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1.
Nucleic Acids Res ; 51(D1): D816-D826, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36300636

RESUMO

Single-nucleotide polymorphisms (SNPs) as the most important type of genetic variation are widely used in describing population characteristics and play vital roles in animal genetics and breeding. Large amounts of population genetic variation resources and tools have been developed in human, which provided solid support for human genetic studies. However, compared with human, the development of animal genetic variation databases was relatively slow, which limits the genetic researches in these animals. To fill this gap, we systematically identified ∼ 499 million high-quality SNPs from 4784 samples of 20 types of animals. On that basis, we annotated the functions of SNPs, constructed high-density reference panels and calculated genome-wide linkage disequilibrium (LD) matrixes. We further developed Animal-SNPAtlas, a user-friendly database (http://gong_lab.hzau.edu.cn/Animal_SNPAtlas/) which includes high-quality SNP datasets and several support tools for multiple animals. In Animal-SNPAtlas, users can search the functional annotation of SNPs, perform online genotype imputation, explore and visualize LD information, browse variant information using the genome browser and download SNP datasets for each species. With the massive SNP datasets and useful tools, Animal-SNPAtlas will be an important fundamental resource for the animal genomics, genetics and breeding community.


Assuntos
Bases de Dados Genéticas , Polimorfismo de Nucleotídeo Único , Animais , Genoma , Genótipo , Desequilíbrio de Ligação
2.
Small ; 20(15): e2307184, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38012533

RESUMO

Aqueous zinc-ion hybrid capacitors (ZIHCs), as ideal candidates for high energy-power supply systems, are restricted by unsatisfied energy density and poor cycling durability for further applications. The construction of a surface-functionalized carbon cathode is an effective strategy for improving the performance of ZIHCs. Herein, a high-performance ZIHC is achieved using oxygen-rich hierarchically porous carbon rods (MDPC-X) prepared by the pyrolysis of a metal-organic framework (MOF) assisted by KOH activation. The MDPC-X samples displayed high electric double-layer capacitance (EDLC) and pseudocapacitance owing to their oxygen-rich surfaces, abundant electroactive sites, and short ions/electron transfer lengths. The surface oxygen functional groups for the reversible chemical adsorption/desorption of Zn2+ are identified using ex situ X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). Consequently, the as-assembled ZIHC exhibited a high capacity of 323.4 F g-1 (161.7 mA h g-1) at 0.5 A g-1 and a retention of 147 F g-1 (73.5 mA h g-1) at an ultrahigh current density of 50 A g-1, corresponding to high energy and power densities of 145.5 W h kg-1 and 45 kW kg-1, respectively. Furthermore, an excellent cycling life with 96.5% of capacity retention is also maintained after 10 000 cycles at 10 A g-1, demonstrating its promising potential for applications.

3.
Small ; 20(5): e2304047, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37752779

RESUMO

Microbial infections based on drug-resistant pathogenic organisms following surgery or trauma and uncontrolled bleeding are the main causes of increased mortality from trauma worldwide. The prevalence of drug-resistant pathogens has led to a significant increase in medical costs and poses a great threat to the normal life of people. This is an important issue in the field of biomedicine, and the emergence of new antimicrobial materials hydrogels holds great promise for solving this problem. Hydrogel is an important material with good biocompatibility, water absorption, oxygen permeability, adhesion, degradation, self-healing, corrosion resistance, and controlled release of drugs as well as structural diversity. Bacteria-disturbing hydrogels have important applications in the direction of surgical treatment, wound dressing, medical device coating, and tissue engineering. This paper reviews the classification of antimicrobial hydrogels, the current status of research, and the potential of antimicrobial hydrogels for one application in biomedicine, and analyzes the current research of hydrogels in biomedical applications from five aspects: metal-loaded hydrogels, drug-loaded hydrogels, carbon-material-loaded hydrogels, hydrogels with fixed antimicrobial activity and biological antimicrobial hydrogels, and provides an outlook on the high antimicrobial activity, biodegradability, biocompatibility, injectability, clinical applicability and future development prospects of hydrogels in this field.


