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1.
Food Chem ; 334: 127567, 2021 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-32707362

RESUMEN

Fruit acidity is an important determinant of peach organoleptic quality, but its regulatory mechanism remains elusive. Measurement of organic acids in ripe fruits of seventy-five peach cultivars revealed the predominant components malate and citrate, accompanied by quinate. Organic acid accumulation increased at early stages of fruit growth, but exhibited a more dramatic reduction in low-acid cultivar during later stages of fruit development compared to high-acid cultivars. Low-acid cultivars showed citrate degradation and less transport of malate into the vacuole due to up- and down-regulation of a GABA pathway gene GAD and a malate transporter gene ALMT9, respectively. The NAD-MDH1 gene might control the rate-limiting step in malate synthesis, while three genes, PDK, PK, and ADH, could affect citrate synthesis through the pyruvate-to-acetyl-CoA-to-citrate pathway. Altogether, these results suggested that malate accumulation is controlled at the level of metabolism and vacuolar storage, while metabolism is crucial for citrate accumulation in peach.


Asunto(s)
Ácidos Carboxílicos/metabolismo , Frutas/metabolismo , Malatos/metabolismo , Proteínas de Plantas/genética , Prunus persica/metabolismo , Acetilcoenzima A/metabolismo , Ácido Cítrico/metabolismo , Frutas/genética , Frutas/crecimiento & desarrollo , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Proteínas de Plantas/metabolismo , Prunus persica/genética , Prunus persica/crecimiento & desarrollo , Ácido Pirúvico/metabolismo , Vacuolas/metabolismo
2.
Gene ; 766: 145142, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32911027

RESUMEN

Rootstocks are among the primary factors that influence fruit yield and quality as well as melon development. To understand the differences in the molecular mechanisms and gene expression networks of fruit development between grafted and nongrafted plants in oriental melon, we performed a comprehensive analysis of the transcriptome and proteome dynamic gene/protein expression profiles during fruit development in oriental melon (Cucumis melo L. var. makuwa). Using pairwise comparisons between grafted and nongrafted samples by transcriptome analysis, we identified a large number of candidate genes involved in hormonal signaling pathways, transcription factors, resistance-related biosynthetic pathways and photosynthesis-related metabolic pathways. Many transcription factor-encoded genes were significantly more strongly expressed in the grafted samples, for example, AP2/ERF, C2H2, MYB, bHLH, and AUX/IAA, which are well-known participants in the regulation of developmental processes and hormonal signaling metabolism. Some differentially expressed genes (DEGs) were enriched in flavonoid biosynthesis and phenylpropanoid biosynthesis and determined plant resistance. In addition, some differentially expressed proteins (DEPs) were enriched in photosynthesis-related pathways, which could improve fruit quality and yield. Moreover, through weighted gene coexpression network analyses, we identified modules of coexpressed genes and hub genes specifically related to grafting for different fruit developmental stages. The results suggested that graft-related modules and hub genes were primarily associated with photosynthate metabolism and hormonal signaling pathways. The results obtained in this study provide a valuable resource for dissecting the role of candidate genes governing graft-related metabolism in oriental melon fruit, suggesting an interesting correlation with the effects of rootstock on fruit development.


Asunto(s)
Cucumis melo/genética , Cucurbitaceae/crecimiento & desarrollo , Cucurbitaceae/genética , Frutas/crecimiento & desarrollo , Frutas/genética , Regulación de la Expresión Génica de las Plantas/genética , Perfilación de la Expresión Génica/métodos , Redes Reguladoras de Genes/genética , Fotosíntesis/genética , Raíces de Plantas/genética , RNA-Seq/métodos , Transducción de Señal/genética , Transcriptoma/genética
3.
Gene ; 764: 145094, 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-32860898

