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1.
Nature ; 632(8027): 1014-1016, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-39112707

RESUMO

Fast radio bursts (FRBs) are millisecond-duration, bright (approximately Jy) extragalactic bursts, whose production mechanism is still unclear1. Recently, two repeating FRBs were found to have a physically associated persistent radio source of non-thermal origin2,3. These two FRBs have unusually large Faraday rotation measure values2,3, probably tracing a dense magneto-ionic medium, consistent with synchrotron radiation originating from a nebula surrounding the FRB source4-8. Recent theoretical arguments predict that, if the observed Faraday rotation measure mostly arises from the persistent radio source region, there should be a simple relation between the persistent radio source luminosity and the rotation measure itself7,9. Here we report the detection of a third, less luminous persistent radio source associated with the repeating FRB source FRB 20201124A at a distance of 413 Mpc, substantially expanding the predicted relation into the low luminosity-low Faraday rotation measure regime (<1,000 rad m-2). At lower values of the Faraday rotation measure, the expected radio luminosity falls below the limit-of-detection threshold for present-day radio telescopes. These findings support the idea that the persistent radio sources observed so far are generated by a nebula in the FRB environment and that FRBs with low Faraday rotation measure may not show a persistent radio source because of a weaker magneto-ionic medium. This is generally consistent with models invoking a young magnetar as the central engine of the FRB, in which the surrounding ionized nebula-or the interacting shock in a binary system-powers the persistent radio source.

2.
Mol Cell ; 82(9): 1724-1736.e7, 2022 05 05.
Artigo em Inglês | MEDLINE | ID: mdl-35320752

RESUMO

7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is hijacked by HIV-1 for viral transcription and replication. Methylphosphate capping enzyme (MePCE) and La-related protein 7 (Larp7) constitutively associate with 7SK to form a core RNP, while P-TEFb and other proteins dynamically assemble to form different complexes. Here, we present the cryo-EM structures of 7SK core RNP formed with two 7SK conformations, circular and linear, and uncover a common RNA-dependent MePCE-Larp7 complex. Together with NMR, biochemical, and cellular data, these structures reveal the mechanism of MePCE catalytic inactivation in the core RNP, unexpected interactions between Larp7 and RNA that facilitate a role as an RNP chaperone, and that MePCE-7SK-Larp7 core RNP serves as a scaffold for switching between different 7SK conformations essential for RNP assembly and regulation of P-TEFb sequestration and release.


Assuntos
Fator B de Elongação Transcricional Positiva , RNA , Conformação Molecular , Fator B de Elongação Transcricional Positiva/genética , Fator B de Elongação Transcricional Positiva/metabolismo , RNA/genética , RNA Nuclear Pequeno/genética , Ribonucleoproteínas/metabolismo , Transcrição Gênica
3.
Nature ; 618(7965): 484-488, 2023 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-37198492

RESUMO

Spider pulsars are millisecond pulsars in short-period (≲12-h) orbits with low-mass (~0.01-0.4 M⊙) companion stars. The pulsars ablate plasma from the companion star, causing time delays and eclipses of the radio emission from the pulsar. The magnetic field of the companion has been proposed to strongly influence both the evolution of the binary system1 and the eclipse properties of the pulsar emission2. Changes in the rotation measure (RM) have been seen in a spider system, implying that there is an increase in the magnetic field near the eclipse3. Here we report a diverse range of evidence for a highly magnetized environment in the spider system PSR B1744 - 24A4, located in the globular cluster Terzan 5. We observe semi-regular profile changes to the circular polarization, V, when the pulsar emission passes close to the companion. This suggests that there is Faraday conversion where the radio wave tracks a reversal in the parallel magnetic field and constrains the companion magnetic field, B (> 10 G). We also see irregular, fast changes in the RM at random orbital phases, implying that the magnetic strength of the stellar wind, B, is greater than 10 mG. There are similarities between the unusual polarization behaviour of PSR B1744 - 24A and some repeating fast radio bursts (FRBs)5-7. Together with the possible binary-produced long-term periodicity of two active repeating FRBs8,9, and the discovery of a nearby FRB in a globular cluster10, where pulsar binaries are common, these similarities suggest that a proportion of FRBs have binary companions.