Assuntos
Anti-Infecciosos , Hidrogéis , Humanos , Hidrogéis/química , Anti-Infecciosos/farmacologia , Bactérias , Bandagens , Antibacterianos/química
4.
Small ; : e2404554, 2024 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-38966908

RESUMO

Chiral inversions of enantiomers have significantly different biological activities, so it is important to develop simple and effective methods to efficiently identify optically pure compounds. Inspired by enzyme catalysis, the construction of chiral microenvironments resembling enzyme pockets in the pore space structure of metal-organic frameworks (MOFs) to achieve asymmetric enantioselective recognition and catalysis has become a new research hotspot. Here, a super-stable porphyrin-containing material PCN-224 is constructed by solvothermal method and a chiral microenvironment around the existing catalytic site of the material is created by post-synthesis modifications of the histidine (His) enantiomers. Experimental and theoretical calculations results show that the modulation of chiral ligands around Zr oxide clusters produces different spatial site resistances, which can greatly affect the adsorption and catalytic level of the enantiomeric molecules of tryptophan guests, resulting in a good enantioselective property of the material. It provides new ideas and possibilities for future chiral recognition and asymmetric catalysis.

5.
Nucleic Acids Res ; 50(D1): D46-D53, 2022 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-34551433

RESUMO

Enhancer RNAs (eRNAs) are a class of non-coding RNAs transcribed from enhancers. As the markers of active enhancers, eRNAs play important roles in gene regulation and are associated with various complex traits and characteristics. With increasing attention to eRNAs, numerous eRNAs have been identified in different human tissues. However, the expression landscape, regulatory network and potential functions of eRNAs in animals have not been fully elucidated. Here, we systematically characterized 185 177 eRNAs from 5085 samples across 10 species by mapping the RNA sequencing data to the regions of known enhancers. To explore their potential functions based on evolutionary conservation, we investigated the sequence similarity of eRNAs among multiple species. In addition, we identified the possible associations between eRNAs and transcription factors (TFs) or nearby genes to decipher their possible regulators and target genes, as well as characterized trait-related eRNAs to explore their potential functions in biological processes. Based on these findings, we further developed Animal-eRNAdb (http://gong_lab.hzau.edu.cn/Animal-eRNAdb/), a user-friendly database for data searching, browsing and downloading. With the comprehensive characterization of eRNAs in various tissues of different species, Animal-eRNAdb may greatly facilitate the exploration of functions and mechanisms of eRNAs.


Assuntos
Bases de Dados Genéticas , Elementos Facilitadores Genéticos/genética , RNA/genética , Software , Animais , Biologia Computacional , Regulação da Expressão Gênica/genética , Regiões Promotoras Genéticas/genética , Transcrição Gênica
6.
Mikrochim Acta ; 191(4): 202, 2024 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-38492117

RESUMO

Chiral self-assembly is the spontaneous organization of individual building blocks from chiral (bio)molecules to macroscopic objects into ordered superstructures. Chiral self-assembly is ubiquitous in nature, such as DNA and proteins, which formed the foundation of biological structures. In addition to chiral (bio) molecules, chiral ordered superstructures constructed by self-assembly have also attracted much attention. Chiral self-assembly usually refers to the process of forming chiral aggregates in an ordered arrangement under various non-covalent bonding such as H-bond, π-π interactions, van der Waals forces (dipole-dipole, electrostatic effects, etc.), and hydrophobic interactions. Chiral assembly involves the spontaneous process, which followed the minimum energy rule. It is essentially an intermolecular interaction force. Self-assembled chiral materials based on chiral recognition in electrochemistry, chiral catalysis, optical sensing, chiral separation, etc. have a broad application potential with the research development of chiral materials in recent years.

