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1.
Nature ; 632(8024): 313-319, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38885695

ABSTRACT

Oligosaccharides have myriad functions throughout biological processes1,2. Chemical synthesis of these structurally complex molecules facilitates investigation of their functions. With a dense concentration of stereocentres and hydroxyl groups, oligosaccharide assembly through O-glycosylation requires simultaneous control of site, stereo- and chemoselectivities3,4. Chemists have traditionally relied on protecting group manipulations for this purpose5-8, adding considerable synthetic work. Here we report a glycosylation platform that enables selective coupling between unprotected or minimally protected donor and acceptor sugars, producing 1,2-cis-O-glycosides in a catalyst-controlled, site-selective manner. Radical-based activation9 of allyl glycosyl sulfones forms glycosyl bromides. A designed aminoboronic acid catalyst brings this reactive intermediate close to an acceptor through a network of non-covalent hydrogen bonding and reversible covalent B-O bonding interactions, allowing precise glycosyl transfer. The site of glycosylation can be switched with different aminoboronic acid catalysts by affecting their interaction modes with substrates. The method accommodates a wide range of sugar types, amenable to the preparation of naturally occurring sugar chains and pentasaccharides containing 11 free hydroxyls. Experimental and computational studies provide insights into the origin of selectivity outcomes.


Subject(s)
Glycosides , Oligosaccharides , Boronic Acids/chemistry , Bromides/chemistry , Catalysis , Glycosides/chemistry , Glycosides/chemical synthesis , Glycosylation , Hydrogen Bonding , Oligosaccharides/chemistry , Oligosaccharides/chemical synthesis , Sulfones/chemistry
2.
EMBO J ; 43(16): 3466-3493, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38965418

ABSTRACT

The gut microbiota and their metabolites are closely linked to obesity-related diseases, such as type 2 diabetes, but their causal relationship and underlying mechanisms remain largely elusive. Here, we found that dysbiosis-induced tyramine (TA) suppresses high-fat diet (HFD)-mediated insulin resistance in both Drosophila and mice. In Drosophila, HFD increases cytosolic Ca2+ signaling in enterocytes, which, in turn, suppresses intestinal lipid levels. 16 S rRNA sequencing and metabolomics revealed that HFD leads to increased prevalence of tyrosine decarboxylase (Tdc)-expressing bacteria and resulting tyramine production. Tyramine acts on the tyramine receptor, TyrR1, to promote cytosolic Ca2+ signaling and activation of the CRTC-CREB complex to transcriptionally suppress dietary lipid digestion and lipogenesis in enterocytes, while promoting mitochondrial biogenesis. Furthermore, the tyramine-induced cytosolic Ca2+ signaling is sufficient to suppress HFD-induced obesity and insulin resistance in Drosophila. In mice, tyramine intake also improves glucose tolerance and insulin sensitivity under HFD. These results indicate that dysbiosis-induced tyramine suppresses insulin resistance in both flies and mice under HFD, suggesting a potential therapeutic strategy for related metabolic disorders, such as diabetes.


Subject(s)
Calcium Signaling , Diet, High-Fat , Gastrointestinal Microbiome , Insulin Resistance , Tyramine , Animals , Tyramine/metabolism , Tyramine/pharmacology , Gastrointestinal Microbiome/drug effects , Diet, High-Fat/adverse effects , Mice , Calcium Signaling/drug effects , Obesity/metabolism , Obesity/microbiology , Obesity/etiology , Male , Drosophila/metabolism , Dysbiosis/metabolism , Dysbiosis/microbiology , Mice, Inbred C57BL , Drosophila melanogaster/microbiology , Drosophila melanogaster/metabolism , Enterocytes/metabolism , Enterocytes/drug effects
3.
Nat Methods ; 21(6): 1103-1113, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38532015

ABSTRACT

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimental settings. Here, we present a multimodality cell segmentation benchmark, comprising more than 1,500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.


