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Oakleaf butterflies in the genus Kallima have a polymorphic wing phenotype, enabling these insects to masquerade as dead leaves. This iconic example of protective resemblance provides an interesting evolutionary paradigm that can be employed to study biodiversity. We integrated multi-omic data analyses and functional validation to infer the evolutionary history of Kallima species and investigate the genetic basis of their variable leaf wing patterns. We find that Kallima butterflies diversified in the eastern Himalayas and dispersed to East and Southeast Asia. Moreover, we find that leaf wing polymorphism is controlled by the wing patterning gene cortex, which has been maintained in Kallima by long-term balancing selection. Our results provide macroevolutionary and microevolutionary insights into a model species originating from a mountain ecosystem.
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Borboletas , Animais , Biodiversidade , Evolução Biológica , Borboletas/genética , Ecossistema , Fenótipo , Asas de AnimaisRESUMO
In recent years, the exploration of genome three-dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. While animals exhibit a characteristic genome topology defined by topologically associating domains (TADs), plants display similar features with a more diverse conformation across species. Employing advanced high-throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato (Solanum lycopersicum). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD-like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.
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Epigenoma , Histonas , Solanum lycopersicum , Solanum lycopersicum/genética , Solanum lycopersicum/metabolismo , Histonas/metabolismo , Histonas/genética , Epigênese Genética , Genoma de Planta , Cromatina/metabolismo , Cromatina/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Regulação da Expressão Gênica de Plantas , Heterocromatina/metabolismo , Heterocromatina/genética , Código das Histonas/genéticaRESUMO
The 3D chromatin organization plays a major role in the control of gene expression. However, our comprehension of the governing principles behind nuclear organization remains incomplete. Particularly, the spatial segregation of loci with similar repressive transcriptional states in plants poses a significant yet poorly understood puzzle. In this study, employing a combination of genetics and advanced 3D genomics approaches, we demonstrated that a redistribution of facultative heterochromatin marks in regions usually occupied by constitutive heterochromatin marks disrupts the 3D genome compartmentalisation. This disturbance, in turn, triggers novel chromatin interactions between genic and transposable element (TE) regions. Interestingly, our results imply that epigenetic features, constrained by genetic factors, intricately mold the landscape of 3D genome organisation. This study sheds light on the profound genetic-epigenetic interplay that underlies the regulation of gene expression within the intricate framework of the 3D genome. Our findings highlight the complexity of the relationships between genetic determinants and epigenetic features in shaping the dynamic configuration of the 3D genome.
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Tumor necrosis factor receptor-associated factor family member-associated NF-κB activator-binding kinase 1 (TBK1) plays a key role in the induction of the type 1 interferon (IFN-I) response, which is an important component of innate antiviral defense. Viruses target calcium (Ca2+) signaling networks, which participate in the regulation of the viral life cycle, as well as mediate the host antiviral response. Although many studies have focused on the role of Ca2+ signaling in the regulation of IFN-I, the relationship between Ca2+ and TBK1 in different infection models requires further elucidation. Here, we examined the effects of the Newcastle disease virus (NDV)-induced increase in intracellular Ca2+ levels on the suppression of host antiviral responses. We demonstrated that intracellular Ca2+ increased significantly during NDV infection, leading to impaired IFN-I production and antiviral immunity through the activation of calcineurin (CaN). Depletion of Ca²+ was found to lead to a significant increase in virus-induced IFN-I production resulting in the inhibition of viral replication. Mechanistically, the accumulation of Ca2+ in response to viral infection increases the phosphatase activity of CaN, which in turn dephosphorylates and inactivates TBK1 in a Ca2+-dependent manner. Furthermore, the inhibition of CaN on viral replication was counteracted in TBK1 knockout cells. Together, our data demonstrate that NDV hijacks Ca2+ signaling networks to negatively regulate innate immunity via the CaN-TBK1 signaling axis. Thus, our findings not only identify the mechanism by which viruses exploit Ca2+ signaling to evade the host antiviral response but also, more importantly, highlight the potential role of Ca2+ homeostasis in the viral innate immune response.IMPORTANCEViral infections disrupt intracellular Ca2+ homeostasis, which affects the regulation of various host processes to create conditions that are conducive for their own proliferation, including the host immune response. The mechanism by which viruses trigger TBK1 activation and IFN-I induction through viral pathogen-associated molecular patterns has been well defined. However, the effects of virus-mediated Ca2+ imbalance on the IFN-I pathway requires further elucidation, especially with respect to TBK1 activation. Herein, we report that NDV infection causes an increase in intracellular free Ca2+ that leads to activation of the serine/threonine phosphatase CaN, which subsequently dephosphorylates TBK1 and negatively regulates IFN-I production. Furthermore, depletion of Ca2+ or inhibition of CaN activity exerts antiviral effects by promoting the production of IFN-I and inhibiting viral replication. Thus, our results reveal the potential role of Ca2+ in the innate immune response to viruses and provide a theoretical reference for the treatment of viral infectious diseases.