4.
PLoS Biol ; 22(6): e3002680, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38865309

RESUMO

CRISPR-Cas12a, often regarded as a precise genome editor, still requires improvements in specificity. In this study, we used a GFP-activation assay to screen 14 new Cas12a nucleases for mammalian genome editing, successfully identifying 9 active ones. Notably, these Cas12a nucleases prefer pyrimidine-rich PAMs. Among these nucleases, we extensively characterized Mb4Cas12a obtained from Moraxella bovis CCUG 2133, which recognizes a YYN PAM (Y = C or T). Our biochemical analysis demonstrates that Mb4Cas12a can cleave double-strand DNA across a wide temperature range. To improve specificity, we constructed a SWISS-MODEL of Mb4Cas12a based on the FnCas12a crystal structure and identified 8 amino acids potentially forming hydrogen bonds at the target DNA-crRNA interface. By replacing these amino acids with alanine to disrupt the hydrogen bond, we tested the influence of each mutation on Mb4Cas12a specificity. Interestingly, the F370A mutation improved specificity with minimal influence on activity. Further study showed that Mb4Cas12a-F370A is capable of discriminating single-nucleotide polymorphisms. These new Cas12a orthologs and high-fidelity variants hold substantial promise for therapeutic applications.


Assuntos
Alelos , Proteínas Associadas a CRISPR , Sistemas CRISPR-Cas , Edição de Genes , Edição de Genes/métodos , Proteínas Associadas a CRISPR/metabolismo , Proteínas Associadas a CRISPR/genética , Humanos , Endodesoxirribonucleases/metabolismo , Endodesoxirribonucleases/genética , Endodesoxirribonucleases/química , Animais , Engenharia de Proteínas/métodos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/química , Polimorfismo de Nucleotídeo Único , Mutação , DNA/metabolismo , DNA/genética , Células HEK293
5.
Nature ; 595(7869): 730-734, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34290403

RESUMO

Hepatocellular carcinoma (HCC)-the most common form of liver cancer-is an aggressive malignancy with few effective treatment options1. Lenvatinib is a small-molecule inhibitor of multiple receptor tyrosine kinases that is used for the treatment of patients with advanced HCC, but this drug has only limited clinical benefit2. Here, using a kinome-centred CRISPR-Cas9 genetic screen, we show that inhibition of epidermal growth factor receptor (EGFR) is synthetic lethal with lenvatinib in liver cancer. The combination of the EGFR inhibitor gefitinib and lenvatinib displays potent anti-proliferative effects in vitro in liver cancer cell lines that express EGFR and in vivo in xenografted liver cancer cell lines, immunocompetent mouse models and patient-derived HCC tumours in mice. Mechanistically, inhibition of fibroblast growth factor receptor (FGFR)  by lenvatinib treatment leads to feedback activation of the EGFR-PAK2-ERK5 signalling axis, which is blocked by EGFR inhibition. Treatment of 12 patients with advanced HCC who were unresponsive to lenvatinib treatment with the combination of lenvatinib plus gefitinib (trial identifier NCT04642547) resulted in meaningful clinical responses. The combination therapy identified here may represent a promising strategy for the approximately 50% of patients with advanced HCC who have high levels of EGFR.


Assuntos
Antineoplásicos/farmacologia , Carcinoma Hepatocelular/metabolismo , Neoplasias Hepáticas/metabolismo , Compostos de Fenilureia/farmacologia , Quinolinas/farmacologia , Animais , Carcinoma Hepatocelular/tratamento farmacológico , Linhagem Celular Tumoral , Resistencia a Medicamentos Antineoplásicos , Receptores ErbB/antagonistas & inibidores , Receptores ErbB/metabolismo , Feminino , Gefitinibe/farmacologia , Humanos , Neoplasias Hepáticas/tratamento farmacológico , Masculino , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Nus , Receptores de Fatores de Crescimento de Fibroblastos , Transdução de Sinais , Ensaios Antitumorais Modelo de Xenoenxerto
6.
Plant Cell ; 35(9): 3604-3625, 2023 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-37325884

