in which IAV infection may further evoke abnormal macrophage polarization, amplify cytokine storms. Melatonin exerts potential effects of anti-inflammation and anti-IAV infection, while its effects on IAV infection-induced AECOPD are poorly understood. METHODS: COPD mice models were established through cigarette smoke exposure for consecutive 24 weeks, evaluated by the detection of lung function. AECOPD mice models were established through the intratracheal atomization of influenza A/H3N2 stocks in COPD mice, and were injected intraperitoneally with melatonin (Mel). Then, The polarization of alveolar macrophages (AMs) was assayed by flow cytometry of bronchoalveolar lavage (BAL) cells. In vitro, the effects of melatonin on macrophage polarization were analyzed in IAV-infected Cigarette smoking extract (CSE)-stimulated Raw264.7 macrophages. Moreover, the roles of the melatonin receptors (MTs) in regulating macrophage polarization and apoptosis were determined using MTs antagonist luzindole. RESULTS: The present results demonstrated that IAV/H3N2 infection deteriorated lung function (reduced FEV20,50/FVC), exacerbated lung damages in COPD mice with higher dual polarization of AMs. Melatonin therapy improved airflow limitation and lung damages of AECOPD mice by decreasing IAV nucleoprotein (IAV-NP) protein levels and the M1 polarization of pulmonary macrophages. Furthermore, in CSE-stimulated Raw264.7 cells, IAV infection further promoted the dual polarization of macrophages accompanied with decreased MT1 expression. Melatonin decreased STAT1 phosphorylation, the levels of M1 markers and IAV-NP via MTs reflected by the addition of luzindole. Recombinant IL-1ß attenuated the inhibitory effects of melatonin on IAV infection and STAT1-driven M1 polarization, while its converting enzyme inhibitor VX765 potentiated the inhibitory effects of melatonin on them. Moreover, melatonin inhibited IAV infection-induced apoptosis by suppressing IL-1ß/STAT1 signaling via MTs. CONCLUSIONS: These findings suggested that melatonin inhibited IAV infection, improved lung function and lung damages of AECOPD via suppressing IL-1ß/STAT1-driven macrophage M1 polarization and apoptosis in a MTs-dependent manner. Melatonin may be considered as a potential therapeutic agent for influenza virus infection-induced AECOPD.


Subject(s)
Apoptosis , Influenza A Virus, H3N2 Subtype , Melatonin , Pulmonary Disease, Chronic Obstructive , Animals , Melatonin/pharmacology , Pulmonary Disease, Chronic Obstructive/drug therapy , Pulmonary Disease, Chronic Obstructive/metabolism , Pulmonary Disease, Chronic Obstructive/virology , Pulmonary Disease, Chronic Obstructive/physiopathology , Mice , Apoptosis/drug effects , RAW 264.7 Cells , Influenza A Virus, H3N2 Subtype/drug effects , Orthomyxoviridae Infections/drug therapy , Orthomyxoviridae Infections/metabolism , Orthomyxoviridae Infections/immunology , Mice, Inbred C57BL , Male , Macrophages/drug effects , Macrophages/metabolism , Disease Progression , Cell Polarity/drug effects , Disease Models, Animal , Macrophages, Alveolar/drug effects , Macrophages, Alveolar/metabolism , Macrophages, Alveolar/virology
19.
Phys Rev Lett ; 132(1): 016501, 2024 Jan 05.
Article in English | MEDLINE | ID: mdl-38242670

ABSTRACT

We use resonant inelastic x-ray scattering (RIXS) at the Fe-L_{3} edge to study the spin excitations of uniaxial-strained and unstrained FeSe_{1-x}S_{x} (0≤x≤0.21) samples. The measurements on unstrained samples reveal dispersive spin excitations in all doping levels, which show only minor doping dependence in energy dispersion, lifetime, and intensity, indicating that high-energy spin excitations are only marginally affected by sulfur doping. RIXS measurements on uniaxial-strained samples reveal that the high-energy spin-excitation anisotropy observed previously in FeSe is also present in the doping range 0200 K in x=0.18 and reaches a maximum around the nematic quantum critical doping (x_{c}≈0.17). Since the spin-excitation anisotropy directly reflects the existence of nematic spin correlations, our results indicate that high-energy nematic spin correlations pervade the regime of nematicity in the phase diagram and are enhanced by the nematic quantum criticality. These results emphasize the essential role of spin fluctuations in driving electronic nematicity and highlight the capability of uniaxial strain in tuning spin excitations in quantum materials hosting strong magnetoelastic coupling and electronic nematicity.

20.
Phys Rev Lett ; 132(23): 235001, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38905668

ABSTRACT

Relativistic positron sources with high spin polarization have important applications in nuclear and particle physics and many frontier fields. However, it is challenging to produce dense polarized positrons. Here we present a simple and effective method to achieve such a positron source by directly impinging a relativistic high-density electron beam on the surface of a solid target. During the interaction, a strong return current of plasma electrons is induced and subsequently asymmetric quasistatic magnetic fields as high as megatesla are generated along the target surface. This gives rise to strong radiative spin flips and multiphoton processes, thus leading to efficient generation of copious polarized positrons. With three-dimensional particle-in-cell simulations, we demonstrate the production of a dense highly polarized multi-GeV positron beam with an average spin polarization above 40% and nC-scale charge per shot. This offers a novel route for the studies of laserless strong-field quantum electrodynamics physics and for the development of high-energy polarized positron sources.

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