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Calcineurina , Cálcio , Imunidade Inata , Vírus da Doença de Newcastle , Proteínas Serina-Treonina Quinases , Replicação Viral , Animais , Humanos , Calcineurina/metabolismo , Cálcio/metabolismo , Sinalização do Cálcio , Linhagem Celular , Células HEK293 , Interferon Tipo I/metabolismo , Interferon Tipo I/imunologia , Doença de Newcastle/imunologia , Doença de Newcastle/virologia , Doença de Newcastle/metabolismo , Vírus da Doença de Newcastle/imunologia , Fosforilação , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas Serina-Treonina Quinases/genéticaRESUMO
BACKGROUND: Machine learning is a potentially effective method for predicting the response to platinum-based treatment for ovarian cancer. However, the predictive performance of various machine learning methods and variables is still a matter of controversy and debate. OBJECTIVE: This study aims to systematically review relevant literature on the predictive value of machine learning for platinum-based chemotherapy responses in patients with ovarian cancer. METHODS: Following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, we systematically searched the PubMed, Embase, Web of Science, and Cochrane databases for relevant studies on predictive models for platinum-based therapies for the treatment of ovarian cancer published before April 26, 2023. The Prediction Model Risk of Bias Assessment tool was used to evaluate the risk of bias in the included articles. Concordance index (C-index), sensitivity, and specificity were used to evaluate the performance of the prediction models to investigate the predictive value of machine learning for platinum chemotherapy responses in patients with ovarian cancer. RESULTS: A total of 1749 articles were examined, and 19 of them involving 39 models were eligible for this study. The most commonly used modeling methods were logistic regression (16/39, 41%), Extreme Gradient Boosting (4/39, 10%), and support vector machine (4/39, 10%). The training cohort reported C-index in 39 predictive models, with a pooled value of 0.806; the validation cohort reported C-index in 12 predictive models, with a pooled value of 0.831. Support vector machine performed well in both the training and validation cohorts, with a C-index of 0.942 and 0.879, respectively. The pooled sensitivity was 0.890, and the pooled specificity was 0.790 in the training cohort. CONCLUSIONS: Machine learning can effectively predict how patients with ovarian cancer respond to platinum-based chemotherapy and may provide a reference for the development or updating of subsequent scoring systems.
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Neoplasias Ovarianas , Humanos , Feminino , Neoplasias Ovarianas/tratamento farmacológico , Bases de Dados Factuais , Aprendizado de Máquina , PubMed , Máquina de Vetores de SuporteRESUMO
Variable renewable energy (VRE) is the most promising form of primary generation under a carbon neutrality target due to its environmental benefits, incentive policy, and technological progress. However, the increasing proportion of VRE generation, such as solar and wind power, has sharply increased integration cost and reduced power grid stability. This study uses portfolio theory to investigate China's optimal power generation portfolio by 2050 considering flexibility constraint and system cost, including technical and integration costs. The results demonstrate that non-fossil-fuel power generation technologies have cost and emission reduction advantages over fossil-fuel-based technologies. VRE generation technologies must be developed in synergy with other forms of power generation when considering flexibility requirement and integration cost. A complete phase-out of fossil-fuel power generation technologies in China appears unlikely in the study period. Gas-fired and coal-fired power generation are the pillar forms of power generation to meet future flexibility needs.