RESUMO

Catalase (CAT) is often phosphorylated and activated by protein kinases to maintain hydrogen peroxide (H2O2) homeostasis and protect cells against stresses, but whether and how CAT is switched off by protein phosphatases remains inconclusive. Here, we identified a manganese (Mn2+)-dependent protein phosphatase, which we named PHOSPHATASE OF CATALASE 1 (PC1), from rice (Oryza sativa L.) that negatively regulates salt and oxidative stress tolerance. PC1 specifically dephosphorylates CatC at Ser-9 to inhibit its tetramerization and thus activity in the peroxisome. PC1 overexpressing lines exhibited hypersensitivity to salt and oxidative stresses with a lower phospho-serine level of CATs. Phosphatase activity and seminal root growth assays indicated that PC1 promotes growth and plays a vital role during the transition from salt stress to normal growth conditions. Our findings demonstrate that PC1 acts as a molecular switch to dephosphorylate and deactivate CatC and negatively regulate H2O2 homeostasis and salt tolerance in rice. Moreover, knockout of PC1 not only improved H2O2-scavenging capacity and salt tolerance but also limited rice grain yield loss under salt stress conditions. Together, these results shed light on the mechanisms that switch off CAT and provide a strategy for breeding highly salt-tolerant rice.


Assuntos
Oryza , Catalase/genética , Catalase/metabolismo , Oryza/metabolismo , Peróxido de Hidrogênio/metabolismo , Proteína Fosfatase 1/metabolismo , Tolerância ao Sal/genética , Homeostase , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
7.
Nat Chem Biol ; 20(3): 344-352, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38052959

RESUMO

Compact Cas9 nucleases hold great promise for therapeutic applications. Although several compact Cas9 nucleases have been developed, many genomic loci still could not be edited due to a lack of protospacer adjacent motifs (PAMs). We previously developed a compact SlugCas9 recognizing an NNGG PAM. Here we demonstrate that SlugCas9 displays comparable activity to SpCas9. We developed a simple phage-assisted evolution to engineer SlugCas9 for unique PAM requirements. Interestingly, we generated a SlugCas9 variant (SlugCas9-NNG) that could recognize an NNG PAM, expanding the targeting scope. We further developed a SlugCas9-NNG-based adenine base editor and demonstrated that it could be delivered by a single adeno-associated virus to disrupt PCSK9 splice donor and splice acceptor. These genome editors greatly enhance our ability for in vivo genome editing.


Assuntos
Bacteriófagos , Sistemas CRISPR-Cas , Sistemas CRISPR-Cas/genética , Pró-Proteína Convertase 9 , Adenina , Endonucleases/genética
8.
Nucleic Acids Res ; 52(D1): D1508-D1518, 2024 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-37897343

RESUMO

Knowledge of the collective activities of individual plants together with the derived clinical effects and targeted disease associations is useful for plant-based biomedical research. To provide the information in complement to the established databases, we introduced a major update of CMAUP database, previously featured in NAR. This update includes (i) human transcriptomic changes overlapping with 1152 targets of 5765 individual plants, covering 74 diseases from 20 027 patient samples; (ii) clinical information for 185 individual plants in 691 clinical trials; (iii) drug development information for 4694 drug-producing plants with metabolites developed into approved or clinical trial drugs; (iv) plant and human disease associations (428 737 associations by target, 220 935 reversion of transcriptomic changes, 764 and 154121 associations by clinical trials of individual plants and plant ingredients); (v) the location of individual plants in the phylogenetic tree for navigating taxonomic neighbors, (vi) DNA barcodes of 3949 plants, (vii) predicted human oral bioavailability of plant ingredients by the established SwissADME and HobPre algorithm, (viii) 21-107% increase of CMAUP data over the previous version to cover 60 222 chemical ingredients, 7865 plants, 758 targets, 1399 diseases, 238 KEGG human pathways, 3013 gene ontologies and 1203 disease ontologies. CMAUP update version is freely accessible at https://bidd.group/CMAUP/index.html.


