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1.
Nature ; 629(8013): 851-860, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38560995

RESUMO

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.


Assuntos
Aves , Evolução Molecular , Genoma , Filogenia , Animais , Aves/genética , Aves/classificação , Aves/anatomia & histologia , Encéfalo/anatomia & histologia , Extinção Biológica , Genoma/genética , Genômica , Densidade Demográfica , Masculino , Feminino
2.
Cell ; 159(1): 176-187, 2014 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-25201530

RESUMO

The lack of in vitro prostate cancer models that recapitulate the diversity of human prostate cancer has hampered progress in understanding disease pathogenesis and therapy response. Using a 3D organoid system, we report success in long-term culture of prostate cancer from biopsy specimens and circulating tumor cells. The first seven fully characterized organoid lines recapitulate the molecular diversity of prostate cancer subtypes, including TMPRSS2-ERG fusion, SPOP mutation, SPINK1 overexpression, and CHD1 loss. Whole-exome sequencing shows a low mutational burden, consistent with genomics studies, but with mutations in FOXA1 and PIK3R1, as well as in DNA repair and chromatin modifier pathways that have been reported in advanced disease. Loss of p53 and RB tumor suppressor pathway function are the most common feature shared across the organoid lines. The methodology described here should enable the generation of a large repertoire of patient-derived prostate cancer lines amenable to genetic and pharmacologic studies.


Assuntos
Técnicas de Cultura , Organoides , Neoplasias da Próstata/patologia , Xenoenxertos , Humanos , Masculino , Metástase Neoplásica/patologia , Organoides/patologia , Farmacologia/métodos , Proteínas Supressoras de Tumor/metabolismo
3.
Cell ; 155(6): 1337-50, 2013 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-24315102

RESUMO

Neural circuits for essential natural behaviors are shaped by selective pressure to coordinate reliable execution of flexible goal-directed actions. However, the structural and functional organization of survival-oriented circuits is poorly understood due to exceptionally complex neuroanatomy. This is exemplified by AGRP neurons, which are a molecularly defined population that is sufficient to rapidly coordinate voracious food seeking and consumption behaviors. Here, we use cell-type-specific techniques for neural circuit manipulation and projection-specific anatomical analysis to examine the organization of this critical homeostatic circuit that regulates feeding. We show that AGRP neuronal circuits use a segregated, parallel, and redundant output configuration. AGRP neuron axon projections that target different brain regions originate from distinct subpopulations, several of which are sufficient to independently evoke feeding. The concerted anatomical and functional analysis of AGRP neuron projection populations reveals a constellation of core forebrain nodes, which are part of an extended circuit that mediates feeding behavior.


Assuntos
Encéfalo/fisiologia , Comportamento Alimentar , Homeostase , Vias Neurais , Neurônios/metabolismo , Proteína Relacionada com Agouti/metabolismo , Animais , Grelina/metabolismo , Camundongos
4.
Nature ; 594(7861): 33-36, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34002091

RESUMO

The extension of the cosmic-ray spectrum beyond 1 petaelectronvolt (PeV; 1015 electronvolts) indicates the existence of the so-called PeVatrons-cosmic-ray factories that accelerate particles to PeV energies. We need to locate and identify such objects to find the origin of Galactic cosmic rays1. The principal signature of both electron and proton PeVatrons is ultrahigh-energy (exceeding 100 TeV) γ radiation. Evidence of the presence of a proton PeVatron has been found in the Galactic Centre, according to the detection of a hard-spectrum radiation extending to 0.04 PeV (ref. 2). Although γ-rays with energies slightly higher than 0.1 PeV have been reported from a few objects in the Galactic plane3-6, unbiased identification and in-depth exploration of PeVatrons requires detection of γ-rays with energies well above 0.1 PeV. Here we report the detection of more than 530 photons at energies above 100 teraelectronvolts and up to 1.4 PeV from 12 ultrahigh-energy γ-ray sources with a statistical significance greater than seven standard deviations. Despite having several potential counterparts in their proximity, including pulsar wind nebulae, supernova remnants and star-forming regions, the PeVatrons responsible for the ultrahigh-energy γ-rays have not yet been firmly localized and identified (except for the Crab Nebula), leaving open the origin of these extreme accelerators.

