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1.
Cell ; 186(3): 560-576.e17, 2023 02 02.
Artigo em Inglês | MEDLINE | ID: mdl-36693374

RESUMO

Downward social mobility is a well-known mental risk factor for depression, but its neural mechanism remains elusive. Here, by forcing mice to lose against their subordinates in a non-violent social contest, we lower their social ranks stably and induce depressive-like behaviors. These rank-decline-associated depressive-like behaviors can be reversed by regaining social status. In vivo fiber photometry and single-unit electrophysiological recording show that forced loss, but not natural loss, generates negative reward prediction error (RPE). Through the lateral hypothalamus, the RPE strongly activates the brain's anti-reward center, the lateral habenula (LHb). LHb activation inhibits the medial prefrontal cortex (mPFC) that controls social competitiveness and reinforces retreats in contests. These results reveal the core neural mechanisms mutually promoting social status loss and depressive behaviors. The intertwined neuronal signaling controlling mPFC and LHb activities provides a mechanistic foundation for the crosstalk between social mobility and psychological disorder, unveiling a promising target for intervention.


Assuntos
Habenula , Status Social , Camundongos , Animais , Recompensa , Comportamento Social , Habenula/fisiologia , Depressão
2.
Cell ; 186(25): 5500-5516.e21, 2023 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-38016470

RESUMO

Most animals require sleep, and sleep loss induces serious pathophysiological consequences, including death. Previous experimental approaches for investigating sleep impacts in mice have been unable to persistently deprive animals of both rapid eye movement sleep (REMS) and non-rapid eye movement sleep (NREMS). Here, we report a "curling prevention by water" paradigm wherein mice remain awake 96% of the time. After 4 days of exposure, mice exhibit severe inflammation, and approximately 80% die. Sleep deprivation increases levels of prostaglandin D2 (PGD2) in the brain, and we found that elevated PGD2 efflux across the blood-brain-barrier-mediated by ATP-binding cassette subfamily C4 transporter-induces both accumulation of circulating neutrophils and a cytokine-storm-like syndrome. Experimental disruption of the PGD2/DP1 axis dramatically reduced sleep-deprivation-induced inflammation. Thus, our study reveals that sleep-related changes in PGD2 in the central nervous system drive profound pathological consequences in the peripheral immune system.


Assuntos
Privação do Sono , Animais , Camundongos , Citocinas/metabolismo , Inflamação , Prostaglandina D2 , Sono/fisiologia , Privação do Sono/genética , Privação do Sono/metabolismo , Síndrome , Humanos , Ratos , Linhagem Celular , Tempestades Ciclônicas , Neutrófilos/metabolismo
3.
Nat Immunol ; 25(2): 268-281, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38195702

RESUMO

Melanoma cells, deriving from neuroectodermal melanocytes, may exploit the nervous system's immune privilege for growth. Here we show that nerve growth factor (NGF) has both melanoma cell intrinsic and extrinsic immunosuppressive functions. Autocrine NGF engages tropomyosin receptor kinase A (TrkA) on melanoma cells to desensitize interferon γ signaling, leading to T and natural killer cell exclusion. In effector T cells that upregulate surface TrkA expression upon T cell receptor activation, paracrine NGF dampens T cell receptor signaling and effector function. Inhibiting NGF, either through genetic modification or with the tropomyosin receptor kinase inhibitor larotrectinib, renders melanomas susceptible to immune checkpoint blockade therapy and fosters long-term immunity by activating memory T cells with low affinity. These results identify the NGF-TrkA axis as an important suppressor of anti-tumor immunity and suggest larotrectinib might be repurposed for immune sensitization. Moreover, by enlisting low-affinity T cells, anti-NGF reduces acquired resistance to immune checkpoint blockade and prevents melanoma recurrence.