Assuntos
Bases de Dados Factuais , Compostos Fitoquímicos , Plantas Medicinais , Humanos , Filogenia , Plantas Medicinais/química , Plantas Medicinais/classificação , Compostos Fitoquímicos/química , Compostos Fitoquímicos/farmacologia , Compostos Fitoquímicos/uso terapêutico
9.
Proc Natl Acad Sci U S A ; 120(8): e2207391120, 2023 02 21.
Artigo em Inglês | MEDLINE | ID: mdl-36787355

RESUMO

Traditional substance use (SU) surveillance methods, such as surveys, incur substantial lags. Due to the continuously evolving trends in SU, insights obtained via such methods are often outdated. Social media-based sources have been proposed for obtaining timely insights, but methods leveraging such data cannot typically provide fine-grained statistics about subpopulations, unlike traditional approaches. We address this gap by developing methods for automatically characterizing a large Twitter nonmedical prescription medication use (NPMU) cohort (n = 288,562) in terms of age-group, race, and gender. Our natural language processing and machine learning methods for automated cohort characterization achieved 0.88 precision (95% CI:0.84 to 0.92) for age-group, 0.90 (95% CI: 0.85 to 0.95) for race, and 94% accuracy (95% CI: 92 to 97) for gender, when evaluated against manually annotated gold-standard data. We compared automatically derived statistics for NPMU of tranquilizers, stimulants, and opioids from Twitter with statistics reported in the National Survey on Drug Use and Health (NSDUH) and the National Emergency Department Sample (NEDS). Distributions automatically estimated from Twitter were mostly consistent with the NSDUH [Spearman r: race: 0.98 (P < 0.005); age-group: 0.67 (P < 0.005); gender: 0.66 (P = 0.27)] and NEDS, with 34/65 (52.3%) of the Twitter-based estimates lying within 95% CIs of estimates from the traditional sources. Explainable differences (e.g., overrepresentation of younger people) were found for age-group-related statistics. Our study demonstrates that accurate subpopulation-specific estimates about SU, particularly NPMU, may be automatically derived from Twitter to obtain earlier insights about targeted subpopulations compared to traditional surveillance approaches.


Assuntos
Estimulantes do Sistema Nervoso Central , Mídias Sociais , Transtornos Relacionados ao Uso de Substâncias , Humanos , Transtornos Relacionados ao Uso de Substâncias/epidemiologia , Prescrições , Demografia
10.
Hum Genomics ; 18(1): 74, 2024 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-38956740

RESUMO

BACKGROUND: Evidence has revealed a connection between cuproptosis and the inhibition of tumor angiogenesis. While the efficacy of a model based on cuproptosis-related genes (CRGs) in predicting the prognosis of peripheral organ tumors has been demonstrated, the impact of CRGs on the prognosis and the immunological landscape of gliomas remains unexplored. METHODS: We screened CRGs to construct a novel scoring tool and developed a prognostic model for gliomas within the various cohorts. Afterward, a comprehensive exploration of the relationship between the CRG risk signature and the immunological landscape of gliomas was undertaken from multiple perspectives. RESULTS: Five genes (NLRP3, ATP7B, SLC31A1, FDX1, and GCSH) were identified to build a CRG scoring system. The nomogram, based on CRG risk and other signatures, demonstrated a superior predictive performance (AUC of 0.89, 0.92, and 0.93 at 1, 2, and 3 years, respectively) in the training cohort. Furthermore, the CRG score was closely associated with various aspects of the immune landscape in gliomas, including immune cell infiltration, tumor mutations, tumor immune dysfunction and exclusion, immune checkpoints, cytotoxic T lymphocyte and immune exhaustion-related markers, as well as cancer signaling pathway biomarkers and cytokines. CONCLUSION: The CRG risk signature may serve as a robust biomarker for predicting the prognosis and the potential viability of immunotherapy responses. Moreover, the key candidate CRGs might be promising targets to explore the underlying biological background and novel therapeutic interventions in gliomas.


