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1.
J Exp Bot ; 73(9): 2859-2874, 2022 May 13.
Artigo em Inglês | MEDLINE | ID: mdl-35560205

RESUMO

Vegetable oils are an indispensable nutritional component of the human diet as well as important raw materials for a variety of industrial applications such as pharmaceuticals, cosmetics, oleochemicals, and biofuels. Oil plant genomes are highly diverse, and their genetic variation leads to a diversity in oil biosynthesis and accumulation along with agronomic traits. This review discusses plant oil biosynthetic pathways, current state of genome assembly, polyploidy and asymmetric evolution of genomes of oil plants and their wild relatives, and research progress of pan-genomics in oil plants. The availability of complete high-resolution genomes and pan-genomes has enabled the identification of structural variations in the genomes that are associated with the diversity of agronomic and environment fitness traits. These and future genomes also provide powerful tools to understand crop evolution and to harvest the rich natural variations to improve oil crops for enhanced productivity, oil quality, and adaptability to changing environments.

3.
Int J Cardiol ; 2022 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-35439585

RESUMO

This is an era of function evaluation for heart, but still there are some structural changes remains to be recognized. Aorto-septal angle (AoSA) is a morphologic description of the heart and adjacent major vessel. Previous studies have shown its potential hemodynamic significance, however, these are conducted in patients with structural heart diseases. The present study investigated its longitudinal change in 140 adults without structural heart disease from 20 to 90 years old and its independent clinical correlates. The findings included: 1. Advanced age, male and presence of sigmoid IVS were independent predictors of a steep AoSA. 2. Females tend to have a wider AoSA compared to age-matched males before 70 years old but they undergo more dramatic decrease with aging so that no gender difference was found beyond 70 years old. 3. Electrocardiographic QRS axis left deviation tends to be correlated with a steeper AoSA. 4. In adults without structural heart disease, no clinically significant association between AoSA and aortic velocity was found. Further prospective study from multi-centers is needed to verify these findings.

4.
J Healthc Eng ; 2022: 7496785, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35463658

RESUMO

Background: The tissues and organs of premature infants are immature and easily damaged by external adverse factors, leading to functional development disorders and abnormalities. Besides, the incidence of premature babies in various countries has an increasing trend, with the incidence rate exceeding 10%. Objective: This study aims to investigate the neurodevelopment and the incidence of various developmental delays, cerebral palsy, autism spectrum disorder, and audio-visual impairment in premature infants under 34 weeks of gestation from birth to 2 years of age, so as to provide the basis for early intervention of premature infants in the clinic. Methods: A cohort of premature infants was established using 263 premature infants with a gestational age of 28-33 + 6 weeks who were born alive from March 1, 2018, to February 28, 2019, in four tertiary hospitals in Shenzhen. In addition, 263 full-term infants of the same sex who were born in the same period in the four hospitals were randomly selected and paired in a ratio of 1 : 1 as the control group. The subjects were assessed for neurodevelopment using the Gesell test scale at 6, 12, 18, and 24 months after birth (premature infants were corrected for months). We calculated the neurodevelopmental indicators of children in each month of age and the incidence of various developmental delays, cerebral palsy, autism spectrum disorder, and audio-visual impairment in the two groups. Results: The results of this study showed that the cohort of premature infants with birth gestational age less than 34 weeks had higher adaptive, fine motor, and personal-social energy domain development quotient (DQ) values from the corrected gestational age of 6 months to the corrected gestational age of 24 months after birth compared with the full-term cohort. And it also achieved catch-up growth in neurological development, but the detection rates of neurodevelopmental abnormalities at the corrected gestational age of 12 and 24 months were higher than those in the full-term cohort. Conclusion: It is important to reduce the disability rate and degree of premature infants by strengthening the systematic management, early promotion and supervision, as well as early intervention for preterm infants with developmental abnormalities who were born at gestational age less than 34 weeks after birth.