7.
Small ; 19(49): e2304172, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37563809

RESUMO

As a promising low-cost and high-safety energy storage candidate, zinc-ion hybrid capacitors (ZIHCs) have received extensive attention. For maximizing the advantages of ZIHC with high energy density and high power density, the structural engineering of the porous carbon materials is the crucial and effective strategy. Herein, an oxygen-enriched hierarchical porous carbon has been fabricated from the pyrolysis of olive leaves combing the chemical activation. The abundant interfacial active sites and short ions/electrons transfer length endow the hierarchical porous carbon cathode with high ions adsorption capacity and fast kinetic behaviors. Meanwhile, the oxygen-rich functional groups can provide extra pseudocapacitance and improve the wettability and conductivity of porous carbon. Benefiting from these advantages, an anti-self-discharge ZIHC device with a high energy-power feature has been assembled. The electrochemical process is studied by ex situ X-ray diffraction (XRD) and scanning electron microscope (SEM) methods. Finally, an excellent energy density of 136.3 W h kg-1 , and high power output of 20 kW kg-1 , as well as long cycle life with 91% capacity retention over 20 000 cycles at 10 A g-1 are realized by as-assembled ZIHC.

8.
Small ; 19(38): e2303059, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37217989

RESUMO

Chirality is a universal phenomenon in molecular and biological systems, denoting an asymmetric configurational property where an object cannot be superimposed onto its mirror image by any kind of translation or rotation, which is ubiquitous on the scale from neutrinos to spiral galaxies. Chirality plays a very important role in the life system. Many biological molecules in the life body show chirality, such as the "codebook" of the earth's biological diversity-DNA, nucleic acid, etc. Intriguingly, living organisms hierarchically consist of homochiral building blocks, for example, l-amino acids and d-sugars with unknown reason. When molecules with chirality interact with these chiral factors, only one conformation favors the positive development of life, that is, the chiral host environment can only selectively interact with chiral molecules of one of the conformations. The differences in chiral interactions are often manifested by chiral recognition, mutual matching, and interactions with chiral molecules, which means that the stereoselectivity of chiral molecules can produce changes in pharmacodynamics and pathology. Here, the latest investigations are summarized including the construction and applications of chiral materials based on natural small molecules as chiral source, natural biomacromolecules as chiral sources, and the material synthesized by design as a chiral source.

9.
Brief Bioinform ; 22(3)2021 05 20.
Artigo em Inglês | MEDLINE | ID: mdl-32392580

RESUMO

P53 is the 'guardian of the genome' and is responsible for regulating cell cycle and apoptosis. The genomic p53 binding regions, where activating transcriptional factors and cofactors like p300 simultaneously bind, are called 'p53-dependent enhancers', which play an important role in tumorigenesis. Current experimental assays generally provide a broad peak of each enhancer element, leaving our knowledge about critical enhancer regions (CERs) limited. Under the inspiration of enhancer dissection by CRISPR-Cas9 screen library on genome-wide p53 binding sites, here we introduce a statistical framework called 'Computational CRISPR Strategy' (CCS), to predict whether a given DNA fragment will be a p53-dependent CER by employing 7-mer as feature extractions along with random forest as the regressor. When training on a p53 CRISPR enhancer dataset, CCS not only accurately fitted the top-ranked enriched single guide RNAs (sgRNAs) but also successfully reproduced two known CERs that were validated by experiments. When applying it to an independent testing dataset on a tilling of a 2K-b genomic region of CRISPR-deCDKN1A-Lib, the trained model shows great generalizability by identifying a CER containing five top-ranked sgRNAs. A feature importance analysis further indicates that top-ranked 7-mers are mapped onto informative TF motifs including POU5F1 and SOX5, which are differentially enriched in p53-dependent CERs and are potential factors to make a general p53 binding site to form a p53-dependent CER, providing the interpretability of the trained model. Our results demonstrate that CCS is an alternative way of the CRISPR experiment to screen the genome for mapping p53-dependent CERs.