5.
Plant J ; 117(3): 924-943, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37902994

RESUMO

Chromoplasts act as a metabolic sink for carotenoids, in which plastoglobules serve as versatile lipoprotein particles. PGs in chloroplasts have been characterized. However, the features of PGs from non-photosynthetic plastids are poorly understood. We found that the development of chromoplast plastoglobules (CPGs) in globular and crystalloid chromoplasts of citrus is associated with alterations in carotenoid storage. Using Nycodenz density gradient ultracentrifugation, an efficient protocol for isolating highly purified CPGs from sweet orange (Citrus sinensis) pulp was established. Forty-four proteins were defined as likely comprise the core proteome of CPGs using comparative proteomics analysis. Lipidome analysis of different chromoplast microcompartments revealed that the nonpolar microenvironment within CPGs was modified by 35 triacylglycerides, two sitosterol esters, and one stigmasterol ester. Manipulation of the CPG-localized gene CsELT1 (esterase/lipase/thioesterase) in citrus calli resulted in increased lipids and carotenoids, which is further evidence that the nonpolar microenvironment of CPGs contributes to carotenoid accumulation and storage in the chromoplasts. This multi-feature analysis of CPGs sheds new light on the role of chromoplasts in carotenoid metabolism, paving the way for manipulating carotenoid content in citrus fruit and other crops.


Assuntos
Citrus sinensis , Citrus , Citrus/genética , Citrus/metabolismo , Multiômica , Carotenoides/metabolismo , Plastídeos/metabolismo , Citrus sinensis/genética , Frutas/genética , Frutas/metabolismo
6.
EMBO Rep ; 24(9): e55060, 2023 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-37477088

RESUMO

Inflammation plays an important role in the initiation and progression of colorectal cancer (CRC) and leads to ß-catenin accumulation in colitis-related CRC. However, the mechanism remains largely unknown. Here, pancreatic progenitor cell differentiation and proliferation factor (PPDPF) is found to be upregulated in CRC and significantly correlated with tumor-node-metastasis (TNM) stages and survival time. Knockout of PPDPF in the intestinal epithelium shortens crypts, decreases the number of stem cells, and inhibits the growth of organoids and the occurrence of azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced CRC. Mechanistically, PPDPF is found to interact with Casein kinase 1α (CK1α), thereby disrupting its binding to Axin, disassociating the ß-catenin destruction complex, decreasing the phosphorylation of ß-catenin, and activating the Wnt/ß-catenin pathway. Furthermore, interleukin 6 (IL6)/Janus kinase 2 (JAK2)-mediated inflammatory signals lead to phosphorylation of PPDPF at Tyr16 and Tyr17, stabilizing the protein. In summary, this study demonstrates that PPDPF is a key molecule in CRC carcinogenesis and progression that connects inflammatory signals to the Wnt/ß-catenin signaling pathway, providing a potential novel therapeutic target.


Assuntos
Neoplasias Colorretais , Interleucina-6 , Humanos , Interleucina-6/efeitos adversos , Interleucina-6/metabolismo , Fosforilação , beta Catenina/metabolismo , Via de Sinalização Wnt , Janus Quinase 2/metabolismo , Neoplasias Colorretais/genética , Proliferação de Células , Linhagem Celular Tumoral , Regulação Neoplásica da Expressão Gênica
7.
Nano Lett ; 2024 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-38856230