Subject(s)
Algorithms , Deep Learning , Image Processing, Computer-Assisted , Single-Cell Analysis , Single-Cell Analysis/methods , Image Processing, Computer-Assisted/methods , Humans , Microscopy/methods , Animals
4.
Nature ; 592(7855): 606-610, 2021 04.
Article in English | MEDLINE | ID: mdl-33658717

ABSTRACT

Intestinal stromal cells are known to modulate the propagation and differentiation of intestinal stem cells1,2. However, the precise cellular and molecular mechanisms by which this diverse stromal cell population maintains tissue homeostasis and repair are poorly understood. Here we describe a subset of intestinal stromal cells, named MAP3K2-regulated intestinal stromal cells (MRISCs), and show that they are the primary cellular source of the WNT agonist R-spondin 1 following intestinal injury in mice. MRISCs, which are epigenetically and transcriptomically distinct from subsets of intestinal stromal cells that have previously been reported3-6, are strategically localized at the bases of colon crypts, and function to maintain LGR5+ intestinal stem cells and protect against acute intestinal damage through enhanced R-spondin 1 production. Mechanistically, this MAP3K2 specific function is mediated by a previously unknown reactive oxygen species (ROS)-MAP3K2-ERK5-KLF2 axis to enhance production of R-spondin 1. Our results identify MRISCs as a key component of an intestinal stem cell niche that specifically depends on MAP3K2 to augment WNT signalling for the regeneration of damaged intestine.


Subject(s)
Intestinal Mucosa/cytology , MAP Kinase Kinase Kinase 2/metabolism , Stem Cell Niche , Stromal Cells/cytology , Animals , Antigens, CD34 , Colitis/pathology , Colitis/prevention & control , Epigenesis, Genetic , Female , Intestinal Mucosa/pathology , Kruppel-Like Transcription Factors/metabolism , Male , Mice , Reactive Oxygen Species/metabolism , Tetraspanin 28 , Thrombospondins/biosynthesis , Thrombospondins/metabolism , Thy-1 Antigens
5.
Proc Natl Acad Sci U S A ; 121(2): e2316396121, 2024 Jan 09.
Article in English | MEDLINE | ID: mdl-38165937

ABSTRACT

Plant epidermal cell walls maintain the mechanical integrity of plants and restrict organ growth. Mechanical analyses can give insights into wall structure and are inputs for mechanobiology models of plant growth. To better understand the intrinsic mechanics of epidermal cell walls and how they may accommodate large deformations during growth, we analyzed a geometrically simple material, onion epidermal strips consisting of only the outer (periclinal) cell wall, ~7 µm thick. With uniaxial stretching by >40%, the wall showed complex three-phase stress-strain responses while cyclic stretching revealed reversible and irreversible deformations and elastic hysteresis. Stretching at varying strain rates and temperatures indicated the wall behaved more like a network of flexible cellulose fibers capable of sliding than a viscoelastic composite with pectin viscosity. We developed an analytic framework to quantify nonlinear wall mechanics in terms of stiffness, deformation, and energy dissipation, finding that the wall stretches by combined elastic and plastic deformation without compromising its stiffness. We also analyzed mechanical changes in slightly dehydrated walls. Their extension became stiffer and more irreversible, highlighting the influence of water on cellulose stiffness and sliding. This study offers insights into the structure and deformation modes of primary cell walls and presents a framework that is also applicable to tissues and whole organs.


Subject(s)
Cell Wall , Cellulose , Cellulose/chemistry , Cell Wall/chemistry , Cell Membrane , Pectins , Plant Epidermis
6.
Proc Natl Acad Sci U S A ; 121(11): e2307803120, 2024 Mar 12.
Article in English | MEDLINE | ID: mdl-38437542