Assuntos
Melanoma , Receptor de Fator de Crescimento Neural , Humanos , Receptor de Fator de Crescimento Neural/genética , Receptor de Fator de Crescimento Neural/metabolismo , Fator de Crescimento Neural/genética , Fator de Crescimento Neural/metabolismo , Tropomiosina , Melanoma/terapia , Receptor trkA/genética , Receptor trkA/metabolismo , Citoproteção , Inibidores de Checkpoint Imunológico , Células T de Memória , Terapia de Imunossupressão , Imunoterapia , Receptores de Antígenos de Linfócitos T
4.
Mol Cell ; 84(2): 327-344.e9, 2024 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-38151018

RESUMO

Mitophagy mediated by BNIP3 and NIX critically regulates mitochondrial mass. Cellular BNIP3 and NIX levels are tightly controlled by SCFFBXL4-mediated ubiquitination to prevent excessive mitochondrial loss and lethal disease. Here, we report that knockout of PPTC7, a mitochondrial matrix protein, hyperactivates BNIP3-/NIX-mediated mitophagy and causes perinatal lethality that is rescued by NIX knockout in mice. Biochemically, the PPTC7 precursor is trapped by BNIP3 and NIX to the mitochondrial outer membrane, where PPTC7 scaffolds assembly of a substrate-PPTC7-SCFFBXL4 holocomplex to degrade BNIP3 and NIX, forming a homeostatic regulatory loop. PPTC7 possesses an unusually weak mitochondrial targeting sequence to facilitate its outer membrane retention and mitophagy control. Starvation upregulates PPPTC7 expression in mouse liver to repress mitophagy, which critically maintains hepatic mitochondrial mass, bioenergetics, and gluconeogenesis. Collectively, PPTC7 functions as a mitophagy sensor that integrates homeostatic and physiological signals to dynamically control BNIP3 and NIX degradation, thereby maintaining mitochondrial mass and cellular homeostasis.


Assuntos
Proteínas de Membrana , Membranas Mitocondriais , Proteínas Mitocondriais , Mitofagia , Proteína Fosfatase 2C , Proteólise , Animais , Camundongos , Proteínas de Membrana/metabolismo , Mitocôndrias/genética , Mitocôndrias/metabolismo , Membranas Mitocondriais/metabolismo , Proteínas Mitocondriais/metabolismo , Mitofagia/genética , Proteína Fosfatase 2C/metabolismo
5.
Mol Cell ; 2023 Aug 25.
Artigo em Inglês | MEDLINE | ID: mdl-37657444

RESUMO

N6-methyladenosine (m6A) RNA modification plays important roles in the governance of gene expression and is temporally regulated in different cell states. In contrast to global m6A profiling in bulk sequencing, single-cell technologies for analyzing m6A heterogeneity are not extensively established. Here, we developed single-nucleus m6A-CUT&Tag (sn-m6A-CT) for simultaneous profiling of m6A methylomes and transcriptomes within a single nucleus using mouse embryonic stem cells (mESCs). m6A-CT is capable of enriching m6A-marked RNA molecules in situ, without isolating RNAs from cells. We adapted m6A-CT to the droplet-based single-cell omics platform and demonstrated high-throughput performance in analyzing nuclei isolated from thousands of cells from various cell types. We show that sn-m6A-CT profiling is sufficient to determine cell identity and allows the generation of cell-type-specific m6A methylome landscapes from heterogeneous populations. These indicate that sn-m6A-CT provides additional dimensions to multimodal datasets and insights into epitranscriptomic landscape in defining cell fate identity and states.