RESUMO

Lithium metal batteries utilizing lithium metal as the anode can achieve a greater energy density. However, it remains challenging to improve low-temperature performance and fast-charging features. Herein, we introduce an electrolyte solvation chemistry strategy to regulate the properties of ethylene carbonate (EC)-based electrolytes through intermolecular interactions, utilizing weakly solvated fluoroethylene carbonate (FEC) to replace EC, and incorporating the low-melting-point solvent 1,2-difluorobenzene (2FB) as a diluent. We identified that the intermolecular interaction between 2FB and solvent can facilitate Li+ desolvation and lower the freezing point of the electrolyte effectively. The resulting electrolyte enables the LiNi0.8Co0.1Mn0.1O2||Li cell to operate at -30 °C for more than 100 cycles while delivering a high capacity of 154 mAh g-1 at 5.0C. We present a solvation structure and interfacial model to analyze the behavior of the formulated electrolyte composition, establishing a relationship with cell performance and also providing insights for the electrolyte design under extreme conditions.

8.
Brief Bioinform ; 23(1)2022 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-34643213

RESUMO

Understanding the impact of non-coding sequence variants on complex diseases is an essential problem. We present a novel ensemble learning framework-CASAVA, to predict genomic loci in terms of disease category-specific risk. Using disease-associated variants identified by GWAS as training data, and diverse sequencing-based genomics and epigenomics profiles as features, CASAVA provides risk prediction of 24 major categories of diseases throughout the human genome. Our studies showed that CASAVA scores at a genomic locus provide a reasonable prediction of the disease-specific and disease category-specific risk prediction for non-coding variants located within the locus. Taking MHC2TA and immune system diseases as an example, we demonstrate the potential of CASAVA in revealing variant-disease associations. A website (http://zhanglabtools.org/CASAVA) has been built to facilitate easily access to CASAVA scores.


Assuntos
Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único , Genoma Humano , Genômica , Humanos , Aprendizado de Máquina
9.
J Transl Med ; 22(1): 469, 2024 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-38760791

RESUMO

BACKGROUND: Colorectal cancer (CRC) remains a major global health challenge, with high incidence and mortality rates. The role of long noncoding RNAs (lncRNAs) in cancer progression has received considerable attention. The present study aimed to investigate the function and mechanisms underlying the role of lncRNA RP11-197K6.1, microRNA-135a-5p (hsa-miR-135a-5p), and DLX5 in CRC development. METHODS: We analyzed RNA sequencing data from The Cancer Genome Atlas Colorectal Cancer dataset to identify the association between lncRNA RP11-197K6.1 and CRC progression. The expression levels of lncRNA RP11-197K6.1 and DLX5 in CRC samples and cell lines were determined by real-time quantitative PCR and western blotting assays. Fluorescence in situ hybridization was used to confirm the cellular localization of lncRNA RP11-197K6.1. Cell migration capabilities were assessed by Transwell and wound healing assays, and flow cytometry was performed to analyze apoptosis. The interaction between lncRNA RP11-197K6.1 and miR-135a-5p and its effect on DLX5 expression were investigated by the dual-luciferase reporter assay. Additionally, a xenograft mouse model was used to study the in vivo effects of lncRNA RP11-197K6.1 on tumor growth, and an immunohistochemical assay was performed to assess DLX5 expression in tumor tissues. RESULTS: lncRNA RP11-197K6.1 was significantly upregulated in CRC tissues and cell lines as compared to that in normal tissues, and its expression was inversely correlated with patient survival. It promoted the migration and metastasis of CRC cells by interacting with miR-135a-5p, alleviated suppression of DLX5 expression, and facilitated tumor growth. CONCLUSION: This study demonstrated the regulatory network and mechanism of action of the lncRNA RP11-197K6.1/miR-135a-5p/DLX5 axis in CRC development. These findings provided insights into the molecular pathology of CRC and suggested potential therapeutic targets for more effective treatment of patients with CRC.