Assuntos
Transtorno do Espectro Autista , Paralisia Cerebral , Transtorno do Espectro Autista/epidemiologia , Paralisia Cerebral/epidemiologia , Criança , Pré-Escolar , Estudos de Coortes , Feminino , Humanos , Lactente , Recém-Nascido , Recém-Nascido Prematuro , Transtornos da Visão
5.
Front Plant Sci ; 13: 828467, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35283921

RESUMO

Coleanthus subtilis (Tratt.) Seidel (Poaceae) is an ephemeral grass from the monotypic genus Coleanthus Seidl, which grows on wet muddy areas such as fishponds or reservoirs. As a rare species with strict habitat requirements, it is protected at international and national levels. In this study, we sequenced its whole chloroplast genome for the first time using the next-generation sequencing (NGS) technology on the Illumina platform, and performed a comparative and phylogenetic analysis with the related species in Poaceae. The complete chloroplast genome of C. subtilis is 135,915 bp in length, with a quadripartite structure having two 21,529 bp inverted repeat regions (IRs) dividing the entire circular genome into a large single copy region (LSC) of 80,100 bp and a small single copy region (SSC) of 12,757 bp. The overall GC content is 38.3%, while the GC contents in LSC, SSC, and IR regions are 36.3%, 32.4%, and 43.9%, respectively. A total of 129 genes were annotated in the chloroplast genome, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The accD gene and the introns of both clpP and rpoC1 genes were missing. In addition, the ycf1, ycf2, ycf15, and ycf68 were pseudogenes. Although the chloroplast genome structure of C. subtilis was found to be conserved and stable in general, 26 SSRs and 13 highly variable loci were detected, these regions have the potential to be developed as important molecular markers for the subfamily Pooideae. Phylogenetic analysis with species in Poaceae indicated that Coleanthus and Phippsia were sister groups, and provided new insights into the relationship between Coleanthus, Zingeria, and Colpodium. This study presents the initial chloroplast genome report of C. subtilis, which provides an essential data reference for further research on its origin.

6.
Ther Apher Dial ; 26(3): 632-639, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-34550646

RESUMO

AIM: To evaluate the cognitive function in dialysis patients over 60 years old and identify the contributing factors. METHODS: A group of elderly dialysis patients in the Department of Nephrology, Pan'an People's Hospital between March 2015 and June 2018 were chosen as the subjects for this study. Patients were divided into two groups, those with cognitive impairment and those with normal cognitive function. Results of their Montreal Cognitive Assessment (MoCA) scores, Controlled Oral Word Association Test (COWAT), Wechsler Adult Intelligence Scale Digit Span subtest (WDMS), and Stanford Diagnostic Math Test (SDMT) were reviewed and analyzed. RESULTS: Among the 110 elderly dialysis patients, 75 patients (68.18%) showed different levels of damage to their cognitive function. Their assessment scores on MoCA (total), MoCA subtests: visuospatial/executive, naming, attention, language, delayed recall, abstraction and orientation, COWAT (total), COWAT1, COWAT2, COWAT3, WMDS-Backward, and SDMT are significantly lower than patients with normal cognitive abilities (p < 0.05). Further analysis showed that the highest percentage (72.00%) of patients had impairment with visuospatial/executive function; and, of the 75 cognitive impaired patients, 37.33% showed cognitive damage in two MoCA subtests simultaneously. Patients with and without cognitive impairment showed a significant (p < 0.05) difference on factors including age, education level, employment status, financial situation, dialysis vintage, serum albumin, and hemoglobin. CONCLUSION: Elderly patients on dialysis have a higher risk of becoming cognitive impaired. The cognitive impairment in elderly dialysis patients was significantly associated with age, dialysis vintage, and levels of serum albumin and hemoglobin.