6.
Nature ; 612(7940): 519-527, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36477534

RESUMO

In mice and humans, sleep quantity is governed by genetic factors and exhibits age-dependent variation1-3. However, the core molecular pathways and effector mechanisms that regulate sleep duration in mammals remain unclear. Here, we characterize a major signalling pathway for the transcriptional regulation of sleep in mice using adeno-associated virus-mediated somatic genetics analysis4. Chimeric knockout of LKB1 kinase-an activator of AMPK-related protein kinase SIK35-7-in adult mouse brain markedly reduces the amount and delta power-a measure of sleep depth-of non-rapid eye movement sleep (NREMS). Downstream of the LKB1-SIK3 pathway, gain or loss-of-function of the histone deacetylases HDAC4 and HDAC5 in adult brain neurons causes bidirectional changes of NREMS amount and delta power. Moreover, phosphorylation of HDAC4 and HDAC5 is associated with increased sleep need, and HDAC4 specifically regulates NREMS amount in posterior hypothalamus. Genetic and transcriptomic studies reveal that HDAC4 cooperates with CREB in both transcriptional and sleep regulation. These findings introduce the concept of signalling pathways targeting transcription modulators to regulate daily sleep amount and demonstrate the power of somatic genetics in mouse sleep research.


Assuntos
Transdução de Sinais , Duração do Sono , Transcrição Gênica , Animais , Camundongos , Regulação da Expressão Gênica , Fosforilação , Transdução de Sinais/fisiologia , Sono de Ondas Lentas/genética , Perfilação da Expressão Gênica
7.
EMBO J ; 42(21): e114220, 2023 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-37691541

RESUMO

DELLA proteins are master regulators of gibberellic acid (GA) signaling through their effects on gene expression. Enhanced DELLA accumulation in rice and wheat varieties has greatly contributed to grain yield increases during the green revolution. However, the molecular basis of DELLA-mediated gene repression remains elusive. In this work, we show that the rice DELLA protein SLENDER RICE1 (SLR1) forms a tripartite complex with Polycomb-repressive complex 2 (PRC2) and the histone deacetylase HDA702 to repress downstream genes by establishing a silent chromatin state. The slr1 mutation and GA signaling resulted in dissociation of PRC2 and HDA702 from GA-inducible genes. Loss-of-function or downregulation of the chromatin regulators impaired SLR1-dependent histone modification and gene repression. Time-resolved analysis of GA signaling revealed that GA-induced transcriptional activation was associated with a rapid increase of H3K9ac followed by H3K27me3 removal. Collectively, these results establish a general epigenetic mechanism for DELLA-mediated gene repression and reveal details of the chromatin dynamics during transcriptional activation stimulated by GA signaling.


Assuntos
Giberelinas , Oryza , Giberelinas/metabolismo , Giberelinas/farmacologia , Oryza/genética , Oryza/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Expressão Gênica , Cromatina/genética , Cromatina/metabolismo , Regulação da Expressão Gênica de Plantas
8.
EMBO J ; 42(13): e113033, 2023 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-36896912

RESUMO

Mitophagy is a fundamental quality control mechanism of mitochondria. Its regulatory mechanisms and pathological implications remain poorly understood. Here, via a mitochondria-targeted genetic screen, we found that knockout (KO) of FBXL4, a mitochondrial disease gene, hyperactivates mitophagy at basal conditions. Subsequent counter screen revealed that FBXL4-KO hyperactivates mitophagy via two mitophagy receptors BNIP3 and NIX. We determined that FBXL4 functions as an integral outer-membrane protein that forms an SCF-FBXL4 ubiquitin E3 ligase complex. SCF-FBXL4 ubiquitinates BNIP3 and NIX to target them for degradation. Pathogenic FBXL4 mutations disrupt SCF-FBXL4 assembly and impair substrate degradation. Fbxl4-/- mice exhibit elevated BNIP3 and NIX proteins, hyperactive mitophagy, and perinatal lethality. Importantly, knockout of either Bnip3 or Nix rescues metabolic derangements and viability of the Fbxl4-/- mice. Together, beyond identifying SCF-FBXL4 as a novel mitochondrial ubiquitin E3 ligase restraining basal mitophagy, our results reveal hyperactivated mitophagy as a cause of mitochondrial disease and suggest therapeutic strategies.