Assuntos
Movimento Celular , Neoplasias Colorretais , Proteínas de Homeodomínio , MicroRNAs , RNA Longo não Codificante , Animais , Feminino , Humanos , Masculino , Camundongos , Pessoa de Meia-Idade , Apoptose , Linhagem Celular Tumoral , Proliferação de Células , Neoplasias Colorretais/genética , Neoplasias Colorretais/patologia , Neoplasias Colorretais/metabolismo , Progressão da Doença , Regulação Neoplásica da Expressão Gênica , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Camundongos Endogâmicos BALB C , Camundongos Nus , MicroRNAs/genética , MicroRNAs/metabolismo , RNA Endógeno Competitivo , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , Fatores de Transcrição/metabolismo , Fatores de Transcrição/genética
10.
Phys Rev Lett ; 132(13): 131002, 2024 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-38613275

RESUMO

We present the measurements of all-particle energy spectrum and mean logarithmic mass of cosmic rays in the energy range of 0.3-30 PeV using data collected from LHAASO-KM2A between September 2021 and December 2022, which is based on a nearly composition-independent energy reconstruction method, achieving unprecedented accuracy. Our analysis reveals the position of the knee at 3.67±0.05±0.15 PeV. Below the knee, the spectral index is found to be -2.7413±0.0004±0.0050, while above the knee, it is -3.128±0.005±0.027, with the sharpness of the transition measured with a statistical error of 2%. The mean logarithmic mass of cosmic rays is almost heavier than helium in the whole measured energy range. It decreases from 1.7 at 0.3 PeV to 1.3 at 3 PeV, representing a 24% decline following a power law with an index of -0.1200±0.0003±0.0341. This is equivalent to an increase in abundance of light components. Above the knee, the mean logarithmic mass exhibits a power law trend towards heavier components, which is reversal to the behavior observed in the all-particle energy spectrum. Additionally, the knee position and the change in power-law index are approximately the same. These findings suggest that the knee observed in the all-particle spectrum corresponds to the knee of the light component, rather than the medium-heavy components.

11.
Chemistry ; 30(22): e202303678, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38373184

RESUMO

The self-assembled resorcinarene capsule C6 shows remarkable photoacidity upon light irradiation, which is here exploited to catalyze olefin hydroarylation reactions in confined space. An experimental pKa* value range of -3.3--2.8 was estimated for the photo-excited hexameric capsule C6*, and consequently an increase in acidity of 8.8 log units was observed with respect to its ground state (pKa=5.5-6.0). This makes the hexameric capsule the first example of a self-assembled supramolecular photoacid. The photoacid C6* can catalyze hydroarylation reaction of olefins with aromatic substrates inside its cavity, while no reaction occurred between them in the absence of irradiation and/or capsule. DFT calculations corroborated a mechanism in which the photoacidity of C6* plays a crucial role in the protonation step of the aromatic substrate. A further proton transfer to olefin with a concomitant C-C bond formation and a final deprotonation step lead to product releasing.

12.
Epilepsy Behav ; 155: 109775, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38640724

RESUMO

INTRODUCTION: Epilepsy is the third most common neurological disorder in elderly people. Patients with epilepsy (PWEs) are more likely to have comorbidities. Social support is very important for PWEs. However, there are many gaps in the research on social support in older PWEs, especially the correlation between social support and comorbidities. METHODS: A cross-sectional study was conducted in three hospitals in China. Social support was assessed using the Social Support Rate Scale. The burden of physical comorbidities was assessed using the CCI, and global disability was assessed using the mRS. The NDDIE was used to assess depression, the GAD7 was used for anxiety, the CDR was used for cognitive status, and the NPI was used for psychotic symptoms. RESULTS: A total of 154 older PWEs participated in the study. There were 97 patients with at least one physical comorbidities. The burden of physical comorbidities was negatively correlated with overall social support (Adj. r = -0.35, P < 0.001) and global disability (Adj. r = -0.45, P < 0.001). In terms of psychiatric comorbidities, anxiety, depression, and cognitive status were not correlated with overall social support (Adj. r = -0.03, -0.02, and -0.11, P > 0.05). Psychotic symptoms were correlated with overall social support (Adj. r = -0.20, P < 0.05). The overall burden of psychiatric comorbidities was associated with overall social support (r = 0.30, P < 0.01). DISCUSSION: Neurologists and social workers should consider more personalized biopsychosocial care to improve the quality of life of older PWEs.