Assuntos
Biomarcadores Tumorais , Glioma , Microambiente Tumoral , Humanos , Glioma/genética , Glioma/imunologia , Glioma/patologia , Microambiente Tumoral/genética , Microambiente Tumoral/imunologia , Prognóstico , Biomarcadores Tumorais/genética , Neoplasias Encefálicas/genética , Neoplasias Encefálicas/imunologia , Neoplasias Encefálicas/patologia , Regulação Neoplásica da Expressão Gênica/genética , Nomogramas , Feminino , Masculino , Perfilação da Expressão Gênica , Pessoa de Meia-Idade
11.
FASEB J ; 38(1): e23389, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-38153347

RESUMO

Serum amyloid A (SAA) are major acute-phase response proteins which actively participate in many inflammatory diseases. This study was designed to explore the function of SAA in acute ocular inflammation and the underlying mechanism. We found that SAA3 was upregulated in endotoxin-induced uveitis (EIU) mouse model, and it was primarily expressed in microglia. Recombinant SAA protein augmented intraocular inflammation in EIU, while the inhibition of Saa3 by siRNA effectively alleviated the inflammatory responses and rescued the retina from EIU-induced structural and functional damage. Further study showed that the recombinant SAA protein activated microglia, causing characteristic morphological changes and driving them further to pro-inflammatory status. The downregulation of Saa3 halted the amoeboid change of microglia, reduced the secretion of pro-inflammatory factors, and increased the expression of tissue-reparative genes. SAA3 also regulated the autophagic activity of microglial cells. Finally, we showed that the above effect of SAA on microglial cells was at least partially mediated through the expression and signaling of Toll-like receptor 4 (TLR4). Collectively, our study suggested that microglial cell-expressed SAA could be a potential target in treating acute ocular inflammation.


Assuntos
Microglia , Proteína Amiloide A Sérica , Animais , Camundongos , Proteína Amiloide A Sérica/genética , Inflamação/induzido quimicamente , Retina , Proteínas de Fase Aguda , Endotoxinas/toxicidade
12.
PLoS Biol ; 20(11): e3001897, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-36449487

RESUMO

Due to different nucleotide preferences at target sites, no single Cas9 is capable of editing all sequences. Thus, this highlights the need to establish a Cas9 repertoire covering all sequences for efficient genome editing. Cas9s with simple protospacer adjacent motif (PAM) requirements are particularly attractive to allow for a wide range of genome editing, but identification of such Cas9s from thousands of Cas9s in the public database is a challenge. We previously identified PAMs for 16 SaCas9 orthologs. Here, we compared the PAM-interacting (PI) domains in these orthologs and found that the serine residue corresponding to SaCas9 N986 was associated with the simple NNGG PAM requirement. Based on this discovery, we identified five additional SaCas9 orthologs that recognize the NNGG PAM. We further identified three amino acids that determined the NNGG PAM requirement of SaCas9. Finally, we engineered Sha2Cas9 and SpeCas9 to generate high-fidelity versions of Cas9s. Importantly, these natural and engineered Cas9s displayed high activities and distinct nucleotide preferences. Our study offers a new perspective to identify SaCas9 orthologs with NNGG PAM requirements, expanding the Cas9 repertoire.


Assuntos
Reconhecimento Psicológico , Serina , Serina/genética , Aminoácidos , Bases de Dados Factuais , Nucleotídeos
13.
Cereb Cortex ; 34(4)2024 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-38642107