RESUMEN

Long chain acyl-CoA synthetases (ACSLs), which drive the conversion of long chain fatty acid into acyl-CoA, an ingredient of lipid synthesis, have been well-acknowledged to exert an indispensable role in many metabolic processes in mammals, especially lipid metabolism. However, in chicken, the evolutionary characteristics, expression profiles and regulatory mechanisms of ACSL gene family are rarely understood. Here, we analyzed the genomic synteny, gene structure, evolutionary event and functional domains of the ACSL gene family members using bioinformatics methods. The spatiotemporal expression profiles of ACSL gene family, and their regulatory mechanism were investigated via bioinformatics analysis incorporated with in vivo and in vitro estrogen-treated experiments. Our results indicated that ACSL2 gene was indeed evolutionarily lost in the genome of chicken. Chicken ACSLs shared an AMP-binding functional domain, as well as highly conversed ATP/AMP and FACS signature motifs, and were clustered into two clades, ACSL1/5/6 and ACSL3/4, based on high sequence similarity, similar gene features and conversed motifs. Chicken ACSLs showed differential tissue expression distributions, wherein the significantly decreased expression level of ACSL1 and the significantly increased expression level of ACSL5 were found, respectively, the expression levels of the other ACSL members remained unchanged in the liver of peak-laying hens versus pre-laying hens. Moreover, the transcription activity of ACSL1, ACSL3 and ACSL4 was silenced and ACSL6 was activated by estrogen, but no response to ACSL5. In conclusion, though having highly conversed functional domains, chicken ACSL gene family is organized into two separate groups, ACSL1/5/6 and ACSL3/4, and exhibits varying expression profiles and estrogen effects. These results not only pave the way for better understanding the specific functions of ACSL genes in avian lipid metabolism, but also provide a valuable evidence for gene family characteristics.


Asunto(s)
Pollos/genética , Coenzima A Ligasas/genética , Evolución Molecular , Metabolismo de los Lípidos/genética , Familia de Multigenes/genética , Acilcoenzima A/metabolismo , Animales , Células Cultivadas , Embrión de Pollo , Pollos/crecimiento & desarrollo , Pollos/metabolismo , Coenzima A Ligasas/metabolismo , Biología Computacional , Estrógenos/metabolismo , Ácidos Grasos/metabolismo , Femenino , Perfilación de la Expresión Génica , Regulación del Desarrollo de la Expresión Génica , Hepatocitos , Cultivo Primario de Células , Dominios Proteicos/genética , Análisis Espacio-Temporal , Sintenía
4.
Gene ; 764: 145105, 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-32882333

RESUMEN

Sarcoma (SARC) represents a group of highly histological and molecular heterogeneous rare malignant tumors with poor prognosis. There are few proposed classifiers for predicting patient's outcome. The Cancer Proteome Atlas (TPCA) and The Cancer Genome Atlas (TCGA) databases provide multi-omics datasets that enable a comprehensive investigation for this disease. The proteomic expression profile of SARC patients along with the clinical information was downloaded. 55 proteins were found to be associated with overall survival (OS) of patients using univariate Cox regression analysis. We developed a prognostic risk signature that comprises seven proteins (AMPKALPHA, CHK1, S6, ARID1A, RBM15, ACETYLATUBULINLYS40, and MSH6) with robust predictive performance using multivariate Cox stepwise regression analysis. Additionally, the signature could be an independent prognostic predictor after adjusting for clinicopathological parameters. Patients in high-risk group also have worse progression free intervals (PFI) than that of patients in low-risk group, but not for disease free intervals (DFI). The signature was validated using transcriptomic profile of SARC patients from TCGA. Potential mechanisms between high- and low-risk groups were identified using differentially expressed genes (DEGs) analysis. These DEGs were primarily enriched in RAS and MPAK signaling pathways. The signature protein molecules are candidate biomarkers for SARC, and the analysis of computational biology in tumor infiltrating lymphocytes and immune checkpoint molecules revealed distinctly immune landscapes of high- and low-risk patients. Together, we constructed a prognostic signature for predicting outcomes for SARC integrating proteomic and transcriptomic profiles, this might have value in guiding clinical practice.