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Carbono , Combustíveis Fósseis , Carbono/análise , Carvão Mineral , Vento , China , Dióxido de Carbono/análise , Centrais ElétricasRESUMO
BACKGROUND: Burnout is a common issue among medical professionals, and one of the well-studied predisposing factors is the Big Five personality traits. However, no studies have explored the relationships between these traits and burnout from a trait-to-component perspective. To understand the specific connections between each Big Five trait and burnout components, as well as the bridging effects of each trait on burnout, we employed network analysis. METHODS: A cluster sampling method was used to select a total of 420 Chinese medical personnel. The 15-item Chinese Big Five Personality Inventory-15 (CBF-PI-15) assessed the Big Five personality traits, while the 15-item Maslach Burnout Inventory-General Survey (MBI-GS) assessed burnout components. Network analysis was used to estimate network structure of Big Five personality traits and burnout components and calculate the bridge expected influence. RESULTS: The study revealed distinct and clear relationships between the Big Five personality traits and burnout components. For instance, Neuroticism was positively related to Doubt significance and Worthwhile, while Conscientiousness was negatively related to Accomplish all tasks. Among the Big Five traits, Neuroticism displayed the highest positive bridge expected influence, while Conscientiousness displayed the highest negative bridge expected influence. CONCLUSIONS: The network model provides a means to investigate the connections between the Big Five personality traits and burnout components among medical professionals. This study offers new avenues for thought and potential targets for burnout prevention and treatment in medical personnel, which can be further explored and tested in clinical settings.
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BACKGROUND: COVID-19 infection continues all over the world, causing serious physical and psychological impacts to patients. Patients with COVID-19 infection suffer from various negative emotional experiences such as anxiety, depression, mania, and alienation, which seriously affect their normal life and is detrimental to the prognosis. Our study is aimed to investigate the effect of psychological capital on alienation among patients with COVID-19 and the mediating role of social support in this relationship. METHODS: The data were collected in China by the convenient sampling. A sample of 259 COVID-19 patients completed the psychological capital, social support and social alienation scale and the structural equation model was adopted to verify the research hypotheses. RESULTS: Psychological capital was significantly and negatively related to the COVID-19 patients' social alienation (p < .01). And social support partially mediated the correlation between psychological capital and patients' social alienation (p < .01). CONCLUSION: Psychological capital is critical to predicting COVID-19 patients' social alienation. Social support plays an intermediary role and explains how psychological capital alleviates the sense of social alienation among patients with COVID-19 infection.
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COVID-19 , Capital Social , Isolamento Social , Apoio Social , COVID-19/psicologia , Humanos , China , Análise de Mediação , Modelos Psicológicos , Masculino , Feminino , Adulto , Pessoa de Meia-Idade , Reprodutibilidade dos Testes , Intervalos de ConfiançaRESUMO
With the increasing number of aged population and growing burden of healthy aging demands, a rational standard for evaluation aging is in urgent need. The advancement of medical testing technology and the prospering of artificial intelligence make it possible to evaluate the biological status of aging from a more comprehensive view. In this review, we introduced common aging biomarkers and concluded several famous aging clocks. Aging biomarkers reflect changes in the organism at a molecular or cellular level over time while aging clocks tend to be more of a generalization of the overall state of the organism. We expect to construct a framework for aging evaluation measurement from both micro and macro perspectives. Especially, population-specific aging clocks and multi-omics aging clocks may better fit the demands to evaluate aging in a comprehensive and multidimensional manner and make a detailed classification to represent different aging rates at tissue/organ levels. This framework will promisingly provide a crucial basis for disease diagnosis and intervention assessment in geroscience.