RESUMO

Glioma is a systemic disease that can induce micro and macro alternations of whole brain. Isocitrate dehydrogenase and vascular endothelial growth factor are proven prognostic markers and antiangiogenic therapy targets in glioma. The aim of this study was to determine the ability of whole brain morphologic features and radiomics to predict isocitrate dehydrogenase status and vascular endothelial growth factor expression levels. This study recruited 80 glioma patients with isocitrate dehydrogenase wildtype and high vascular endothelial growth factor expression levels, and 102 patients with isocitrate dehydrogenase mutation and low vascular endothelial growth factor expression levels. Virtual brain grafting, combined with Freesurfer, was used to compute morphologic features including cortical thickness, LGI, and subcortical volume in glioma patient. Radiomics features were extracted from multiregional tumor. Pycaret was used to construct the machine learning pipeline. Among the radiomics models, the whole tumor model achieved the best performance (accuracy 0.80, Area Under the Curve 0.86), while, after incorporating whole brain morphologic features, the model had a superior predictive performance (accuracy 0.82, Area Under the Curve 0.88). The features contributed most in predicting model including the right caudate volume, left middle temporal cortical thickness, first-order statistics, shape, and gray-level cooccurrence matrix. Pycaret, based on morphologic features, combined with radiomics, yielded highest accuracy in predicting isocitrate dehydrogenase mutation and vascular endothelial growth factor levels, indicating that morphologic abnormalities induced by glioma were associated with tumor biology.


Assuntos
Neoplasias Encefálicas , Glioma , Humanos , Fator A de Crescimento do Endotélio Vascular/genética , Neoplasias Encefálicas/diagnóstico por imagem , Neoplasias Encefálicas/genética , Isocitrato Desidrogenase/genética , Imageamento por Ressonância Magnética , Glioma/diagnóstico por imagem , Glioma/genética , Encéfalo/diagnóstico por imagem , Encéfalo/patologia , Mutação , Estudos Retrospectivos
14.
Cereb Cortex ; 34(1)2024 01 14.
Artigo em Inglês | MEDLINE | ID: mdl-38112602

RESUMO

Systemic infiltration is a hallmark of diffuse midline glioma pathogenesis, which can trigger distant disturbances in cortical structure. However, the existence and effects of these changes have been underexamined. This study aimed to investigate whole-brain cortical myelin and thickness alternations induced by diffuse midline glioma. High-resolution T1- and T2-weighted images were acquired from 90 patients with diffuse midline glioma with H3 K27-altered and 64 patients with wild-type and 86 healthy controls. Cortical thickness and myelin content was calculated using Human Connectome Project pipeline. Significant differences in cortical thickness and myelin content were detected among groups. Short-term survival prediction model was constructed using automated machine learning. Compared with healthy controls, diffuse midline glioma with H3 K27-altered patients showed significantly reduced cortical myelin in bilateral precentral gyrus, postcentral gyrus, insular, parahippocampal gyrus, fusiform gyrus, and cingulate gyrus, whereas diffuse midline glioma with H3 K27 wild-type patients exhibited well-preserved myelin content. Furtherly, when comparing diffuse midline glioma with H3 K27-altered and diffuse midline glioma with H3 K27 wild-type, the decreased cortical thickness in parietal and occipital regions along with demyelination in medial orbitofrontal cortex was observed in diffuse midline glioma with H3 K27-altered. Notably, a combination of cortical features and tumor radiomics allowed short-term survival prediction with accuracy 0.80 and AUC 0.84. These findings may aid clinicians in tailoring therapeutic approaches based on cortical characteristics, potentially enhancing the efficacy of current and future treatment modalities.


Assuntos
Neoplasias Encefálicas , Glioma , Humanos , Neoplasias Encefálicas/diagnóstico por imagem , Histonas/genética , Glioma/diagnóstico por imagem , Bainha de Mielina , Encéfalo/patologia , Mutação
15.
Nucleic Acids Res ; 51(D1): D621-D628, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36624664

RESUMO

Quantitative activity and species source data of natural products (NPs) are important for drug discovery, medicinal plant research, and microbial investigations. Activity values of NPs against specific targets are useful for discovering targeted therapeutic agents and investigating the mechanism of medicinal plants. Composition/concentration values of NPs in individual species facilitate the assessments and investigations of the therapeutic quality of herbs and phenotypes of microbes. Here, we describe an update of the NPASS natural product activity and species source database previously featured in NAR. This update includes: (i) new data of ∼95 000 records of the composition/concentration values of ∼1 490 NPs/NP clusters in ∼390 species, (ii) extended data of activity values of ∼43 200 NPs against ∼7 700 targets (∼40% and ∼32% increase, respectively), (iii) extended data of ∼31 600 species sources of ∼94 400 NPs (∼26% and ∼32% increase, respectively), (iv) new species types of ∼440 co-cultured microbes and ∼420 engineered microbes, (v) new data of ∼66 600 NPs without experimental activity values but with estimated activity profiles from the established chemical similarity tool Chemical Checker, (vi) new data of the computed drug-likeness properties and the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties for all NPs. NPASS update version is freely accessible at http://bidd.group/NPASS.