Assuntos
Doenças Mitocondriais , Mitofagia , Camundongos , Animais , Mitofagia/fisiologia , Mitocôndrias/metabolismo , Doenças Mitocondriais/metabolismo , Ubiquitina-Proteína Ligases/genética , Ubiquitina-Proteína Ligases/metabolismo , Ubiquitinas/metabolismo , Proteínas Mitocondriais/genética , Proteínas Mitocondriais/metabolismo
9.
Plant Cell ; 36(2): 227-245, 2024 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-37772963

RESUMO

Biomolecular condensates are dynamic structures formed through diverse mechanisms, including liquid-liquid phase separation. These condensates have emerged as crucial regulators of cellular processes in eukaryotic cells, enabling the compartmentalization of specific biological reactions while allowing for dynamic exchange of molecules with the surrounding environment. RNA silencing, a conserved gene regulatory mechanism mediated by small RNAs (sRNAs), plays pivotal roles in various biological processes. Multiple types of biomolecular condensate, including dicing bodies, processing bodies, small interfering RNA bodies, and Cajal bodies, have been identified as key players in RNA silencing pathways. These biomolecular condensates provide spatial compartmentation for the biogenesis, loading, action, and turnover of small RNAs. Moreover, they actively respond to stresses, such as viral infections, and modulate RNA silencing activities during stress responses. This review summarizes recent advances in understanding of dicing bodies and other biomolecular condensates involved in RNA silencing. We explore their formation, roles in RNA silencing, and contributions to antiviral resistance responses. This comprehensive overview provides insights into the functional significance of biomolecular condensates in RNA silencing and expands our understanding of their roles in gene expression and stress responses in plants.


Assuntos
Condensados Biomoleculares , RNA , Interferência de RNA , Células Eucarióticas , RNA Interferente Pequeno , Separação de Fases
10.
Plant Cell ; 2024 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-38819320

RESUMO

The brassinosteroid (BR) receptor BRASSINOSTEROID-INSENSITIVE 1 (BRI1) plays a critical role in plant growth and development. Although much is known about how BR signaling regulates growth and development in many crop species, the role of StBRI1 in regulating potato (Solanum tuberosum) tuber development is not well understood. To address this question, a series of comprehensive genetic and biochemical methods were applied in this investigation. It was determined that StBRI1 and Solanum tuberosum PLASMA MEMBRANE (PM) PROTON ATPASE2 (PHA2), a PM-localized proton ATPase, play important roles in potato tuber development. The individual overexpression of StBRI1 and PHA2 led to a 22% and 25% increase in tuber yield per plant, respectively. Consistent with the genetic evidence, in vivo interaction analysis using double transgenic lines and PM H+-ATPase activity assays indicated that StBRI1 interacts with the C-terminus of PHA2, which restrains the intramolecular interaction of the PHA2 C-terminus with the PHA2 central loop to attenuate autoinhibition of PM H+-ATPase activity, resulting in increased PHA2 activity. Furthermore, the extent of PM H+-ATPase autoinhibition involving phosphorylation-dependent mechanisms corresponds to phosphorylation of the penultimate Thr residue (Thr-951) in PHA2. These results suggest that StBRI1 phosphorylates PHA2 and enhances its activity, which subsequently promotes tuber development. Altogether, our results uncover a BR-StBRI1-PHA2 module that regulates tuber development and suggest a prospective strategy for improving tuberous crop growth and increasing yield via the cell surface-based BR signaling pathway.

11.
Nature ; 598(7879): 174-181, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34616072

RESUMO

Dendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types1,2, yet our knowledge of its diversity remains limited. Here, to systematically examine complete single-neuron morphologies on a brain-wide scale, we established a pipeline encompassing sparse labelling, whole-brain imaging, reconstruction, registration and analysis. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice. We identified 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. Extensive projectional diversity was found within each of these major types, on the basis of which some types were clustered into more refined subtypes. This diversity follows a set of generalizable principles that govern long-range axonal projections at different levels, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. Although clear concordance with transcriptomic profiles is evident at the level of major projection type, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell cross-modality studies. Overall, our study demonstrates the crucial need for quantitative description of complete single-cell anatomy in cell-type classification, as single-cell morphological diversity reveals a plethora of ways in which different cell types and their individual members may contribute to the configuration and function of their respective circuits.