ABSTRACT

Lipid nanoparticle (LNP) formulations are a proven method for the delivery of nucleic acids for gene therapy as exemplified by the worldwide rollout of LNP-based RNAi therapeutics and mRNA vaccines. However, targeting specific tissues or cells is still a major challenge. After LNP administration, LNPs interact with biological fluids (i.e., blood), components of which adsorb onto the LNP surface forming a layer of biomolecules termed the "biomolecular corona (BMC)" which affects LNP stability, biodistribution, and tissue tropism. The mechanisms by which the BMC influences tissue- and cell-specific targeting remains largely unknown, due to the technical challenges in isolating LNPs and their corona from complex biological media. In this study, we present a new technique that utilizes magnetic LNPs to isolate LNP-corona complexes from unbound proteins present in human serum. First, we developed a magnetic LNP formulation, containing >40 superparamagnetic iron oxide nanoparticles (IONPs)/LNP, the resulting LNPs containing iron oxide nanoparticles (IOLNPs) displayed a similar particle size and morphology as LNPs loaded with nucleic acids. We further demonstrated the isolation of the IOLNPs and their corresponding BMC from unbound proteins using a magnetic separation (MS) system. The BMC profile of LNP from the MS system was compared to size exclusion column chromatography and further analyzed via mass spectrometry, revealing differences in protein abundances. This new approach enabled a mild and versatile isolation of LNPs and its corona, while maintaining its structural integrity. The identification of the BMC associated with an intact LNP provides further insight into LNP interactions with biological fluids.


Subject(s)
Liposomes , Nanoparticles , Nucleic Acids , Humans , Tissue Distribution , Magnetic Phenomena
7.
Brief Bioinform ; 25(2)2024 Jan 22.
Article in English | MEDLINE | ID: mdl-38485768

ABSTRACT

Enhancers, noncoding DNA fragments, play a pivotal role in gene regulation, facilitating gene transcription. Identifying enhancers is crucial for understanding genomic regulatory mechanisms, pinpointing key elements and investigating networks governing gene expression and disease-related mechanisms. Existing enhancer identification methods exhibit limitations, prompting the development of our novel multi-input deep learning framework, termed Enhancer-MDLF. Experimental results illustrate that Enhancer-MDLF outperforms the previous method, Enhancer-IF, across eight distinct human cell lines and exhibits superior performance on generic enhancer datasets and enhancer-promoter datasets, affirming the robustness of Enhancer-MDLF. Additionally, we introduce transfer learning to provide an effective and potential solution to address the prediction challenges posed by enhancer specificity. Furthermore, we utilize model interpretation to identify transcription factor binding site motifs that may be associated with enhancer regions, with important implications for facilitating the study of enhancer regulatory mechanisms. The source code is openly accessible at https://github.com/HaoWuLab-Bioinformatics/Enhancer-MDLF.


Subject(s)
Deep Learning , Enhancer Elements, Genetic , Humans , Genomics/methods , Gene Expression Regulation , Promoter Regions, Genetic
8.
PLoS Pathog ; 20(2): e1011928, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38324558

ABSTRACT

The subgroup J avian leukosis virus (ALV-J), a retrovirus, uses its gp85 protein to bind to the receptor, the chicken sodium hydrogen exchanger isoform 1 (chNHE1), facilitating viral invasion. ALV-J is the main epidemic subgroup and shows noteworthy mutations within the receptor-binding domain (RBD) region of gp85, especially in ALV-J layer strains in China. However, the implications of these mutations on viral replication and transmission remain elusive. In this study, the ALV-J layer strain JL08CH3-1 exhibited a more robust replication ability than the prototype strain HPRS103, which is related to variations in the gp85 protein. Notably, the gp85 of JL08CH3-1 demonstrated a heightened binding capacity to chNHE1 compared to HPRS103-gp85 binding. Furthermore, we showed that the specific N123I mutation within gp85 contributed to the enhanced binding capacity of the gp85 protein to chNHE1. Structural analysis indicated that the N123I mutation primarily enhanced the stability of gp85, expanded the interaction interface, and increased the number of hydrogen bonds at the interaction interface to increase the binding capacity between gp85 and chNHE1. We found that the N123I mutation not only improved the viral replication ability of ALV-J but also promoted viral shedding in vivo. These comprehensive data underscore the notion that the N123I mutation increases receptor binding and intensifies viral replication.