Assuntos
Ansiedade , Comorbidade , Depressão , Epilepsia , Apoio Social , Humanos , Masculino , Feminino , Estudos Transversais , China/epidemiologia , Idoso , Epilepsia/epidemiologia , Epilepsia/psicologia , Pessoa de Meia-Idade , Depressão/epidemiologia , Depressão/psicologia , Ansiedade/epidemiologia , Ansiedade/psicologia , Idoso de 80 Anos ou mais , Transtornos Mentais/epidemiologia , Transtornos Mentais/psicologia , Idade de Início , Efeitos Psicossociais da Doença
13.
Biomed Eng Online ; 23(1): 44, 2024 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-38705993

RESUMO

BACKGROUND: Osteocytes are critical mechanosensory cells in bone, and mechanically stimulated osteocytes produce exosomes that can induce osteogenesis. MicroRNAs (miRNAs) are important constituents of exosomes, and some miRNAs in osteocytes regulate osteogenic differentiation; previous studies have indicated that some differentially expressed miRNAs in mechanically strained osteocytes likely influence osteoblastic differentiation. Therefore, screening and selection of miRNAs that regulate osteogenic differentiation in exosomes of mechanically stimulated osteocytes are important. RESULTS: A mechanical tensile strain of 2500 µÎµ at 0.5 Hz 1 h per day for 3 days, elevated prostaglandin E2 (PGE2) and insulin-like growth factor-1 (IGF-1) levels and nitric oxide synthase (NOS) activity of MLO-Y4 osteocytes, and promoted osteogenic differentiation of MC3T3-E1 osteoblasts. Fourteen miRNAs differentially expressed only in MLO-Y4 osteocytes which were stimulated with mechanical tensile strain, were screened, and the miRNAs related to osteogenesis were identified. Four differentially expressed miRNAs (miR-1930-3p, miR-3110-5p, miR-3090-3p, and miR-3058-3p) were found only in mechanically strained osteocytes, and the four miRNAs, eight targeted mRNAs which were differentially expressed only in mechanically strained osteoblasts, were also identified. In addition, the mechanically strained osteocyte-derived exosomes promoted the osteoblastic differentiation of MC3T3-E1 cells in vitro, the exosomes were internalized by osteoblasts, and the up-regulated miR-3110-5p and miR-3058-3p in mechanically strained osteocytes, were both increased in the exosomes, which was verified via reverse transcription quantitative polymerase chain reaction (RT-qPCR). CONCLUSIONS: In osteocytes, a mechanical tensile strain of 2500 µÎµ at 0.5 Hz induced the fourteen differentially expressed miRNAs which probably were in exosomes of osteocytes and involved in osteogenesis. The mechanically strained osteocyte-derived exosomes which contained increased miR-3110-5p and miR-3058-3p (two of the 14 miRNAs), promoted osteoblastic differentiation.


Assuntos
Exossomos , MicroRNAs , Osteócitos , Osteogênese , Estresse Mecânico , Animais , Camundongos , Linhagem Celular , Exossomos/metabolismo , Regulação da Expressão Gênica , MicroRNAs/genética , MicroRNAs/metabolismo , Osteoblastos/citologia , Osteoblastos/metabolismo , Osteócitos/citologia , Osteócitos/metabolismo , Osteogênese/genética
14.
Environ Res ; 260: 119634, 2024 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-39029729