Assuntos
Encéfalo/citologia , Forma Celular , Neurônios/classificação , Neurônios/metabolismo , Análise de Célula Única , Atlas como Assunto , Biomarcadores/metabolismo , Encéfalo/anatomia & histologia , Encéfalo/embriologia , Encéfalo/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Humanos , Neocórtex/anatomia & histologia , Neocórtex/citologia , Neocórtex/embriologia , Neocórtex/metabolismo , Neurogênese , Neuroglia/citologia , Neurônios/citologia , RNA-Seq , Reprodutibilidade dos Testes
12.
Proc Natl Acad Sci U S A ; 121(5): e2305770121, 2024 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-38227645

RESUMO

Acylated peptides composed of glucagon-like peptide-1 receptor agonists modified with a fatty acid side chain are an important class of therapeutics for type 2 diabetes and obesity but are susceptible to an unusual physical instability in the presence of hydrophobic surfaces, i.e., spontaneous emulsification, also known as ouzo formation in practice. In this work, light scattering, small-angle X-ray scattering, and circular dichroism measurements are used to characterize the physical properties of the semaglutide colloidal phase, including size distribution, shape, secondary structure, internal structure, and internal composition, as a function of solution physico-chemical conditions. The existence and size of the colloids formed are successfully predicted by a classical Rayleigh model, which identifies the parameters controlling their size and formation. Colloid formation is found to be catalyzed by hydrophobic surfaces, and formation rates are modeled as an autocatalytic reaction, enabling the formation of a master curve for various surfaces that elucidates the mechanism. Surfaces differ due to differences in surface wettability, which can be correlated with Hansen solubility parameters. This work provides insights into this unusual colloidal phenomenon and guides the peptide synthesis process and drug product formulation in the pharmaceutical industry.


Assuntos
Diabetes Mellitus Tipo 2 , Humanos , Peptídeos Semelhantes ao Glucagon , Molhabilidade , Peptídeos , Coloides/química , Receptor do Peptídeo Semelhante ao Glucagon 1/agonistas , Hipoglicemiantes
13.
Chem Rev ; 124(7): 3813-3931, 2024 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-38512224

RESUMO

The breadth and importance of polymerized ionic liquids (PILs) are steadily expanding, and this review updates advances and trends in syntheses, properties, and applications over the past five to six years. We begin with an historical overview of the genesis and growth of the PIL field as a subset of materials science. The genesis of ionic liquids (ILs) over nano to meso length-scales exhibiting 0D, 1D, 2D, and 3D topologies defines colloidal ionic liquids, CILs, which compose a subclass of PILs and provide a synthetic bridge between IL monomers (ILMs) and micro to macro-scale PIL materials. The second focus of this review addresses design and syntheses of ILMs and their polymerization reactions to yield PILs and PIL-based materials. A burgeoning diversity of ILMs reflects increasing use of nonimidazolium nuclei and an expanding use of step-growth chemistries in synthesizing PIL materials. Radical chain polymerization remains a primary method of making PILs and reflects an increasing use of controlled polymerization methods. Step-growth chemistries used in creating some CILs utilize extensive cross-linking. This cross-linking is enabled by incorporating reactive functionalities in CILs and PILs, and some of these CILs and PILs may be viewed as exotic cross-linking agents. The third part of this update focuses upon some advances in key properties, including molecular weight, thermal properties, rheology, ion transport, self-healing, and stimuli-responsiveness. Glass transitions, critical solution temperatures, and liquidity are key thermal properties that tie to PIL rheology and viscoelasticity. These properties in turn modulate mechanical properties and ion transport, which are foundational in increasing applications of PILs. Cross-linking in gelation and ionogels and reversible step-growth chemistries are essential for self-healing PILs. Stimuli-responsiveness distinguishes PILs from many other classes of polymers, and it emphasizes the importance of segmentally controlling and tuning solvation in CILs and PILs. The fourth part of this review addresses development of applications, and the diverse scope of such applications supports the increasing importance of PILs in materials science. Adhesion applications are supported by ionogel properties, especially cross-linking and solvation tunable interactions with adjacent phases. Antimicrobial and antifouling applications are consequences of the cationic nature of PILs. Similarly, emulsion and dispersion applications rely on tunable solvation of functional groups and on how such groups interact with continuous phases and substrates. Catalysis is another significant application, and this is an historical tie between ILs and PILs. This component also provides a connection to diverse and porous carbon phases templated by PILs that are catalysts or serve as supports for catalysts. Devices, including sensors and actuators, also rely on solvation tuning and stimuli-responsiveness that include photo and electrochemical stimuli. We conclude our view of applications with 3D printing. The largest components of these applications are energy related and include developments for supercapacitors, batteries, fuel cells, and solar cells. We conclude with our vision of how PIL development will evolve over the next decade.