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Inteligência Artificial , Proteínas CLOCK , BiomarcadoresRESUMO
We numerically explored the enhanced performance and physical mechanism of semiconductor laser (SL) based reservoir computation (RC) with double optoelectronic feedback (DOEF). One-step and multistep Santa Fe time series predictions were used as standard test benchmarks in this work. We found that in the optimized parameter region the normalized mean square error (NMSE) of an SL-based RC under DOEF is smaller than an SL-based RC with single optoelectronic feedback (SOEF). In addition, the performance improvement is more obvious for multistep prediction, which is particularly suitable for more complex tasks that requires a higher memory capability (MC). The enriched node states (optical intensity of the virtual nodes for each sample) and the enhanced MC of the proposed DOEF were verified by a comparison to SOEF under the optimized feedback strength. The influence of the feedback strength and the delay difference on the NMSE and the MC was also investigated. Our study should be helpful in the design of a high-performance optoelectronic RC based on an SL.
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Objective: To investigate the application of atorvastatin (AT) combined with ezetimibe (EZ) in elderly patients with hypertension (HY) combined with type 2 diabetes mellitus (T2DM) and the significance analysis of changes in serum bilirubin levels during treatment. Methods: One hundred and twelve elderly patients with HY combined with T2DM admitted to our hospital from September 2019 to March 2022 were selected and divided into a control group (AT) and a combined group (AT + EZ) according to the random number table method, with 56 cases in each group. It revealed that blood glucose, lipid function, inflammatory factors, and serum bilirubin [(total bilirubin, direct bilirubin (DBIL), indirect bilirubin (IBIL))] were also compared in both groups. The combined group was divided into high and low expression groups according to the mean total bilirubin value, and the incidence of adverse reactions was compared between the two groups. Results: Glucose, lipid function, and inflammatory factors were lower in the combined group than in the control group (P < .05). Total bilirubin, DBIL, and IBIL were higher in the combined group than in the control group (P < .05). The total incidence of adverse reactions in the high expression group was significantly lower than that in the low expression group (12.50% vs. 28.57%, P < .05). Conclusion: AT combined with EZ can effectively improve glucose, lipids, inflammation and upregulate serum bilirubin in patients with HY combined with T2DM.
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Diabetes Mellitus Tipo 2 , Hipertensão , Humanos , Idoso , Atorvastatina/uso terapêutico , Diabetes Mellitus Tipo 2/tratamento farmacológico , Ezetimiba/uso terapêutico , Bilirrubina , Hipertensão/tratamento farmacológico , GlucoseRESUMO
BACKGROUND: Diabetes was commonly seen in chronic total occlusion (CTO) patients but data regarding the impact of successful percutaneous coronary intervention (PCI) on clinical outcome of CTO patients with diabetes was controversial. And importantly, no studies have compared quality of life (QOL) after CTO-PCI in patients with and without diabetes. METHODS: Consecutive patients undergoing elective CTO-PCI were prospectively enrolled from Apr. 2018 to May 2021. Patients were subdivided into 2 groups: Diabetes and No Diabetes. Detailed baseline characteristics, assessment of symptoms and QOL, angiographic and procedural details, in-hospital complications, and 1 month and 1 year follow-up data were collected. These data were analyzed accordingly for risk predictors of clinical outcome in patients who have diabetes and received successful CTO-PCI. RESULTS: A total of 1076 patients underwent CTO-PCI attempts. Diabetes was present in 374 (34.76%) patients, who had more hypertension, previous PCI and stroke. Regarding the coronary lesions, diabetic patients suffered more LCX lesion, multivessel disease, number of lesions per patient, blunt stump, calcification and higher J-CTO score (p < 0.05). In-hospital major adverse cardiac event (MACE) (4.13% vs. 5.35%; p = 0.362) was similar in the two groups. At 1 month and 1 year follow-up after successful CTO-PCI, the incidence of MACE and all-cause mortality were also similar in the two groups (p > 0.05). Number of lesions per patient was an independent risk factor of MACE and all-cause mortality (p < 0.001) 1 year after successful CTO-PCI. Symptom and QOL were markedly improved regardless of diabetes both at 1 month and 1 year follow-up, and importantly, patients with diabetes showed similar degrees of improvement to those without diabetes (P > 0.05). CONCLUSIONS: Successful CTO-PCI could represent an effective strategy improving clinical outcome, symptoms and QOL in CTO patients with diabetes.