Asunto(s)
Biomarcadores de Tumor/genética , Regulación Neoplásica de la Expresión Génica/inmunología , Pruebas Genéticas/métodos , Sarcoma/mortalidad , Microambiente Tumoral/inmunología , Antineoplásicos Inmunológicos/farmacología , Antineoplásicos Inmunológicos/uso terapéutico , Antígeno B7-H1/antagonistas & inhibidores , Antígeno B7-H1/genética , Antígeno B7-H1/inmunología , Antígeno CTLA-4/antagonistas & inhibidores , Antígeno CTLA-4/genética , Antígeno CTLA-4/inmunología , Conjuntos de Datos como Asunto , Femenino , Estudios de Seguimiento , Perfilación de la Expresión Génica , Humanos , Estimación de Kaplan-Meier , Linfocitos Infiltrantes de Tumor/inmunología , Linfocitos Infiltrantes de Tumor/metabolismo , Masculino , Persona de Mediana Edad , Valor Predictivo de las Pruebas , Pronóstico , Receptor de Muerte Celular Programada 1/antagonistas & inhibidores , Receptor de Muerte Celular Programada 1/genética , Receptor de Muerte Celular Programada 1/inmunología , Supervivencia sin Progresión , Mapeo de Interacción de Proteínas , Proteómica , Curva ROC , Sarcoma/tratamiento farmacológico , Sarcoma/genética , Sarcoma/inmunología , Transcriptoma/genética , Microambiente Tumoral/efectos de los fármacos , Microambiente Tumoral/genética
5.
Chemosphere ; 262: 127891, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32799150

RESUMEN

Fluoride generally exists in the natural environment, and has been reported to induce serious environmental hazard to animals, plants, and even humans via ecological cycle. Silkworm, Bombyx mori, which showed significant growth and reproductivity reduction when exposed to fluoride, has become a model to evaluate the toxicity of fluoride. However, the detailed mechanism underlying fluoride toxicity and corresponding transport proteins remain unclear. In this study, we performed RNA-seq of the larval midgut and fat body with fluoride exposure and normal treatment. Differential analysis showed that there were 4405 differentially expressed genes in fat body and 4430 DEGs in midgut with fluoride stress. By Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, we identified several key pathways involved in the fluoride exposure and poisoning. We focused on the oxidative phosphorylation and MAPK signal pathway. QRT-PCR confirmed that oxidative phosphorylation process was remarkably inhibited by fluoride exposure and resulted in the blocking of ATP synthesis. The MAPK signal pathway was stimulated via phosphorylation signal transduction. Moreover, by protein structure analysis combined with the DEGs, we screen 36 potential membrane proteins which might take part in transporting fluoride. Taken together, the results of our study expanded the underlying mechanisms of fluoride poisoning on silkworm larval growth and development, and implied potential fluoride transport proteins in silkworm.


Asunto(s)
Bombyx/fisiología , Fluoruros/toxicidad , Sustancias Peligrosas/toxicidad , Tejido Adiposo/metabolismo , Animales , Bombyx/metabolismo , Sistema Digestivo/metabolismo , Cuerpo Adiposo/metabolismo , Perfilación de la Expresión Génica/métodos , Inactivación Metabólica , Larva/genética , Transcriptoma/fisiología
6.
Sci Total Environ ; 752: 142172, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-33207499

RESUMEN

The biotic enzymatic reduction of mercury II [Hg(II)] to elemental Hg [Hg(0)] is an important pathway for Hg detoxification in natural ecosystems. However, the mechanisms of Hg(II) volatilization and resistance in fungi have not been understood completely. In the present study, we investigated the mechanisms of Hg(II) volatilization and resistance in the fungus Lecythophora sp. DC-F1. Hg(II) volatilization occurred during the investigation via the reduction of Hg(II) to Hg(0) in DC-F1. Comparative transcriptome analyses of DC-F1 revealed 3439 differentially expressed genes under 10 mg/L Hg(II) stress, among which 2770 were up-regulated and 669 were down-regulated. Functional enrichment analyses of genes and pathways further suggested that the Hg(II) resistance of DC-F1 is a multisystem collaborative process with three important transcriptional responses to Hg(II) stress: a mer-mediated Hg detoxification system, a thiol compound metabolism, and a cell reactive oxygen species stress response system. The phylogenetic analysis of merA protein homologs suggests that the Hg(II) reduction by merA is widely distributed in fungi. Overall, this study provides evidence for the reduction of Hg(II) to Hg(0) in fungi via the mer-mediated Hg detoxification system and offers a comprehensive explanation for its role within Hg biogeochemical cycling. These findings offer a strong theoretical basis for the application of fungi in the bioremediation of Hg-contaminated envionments.