RESUMO

The process of harmless treatment of livestock manure produces a large amount of odor, which poses a potential threat to human and livestock health. A vertical fermentation tank system is commonly used for the environmentally sound treatment of chicken manure in China, but the composition and concentration of the odor produced and the factors affecting odor emissions remain unclear. In this study, we investigated the types and concentrations of odors produced in the mixing room (MR), vertical fermenter (VF), and aging room (AR) of the system, and analyzed the effects of bacterial communities and metabolic genes on odor production. The results revealed that 34, 26 and 26 odors were detected in the VF, MR and AR, respectively. The total odor concentration in the VF was 66613 ± 10097, which was significantly greater than that in the MR (1157 ± 675) and AR (1143 ± 1005) (P < 0.001), suggesting that the VF was the main source of odor in the vertical fermentation tank system. Methyl mercaptan had the greatest contribution to the odor produced by VF, reaching 47.82%, and the concentration was 0.6145 ± 0.2164 mg/m3. The abundance of metabolic genes did not correlate significantly with odor production, but PICRUSt analysis showed that cysteine and methionine metabolism involved in methyl mercaptan production was significantly more enriched in MR and VF than in AR. Bacillus was the most abundant genus in the VF, with a relative abundance significantly greater than that in the MR (P < 0.05). The RDA results revealed that Bacillus was significantly and positively correlated with methyl mercaptan. The use of large-scale aerobic fermentation systems to treat chicken manure needs to focused on the production of methyl mercaptan.

15.
Appl Microbiol Biotechnol ; 108(1): 46, 2024 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38183474

RESUMO

Fecal microbiota transplantation (FMT) has been shown to improve gut dysbiosis in dogs; however, it has not completely been understood in police dogs. This study aimed to investigate the effects of FMT on performance and gut microflora in Kunming police dogs. Twenty Wolf Cyan dogs were randomly assigned to receive physiological saline or fecal suspension at low, medium, or high doses through oral gavage for 14 days. Growth performance, police performance, serum biochemical profiling, and gut microflora were determined 2-week post-FMT. Dogs after FMT treatment were also subjected to an hour road transportation and then were evaluated for serum stress indicators. Overall, FMT enhanced the growth performance and alleviated diarrhea rate in Kunming dogs with the greatest effects occurring in the low dose FMT (KML) group. The improvement of FMT on police performance was also determined. These above alterations were accompanied by changed serum biochemical parameters as indicated by elevated total protein and albumin and reduced total cholesterol and glycerol. Furthermore, the serum stress indicators after road transportation in dog post-FMT significantly decreased. Increased bacterial diversity and modified bacterial composition were found in the feces of dogs receiving FMT. The fecal samples from FMT dogs were characterized by higher abundances of the genera Lactobacillus, Prevotella, and Fusobacterium and lower concentrations of Cetobacterium, Allobaculum, Bifidobacterium, and Streptococcus. The present study supports a potential benefit of FMT on police performance in Kunming dogs. KEY POINTS: • FMT improves the growth performance and reduces diarrhea rates in Kunming police dogs. • FMT alleviates the serum stress profiles after road transportation in Kunming police dogs. • FMT modifies the gut microbiota composition of Kunming police dogs.


Assuntos
Transplante de Microbiota Fecal , Cães Trabalhadores , Cães , Animais , Fezes , Bifidobacterium , Diarreia
16.
Nucleic Acids Res ; 50(20): 11455-11469, 2022 11 11.
Artigo em Inglês | MEDLINE | ID: mdl-36416268

RESUMO

We present a systematic structural and energetic characterization of phosphate(OP)-nucleobase anion…π stacking interactions in RNAs. We observed OP-nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from the stacking between a phosphate and a guanine or a uracil two-residue upstream in specific U-turns, such interactions in RNA have been scarcely characterized to date. Our QM calculations showed an energy minimum at a distance between the OP atom and the nucleobase plane centroid slightly below 3 Å for all the nucleobases. By sliding the OP atom over the nucleobase plane we localized the optimal mutual positioning of the stacked moieties, corresponding to an energy minimum below -6 kcal•mol-1, for all the nucleobases, consistently with the projections of the OP atoms over the different π-rings we observed in experimental occurrences. We also found that the strength of the interaction clearly correlates with its electrostatic component, pointing to it as the most relevant contribution. Finally, as OP-uracil and OP-guanine interactions represent together 86% of the instances we detected, we also proved their stability under dynamic conditions in model systems simulated by state-of-the art DFT-MD calculations.