Assuntos
Disfunção Cognitiva , Diálise Renal , Adulto , Idoso , Disfunção Cognitiva/epidemiologia , Disfunção Cognitiva/etiologia , Função Executiva , Humanos , Pessoa de Meia-Idade , Testes Neuropsicológicos , Albumina Sérica
7.
Genome Biol ; 23(1): 16, 2022 01 10.
Artigo em Inglês | MEDLINE | ID: mdl-35012611

RESUMO

Many circular RNAs (circRNAs) are produced from back-splicing of exons of precursor mRNAs and are generally co-expressed with cognate linear RNAs. Methods for circRNA-specific knockout are lacking, largely due to sequence overlaps between forms. Here, we use base editors (BEs) for circRNA depletion. By targeting splice sites involved in both back-splicing and canonical splicing, BEs can repress circular and linear RNAs. Targeting sites predominantly for circRNA biogenesis, BEs could efficiently repress the production of circular but not linear RNAs. As hundreds of exons are predominantly back-spliced to produce circRNAs, this provides an efficient method to deplete circRNAs for functional study.


Assuntos
Splicing de RNA , RNA Circular , Éxons , RNA/genética , Precursores de RNA
8.
Mol Cell ; 82(2): 420-434.e6, 2022 01 20.
Artigo em Inglês | MEDLINE | ID: mdl-34951963

RESUMO

Exon back-splicing-generated circular RNAs, as a group, can suppress double-stranded RNA (dsRNA)-activated protein kinase R (PKR) in cells. We have sought to synthesize immunogenicity-free, short dsRNA-containing RNA circles as PKR inhibitors. Here, we report that RNA circles synthesized by permuted self-splicing thymidylate synthase (td) introns from T4 bacteriophage or by Anabaena pre-tRNA group I intron could induce an immune response. Autocatalytic splicing introduces ∼74 nt td or ∼186 nt Anabaena extraneous fragments that can distort the folding status of original circular RNAs or form structures themselves to provoke innate immune responses. In contrast, synthesized RNA circles produced by T4 RNA ligase without extraneous fragments exhibit minimized immunogenicity. Importantly, directly ligated circular RNAs that form short dsRNA regions efficiently suppress PKR activation 103- to 106-fold higher than reported chemical compounds C16 and 2-AP, highlighting the future use of circular RNAs as potent inhibitors for diseases related to PKR overreaction.


Assuntos
Inibidores de Proteínas Quinases/farmacologia , RNA Circular/farmacologia , eIF-2 Quinase/antagonistas & inibidores , Células A549 , Bacteriófago T4/enzimologia , Bacteriófago T4/genética , Células HEK293 , Células HeLa , Humanos , Imunidade Inata/efeitos dos fármacos , Íntrons , Conformação de Ácido Nucleico , Inibidores de Proteínas Quinases/imunologia , RNA Ligase (ATP)/genética , RNA Ligase (ATP)/metabolismo , Precursores de RNA/genética , Precursores de RNA/metabolismo , RNA Circular/genética , RNA Circular/imunologia , Timidilato Sintase/genética , Timidilato Sintase/metabolismo , Proteínas Virais/genética , Proteínas Virais/metabolismo , eIF-2 Quinase/metabolismo
9.
Curr Opin Genet Dev ; 72: 128-137, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34933201

RESUMO

Long non-coding RNAs (lncRNAs) associate with RNA-binding proteins (RBPs) to form lncRNA-protein complexes that act in a wide range of biological processes. Understanding the molecular mechanism of how a lncRNA-protein complex is assembled and regulated is key for their cellular functions. In this mini-review, we outline molecular methods used to identify lncRNA-protein interactions from large-scale to individual levels using bulk cells as well as those recently developed imaging and single-molecule approaches that are capable of visualizing RNA-protein assemblies in single cells and in real-time. Focusing on the latter group of approaches, we discuss their applications and limitations, which nevertheless have enabled quantification and comprehensive dissection of RNA-protein interactions possible.