Assuntos
Produtos Biológicos , Pesquisa Biomédica , Bases de Dados Factuais , Descoberta de Drogas , Preparações Farmacêuticas/isolamento & purificação
16.
Proc Natl Acad Sci U S A ; 119(5)2022 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-35074868

RESUMO

A major goal of linguistics and cognitive science is to understand what class of learning systems can acquire natural language. Until recently, the computational requirements of language have been used to argue that learning is impossible without a highly constrained hypothesis space. Here, we describe a learning system that is maximally unconstrained, operating over the space of all computations, and is able to acquire many of the key structures present in natural language from positive evidence alone. We demonstrate this by providing the same learning model with data from 74 distinct formal languages which have been argued to capture key features of language, have been studied in experimental work, or come from an interesting complexity class. The model is able to successfully induce the latent system generating the observed strings from small amounts of evidence in almost all cases, including for regular (e.g., an , [Formula: see text], and [Formula: see text]), context-free (e.g., [Formula: see text], and [Formula: see text]), and context-sensitive (e.g., [Formula: see text], and xx) languages, as well as for many languages studied in learning experiments. These results show that relatively small amounts of positive evidence can support learning of rich classes of generative computations over structures. The model provides an idealized learning setup upon which additional cognitive constraints and biases can be formalized.


Assuntos
Aprendizagem/fisiologia , Linguística/métodos , Humanos , Idioma
17.
Nano Lett ; 24(22): 6625-6633, 2024 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-38788161

RESUMO

All-solid-state lithium-sulfur batteries (ASSLSBs) are promising next-generation battery technologies with a high energy density and excellent safety. Because of the insulating nature of sulfur/Li2S, conventional cathode designs focus on developing porous hosts with high electronic conductivities such as porous carbon. However, carbon hosts boost the decomposition of sulfide electrolytes and suffer from sulfur detachment due to their weak bonding with sulfur/Li2S, resulting in capacity decays. Herein, we propose a counterintuitive design concept of host materials in which nonconductive polar mesoporous hosts can enhance the cycling life of ASSLSBs through mitigating the decomposition of adjacent electrolytes and bonding sulfur/Li2S steadily to avoid detachment. By using a mesoporous SiO2 host filled with 70 wt % sulfur as the cathode, we demonstrate steady cycling in ASSLSBs with a capacity reversibility of 95.1% in the initial cycle and a discharge capacity of 1446 mAh/g after 500 cycles at C/5 based on the mass of sulfur.

18.
J Infect Dis ; 230(3): e524-e535, 2024 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-38412342

RESUMO

BACKGROUND: Coinfection of human immunodeficiency virus type 1 (HIV-1) is the most significant risk factor for tuberculosis (TB). The immune responses of the lung are essential to restrict the growth of Mycobacterium tuberculosis and avoid the emergence of the disease. Nevertheless, there is still limited knowledge about the local immune response in people with HIV-1-TB coinfection. METHODS: We employed single-cell RNA sequencing (scRNA-seq) on bronchoalveolar lavage fluid from 9 individuals with HIV-1-TB coinfection and 10 with pulmonary TB. RESULTS: A total of 19 058 cells were grouped into 4 major cell types: myeloid cells, T/natural killer (NK) cells, B cells, and epithelial cells. The myeloid cells and T/NK cells were further divided into 10 and 11 subsets, respectively. The proportions of dendritic cell subsets, CD4+ T cells, and NK cells were lower in the HIV-1-TB coinfection group compared to the TB group, while the frequency of CD8+ T cells was higher. Additionally, we identified numerous differentially expressed genes between the CD4+ and CD8+ T-cell subsets between the 2 groups. CONCLUSIONS: HIV-1 infection not only affects the abundance of immune cells in the lungs but also alters their functions in patients with pulmonary TB.