Assuntos
Fosfatos , RNA , Termodinâmica , RNA/química , Guanina/química , Uracila , Ânions , RNA não Traduzido
17.
PLoS Genet ; 17(8): e1009701, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34407067

RESUMO

Trait evolution among a set of species-a central theme in evolutionary biology-has long been understood and analyzed with respect to a species tree. However, the field of phylogenomics, which has been propelled by advances in sequencing technologies, has ushered in the era of species/gene tree incongruence and, consequently, a more nuanced understanding of trait evolution. For a trait whose states are incongruent with the branching patterns in the species tree, the same state could have arisen independently in different species (homoplasy) or followed the branching patterns of gene trees, incongruent with the species tree (hemiplasy). Another evolutionary process whose extent and significance are better revealed by phylogenomic studies is gene flow between different species. In this work, we present a phylogenomic method for assessing the role of hybridization and introgression in the evolution of polymorphic or monomorphic binary traits. We apply the method to simulated evolutionary scenarios to demonstrate the interplay between the parameters of the evolutionary history and the role of introgression in a binary trait's evolution (which we call xenoplasy). Very importantly, we demonstrate, including on a biological data set, that inferring a species tree and using it for trait evolution analysis in the presence of gene flow could lead to misleading hypotheses about trait evolution.


Assuntos
Biologia Computacional/métodos , Introgressão Genética/genética , Locos de Características Quantitativas , Evolução Molecular , Especiação Genética , Modelos Genéticos , Fenótipo , Filogenia
18.
Proc Natl Acad Sci U S A ; 118(32)2021 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-34353917

RESUMO

The increasing complexity of different cell types revealed by single-cell analysis of tissues presents challenges in efficiently elucidating their functions. Here we show, using prostate as a model tissue, that primary organoids and freshly isolated epithelial cells can be CRISPR edited ex vivo using Cas9-sgRNA (guide RNA) ribotnucleoprotein complex technology, then orthotopically transferred in vivo into immunocompetent or immunodeficient mice to generate cancer models with phenotypes resembling those seen in traditional genetically engineered mouse models. Large intrachromosomal (∼2 Mb) or multigenic deletions can be engineered efficiently without the need for selection, including in isolated subpopulations to address cell-of-origin questions.


Assuntos
Deleção Cromossômica , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Edição de Genes/métodos , Próstata/citologia , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Animais , Proteína 9 Associada à CRISPR/genética , Células Epiteliais , Genes Supressores de Tumor , Humanos , Masculino , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Organoides , Neoplasias da Próstata/genética , Neoplasias da Próstata/patologia , RNA Guia de Cinetoplastídeos , Ribonucleoproteínas/genética , Regulador Transcricional ERG/genética , Ensaios Antitumorais Modelo de Xenoenxerto
19.
Ecotoxicol Environ Saf ; 273: 116142, 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38394757