Assuntos
RNA Longo não Codificante , Proteínas de Ligação a RNA , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo
10.
J Exp Bot ; 2021 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-34727176

RESUMO

Vegetable oils are indispensable nutritional components of human diet as well as important raw materials for a variety of industrial applications such as pharmaceuticals, cosmetics, oleochemicals and biofuels. The oil plant genomes are highly diverse, and the genetic variation leads to the diversity in oil biosynthesis and accumulation along with agronomic traits. This review discusses the plant oil biosynthetic pathways, the current state of genome assembly, the polyploidy and asymmetric evolution genomes of oil plants and their wild relatives, and the research progress of pan-genomics in oil plants. The availability of complete high-resolution genomes and pangenomes has enabled the identification of structural variations in the genomes that are associated with the diversity of agronomic and environment fitness traits. These and more future genomes also provide powerful tools to understand crop evolution and to harvest the rich natural variations to improve oil crops for enhanced productivity, oil quality, and adaptability to changing environments.

11.
Genome Biol ; 22(1): 304, 2021 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-34736486

RESUMO

BACKGROUND: Coconut is an important tropical oil and fruit crop whose evolutionary position renders it a fantastic species for the investigation of the evolution of monocot chromosomes and the subsequent differentiation of ancient plants. RESULTS: Here, we report the assembly and annotation of reference-grade genomes of Cn. tall and Cn. dwarf, whose genome sizes are 2.40 Gb and 2.39 Gb, respectively. The comparative analysis reveals that the two coconut subspecies diverge about 2-8 Mya while the conserved Arecaceae-specific whole-genome duplication (ω WGD) occurs approximately 47-53 Mya. It additionally allows us to reconstruct the ancestral karyotypes of the ten ancient monocot chromosomes and the evolutionary trajectories of the 16 modern coconut chromosomes. Fiber synthesis genes in Cn. tall, related to lignin and cellulose synthesis, are found at a higher copy number and expression level than dwarf coconuts. Integrated multi-omics analysis reveals that the difference in coconut plant height is the result of altered gibberellin metabolism, with both the GA20ox copy number and a single-nucleotide change in the promoter together leading to the difference in plant height between Cn. tall and Cn. dwarf. CONCLUSION: We provide high-quality coconut genomes and reveal the genetic basis of trait differences between two coconuts through multi-omics analysis. We also reveal that the selection of plant height has been targeted for the same gene for millions of years, not only in natural selection of ancient plant as illustrated in coconut, but also for artificial selection in cultivated crops such as rice and maize.


Assuntos
Cromossomos de Plantas , Cocos/genética , Evolução Molecular , Genoma de Planta , Vias Biossintéticas , Cocos/anatomia & histologia , Cocos/metabolismo , Genômica , Cariótipo
12.
Heliyon ; 7(11): e08361, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34841101

RESUMO

Dioxin pollution has been problematic in Taiwan. Although the government has established emission standards and emission inventory to control dioxin pollution, such efforts only apply to pollution emissions; no attempt has been made to understand the flow of dioxins in different environmental media. In this study, the STELLA software was used to model the flow pattern of dioxins in various media. This model and the RAIDAR model established by the Canadian Environmental Model Research Center were used to simulate dioxin flow in Taiwan, and their results were compared with the measured values. The accuracies of the RAIDAR and STELLA models were 63.92% and 49.78%, respectively. This shows that the simulation with the STELLA model provided results closer to the measured values and that the error was less than ten times that of the RAIDAR model, indicating that the proposed model is predictive. In addition, we used the results of a system dynamics model for dioxin flow and an air resource co-benefits (ARCoB) model to apply the obtained results to the energy sector to quantify the co-benefits of reducing dioxin, greenhouse gas, and air pollutant emissions on the basis of the policy target for the year 2030. The total co-benefits of natural gas and renewable energy (RE) scenarios were US$9.63 billion and US$12.57 billion, respectively; the benefit-cost ratios were 2.89 and 20.67, respectively. The development of an RE policy as an alternative to a coal-fired power generation policy will contribute to the best co-benefits of integrated reductions and will also contribute to human health.