Assuntos
Líquido da Lavagem Broncoalveolar , Coinfecção , Infecções por HIV , HIV-1 , Análise de Célula Única , Tuberculose Pulmonar , Humanos , Tuberculose Pulmonar/imunologia , Tuberculose Pulmonar/complicações , Infecções por HIV/complicações , Infecções por HIV/imunologia , Coinfecção/virologia , Coinfecção/imunologia , Coinfecção/microbiologia , HIV-1/imunologia , Masculino , Adulto , Líquido da Lavagem Broncoalveolar/microbiologia , Líquido da Lavagem Broncoalveolar/virologia , Líquido da Lavagem Broncoalveolar/imunologia , Feminino , Mycobacterium tuberculosis/imunologia , Pessoa de Meia-Idade , Linfócitos T CD4-Positivos/imunologia , Linfócitos T CD8-Positivos/imunologia , Células Matadoras Naturais/imunologia , Pulmão/microbiologia , Pulmão/imunologia , Pulmão/virologia
19.
J Mol Cell Cardiol ; 192: 65-78, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38761989

RESUMO

Endothelial dysfunction is a central contributor to the development of most cardiovascular diseases and is characterised by the reduced synthesis or bioavailability of the vasodilator nitric oxide together with other abnormalities such as inflammation, senescence, and oxidative stress. The use of patient-specific and genome-edited human pluripotent stem cell-derived endothelial cells (hPSC-ECs) has shed novel insights into the role of endothelial dysfunction in cardiovascular diseases with strong genetic components such as genetic cardiomyopathies and pulmonary arterial hypertension. However, their utility in studying complex multifactorial diseases such as atherosclerosis, metabolic syndrome and heart failure poses notable challenges. In this review, we provide an overview of the different methods used to generate and characterise hPSC-ECs before comprehensively assessing their effectiveness in cardiovascular disease modelling and high-throughput drug screening. Furthermore, we explore current obstacles that will need to be overcome to unleash the full potential of hPSC-ECs in facilitating patient-specific precision medicine. Addressing these challenges holds great promise in advancing our understanding of intricate cardiovascular diseases and in tailoring personalised therapeutic strategies.


Assuntos
Doenças Cardiovasculares , Células Endoteliais , Humanos , Doenças Cardiovasculares/metabolismo , Doenças Cardiovasculares/patologia , Células Endoteliais/metabolismo , Animais , Células-Tronco Pluripotentes/metabolismo , Endotélio Vascular/metabolismo , Endotélio Vascular/patologia
20.
J Am Chem Soc ; 146(43): 29857-29864, 2024 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-39412244

RESUMO

The asymmetric functionalization of unstrained C(sp3)-C(sp3) bonds could be a powerful strategy to stereoselectively reconstruct the backbone of an organic compound, but such reactions are rare. Although allylic substitutions have been used frequently to construct C-C bonds by the cleavage of more reactive C-X bonds (X is usually an O atom of an ester) by transition metals, the reverse process that involves the replacement of a C-C bond with a C-heteroatom bond is rare and generally considered thermodynamically unfavorable. We show that an unstrained, inert allylic C-C σ bond can be converted to a C-N bond stereoselectively via a designed solubility-control strategy, which makes the thermodynamically unfavorable process possible. The C-C bond amination occurs with a range of amine nucleophiles and cleaves multiple classes of alkyl C-C bonds in good yields with high enantioselectivity. A novel resolution strategy is also reported that transforms racemic allylic amines to the corresponding optically active allylic amine by the sequential conversion of a C-N bond to a C-C bond and back to a C-N bond. Mechanistic studies show that formation of the C-N bond is the rate-limiting step and is driven by the low solubility of the salt formed from the cleaved alkyl group in a nonpolar solvent.

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