Assuntos
Elementos Facilitadores Genéticos , Genes p53 , Sistemas CRISPR-Cas , Conjuntos de Dados como Assunto , Humanos , RNA Guia de Cinetoplastídeos/genética
10.
Brief Bioinform ; 22(6)2021 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-34015824

RESUMO

Expression quantitative trait loci (eQTL) analysis has been widely used in interpreting disease-associated loci through correlating genetic variant loci with the expression of specific genes. RNA-sequencing (RNA-Seq), which can quantify gene expression at the genome-wide level, is often used in eQTL identification. Since different normalization methods of gene expression have substantial impacts on RNA-seq downstream analysis, it is of great necessity to systematically compare the effects of these methods on eQTL identification. Here, by using RNA-seq and genotype data of four different cancers in The Cancer Genome Atlas (TCGA) database, we comprehensively evaluated the effect of eight commonly used normalization methods on eQTL identification. Our results showed that the application of different methods could cause 20-30% differences in the final results of eQTL identification. Among these methods, COUNT, Median of Ratio (MED) and Trimmed Mean of M-values (TMM) generated similar results for identifying eQTLs, while Fragments Per Kilobase Million (FPKM) or RANK produced more differential results compared with other methods. Based on the accuracy and receiver operating characteristic (ROC) curve, the TMM method was found to be the optimal method for normalizing gene expression data in eQTLs analysis. In addition, we also evaluated the performance of different pairwise combinations of these methods. As a result, compared with single normalization methods, the combination of methods can not only identify more cis-eQTLs, but also improve the performance of the ROC curve. Overall, this study provides a comprehensive comparison of normalization methods for identifying eQTLs from RNA-seq data, and proposes some practical recommendations for diverse scenarios.


Assuntos
Biologia Computacional , Estudos de Associação Genética/métodos , Predisposição Genética para Doença , Locos de Características Quantitativas , Algoritmos , Biologia Computacional/métodos , Bases de Dados Genéticas , Expressão Gênica , Genótipo , Humanos , Curva ROC , Reprodutibilidade dos Testes , Fluxo de Trabalho
11.
BMC Cancer ; 23(1): 868, 2023 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-37715133

RESUMO

BACKGROUND: Novel and effective immunotherapies are required for refractory or recurrent sarcomas. Transforming growth factor-beta (TGF-ß) is a diverse regulatory and fibrogenic protein expressed in multiple sarcoma tumors that promotes epithelial-mesenchymal transition and excessive deposition of extracellular matrix. This study evaluated the efficacy and safety of the anti-PD-L1/TGF-ß antibody TQB2858 in patients with refractory osteosarcoma and alveolar soft part sarcoma (ASPS). METHODS: This single-arm phase 1b exploratory study included patients with refractory osteosarcoma or ASPS who had previously undergone at least two lines of systemic therapy. Patients were administered 1200 mg of TQB2858 once every 3 weeks. The primary endpoint was objective response rate (ORR), with null and alternative hypotheses of ORR ≤5% and ≥20%, respectively. Exploratory biomarker analyses using immunohistochemistry (IHC) staining (for PD-L1 and TGF-ß) were performed on pre-treatment tumor samples. RESULTS: Eleven eligible patients were included in this study. TQB2858 did not demonstrate evidence of efficacy as 0/5 osteosarcomas had any objective response, while 2/6 ASPS showed a partial response. The median progression-free survivals were 1.51 (1.38, Not Evaluable) and 2.86 (1.38, Not Evaluable) months for the osteosarcoma and ASPS groups, respectively. None of the administered cycles met the criteria for unacceptable toxicity. Other Grade 3 toxicities included abnormal liver function and elevation of γ-glutamyl transferase. IHC analysis revealed that functional enrichment in the TGF-ß pathway or PD-L1 was not associated with treatment outcomes. CONCLUSIONS: The combination of PD-L1 and TQB2858 did not significantly improve the ORR in patients with recurrent osteosarcoma. However, it improved immunogenic responses in ASPS, even after progression upon anti-PD-1/PD-L1 therapy, with an acceptable safety profile. IHC profiling with pathway enrichment analysis may not have any predictive value for survival outcomes. TRIAL REGISTRATION: Prospectively registered in the Ethical Review Committee of Peking University People's Hospital. The trial registration number is 2021PHA105-001 and 2021PHA140-001 and the registration date was March 2, 2022. CLINICALTRIALS: gov Identifier CTR20213001 and CTR20220390.