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Oclusão Coronária , Diabetes Mellitus , Intervenção Coronária Percutânea , Humanos , Intervenção Coronária Percutânea/efeitos adversos , Oclusão Coronária/diagnóstico por imagem , Oclusão Coronária/cirurgia , Qualidade de Vida , Angiografia Coronária , Resultado do Tratamento , Fatores de Risco , Diabetes Mellitus/diagnóstico , Diabetes Mellitus/epidemiologia , Diabetes Mellitus/etiologia , Doença Crônica , Sistema de RegistrosRESUMO
A regional healthcare coalition enables its member hospitals to conduct an integrated emergency supply management, which is seldom addressed in the existing literature. In this work, we propose a two-stage stochastic emergency supply planning model to facilitate cooperation and coordination in a regional healthcare coalition. Our model integrates pre-disaster emergency supplies pre-positioning and post-disaster emergency supplies transshipment and procurement and considers two planning goals, i.e., minimizing the expected total cost and the maximum supply shortage rate. With some comparison models and a case study on the West China Hospital coalition of Sichuan Province, China, under the background of the COVID-19 epidemic, we demonstrate the effectiveness and benefits of our model and obtain various managerial insights and policy suggestions for practice. We highlight the importance of conducting integrated management of emergency supplies pre-positioning, transshipment and procurement in the regional healthcare coalition for better preparation and responding to future potential disasters.
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BACKGROUND: Cervical cancer continues to be one of the leading causes of cancer deaths among females in low and middle-income countries. In this study, we aimed to assess the independent prognostic value of clinical and potential prognostic factors in progression-free survival (PFS) in cervical cancer. METHODS: We conducted a retrospective study on 92 cervical cancer patients treated from 2017 to 2019 at the Zhuhai Hospital of Traditional Chinese and Western Medicine. Tumor characteristics, treatment options, progression-free survival and follow-up information were collected. Kaplan-Meier method was used to assess the PFS. RESULTS: Results showed that the number of retrieved lymph nodes had a statistically significant effect on PFS of cervical cancer patients (P = 0.002). Kaplan-Meier survival curve analysis showed that cervical cancer patients with initial symptoms age 25-39 had worse survival prognoses (P = 0.020). And the using of uterine manipulator in laparoscopic treatment showed a better prognosis (P < 0.001). A novel discovery of our study was to verify the prognostic values of retrieved lymph nodes count combining with FIGO staging system, which had never been investigated in cervical cancer before. According to the Kaplan-Meier survival curve analysis and receiver operating characteristic (ROC) curve analysis, significant improvements were found after the combination of retrieved lymph nodes count and FIGO stage in predicting PFS for cervical cancer patients (P < 0.001, AUC = 0.826, 95% CI: 0.689-0.962). CONCLUSION: Number of retrieved lymph nodes, initial symptoms age, uterine manipulator, and retrieved lymph nodes count combining with FIGO staging system could be potential prognostic factors for cervical cancer patients.
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Neoplasias do Colo do Útero/mortalidade , Adulto , Idoso , Feminino , Humanos , Excisão de Linfonodo , Pessoa de Meia-Idade , Estadiamento de Neoplasias , Prognóstico , Estudos Retrospectivos , Neoplasias do Colo do Útero/patologiaRESUMO
Liquid chromatography-mass spectrometry (LC-MS)-based proteomics approaches have been widely used to identify residual host-cell proteins (HCPs) in support of process and product characterization for protein therapeutics. Particularly, these methods can provide a general and unbiased approach for the detection of HCPs and may generate critical information on HCPs that are outside the coverage provided by a conventional immunoassay. A significant technical hurdle for HCP analysis is the overwhelmingly large background of biotherapeutic that obscures HCP detection and quantification. In this work, we developed a method that relies on hydrophilic interaction chromatography (HILIC) for HCP enrichment followed by in situ concentration and digestion prior to LC-MS analysis. This approach has enabled detection of HCPs in a drug substance that were not observed in other conventional flow rate LC-MS strategies. For example, 28% of HCPs identified in NISTmAb (20 out of 71) were not previously published or identified by established methods such as the native digestion technique. For an IgG1 protein spiked with 1000 ppm HCP standards, we detected 83 HCPs, 61 out of which were not identified by the native digestion method. Similar improvement in performance was demonstrated for an Fc-fusion protein therapeutic. Our method can be readily implemented in most protein mass spectrometry laboratories to support process development for protein therapeutics.