14.
Cell ; 147(2): 447-58, 2011 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-22000021

RESUMO

Spinal opioid-induced itch, a prevalent side effect of pain management, has been proposed to result from pain inhibition. We now report that the µ-opioid receptor (MOR) isoform MOR1D is essential for morphine-induced scratching (MIS), whereas the isoform MOR1 is required only for morphine-induced analgesia (MIA). MOR1D heterodimerizes with gastrin-releasing peptide receptor (GRPR) in the spinal cord, relaying itch information. We show that morphine triggers internalization of both GRPR and MOR1D, whereas GRP specifically triggers GRPR internalization and morphine-independent scratching. Providing potential insight into opioid-induced itch prevention, we demonstrate that molecular and pharmacologic inhibition of PLCß3 and IP3R3, downstream effectors of GRPR, specifically block MIS but not MIA. In addition, blocking MOR1D-GRPR association attenuates MIS but not MIA. Together, these data suggest that opioid-induced itch is an active process concomitant with but independent of opioid analgesia, occurring via the unidirectional cross-activation of GRPR signaling by MOR1D heterodimerization.


Assuntos
Analgesia , Analgésicos Opioides/administração & dosagem , Morfina/administração & dosagem , Dor/tratamento farmacológico , Prurido/induzido quimicamente , Receptores da Bombesina/metabolismo , Receptores Opioides mu/metabolismo , Sequência de Aminoácidos , Animais , Camundongos , Camundongos Knockout , Dados de Sequência Molecular , Receptores da Bombesina/genética , Receptores Opioides mu/genética , Transdução de Sinais
15.
Nature ; 586(7827): 145-150, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32968273

RESUMO

Natural products serve as chemical blueprints for most antibiotics in clinical use. The evolutionary process by which these molecules arise is inherently accompanied by the co-evolution of resistance mechanisms that shorten the clinical lifetime of any given class of antibiotics1. Virginiamycin acetyltransferase (Vat) enzymes are resistance proteins that provide protection against streptogramins2, potent antibiotics against Gram-positive bacteria that inhibit the bacterial ribosome3. Owing to the challenge of selectively modifying the chemically complex, 23-membered macrocyclic scaffold of group A streptogramins, analogues that overcome the resistance conferred by Vat enzymes have not been previously developed2. Here we report the design, synthesis, and antibacterial evaluation of group A streptogramin antibiotics with extensive structural variability. Using cryo-electron microscopy and forcefield-based refinement, we characterize the binding of eight analogues to the bacterial ribosome at high resolution, revealing binding interactions that extend into the peptidyl tRNA-binding site and towards synergistic binders that occupy the nascent peptide exit tunnel. One of these analogues has excellent activity against several streptogramin-resistant strains of Staphylococcus aureus, exhibits decreased rates of acetylation in vitro, and is effective at lowering bacterial load in a mouse model of infection. Our results demonstrate that the combination of rational design and modular chemical synthesis can revitalize classes of antibiotics that are limited by naturally arising resistance mechanisms.