Subject(s)
Avian Leukosis Virus , Avian Leukosis , Poultry Diseases , Animals , Avian Leukosis Virus/genetics , Avian Leukosis Virus/chemistry , Mutation , Chickens , Protein Isoforms/genetics , Viral Envelope Proteins/genetics
9.
Immunity ; 46(6): 992-1004.e5, 2017 06 20.
Article in English | MEDLINE | ID: mdl-28636969

ABSTRACT

RNA interference (RNAi) functions as a potent antiviral immunity in plants and invertebrates; however, whether RNAi plays antiviral roles in mammals remains unclear. Here, using human enterovirus 71 (HEV71) as a model, we showed HEV71 3A protein as an authentic viral suppressor of RNAi during viral infection. When the 3A-mediated RNAi suppression was impaired, the mutant HEV71 readily triggered the production of abundant HEV71-derived small RNAs with canonical siRNA properties in cells and mice. These virus-derived siRNAs were produced from viral dsRNA replicative intermediates in a Dicer-dependent manner and loaded into AGO, and they were fully active in degrading cognate viral RNAs. Recombinant HEV71 deficient in 3A-mediated RNAi suppression was significantly restricted in human somatic cells and mice, whereas Dicer deficiency rescued HEV71 infection independently of type I interferon response. Thus, RNAi can function as an antiviral immunity, which is induced and suppressed by a human virus, in mammals.


Subject(s)
Enterovirus A, Human/immunology , Enterovirus Infections/immunology , Immunity , RNA Interference , RNA, Viral/immunology , Animals , Argonaute Proteins/metabolism , Clustered Regularly Interspaced Short Palindromic Repeats , Enterovirus A, Human/genetics , HEK293 Cells , Humans , Mammals , Mice , Mice, 129 Strain , Mice, Knockout , Mutation/genetics , Ribonuclease III/metabolism , Viral Proteins/immunology
10.
Circ Res ; 135(8): 856-872, 2024 Sep 27.
Article in English | MEDLINE | ID: mdl-39224974

ABSTRACT

BACKGROUND: Chronic inflammation initiated by inflammatory monocytes underlies the pathogenesis of atherosclerosis. However, approaches that can effectively resolve chronic low-grade inflammation targeting monocytes are not readily available. The small chemical compound 4-phenylbutyric acid (4-PBA) exhibits broad anti-inflammatory effects in reducing atherosclerosis. Selective delivery of 4-PBA reprogrammed monocytes may hold novel potential in providing targeted and precision therapeutics for the treatment of atherosclerosis. METHODS: Systems analyses integrating single-cell RNA sequencing and complementary immunologic approaches characterized key resolving characteristics as well as defining markers of reprogrammed monocytes trained by 4-PBA. Molecular mechanisms responsible for monocyte reprogramming were assessed by integrated biochemical and genetic approaches. The intercellular propagation of homeostasis resolution was evaluated by coculture assays with donor monocytes trained by 4-PBA and recipient naive monocytes. The in vivo effects of monocyte resolution and atherosclerosis prevention by 4-PBA were assessed with the high-fat diet-fed ApoE-/- mouse model with IP 4-PBA administration. Furthermore, the selective efficacy of 4-PBA-trained monocytes was examined by IV transfusion of ex vivo trained monocytes by 4-PBA into recipient high-fat diet-fed ApoE-/- mice. RESULTS: In this study, we found that monocytes can be potently reprogrammed by 4-PBA into an immune-resolving state characterized by reduced adhesion and enhanced expression of anti-inflammatory mediator CD24. Mechanistically, 4-PBA reduced the expression of ICAM-1 (intercellular adhesion molecule 1) via reducing peroxisome stress and attenuating SYK (spleen tyrosine kinase)-mTOR (mammalian target of rapamycin) signaling. Concurrently, 4-PBA enhanced the expression of resolving mediator CD24 through promoting PPARγ (peroxisome proliferator-activated receptor γ) neddylation mediated by TOLLIP (toll-interacting protein). 4-PBA-trained monocytes can effectively propagate anti-inflammation activity to neighboring monocytes through CD24. Our data further demonstrated that 4-PBA-trained monocytes effectively reduce atherosclerosis pathogenesis when administered in vivo. CONCLUSIONS: Our study describes a robust and effective approach to generate resolving monocytes, characterizes novel mechanisms for targeted monocyte reprogramming, and offers a precision therapeutics for atherosclerosis based on delivering reprogrammed resolving monocytes.