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Cromatografia Líquida/métodos , Proteínas/química , Proteínas/uso terapêutico , Animais , Anticorpos Monoclonais , Anticorpos Monoclonais Humanizados , Células CHO , Cricetulus , Imunoglobulina G/química , Espectrometria de Massas em Tandem/métodos , Tripsina/metabolismoRESUMO
BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNAs that play important roles by regulating other genes. Rosa rugosa Thunb. is an important ornamental and edible plant, yet there are only a few studies on the miRNAs and their functions in R. rugosa. RESULTS: We sequenced 10 samll RNA profiles from the roots, petals, pollens, stamens, and leaves and 4 RNA-seq profiles in leaves and petals to analysis miRNA, phasiRNAs and mRNAs in R. rugosa. In addition, we acquired a degradome sequencing profile from leaf of R. rugosa to identify miRNA and phasiRNA targets using the SeqTar algorithm. We have identified 321 conserved miRNA homologs including primary transcripts for 25 conserved miRNAs, and 22 novel miRNAs. We identified 592 putative targets of the conserved miRNAs or tasiRNAs that showed significant accumulations of degradome reads. We found differential expression patterns of conserved miRNAs in five different tissues of R. rugosa. We identified three hundred and thirty nine 21 nucleotide (nt) PHAS loci, and forty nine 24 nt PHAS loci, respectively. Our results suggest that miR482 triggers generations of phasiRNAs by targeting nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes in R. rugosa. Our results also suggest that the deregulated genes in leaves and petals are significantly enriched in GO terms and KEGG pathways related to metabolic processes and photosynthesis. CONCLUSIONS: These results significantly enhanced our knowledge of the miRNAs and phasiRNAs, as well as their potential functions, in R. rugosa.
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Sequenciamento de Nucleotídeos em Larga Escala/métodos , MicroRNAs/genética , Proteínas de Plantas/genética , RNA de Plantas/genética , RNA Interferente Pequeno/genética , Rosa/genética , Biologia Computacional , Regulação da Expressão Gênica de Plantas , Folhas de Planta/genéticaRESUMO
BACKGROUND: MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. However, the watermelon miRNAs and phasiRNAs and their functions are not well explored. RESULTS: Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, petals, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed using the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 127 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. CONCLUSIONS: The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.
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Citrullus/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , MicroRNAs/genética , RNA Interferente Pequeno/genética , Análise de Sequência de RNA/métodos , Biologia Computacional , Flores/genética , Frutas/genética , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Folhas de Planta/genética , RNA de Plantas/genéticaRESUMO
BACKGROUND: Alfalfa (Medicago sativa L.) is a forage legume with significant agricultural value worldwide. MicroRNAs (miRNAs) are key components of post-transcriptional gene regulation and essentially regulate many aspects of plant growth and development. Although miRNAs were reported in alfalfa, their expression profiles in different tissues and the discovery of novel miRNAs as well as their targets have not been described in this plant species. RESULTS: To identify tissue-specific miRNA profiles in whole plants, shoots and roots of three different alfalfa genotypes (Altet-4, NECS-141and NF08ALF06) were used. Small RNA libraries were generated and sequenced using a high-throughput sequencing platform. Analysis of these libraries enabled identification of100 miRNA families; 21 of them belong to the highly conserved families while the remaining 79 families are conserved at the minimum between M. sativa and the model legume and close relative, M. truncatula. The profiles of the six abundantly expressed miRNA families (miR156, miR159, miR166, miR319, miR396 and miR398) were relatively similar between the whole plants, roots and shoots of these three alfalfa genotypes. In contrast, robust differences between shoots and roots for miR160 and miR408 levels were evident, and their expression was more abundant in the shoots. Additionally, 17 novel miRNAs were identified and the relative abundance of some of these differed between tissue types. Further, the generation and analysis of degradome libraries from the three alfalfa genotypes enabled confirmation of 69 genes as targets for 31 miRNA families in alfalfa. CONCLUSIONS: The miRNA profiles revealed both similarities and differences in the expression profiles between tissues within a genotype as well as between the genotypes. Among the highly conserved miRNA families, miR166 was the most abundantly expressed in almost all tissues from the three genotypes. The identification of conserved and novel miRNAs as well as their targets in different tissues of multiple genotypes increased our understanding of miRNA-mediated gene regulation in alfalfa and could provide valuable insights for practical research and plant improvement applications in alfalfa and related legume species.