Assuntos
Antineoplásicos Imunológicos , Neoplasias Ósseas , Osteossarcoma , Sarcoma Alveolar de Partes Moles , Neoplasias de Tecidos Moles , Humanos , Povo Asiático , Neoplasias Ósseas/tratamento farmacológico , População do Leste Asiático , Osteossarcoma/tratamento farmacológico , Sarcoma Alveolar de Partes Moles/tratamento farmacológico , Neoplasias de Tecidos Moles/tratamento farmacológico , Fator de Crescimento Transformador beta/antagonistas & inibidores , Antígeno B7-H1/antagonistas & inibidores , Antineoplásicos Imunológicos/uso terapêutico , Anticorpos/uso terapêutico
12.
Arch Microbiol ; 205(4): 118, 2023 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-36928985

RESUMO

Alzheimer's disease (AD), the most prevalent neurodegenerative disease, has a significant relationship with alteration of the gut microbiota (GM), and the GM-gut-brain axis has been explored to find novel therapeutic approaches for AD. The present study aimed to evaluate the effect of human Lactobacillaceae (HLL) on cognitive function in APP/PS1 mice. The results showed that HLL treatment significantly improved the cognitive function of mice via MWM and NOR tests. Furthermore, the expression of Aß plaques, tau phosphorylation and neuroinflammation were markedly reduced in the hippocampus. Meanwhile, HLL treatment significantly increased the activity of GSH-PX and decreased the expression levels of IL-6 and MDA in the brain, and simultaneously increased the abundance of beneficial bacteria and restrained pathogenic bacteria in the intestine. Interestingly, significant correlations were observed between significant changes in abundance of GMs and AD-related markers. Collectively, these findings reveal that HLL is a promising therapeutic agent and potential probiotics, which might improve the cognitive function and AD pathologies.


Assuntos
Doença de Alzheimer , Disfunção Cognitiva , Microbioma Gastrointestinal , Lactobacillaceae , Doenças Neurodegenerativas , Animais , Humanos , Camundongos , Doença de Alzheimer/tratamento farmacológico , Doença de Alzheimer/metabolismo , Doença de Alzheimer/patologia , Peptídeos beta-Amiloides/metabolismo , Peptídeos beta-Amiloides/uso terapêutico , Disfunção Cognitiva/microbiologia , Disfunção Cognitiva/terapia , Modelos Animais de Doenças , Camundongos Transgênicos , Doenças Neurodegenerativas/microbiologia , Doenças Neuroinflamatórias
13.
Inflamm Res ; 72(4): 879-892, 2023 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-36912917

RESUMO

BACKGROUND: Monocytes/macrophages play critical roles in inflammation and cardiac remodeling following myocardial infarction (MI). The cholinergic anti-inflammatory pathway (CAP) modulates local and systemic inflammatory responses by activating α7 nicotinic acetylcholine receptors (α7nAChR) in monocytes/macrophages. We investigated the effect of α7nAChR on MI-induced monocyte/macrophage recruitment and polarization and its contribution to cardiac remodeling and dysfunction. METHODS: Adult male Sprague Dawley rats underwent coronary ligation and were intraperitoneally injected with the α7nAChR-selective agonist PNU282987 or the antagonist methyllycaconitine (MLA). RAW264.7 cells were stimulated with lipopolysaccharide (LPS) + interferon-gamma (IFN-γ) and treated with PNU282987, MLA, and S3I-201 (a STAT3 inhibitor). Cardiac function was evaluated by echocardiography. Masson's trichrome and immunofluorescence were used to detect cardiac fibrosis, myocardial capillary density, and M1/M2 macrophages. Western blotting was used to detect protein expression, and the proportion of monocytes was measured using flow cytometry. RESULTS: Activating the CAP with PNU282987 significantly improved cardiac function and reduced cardiac fibrosis and 28-day mortality after MI. On days 3 and 7 post-MI, PNU282987 reduced the percentage of peripheral CD172a + CD43low monocytes and the infiltration of M1 macrophages in the infarcted hearts, whereas it increased the recruitment of peripheral CD172a + CD43high monocytes and M2 macrophages. Conversely, MLA exerted the opposite effects. In vitro, PNU282987 inhibited M1 macrophage polarization and promoted M2 macrophage polarization in LPS + IFN-γ-stimulated RAW264.7 cells. These PNU282987-induced changes in LPS + IFN-γ-stimulated RAW264.7 cells were reversed by administering S3I-201. CONCLUSION: Activating α7nAChR inhibits the early recruitment of pro-inflammatory monocytes/macrophages during MI and improves cardiac function and remodeling. Our findings suggest a promising therapeutic target for regulating monocyte/macrophage phenotypes and promoting healing after MI.