Asunto(s)
Mercurio , Ecosistema , Hongos , Perfilación de la Expresión Génica , Filogenia , Transcriptoma , Volatilización
7.
Gene ; 766: 145077, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32941951

RESUMEN

Newcastle disease virus (NDV) is a contagious poultry paramyxovirus, leading to substantial economic losses to the poultry industry. Here, RNA-seq was carried out to investigate the altered expression of immune-related genes in chicken thymus within 96 h in response to NDV infection. In NDV-infected chicken thymus tissues, comparative transcriptome analysis revealed 1386 differentially expressed genes (DEGs) at 24 h with 989 up- and 397 down-regulated genes, 728 DEGs at 48 h with 567 up- and 161 down-regulated genes, 1514 DEGs at 72 h with 1016 up- and 498 down-regulated genes, and 1196 DEGs at 96 h with 522 up- and 674 down-regulated genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these candidate targets mainly participate in biological processes or biochemical, metabolic and signal transduction processes. Notably, there is large enrichment in biological processes, cell components and metabolic processes, which may be related to NDV pathogenicity. In addition, the expression of five immune-related DEGs identified by RNA-seq was validated by quantitative real-time polymerase chain reaction (qRT-PCR). Our results indicated that the expression levels of AvBD5, IL16, IL22 and IL18R1 were obviously up-regulated, and Il-18 expression was also changed, but not significantly, which play key roles in the defense against NDV. Overall, we identified several candidate targets that may be involved in the regulation of NDV infection, which provide new insights into the complicated regulatory mechanisms of virus-host interactions, and explore new strategies for protecting chickens against the virus.


Asunto(s)
Pollos/genética , Pollos/inmunología , Enfermedad de Newcastle/genética , Enfermedad de Newcastle/inmunología , Virus de la Enfermedad de Newcastle/inmunología , Transcriptoma/genética , Vacunas Virales/inmunología , Animales , Pollos/virología , Regulación hacia Abajo/inmunología , Perfilación de la Expresión Génica/métodos , Enfermedad de Newcastle/virología , Enfermedades de las Aves de Corral/genética , Enfermedades de las Aves de Corral/inmunología , Enfermedades de las Aves de Corral/virología , Análisis de Secuencia de ARN/métodos , Transcriptoma/inmunología , Regulación hacia Arriba/inmunología
8.
Gene ; 766: 145119, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32946928

RESUMEN

BACKGROUND: Cervical cancer is the fourth most commonly diagnosed cancer in women worldwide. The metastasis and invasion of this type of cancer are closely related to the tumor microenvironment. Immune cells and stromal cells dominate the tumor microenvironment in cervical cancer. Therefore, we should further investigate the complex interplay between the tumor progression with immune cells or stromal cells. METHODS: We downloaded the gene expression profiles and clinical data of 307 patients with cervical cancers based on the TCGA database. Subsequently, the Estimation of Stromal and Immune cells in Malignant Tumours using Expression data (ESTIMATE) algorithm was used to calculate the scores of stromal cells and immune cells in order to uncover differential expressed genes, and we analyzed the correlation between their scores and patient survival. Then the Cell type Identification By Estimating Relative Subsets Of known RNA Transcripts (CIBERSORT) deconvolution algorithm was applied to quantify the fraction and infiltration of 22 types of immune cells in cervical cancer. Moreover, we also used R language packs and network tools to analyze GO term, gene enrichment pathway, and protein-protein relationship to trace down genes related to inflammation and immune regulation. RESULTS: The gene expression profiles and corresponding clinical data of 307 patients were obtained from TCGA database. The results showed that the scores were statistically significant between the high immunescore group and the low immunescore group. And the low immunescore group had shorter survival period than the high scores group (P = 0.035). Among the 22 types of immune cells, only T cells and mast cells were significantly related to the survival rate of cervical cancer patients. Moreover, PPI network analysis revealed that CCR5 and CXCL9, -10, -11/CXCR3 axis might be a new target for cervical cancer treatment. Finally, Kaplan-Meier survival curves found outnine representative genes significantly related to survival rate including BTNL8, CCR7, CD1E, CD6, CD27, CD79A, GRAP2, SP1B, LY9. CONCLUSIONS: These genes can be used as markers for the prognosis and diagnosis of cervical cancer and also might be used as treatment targets.