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Genótipo , Medicago sativa/genética , MicroRNAs/genética , Sequência de Bases , Perfilação da Expressão Gênica , Biblioteca Gênica , Variação Genética , Anotação de Sequência Molecular , Especificidade de Órgãos , RNA de Plantas/genéticaRESUMO
BACKGROUND: Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), an important traditional Chinese herbal medicinal plant species. METHODS: Here we performed a genome-wide discovery of phasiRNAs and its host PHAS loci in P. notoginseng by analyzing small RNA sequencing profiles. Degradome sequencing profile was used to identify the trigger miRNAs of these phasiRNAs and potential targets of phasiRNAs. We also used RLM 5'-RACE to validate some of the identified phasiRNA targets. RESULTS: After analyzing 24 small RNA sequencing profiles of P. notoginseng, 204 and 90 PHAS loci that encoded 21 and 24 nucleotide (nt) phasiRNAs, respectively, were identified. Furthermore, we found that phasiRNAs produced from some pentatricopeptide repeat-contain (PPR) genes target another layer of PPR genes as validated by both the degradome sequencing profile and RLM 5'-RACE analysis. We also found that miR171 with 21 nt triggers the generations of 21 nt phasiRNAs from its conserved targets. CONCLUSIONS: We validated that some phasiRNAs generated from PPRs and TASL genes are functional by targeting other PPRs in trans. These results provide the first set of PHAS loci and phasiRNAs in P. notoginseng, and enhance our understanding of PHAS in plants.
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Genoma de Planta , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Panax notoginseng/genética , Proteínas de Plantas/genética , RNA Interferente Pequeno/genética , Análise de Sequência de RNA/métodos , Regulação da Expressão Gênica de Plantas , RNA Interferente Pequeno/classificaçãoRESUMO
Mutation of PKD1, encoding the protein polycystin-1 (PC1), is the main cause of autosomal dominant polycystic kidney disease (ADPKD). The signaling pathways downstream of PC1 in ADPKD are still not fully understood. Here, we provide genetic evidence for the necessity of Gα12 (encoded by Gna12, hereafter Gα12) for renal cystogenesis induced by Pkd1 knockout. There was no phenotype in mice with deletion of Gα12 (Gα12-/-). Polyinosine-polycytosine (pI:pC)-induced deletion of Pkd1 (Mx1Cre+Pkd1f/fGα12+/+) in 1-week-old mice resulted in multiple kidney cysts by 9â weeks, but the mice with double knockout of Pkd1 and Gα12 (Mx1Cre+Pkd1f/fGα12-/-) had no structural and functional abnormalities in the kidneys. These mice could survive more than one year without kidney abnormalities except multiple hepatic cysts in some mice, which indicates that the effect of Gα12 on cystogenesis is kidney specific. Furthermore, Pkd1 knockout promoted Gα12 activation, which subsequently decreased cell-matrix and cell-cell adhesion by affecting the function of focal adhesion and E-cadherin, respectively. Our results demonstrate that Gα12 is required for the development of kidney cysts induced by Pkd1 mutation in mouse ADPKD.