13.
Ann N Y Acad Sci ; 1506(1): 118-141, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34791665

RESUMO

The human transcriptome contains many types of noncoding RNAs, which rival the number of protein-coding species. From long noncoding RNAs (lncRNAs) that are over 200 nucleotides long to piwi-interacting RNAs (piRNAs) of only 20 nucleotides, noncoding RNAs play important roles in regulating transcription, epigenetic modifications, translation, and cell signaling. Roles for noncoding RNAs in disease mechanisms are also being uncovered, and several species have been identified as potential drug targets. On May 11-14, 2021, the Keystone eSymposium "Noncoding RNAs: Biology and Applications" brought together researchers working in RNA biology, structure, and technologies to accelerate both the understanding of RNA basic biology and the translation of those findings into clinical applications.


Assuntos
Congressos como Assunto/tendências , Epigênese Genética/genética , Marcação de Genes/tendências , RNA não Traduzido/administração & dosagem , RNA não Traduzido/genética , Relatório de Pesquisa , Animais , Sistemas de Liberação de Medicamentos/métodos , Sistemas de Liberação de Medicamentos/tendências , Marcação de Genes/métodos , Humanos , MicroRNAs/administração & dosagem , MicroRNAs/genética , RNA Longo não Codificante/administração & dosagem , RNA Longo não Codificante/genética , RNA Interferente Pequeno/administração & dosagem , RNA Interferente Pequeno/genética , Pequeno RNA não Traduzido/administração & dosagem , Pequeno RNA não Traduzido/genética , Transdução de Sinais/genética
14.
Comput Biol Med ; 138: 104929, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34655900

RESUMO

Cholera is a severe small intestine bacterial disease caused by consumption of water and food contaminated with Vibrio cholera. The disease causes watery diarrhea leading to severe dehydration and even death if left untreated. In the past few decades, V. cholerae has emerged as multidrug-resistant enteric pathogen due to its rapid ability to adapt in detrimental environmental conditions. This research study aimed to design inhibitors of a master virulence gene expression regulator, HapR. HapR is critical in regulating the expression of several set of V. cholera virulence genes, quorum-sensing circuits and biofilm formation. A blind docking strategy was employed to infer the natural binding tendency of diverse phytochemicals extracted from medicinal plants by exposing the whole HapR structure to the screening library. Scoring function criteria was applied to prioritize molecules with strong binding affinity (binding energy < -11 kcal/mol) and as such two compounds: Strychnogucine A and Galluflavanone were filtered. Both the compounds were found favourably binding to the conserved dimerization interface of HapR. One rare binding conformation of Strychnogucine A was noticed docked at the elongated cavity formed by α1, α4 and α6 (binding energy of -12.5 kcal/mol). The binding stability of both top leads at dimer interface and elongated cavity was further estimated using long run of molecular dynamics simulations, followed by MMGB/PBSA binding free energy calculations to define the dominance of different binding energies. In a nutshell, this study presents computational evidence on antibacterial potential of phytochemicals capable of directly targeting bacterial virulence and highlight their great capacity to be utilized in the future experimental studies to stop the evolution of antibiotic resistance evolution.


Assuntos
Vibrio cholerae , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Regulação Bacteriana da Expressão Gênica , Compostos Fitoquímicos , Percepção de Quorum , Vibrio cholerae/genética , Vibrio cholerae/metabolismo
15.
Mol Cell ; 81(20): 4111-4113, 2021 10 21.
Artigo em Inglês | MEDLINE | ID: mdl-34686312

RESUMO

Chen et al. (2021) have identified many internal ribosome entry site-like elements that can potentially drive circRNA translation. Dozens of such element-containing circRNAs-encoded peptides are validated, among which a circFGFR1-encoded protein acts as an antagonist of FGFR1.