Asunto(s)
Regulación Neoplásica de la Expresión Génica/genética , Transcriptoma/genética , Microambiente Tumoral/genética , Neoplasias del Cuello Uterino/genética , Adulto , Biomarcadores de Tumor/genética , Manejo de Datos , Femenino , Perfilación de la Expresión Génica/métodos , Humanos , Estimación de Kaplan-Meier , Persona de Mediana Edad , Pronóstico , Mapas de Interacción de Proteínas/genética , Células del Estroma/patología , Neoplasias del Cuello Uterino/patología , Adulto Joven
9.
Gene ; 766: 145156, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32949696

RESUMEN

Plant Glycogen Synthase Kinase 3 (GSK3)/SHAGGY-like kinase (GSK) proteins play important roles in modulating growth, development, and stress responses in several plant species. However, little is known about the members of the potato GSK (StGSK) family. Here, nine StGSK genes were identified and phylogenetically grouped into four clades. Gene duplication analysis revealed that segmental duplication contributed to the expansion of the StGSK family. Gene structure and motif pattern analyses indicated that similar exon/intron and motif organizations were found in StGSKs from the same clade. Conserved motif and kinase activity analyses indicated that the StGSKs encode active protein kinases, and they were shown to be distributed throughout whole cells. Cis-acting regulatory element analysis revealed the presence of many growth-, hormone-, and stress-responsive elements within the promoter regions of the StGSKs, which is consistent with their expression in different organs, and their altered expression in response to hormone and stress treatments. Association network analysis indicated that various proteins, including two confirmed BES1 family transcription factors, potentially interact with StGSKs. Overexpression of StSK21 provides enhanced sensitivity to salt stress in Arabidopsis thaliana plants. Overall, these results reveal that StGSK proteins are active protein kinases with purported functions in regulating growth, development, and stress responses.


Asunto(s)
Regulación de la Expresión Génica de las Plantas/genética , Genes de Plantas/genética , Familia de Multigenes/genética , Proteínas de Plantas/genética , Estrés Salino/genética , Solanum tuberosum/genética , Estrés Fisiológico/genética , Arabidopsis/genética , Cromosomas de las Plantas/genética , Duplicación de Gen/genética , Perfilación de la Expresión Génica/métodos , Estudio de Asociación del Genoma Completo/métodos , Filogenia , Reguladores del Crecimiento de las Plantas/genética , Factores de Transcripción/genética
10.
Gene ; 766: 145157, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32949697

RESUMEN

Glycolytic potential (GP) calculated based on glucose, glycogen, glucose-6-phosphate, and lactate contents is a critical factor for multiple meat quality characteristics. However, the genetic basis of glycolytic metabolism is still unclear. In this study, we constructed six RNA-Seq libraries using longissimus dorsi (LD) muscles from pigs divergent for GP phenotypic values and generated the whole genome-wide gene expression profiles. Furthermore, we identified 25,880 known and 220 novel genes from these skeletal muscle libraries, and 222 differentially expressed genes (DEGs) between the higher and lower GP groups. Notably, we found that the Lactate dehydrogenase B (LDHB) and Fructose-2, 6-biphosphatase 3 (PFKFB3) expression levels were higher in the higher GP group than the lower GP group, and positively correlated with GP and lactic acid (LA), and reversely correlated with pH value at 45 min postmortem (pH45min). Besides, LDHB and PFKFB3 expression were positively correlated with drip loss measured at 48 h postmortem (DL48h) and drip loss measured at 24 h postmortem (DL24h). Collectively, we identified a serial of DEGs as the potential key candidate genes affecting GP and found that LDHB and PFKFB3 are closely related to GP and GP-related traits. Our results lay a solid basis for in-depth studies of the regulatory mechanisms on GP and GP-related traits in pigs.