Assuntos
Antibacterianos/síntese química , Antibacterianos/farmacologia , Desenho de Fármacos , Farmacorresistência Bacteriana/efeitos dos fármacos , Estreptogramina Grupo A/síntese química , Estreptogramina Grupo A/farmacologia , Acetilação/efeitos dos fármacos , Acetiltransferases/genética , Acetiltransferases/metabolismo , Animais , Antibacterianos/classificação , Carga Bacteriana/efeitos dos fármacos , Sítios de Ligação , Microscopia Crioeletrônica , Feminino , Técnicas In Vitro , Camundongos , Testes de Sensibilidade Microbiana , Modelos Moleculares , RNA de Transferência/metabolismo , Ribossomos/efeitos dos fármacos , Ribossomos/metabolismo , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/genética , Staphylococcus aureus/metabolismo , Estreptogramina Grupo A/química , Estreptogramina Grupo A/classificação , Virginiamicina/análogos & derivados , Virginiamicina/química , Virginiamicina/metabolismo
16.
Nucleic Acids Res ; 52(9): e46, 2024 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-38647069

RESUMO

SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multi-omic cellular profiles. It is conveniently available as an open-source R package.


Assuntos
Análise de Célula Única , Software , Análise de Célula Única/métodos , Humanos , Anotação de Sequência Molecular , Algoritmos , Biologia Computacional/métodos , Análise de Sequência de RNA/métodos , Perfilação da Expressão Gênica/métodos , Sequenciamento de Cromatina por Imunoprecipitação/métodos , Análise por Conglomerados
17.
Proc Natl Acad Sci U S A ; 120(21): e2216765120, 2023 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-37186862

RESUMO

Urbanization extensively modifies surface roughness and properties, impacting regional climate and hydrological cycles. Urban effects on temperature and precipitation have drawn considerable attention. These associated physical processes are also closely linked to clouds' formation and dynamics. Cloud is one of the critical components in regulating urban hydrometeorological cycles but remains less understood in urban-atmospheric systems. We analyzed satellite-derived cloud patterns spanning two decades over 447 US cities and quantified the urban-influenced cloud patterns diurnally and seasonally. The systematic assessment suggests that most cities experience enhanced daytime cloud cover in both summer and winter; nocturnal cloud enhancement prevails in summer by 5.8%, while there is modest cloud suppression in winter nights. Statistically linking the cloud patterns with city properties, geographic locations, and climate backgrounds, we found that larger city size and stronger surface heating are primarily responsible for summer local cloud enhancement diurnally. Moisture and energy background control the urban cloud cover anomalies seasonally. Under strong mesoscale circulations induced by terrains and land-water contrasts, urban clouds exhibit considerable nighttime enhancement during warm seasons, which is relevant to strong urban surface heating interacting with these circulations, but other local and climate impacts remain complicated and inconclusive. Our research unveils extensive urban influences on local cloud patterns, but the effects are diverse depending on time, location, and city properties. The comprehensive observational study on urban-cloud interactions calls for more in-depth research on urban cloud life cycles and their radiative and hydrologic implications under the urban warming context.