Assuntos
Sítios Internos de Entrada Ribossomal , RNA Circular , Regulação da Expressão Gênica
16.
Methods ; 196: 1-2, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34601050
17.
RNA ; 27(12): 1427-1440, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34526358

RESUMO

Although long noncoding RNAs (lncRNAs) are generally expressed at low levels, emerging evidence has revealed that many play important roles in gene regulation by a variety of mechanisms as they engage with proteins. Given that the abundance of proteins often greatly exceeds that of their interacting lncRNAs, quantification of the relative abundance, or even the exact stoichiometry in some cases, within lncRNA-protein complexes is helpful for understanding of the mechanism(s) of action of lncRNAs. We discuss methods used to examine lncRNA and protein expression at the single cell, subcellular, and suborganelle levels, the average and local lncRNA concentration in cells, as well as how lncRNAs can modulate the functions of their interacting proteins even at a low stoichiometric concentration.


Assuntos
RNA Longo não Codificante/metabolismo , Proteínas de Ligação a RNA/metabolismo , Ribonucleoproteínas/metabolismo , Animais , Regulação da Expressão Gênica , Humanos , RNA Longo não Codificante/genética , Proteínas de Ligação a RNA/genética , Ribonucleoproteínas/genética
18.
Methods Mol Biol ; 2372: 179-192, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34417752

RESUMO

Accumulated lines of evidence have revealed that a large number of circular RNAs are produced in transcriptomes from fruit fly to mouse and human. Unlike linear RNAs shaped with 5' cap and 3' tail, circular RNAs are characterized by covalently closed loop structures without open terminals, thus required specific treatments for their identification and validation. Here, we describe a detailed pipeline for the characterization of circular RNAs. It has been successfully applied to the study of circular intronic RNAs (ciRNAs) derived from intron lariats and circular RNAs (circRNAs) produced from back spliced exons in human.


Assuntos
RNA Circular/genética , Animais , Éxons , Íntrons/genética , Camundongos , RNA/genética , RNA/metabolismo , Splicing de RNA
19.
Sci China Life Sci ; 64(11): 1795-1809, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34453665

RESUMO

Circular intronic RNAs (ciRNAs) escaping from DBR1 debranching of intron lariats are co-transcriptionally produced from pre-mRNA splicing, but their turnover and mechanism of action have remained elusive. We report that RNase H1 degrades a subgroup of ciRNAs in human cells. Many ciRNAs contain high GC% and tend to form DNA:RNA hybrids (R-loops) for RNase H1 cleavage, a process that appears to promote Pol II transcriptional elongation at ciRNA-producing loci. One ciRNA, ciankrd52, shows a stronger ability of R-loop formation than that of its cognate pre-mRNA by maintaining a locally open RNA structure in vitro. This allows the release of pre-mRNA from R-loops by ci-ankrd52 replacement and subsequent ciRNA removal via RNase H1 for efficient transcriptional elongation. We propose that such an R-loop dependent ciRNA degradation likely represents a mechanism that on one hand limits ciRNA accumulation by recruiting RNase H1 and on the other hand resolves R-loops for transcriptional elongation at some GC-rich ciRNA-producing loci.


Assuntos
RNA Polimerase II/metabolismo , Splicing de RNA , RNA Circular/metabolismo , Ribonuclease H/metabolismo , Humanos , Íntrons , Desnaturação de Ácido Nucleico
20.
Genome Biol ; 22(1): 221, 2021 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-34376223

RESUMO

Single-cell RNA-seq (scRNA-seq) profiles gene expression with high resolution. Here, we develop a stepwise computational method-called SCAPTURE to identify, evaluate, and quantify cleavage and polyadenylation sites (PASs) from 3' tag-based scRNA-seq. SCAPTURE detects PASs de novo in single cells with high sensitivity and accuracy, enabling detection of previously unannotated PASs. Quantified alternative PAS transcripts refine cell identity analysis beyond gene expression, enriching information extracted from scRNA-seq data. Using SCAPTURE, we show changes of PAS usage in PBMCs from infected versus healthy individuals at single-cell resolution.


Assuntos
Aprendizado Profundo , Poliadenilação , RNA-Seq , Análise de Célula Única , COVID-19/diagnóstico , Humanos , SARS-CoV-2 , Sensibilidade e Especificidade , Análise de Sequência de RNA , Transcriptoma
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