Asunto(s)
Glucólisis/genética , Músculo Esquelético/metabolismo , Porcinos/genética , Transcriptoma/genética , Animales , Perfilación de la Expresión Génica/métodos , Glucosa/genética , Glucógeno/genética , Isoenzimas/genética , L-Lactato Deshidrogenasa/genética , Ácido Láctico/metabolismo , Carne , Fenotipo , Fosfofructoquinasa-2/genética , Porcinos/metabolismo
11.
Nat Commun ; 11(1): 5541, 2020 11 02.
Artículo en Inglés | MEDLINE | ID: mdl-33139723

RESUMEN

The bacterium Neisseria meningitidis causes life-threatening meningitis and sepsis. Here, we construct a complete collection of defined mutants in protein-coding genes of this organism, identifying all genes that are essential under laboratory conditions. The collection, named NeMeSys 2.0, consists of individual mutants in 1584 non-essential genes. We identify 391 essential genes, which are associated with basic functions such as expression and preservation of genome information, cell membrane structure and function, and metabolism. We use this collection to shed light on the functions of diverse genes, including a gene encoding a member of a previously unrecognised class of histidinol-phosphatases; a set of 20 genes required for type IV pili function; and several conditionally essential genes encoding antitoxins and/or immunity proteins. We expect that NeMeSys 2.0 will facilitate the phenotypic profiling of a major human bacterial pathogen.


Asunto(s)
Genes Bacterianos/genética , Genes Esenciales/genética , Mutación , Neisseria meningitidis/genética , Neisseria meningitidis/metabolismo , Fenotipo , Proteínas Bacterianas/metabolismo , Biología Computacional , Proteínas Fimbrias/genética , Proteínas Fimbrias/metabolismo , Fimbrias Bacterianas/genética , Fimbrias Bacterianas/metabolismo , Perfilación de la Expresión Génica , Regulación Bacteriana de la Expresión Génica , Genoma Bacteriano , Humanos , Neisseria meningitidis/patogenicidad
12.
Nat Commun ; 11(1): 5660, 2020 11 09.
Artículo en Inglés | MEDLINE | ID: mdl-33168830

RESUMEN

Human endogenous retroviruses (HERV) form a substantial part of the human genome, but mostly remain transcriptionally silent under strict epigenetic regulation, yet can potentially be reactivated by malignant transformation or epigenetic therapies. Here, we evaluate the potential for T cell recognition of HERV elements in myeloid malignancies by mapping transcribed HERV genes and generating a library of 1169 potential antigenic HERV-derived peptides predicted for presentation by 4 HLA class I molecules. Using DNA barcode-labeled MHC-I multimers, we find CD8+ T cell populations recognizing 29 HERV-derived peptides representing 18 different HERV loci, of which HERVH-5, HERVW-1, and HERVE-3 have more profound responses; such HERV-specific T cells are present in 17 of the 34 patients, but less frequently in healthy donors. Transcriptomic analyses reveal enhanced transcription of the HERVs in patients; meanwhile DNA-demethylating therapy causes a small and heterogeneous enhancement in HERV transcription without altering T cell recognition. Our study thus uncovers T cell recognition of HERVs in myeloid malignancies, thereby implicating HERVs as potential targets for immunotherapeutic therapies.


Asunto(s)
Retrovirus Endógenos/genética , Neoplasias Hematológicas/virología , Linfocitos T/metabolismo , Linfocitos T/virología , Linfocitos T CD8-positivos , Epigénesis Genética , Epítopos de Linfocito T , Perfilación de la Expresión Génica , Neoplasias Hematológicas/genética , Neoplasias Hematológicas/terapia , Humanos , Inmunoterapia , Monitorización Inmunológica , Células Mieloides , Neoplasias
13.
Zhongguo Zhong Yao Za Zhi ; 45(19): 4606-4616, 2020 Oct.
Artículo en Chino | MEDLINE | ID: mdl-33164424

RESUMEN

Prunus mume "Langmei" is a relict tree species, which fruit has good medicinal value. To understand the biosynthesis pathway of citric acid, the Illumina HiSeq XTen high-throughput sequencing technology was used to get the transcriptome from "Langmei". A total of 38 936 unigenes were obtained by assembling the fruit transcripts, of which 28 311 unigenes were successfully annotated in public databases, 15 193 unigenes were mapped to 265 KEGG metabolic pathways, and 18 908 unigenes were classified into 59 GO functional subclasses, 103 unigenes encoding 15 key enzymes involved in citric acid synthesis pathway were identified and analyzed. The structural model of citrate synthetase in "Langmei" showed that it was a homodimer and the secondary structure of each monomer was mainly composed of alpha helixes. Moreover, the residues in the active site of the citrate synthetase were highly conserved. This study provides a valuable resource for identifying candidate genes involved in the citric acid biosynthesis pathway, and will promote the development and sustainable utilization of genetic resources of "Langmei".