RESUMO

BACKGROUND: The relationship between brominated flame retardants (BFRs) exposure and the human liver was still not well understood. METHODS: A total of 3108 participants (age > 12) from the National Health and Nutrition Examination Survey (NHANES) database spanning from 2005 to 2016 were included as the study population, with nine BFRs exhibiting a detection rate of over 70% serving as the exposure factor. The singular effects and combined effects of BFRs exposure on liver injury, non-alcoholic fatty liver disease (NAFLD), and advanced hepatic fibrosis (AHF) were evaluated separately. Finally, COX regression was employed to explore the hazard ratios associated with individual BFRs. RESULTS: In our analysis of individual exposures, we found significant positive association of PBB153 with alanine aminotransferase (ALT), PBB153 with aspartate aminotransferase (AST), PBDE47, PBDE85, PBDE99, PBDE100, and PBDE154 with alkaline phosphatase (ALP), PBDE28 and PBB153 with gamma-glutamyl transaminase (GGT), PBB153 with the risk of NAFLD and AHF; and significant negative association of PBB153 with ALP, PBDE28, PBDE47, PBDE99, PBDE100, PBDE85, PBDE209, and PBDE154 with albumin (ALB), PBB153 with AST/ALT. The nonlinear analysis results from Restricted Cubic Spline (RCS) further validated these associations (all P<0.05). In the mixed analysis combining Weighted Quantile Sum (WQS) regression and Quantile G-computation (QGC) analysis, BFRs were positively associated with ALT (ß>0, P<0.001), GGT (ß>0, P<0.001), and the risk of NAFLD (OR>1, P=0.007). Conversely, BFRs exhibited significant negative correlations with ALP (ß<0, P<0.001), ALB (ß<0, P<0.001), and AST/ALT (ß<0, P<0.001). Furthermore, the COX regression analysis revealed that PBB153 had the highest hazard ratio among the BFRs. CONCLUSIONS: BFR exposure may increase the risk of liver injury and NAFLD, with no significant association with AHF risk. The impact of BFR exposure on liver health should not be overlooked, especially in individuals residing in impoverished areas.


Assuntos
Retardadores de Chama , Hepatopatia Gordurosa não Alcoólica , Bifenil Polibromatos , Humanos , Hepatopatia Gordurosa não Alcoólica/induzido quimicamente , Hepatopatia Gordurosa não Alcoólica/epidemiologia , Retardadores de Chama/toxicidade , Retardadores de Chama/análise , Inquéritos Nutricionais , Fígado , Fosfatase Alcalina , Alanina Transaminase , Cirrose Hepática
20.
Chem Biodivers ; 21(5): e202400031, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38448389

RESUMO

Ulcerative colitis has been widely concerned for its persistent upward trend, and the sustained overproduction of pro-inflammatory cytokines such as IL-6 remains a crucial factor in the development of UC. Therefore, the identification of new effective drugs to block inflammatory responses is an urgent and viable therapeutic strategy for UC. In our research, twenty-three 6-acylamino/sulfonamido benzoxazolone derivatives were synthesized, characterized, and evaluated for anti-inflammatory activity against NO and IL-6 production in LPS-induced RAW264.7 cells. The results demonstrated that most of the target compounds were capable of reducing the overexpression of NO and IL-6 to a certain degree. For the most active compounds 3i, 3j and 3 l, the inhibitory activities were superior or equivalent to those of the positive drug celecoxib with a dose-dependent relationship. Furthermore, animal experiments revealed that active derivatives 3i, 3j and 3 l exhibited definitive therapeutical effect on DSS induced ulcerative colitis in mice by mitigating weight loss and DAI score while decreasing levels of pro-inflammatory cytokines such as IL-6 and IFN-γ, simultaneously increasing production of anti-inflammatory cytokines IL-10. In addition, compounds 3i, 3j and 3 l could also inhibit the oxidative stress to alleviate ulcerative colitis by decreasing MDA and MPO levels. These finding demonstrated that compounds 3i, 3j and 3 l hold significant potential as novel therapeutic agents for ulcerative colitis.


Assuntos
Benzoxazóis , Colite Ulcerativa , Interleucina-6 , Animais , Colite Ulcerativa/tratamento farmacológico , Camundongos , Interleucina-6/antagonistas & inibidores , Interleucina-6/metabolismo , Benzoxazóis/química , Benzoxazóis/farmacologia , Benzoxazóis/síntese química , Células RAW 264.7 , Relação Estrutura-Atividade , Lipopolissacarídeos/antagonistas & inibidores , Lipopolissacarídeos/farmacologia , Óxido Nítrico/antagonistas & inibidores , Óxido Nítrico/metabolismo , Óxido Nítrico/biossíntese , Anti-Inflamatórios/química , Anti-Inflamatórios/farmacologia , Anti-Inflamatórios/síntese química , Anti-Inflamatórios/uso terapêutico , Sulfato de Dextrana , Descoberta de Drogas , Estrutura Molecular , Relação Dose-Resposta a Droga
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