Assuntos
Infarto do Miocárdio , Receptor Nicotínico de Acetilcolina alfa7 , Ratos , Animais , Masculino , Receptor Nicotínico de Acetilcolina alfa7/metabolismo , Remodelação Ventricular , Lipopolissacarídeos/farmacologia , Ratos Sprague-Dawley , Macrófagos/metabolismo , Transdução de Sinais , Interferon gama/metabolismo , Fibrose
14.
Can J Microbiol ; 69(4): 158-169, 2023 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-36669152

RESUMO

This study explored the effects of Lactiplantibacillus plantarum (previously Lactobacillus plantarum) BW2013 on mucosal integrity and gut microbiota of mice with dextran sulfate sodium (DSS)-induced colitis. The results show that the clinical symptoms in DSS-modelled ulcerative colitis (UC) were improved by L. plantarum BW2013 via decreasing disease activity index scores and suppressing inflammatory cell infiltration. Furthermore, L. plantarum BW2013 decreased the levels of diamine oxidase activity, myeloperoxidase, and D-lactic acid. The mRNA expression of ZO-1, occludin, and claudin-1 was upregulated by L. plantarum BW2013, which also increased IL-10 and reduced TNF-α, IL-1ß, and IL-6 in the colon. 16S rDNA sequencing showed that L. plantarum BW2013 enhanced α-diversity. L. plantarum BW2013 upregulated significantly the abundance of unidentfied Lachnospiraceae, Lactococcus, Rikenella, Lactobacillus, and Odoribacter, which had an inhibitory effect on inflammation and a protective effect on the integrity of the mucosa. These results demonstrate that L. plantarum BW2013 alleviates DSS-modelled UC by protecting mucosal integrity and ameliorating the composition of gut microbiota.


Assuntos
Colite Ulcerativa , Colite , Microbioma Gastrointestinal , Animais , Camundongos , Colite/induzido quimicamente , Colite Ulcerativa/induzido quimicamente , Colite Ulcerativa/metabolismo , Mucosa Intestinal/metabolismo , Modelos Animais de Doenças , Camundongos Endogâmicos C57BL
15.
Nucleic Acids Res ; 49(D1): D1480-D1488, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33137192

RESUMO

Genotype imputation is a process that estimates missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs), boost the power to identify genetic association and promote the combination of genetic studies. However, there has been a lack of high-quality reference panels for most plants, which greatly hinders the application of genotype imputation. Here, we developed Plant-ImputeDB (http://gong_lab.hzau.edu.cn/Plant_imputeDB/), a comprehensive database with reference panels of 12 plant species for online genotype imputation, SNP and block search and free download. By integrating genotype data and whole-genome resequencing data of plants from various studies and databases, the current Plant-ImputeDB provides high-quality reference panels of 12 plant species, including ∼69.9 million SNPs from 34 244 samples. It also provides an easy-to-use online tool with the option of two popular tools specifically designed for genotype imputation. In addition, Plant-ImputeDB accepts submissions of different types of genomic variations, and provides free and open access to all publicly available data in support of related research worldwide. In general, Plant-ImputeDB may serve as an important resource for plant genotype imputation and greatly facilitate the research on plant genetic research.