Subject(s)
Atherosclerosis , Inflammation , Monocytes , Phenylbutyrates , Animals , Atherosclerosis/metabolism , Atherosclerosis/drug therapy , Atherosclerosis/pathology , Atherosclerosis/prevention & control , Monocytes/metabolism , Monocytes/drug effects , Mice , Inflammation/metabolism , Phenylbutyrates/pharmacology , Mice, Inbred C57BL , Humans , Male , Intercellular Adhesion Molecule-1/metabolism , Intercellular Adhesion Molecule-1/genetics , Mice, Knockout, ApoE , PPAR gamma/metabolism , Cellular Reprogramming/drug effects , Cells, Cultured , Anti-Inflammatory Agents/pharmacology
11.
Chem Rev ; 2024 Oct 25.
Article in English | MEDLINE | ID: mdl-39454031

ABSTRACT

The copolymerization of CO2 and epoxides presents a transformative approach to converting greenhouse gases into aliphatic polycarbonates (CO2-PCs), thereby reducing the polymer industry's dependence on fossil resources. Over the past 50 years, a wide array of metallic catalysts, both heterogeneous and homogeneous, have been developed to achieve precise control over polymer selectivity, sequence, regio-, and stereoselectivity. This review details the evolution of metal-based catalysts, with a particular focus on the emergence of organoborane catalysts, and explores how these catalysts effectively address kinetic and thermodynamic challenges in CO2/epoxides copoly2merization. Advances in the synthesis of CO2-PCs with varied sequence and chain architectures through diverse polymerization protocols are examined, alongside the applications of functional CO2-PCs produced by incorporating different epoxides. The review also underscores the contributions of computational techniques to our understanding of copolymerization mechanisms and highlights recent advances in the closed-loop chemical recycling of CO2-sourced polycarbonates. Finally, the industrialization efforts of CO2-PCs are discussed, offering readers a comprehensive understanding of the evolution and future potential of epoxide copolymerization with CO2.

12.
Proc Natl Acad Sci U S A ; 120(41): e2304988120, 2023 10 10.
Article in English | MEDLINE | ID: mdl-37782782

ABSTRACT

Previous evaluations on the biophysical potential of forest carbon sink have focused on forestation area distribution and the associated carbon stock for equilibrium-state forests after centuries-long growth. These approaches, however, have limited relevance for climate policies because they ignore the near-term and mid-term decadal carbon uptake dynamics and suitable forest species for forestation. This study developed a forestation roadmap to support China's "carbon neutrality" objective in 2060 by addressing three key questions of forestation: where, with what forest species, and when to afforest. The results yielded a high-confidence potential forestation map for China at a resolution of 1 km with the identified optimal native forest type or species. Our analysis revealed an additional 78 Mha suitable for forestation up to the 2060s, a 43% increase on the current forest area. Selecting forest species for maximal carbon stock in addition to maximizing local environmental suitability enabled almost a doubling in forest carbon sink potential. Progressive forestation of this area can fix a considerable amount of CO2 and compensate for the carbon sink decline in existing forests. Altogether, the entire forest ecosystem can support a persistent biophysical carbon sink potential of 0.4 Pg C y-1 by 2060 and 0.2 Pg C y-1 by 2100, offsetting 7 to 14% of the current national fossil CO2 emissions. Our research provides an example of building a forestation roadmap toward a sustained forest carbon sink, which creates a critical time window for the emission cuts required by the goal of carbon neutrality.


Subject(s)
Ecosystem , Trees , Carbon/analysis , Carbon Dioxide/analysis , Forests , China , Carbon Sequestration
13.
PLoS Genet ; 19(9): e1010923, 2023 09.
Article in English | MEDLINE | ID: mdl-37676887