18.
Proc Natl Acad Sci U S A ; 120(11): e2219523120, 2023 03 14.
Artigo em Inglês | MEDLINE | ID: mdl-36893269

RESUMO

The continuous evolution of SARS-CoV-2 variants complicates efforts to combat the ongoing pandemic, underscoring the need for a dynamic platform for the rapid development of pan-viral variant therapeutics. Oligonucleotide therapeutics are enhancing the treatment of numerous diseases with unprecedented potency, duration of effect, and safety. Through the systematic screening of hundreds of oligonucleotide sequences, we identified fully chemically stabilized siRNAs and ASOs that target regions of the SARS-CoV-2 genome conserved in all variants of concern, including delta and omicron. We successively evaluated candidates in cellular reporter assays, followed by viral inhibition in cell culture, with eventual testing of leads for in vivo antiviral activity in the lung. Previous attempts to deliver therapeutic oligonucleotides to the lung have met with only modest success. Here, we report the development of a platform for identifying and generating potent, chemically modified multimeric siRNAs bioavailable in the lung after local intranasal and intratracheal delivery. The optimized divalent siRNAs showed robust antiviral activity in human cells and mouse models of SARS-CoV-2 infection and represent a new paradigm for antiviral therapeutic development for current and future pandemics.


Assuntos
COVID-19 , Humanos , Animais , Camundongos , RNA Interferente Pequeno/genética , COVID-19/terapia , SARS-CoV-2/genética , Antivirais/farmacologia , Antivirais/uso terapêutico , Oligonucleotídeos , Pulmão
19.
Plant J ; 117(1): 193-211, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37812678

RESUMO

Soil salinity severely threatens plant growth and crop yields. The utilization of PGPR is an effective strategy for enhancing plant salt tolerance, but the mechanisms involved in this process have rarely been reported. In this study, we investigated the effects of Bacillus subtilis CNBG-PGPR-1 on improving plant salt tolerance and elucidated the molecular pathways involved. The results showed that CNBG-PGPR-1 significantly improved the cellular homeostasis and photosynthetic efficiency of leaves and reduced ion toxicity and osmotic stress caused by salt in tomato. Transcriptome analysis uncovered that CNBG-PGPR-1 enhanced plant salt tolerance through the activation of complex molecular pathways, with plant hormone signal transduction playing an important role. Comparative analysis and pharmacological experiments confirmed that the ethylene pathway was closely related to the beneficial effect of CNBG-PGPR-1 on improving plant salt tolerance. Furthermore, we found that methionine, a precursor of ethylene synthesis, significantly accumulated in response to CNBG-PGPR-1 in tomato. Exogenous L-methionine largely mimicked the beneficial effects of CNBG-PGPR-1 and activated the expression of ethylene pathway-related genes, indicating CNBG-PGPR-1 induces methionine accumulation to regulate the ethylene pathway in tomato. Finally, CNBG-PGPR-1 reduced salt-induced ROS by activating ROS scavenger-encoding genes, mainly involved in GSH metabolism and POD-related genes, which were also closely linked to methionine metabolism. Overall, our studies demonstrate that CNBG-PGPR-1-induced methionine is a key regulator in enhancing plant salt tolerance through the ethylene pathway and ROS scavenging, providing a novel understanding of the mechanism by which beneficial microbes improve plant salt tolerance.


Assuntos
Solanum lycopersicum , Solanum lycopersicum/genética , Bacillus subtilis/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Metionina , Tolerância ao Sal , Etilenos/metabolismo , Racemetionina
20.
Nat Mater ; 23(2): 237-243, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37974006

RESUMO

Dielectric polymers are ubiquitous as electrical insulation in electronic devices and electrical systems. Electrical degradation of dielectric polymers tends to initiate catastrophic failure of numerous devices and systems, but its detection and early warning remain challenging. Here we report a general material strategy that signals the electrical degradation of dielectric polymers by autonomously presenting a visually discernible warning in the form of a pronounced colour change. This colour change is induced by the chromogenic response of molecular indicators blended with the polymer, which are chemically activated by the oxygen radicals generated in situ during the electrical degradation of the polymer. We unveil that the structural degradation and electrical properties of the dielectric polymer are quantitatively correlated with the colour difference. Such a chromogenic process is autonomous without the need of human intervention or other external energy, thus offering the convenience to lower or even eliminate the risk of dielectric failure.

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