Assuntos
Bases de Dados Genéticas , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Genótipo , Proteínas de Plantas/genética , Plantas/genética , Arabidopsis/genética , Arabidopsis/metabolismo , Produtos Agrícolas , Estudos de Associação Genética , Internet , Anotação de Sequência Molecular , Melhoramento Vegetal/métodos , Proteínas de Plantas/metabolismo , Plantas/classificação , Plantas/metabolismo , Polimorfismo de Nucleotídeo Único , Padrões de Referência , Software
16.
Nucleic Acids Res ; 49(D1): D47-D54, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-32986825

RESUMO

Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism that recognizes different polyadenylation signals on transcripts, resulting in transcripts with different lengths of 3' untranslated regions and thereby influencing a series of biological processes. Recent studies have highlighted the important roles of APA in human. However, APA profiles in other animals have not been fully recognized, and there is no database that provides comprehensive APA information for other animals except human. Here, by using the RNA sequencing data collected from public databases, we systematically characterized the APA profiles in 9244 samples of 18 species. In total, we identified 342 952 APA events with a median of 17 020 per species using the DaPars2 algorithm, and 315 691 APA events with a median of 17 953 per species using the QAPA algorithm in these 18 species, respectively. In addition, we predicted the polyadenylation sites (PAS) and motifs near PAS of these species. We further developed Animal-APAdb, a user-friendly database (http://gong_lab.hzau.edu.cn/Animal-APAdb/) for data searching, browsing and downloading. With comprehensive information of APA events in different tissues of different species, Animal-APAdb may greatly facilitate the exploration of animal APA patterns and novel mechanisms, gene expression regulation and APA evolution across tissues and species.


Assuntos
Processamento Alternativo , Biologia Computacional/métodos , Bases de Dados Genéticas , Poliadenilação , RNA Mensageiro/genética , Software , Regiões 3' não Traduzidas , Animais , Humanos , Motivos de Nucleotídeos , Navegador
17.
World J Surg Oncol ; 21(1): 187, 2023 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-37344874

RESUMO

BACKGROUND: Computer-assisted navigation has made bone sarcoma resections more precise. However, further clinical studies involving accuracy analyses under navigation are still warranted. METHODS: A retrospective study for analysis of computer-assisted navigation accuracy was carried out. Between September 2008 and November 2017, 39 cases of bone sarcomas around the knee joint were resected under computer-assisted navigation. The control group comprised 117 cases of bone sarcomas around the knee treated by limb salvage surgery wherein bony cutting was achieved freehand. The length difference (LD) was defined as the specimen length minus the planned resection length. The LDs were detected in both groups and compared. The margin accuracy (MA) was defined as the achieved margin minus the desired margin at the bone cutting site and was detected in the navigation group. RESULTS: The LDs between the postoperative specimen length and the preoperative planned length were compared. In the navigation group, the LD was 0.5 ± 2.5 mm (range, - 5 to 5 mm), while in the freehand group, the LD was 3.4 ± 9.6 mm (range, - 20 to 29 mm), with a significant difference (P < 0.01). In the absolute value analysis, the LD absolute value was 2.0 ± 1.6 mm in the navigation group and 8.3 ± 6.0 mm in the freehand group, with a significant difference (P < 0.01). In the navigation group, the MA was 0.3 ± 1.5 mm (range, - 3 to 3 mm) and the MA absolute value was 1.1 ± 1.0 mm. CONCLUSIONS: Better accuracy can be achieved when computer-assisted navigation is conducted for bone sarcoma resection around the knee. LEVEL OF EVIDENCE: IV.


Assuntos
Neoplasias Ósseas , Osteossarcoma , Sarcoma , Cirurgia Assistida por Computador , Humanos , Estudos Retrospectivos , Osteossarcoma/cirurgia , Neoplasias Ósseas/cirurgia , Sarcoma/cirurgia , Articulação do Joelho/cirurgia , Computadores
18.
Mikrochim Acta ; 190(6): 230, 2023 05 20.
Artigo em Inglês | MEDLINE | ID: mdl-37208529