ABSTRACT

Circular RNAs (circRNAs) have been recognized as critical regulators of skeletal muscle development. Myocyte enhancer factor 2A (MEF2A) is an evolutionarily conserved transcriptional factor that regulates myogenesis. However, it remains unclear whether MEF2A produces functional circRNAs. In this study, we identified two evolutionarily conserved circular MEF2A RNAs (circMEF2As), namely circMEF2A1 and circMEF2A2, in chicken and mouse muscle stem cells. Our findings revealed that circMEF2A1 promotes myogenesis by regulating the miR-30a-3p/PPP3CA/NFATC1 axis, whereas circMEF2A2 facilitates myogenic differentiation by targeting the miR-148a-5p/SLIT3/ROBO2/ß-catenin signaling pathway. Furthermore, in vivo experiments demonstrated that circMEF2As both promote skeletal muscle growth. We also discovered that the linear MEF2A mRNA-derived MEF2A protein binds to its own promoter region, accelerating the transcription of MEF2A and upregulating the expression of both linear MEF2A and circMEF2As, forming a MEF2A autoregulated positive feedback loop. Moreover, circMEF2As positively regulate the expression of linear MEF2A by adsorbing miR-30a-3p and miR-148a-5p, which directly contribute to the MEF2A autoregulated feedback loop. Importantly, we found that mouse circMEF2As are essential for the myogenic differentiation of C2C12 cells. Collectively, our results demonstrated the evolution, function, and underlying mechanisms of circMEF2As in animal myogenesis, which may provide novel insight for both the farm animal meat industry and human medicine.


Subject(s)
MicroRNAs , RNA, Circular , Animals , Humans , Mice , Cell Differentiation , MEF2 Transcription Factors/genetics , MicroRNAs/genetics , Muscle Development/genetics , RNA, Circular/genetics
14.
Proc Natl Acad Sci U S A ; 120(11): e2220697120, 2023 03 14.
Article in English | MEDLINE | ID: mdl-36888658

ABSTRACT

The ocean is a net source of the greenhouse gas and ozone-depleting substance, nitrous oxide (N2O), to the atmosphere. Most of that N2O is produced as a trace side product during ammonia oxidation, primarily by ammonia-oxidizing archaea (AOA), which numerically dominate the ammonia-oxidizing community in most marine environments. The pathways to N2O production and their kinetics, however, are not completely understood. Here, we use 15N and 18O isotopes to determine the kinetics of N2O production and trace the source of nitrogen (N) and oxygen (O) atoms in N2O produced by a model marine AOA species, Nitrosopumilus maritimus. We find that during ammonia oxidation, the apparent half saturation constants of nitrite and N2O production are comparable, suggesting that both processes are enzymatically controlled and tightly coupled at low ammonia concentrations. The constituent atoms in N2O are derived from ammonia, nitrite, O2, and H2O via multiple pathways. Ammonia is the primary source of N atoms in N2O, but its contribution varies with ammonia to nitrite ratio. The ratio of 45N2O to 46N2O (i.e., single or double labeled N) varies with substrate ratio, leading to widely varying isotopic signatures in the N2O pool. O2 is the primary source for O atoms. In addition to the previously demonstrated hybrid formation pathway, we found a substantial contribution by hydroxylamine oxidation, while nitrite reduction is an insignificant source of N2O. Our study highlights the power of dual 15N-18O isotope labeling to disentangle N2O production pathways in microbes, with implications for interpretation of pathways and regulation of marine N2O sources.


Subject(s)
Ammonia , Archaea , Archaea/metabolism , Ammonia/metabolism , Nitrification , Nitrites/metabolism , Isotope Labeling , Oxygen/metabolism , Oxidation-Reduction , Nitrous Oxide/metabolism
15.
Circulation ; 149(21): 1670-1688, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38314577