RESUMO

Chiral materials have drawn the widespread attention for their its chiral recognition ability. The design and synthesis of chiral material are of importance owing to the unpredictability in controlling chirality during the synthesis process. To circumvent problems, a chiral MOF (D-His-ZIF-8) was synthesized by ligand exchange of 2-methylimidazole (Hmim) on ZIF-8 by D-histidine (D-His), which can be treated as chiral host to distinguish amino acid enantiomers. The obtained D-His-ZIF-8 can provide chiral nanochannels for amino acid guests. Meanwhile, polynary transition-metal ion (Co2+ and Fe3+) coordinating with polydopamine (PDA) wrapped on the surface of D-His-ZIF-8 can increase the active sites. The electrochemical chiral recognition behavior showed that D-His-ZIF-8@CoFe-PDA exhibited good recognition of the tryptophan enantiomer (L/D-Trp) (working potential of -0.2 V vs. Hg/HgCl2). The LOD and LOQ of L-Trp were 0.066 mM and 0.22 mM, respectively, while the LOD and LOQ of D-Trp were 0.15 mM and 0.50 mM, respectively. Finally, the usefulness of D-His-ZIF-8@CoFe-PDA/GCE was evaluated with a recovery of 94.4-103%. The analysis of real  samples shows that D-His-ZIF-8@CoFe-PDA/GCE is a feasible sensing platform for the detection of L-Trp and D-Trp.


Assuntos
Técnicas Biossensoriais , Polímeros , Polímeros/química , Triptofano/química , Histidina , Estereoisomerismo
19.
Mikrochim Acta ; 190(2): 61, 2023 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-36662318

RESUMO

Chirality plays a key role in many fields of natural sciences as well as life sciences. Chiral materials are widely developed and used for electrochemical chiral recognition. In recent years, carbon quantum dots (CQDs) have been widely used as a novel carbon nanomaterial due to their excellent charge transfer properties, good biocompatibility, and low cost. The special structure of π-conjugated porphyrin attracts attention. Supramolecular self-assembly shows a way to construct chiral materials by self-assembling simple molecules into chiral composites. Herein, we demonstrate the self-assembly of achiral porphyrins induced by chiral carbon quantum dots assembled from L- and or D-tryptophan (L- and or D-Trp) with carbon quantum dots, resulting in 5,10,15,20-tetrakis (4-carboxyPheyl) (TCPP) self-assembled structure. The electrochemical chiral recognition of chiral self-assembled materials was studied using Phenylalanine (Phe) enantiomer as a chiral analyte. Electrochemical chiral recognition results showed that the chiral self-assembled materials induced by chiral templates have a good ability to discriminate Phe enantiomers. Therefore, this research provides a new idea for the synthesis of chiral composites and further expands applications to electrochemical chiral recognition.


Assuntos
Nanoestruturas , Porfirinas , Porfirinas/química , Fenilalanina/química , Triptofano , Carbono
20.
Br J Clin Pharmacol ; 88(5): 2456-2472, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-34729817

RESUMO

AIMS: A lot of medication risks related to high-dose methotrexate (HDMTX) therapy still remain to be identified and standardized. This study aims to establish an evidence-based practice guideline for individualized medication of HDMTX. METHODS: The practice guideline was launched by the Division of Therapeutic Drug Monitoring, Chinese Pharmacological Society. The guideline was developed following the WHO handbook for guideline development and the methodology of evidence-based medicine (EBM). The guideline was initially registered in the International Practice Guidelines Registry Platform (IPGRP-2017CN021). Systematic reviews were conducted to synthesize available evidence. A multicentre cross-sectional study was conducted using questionnaires to evaluate patients' perception and willingness concerning individualized medication of HDMTX. The Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach was used to rate the quality of evidence and to grade the strength of recommendations. RESULTS: Multidisciplinary working groups were included in this guideline, including clinicians, pharmacists, methodologists, pharmacologists and pharmacoeconomic specialists. A total of 124 patients were involved to integrate patient values and preferences. Finally, the guideline presents 28 recommendations, regarding evaluation prior to administration (renal function, liver function, pleural effusion, comedications, genetic testing), pre-treatment and routine dosing regimen, therapeutic drug monitoring (necessity, method, timing, target concentration), leucovorin rescue (initial timing, dosage regimen and optimization), and management of toxicities. Of these, 12 are strong recommendations. CONCLUSIONS: We developed an evidence-based practice guideline with respect to HDMTX medication using a rigorous and multidisciplinary approach. This guideline provides comprehensive and practical recommendations involving the whole process of HDMTX administration to health care providers.


Assuntos
Monitoramento de Medicamentos , Metotrexato , China , Estudos Transversais , Medicina Baseada em Evidências/métodos , Humanos , Metotrexato/efeitos adversos
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