ABSTRACT

BACKGROUND: Preeclampsia is a serious disease of pregnancy that lacks early diagnosis methods or effective treatment, except delivery. Dysregulated uterine immune cells and spiral arteries are implicated in preeclampsia, but the mechanistic link remains unclear. METHODS: Single-cell RNA sequencing and spatial transcriptomics were used to identify immune cell subsets associated with preeclampsia. Cell-based studies and animal models including conditional knockout mice and a new preeclampsia mouse model induced by recombinant mouse galectin-9 were applied to validate the pathogenic role of a CD11chigh subpopulation of decidual macrophages (dMφ) and to determine its underlying regulatory mechanisms in preeclampsia. A retrospective preeclampsia cohort study was performed to determine the value of circulating galectin-9 in predicting preeclampsia. RESULTS: We discovered a distinct CD11chigh dMφ subset that inhibits spiral artery remodeling in preeclampsia. The proinflammatory CD11chigh dMφ exhibits perivascular enrichment in the decidua from patients with preeclampsia. We also showed that trophoblast-derived galectin-9 activates CD11chigh dMφ by means of CD44 binding to suppress spiral artery remodeling. In 3 independent preeclampsia mouse models, placental and plasma galectin-9 levels were elevated. Galectin-9 administration in mice induces preeclampsia-like phenotypes with increased CD11chigh dMφ and defective spiral arteries, whereas galectin-9 blockade or macrophage-specific CD44 deletion prevents such phenotypes. In pregnant women, increased circulating galectin-9 levels in the first trimester and at 16 to 20 gestational weeks can predict subsequent preeclampsia onset. CONCLUSIONS: These findings highlight a key role of a distinct perivascular inflammatory CD11chigh dMφ subpopulation in the pathogenesis of preeclampsia. CD11chigh dMφ activated by increased galectin-9 from trophoblasts suppresses uterine spiral artery remodeling, contributing to preeclampsia. Increased circulating galectin-9 may be a biomarker for preeclampsia prediction and intervention.


Subject(s)
Decidua , Galectins , Macrophages , Pre-Eclampsia , Vascular Remodeling , Pre-Eclampsia/metabolism , Pre-Eclampsia/immunology , Pregnancy , Female , Animals , Galectins/metabolism , Macrophages/metabolism , Macrophages/immunology , Macrophages/pathology , Mice , Humans , Decidua/metabolism , Decidua/pathology , Mice, Knockout , Uterus/metabolism , Uterus/blood supply , Disease Models, Animal , Hyaluronan Receptors/metabolism , Hyaluronan Receptors/genetics , Retrospective Studies , Mice, Inbred C57BL , CD11 Antigens
16.
Mol Biol Evol ; 41(6)2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38829799

ABSTRACT

Global climate change has led to shifts in the distribution ranges of many terrestrial species, promoting their migration from lower altitudes or latitudes to higher ones. Meanwhile, successful invaders have developed genetic adaptations enabling the colonization of new environments. Over the past 40 years, Rattus tanezumi (RT) has expanded into northern China (Northwest and North China) from its southern origins. We studied the cold adaptation of RT and its potential for northward expansion by comparing it with sympatric Rattus norvegicus (RN), which is well adapted to cold regions. Through population genomic analysis, we revealed that the invading RT rats have split into three distinct populations: the North, Northwest, and Tibetan populations. The first two populations exhibited high genetic diversity, while the latter population showed remarkably low genetic diversity. These rats have developed various genetic adaptations to cold, arid, hypoxic, and high-UV conditions. Cold acclimation tests revealed divergent thermoregulation between RT and RN. Specifically, RT exhibited higher brown adipose tissue activity and metabolic rates than did RN. Transcriptome analysis highlighted changes in genes regulating triglyceride catabolic processes in RT, including Apoa1 and Apoa4, which were upregulated, under selection and associated with local adaptation. In contrast, RN showed changes in carbohydrate metabolism genes. Despite the cold adaptation of RT, we observed genotypic and phenotypic constraints that may limit its ability to cope with severe low temperatures farther north. Consequently, it is less likely that RT rats will invade and overlap with RN rats in farther northern regions.


Subject(s)
Acclimatization , Cold Temperature , Animals , Rats , Acclimatization/genetics , China , Phenotype , Genetic Variation , Adaptation, Physiological/genetics , Body Temperature Regulation/genetics , Climate Change
17.
Brief Bioinform ; 24(5)2023 09 20.
Article in English | MEDLINE | ID: mdl-37466138

ABSTRACT

Accurately identifying phage-host relationships from their genome sequences is still challenging, especially for those phages and hosts with less homologous sequences. In this work, focusing on identifying the phage-host relationships at the species and genus level, we propose a contrastive learning based approach to learn whole-genome sequence embeddings that can take account of phage-host interactions (PHIs). Contrastive learning is used to make phages infecting the same hosts close to each other in the new representation space. Specifically, we rephrase whole-genome sequences with frequency chaos game representation (FCGR) and learn latent embeddings that 'encapsulate' phages and host relationships through contrastive learning. The contrastive learning method works well on the imbalanced dataset. Based on the learned embeddings, a proposed pipeline named CL4PHI can predict known hosts and unseen hosts in training. We compare our method with two recently proposed state-of-the-art learning-based methods on their benchmark datasets. The experiment results demonstrate that the proposed method using contrastive learning improves the prediction accuracy on known hosts and demonstrates a zero-shot prediction capability on unseen hosts. In terms of potential applications, the rapid pace of genome sequencing across different species has resulted in a vast amount of whole-genome sequencing data that require efficient computational methods for identifying phage-host interactions. The proposed approach is expected to address this need by efficiently processing whole-genome sequences of phages and prokaryotic hosts and capturing features related to phage-host relationships for genome sequence representation. This approach can be used to accelerate the discovery of phage-host interactions and aid in the development of phage-based therapies for infectious diseases.


Subject(s)
Bacteriophages , Bacteriophages/genetics , Genome, Viral , Whole Genome Sequencing , Chromosome Mapping
18.
Bioinformatics ; 40(6)2024 06 03.
Article in English | MEDLINE | ID: mdl-38851878

ABSTRACT

SUMMARY: Functional interpretation of biological entities such as differentially expressed genes is one of the fundamental analyses in bioinformatics. The task can be addressed by using biological pathway databases with enrichment analysis (EA). However, textual description of biological entities in public databases is less explored and integrated in existing tools and it has a potential to reveal new mechanisms. Here, we present a new R package biotextgraph for graphical summarization of omics' textual description data which enables assessment of functional similarities of the lists of biological entities. We illustrate application examples of annotating gene identifiers in addition to EA. The results suggest that the visualization based on words and inspection of biological entities with text can reveal a set of biologically meaningful terms that could not be obtained by using biological pathway databases alone. The results suggest the usefulness of the package in the routine analysis of omics-related data. The package also offers a web-based application for convenient querying. AVAILABILITY AND IMPLEMENTATION: The package, documentation, and web server are available at: https://github.com/noriakis/biotextgraph.


Subject(s)
Computational Biology , Software , Computational Biology/methods
19.
Nat Mater ; 23(1): 71-78, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37919349

ABSTRACT

Light scattered or radiated from a material carries valuable information on the said material. Such information can be uncovered by measuring the light field at different angles and frequencies. However, this technique typically requires a large optical apparatus, hampering the widespread use of angle-resolved spectroscopy beyond the lab. Here we demonstrate compact angle-resolved spectral imaging by combining a tunable metasurface-based spectrometer array and a metalens. With this approach, even with a miniaturized spectrometer footprint of only 4 × 4 µm2, we demonstrate a wavelength accuracy of 0.17 nm, spectral resolution of 0.4 nm and a linear dynamic range of 149 dB. Moreover, our spectrometer has a detection limit of 1.2 fJ, and can be patterned to an array for spectral imaging. Placing such a spectrometer array directly at the back focal plane of a metalens, we achieve an angular resolution of 4.88 × 10-3 rad. Our angle-resolved spectrometers empowered by metalenses can be employed towards enhancing advanced optical imaging and spectral analysis applications.

20.
Nat Mater ; 23(9): 1193-1199, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39080501

ABSTRACT

The question of whether all materials can solidify into the glassy form proposed by Turnbull half a century ago remains unsolved. Some of the simplest systems of monatomic metals have not been vitrified, especially the close-packed face-centred cubic metals. Here we report the vitrification of gold, which is notoriously difficult to be vitrified, and several similar close-packed face-centred cubic and hexagonal metals using a method of picosecond pulsed laser ablation in a liquid medium. The vitrification occurs through the rapid cooling during laser ablation and the inhibition of nucleation by the liquid medium. Using this method, a large number of atomic configurations, including glassy configurations, can be generated simultaneously, from which a stable glass state can be sampled. Simulations demonstrate that the favourable stability of monatomic metals stems from the strong topological frustration of icosahedra-like clusters. Our work breaks the limitation of the glass-forming ability of matter, indicating that vitrification is an intrinsic property of matter and providing a strategy for the preparation and design of metallic glasses from an atomic configuration perspective.

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