Asunto(s)
Ácido Cítrico , Frutas , Frutas/genética , Perfilación de la Expresión Génica , Secuenciación de Nucleótidos de Alto Rendimiento , Transcriptoma
14.
J Transl Med ; 18(1): 408, 2020 10 31.
Artículo en Inglés | MEDLINE | ID: mdl-33129318

RESUMEN

COronaVIrus Disease 19 (COVID-19) is caused by the infection of the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2). Although the main clinical manifestations of COVID-19 are respiratory, many patients also display acute myocardial injury and chronic damage to the cardiovascular system. Understanding both direct and indirect damage caused to the heart and the vascular system by SARS-CoV-2 infection is necessary to identify optimal clinical care strategies. The homeostasis of the cardiovascular system requires a tight regulation of the gene expression, which is controlled by multiple types of RNA molecules, including RNA encoding proteins (messenger RNAs) (mRNAs) and those lacking protein-coding potential, the noncoding-RNAs. In the last few years, dysregulation of noncoding-RNAs has emerged as a crucial component in the pathophysiology of virtually all cardiovascular diseases. Here we will discuss the potential role of noncoding RNAs in COVID-19 disease mechanisms and their possible use as biomarkers of clinical use.


Asunto(s)
Enfermedades Cardiovasculares/complicaciones , Infecciones por Coronavirus/complicaciones , Neumonía Viral/complicaciones , ARN no Traducido , Animales , Arritmias Cardíacas/complicaciones , Betacoronavirus , Cardiomegalia/complicaciones , Enfermedades Cardiovasculares/genética , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Homeostasis , Humanos , Inflamación/complicaciones , Ratones , Pandemias , Peptidil-Dipeptidasa A/genética , Sistema Renina-Angiotensina , Transcriptoma
15.
Mar Pollut Bull ; 160: 111673, 2020 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-33181946

RESUMEN

Heavy metal pollution arising from agricultural and industrial activities poses a significant threat to the aquatic environment, especially the increasing levels of chromium (Cr) that is exacerbating marine pollution. Given the economic importance of the Pacific white shrimp Litopenaeus vannamei (L. vannamei), understanding the impact of marine Cr pollution is deemed to be significant. In this study, we used the transcriptome sequencing (RNA-seq) technique to characterize the molecular mechanism of Cr exposure in L. vannamei. Gene ontology enrichment analysis showed substrate-specific and ion transport-related functions were mainly influenced by Cr exposure. We further identified genes involved in protein digestion and absorption (PEPT1, BAT1, MDU1), chemical carcinogenesis (GST and UGTs), ABC transporters (ABCC2), apoptosis (CAPN1, CASP10, PARP), implying the potentially Cr disintoxication mechanisms in L. vannamei. Genes within pancreatic secretion (ALT, LDH), lysosome (CTSL and HEXB), and peroxisome (ACOX1, ECI2, NUDT12) pathways implied the potentially Cr toxicity mechanisms in L. vannamei.


Asunto(s)
Cromo , Penaeidae , Animales , Cromo/toxicidad , Perfilación de la Expresión Génica , Ontología de Genes , Penaeidae/genética , Transcriptoma
16.
Signal Transduct Target Ther ; 5(1): 240, 2020 10 15.
Artículo en Inglés | MEDLINE | ID: mdl-33060566

RESUMEN

The COVID-19 pandemic has emerged as a global health emergency due to its association with severe pneumonia and relative high mortality. However, the molecular characteristics and pathological features underlying COVID-19 pneumonia remain largely unknown. To characterize molecular mechanisms underlying COVID-19 pathogenesis in the lung tissue using a proteomic approach, fresh lung tissues were obtained from newly deceased patients with COVID-19 pneumonia. After virus inactivation, a quantitative proteomic approach combined with bioinformatics analysis was used to detect proteomic changes in the SARS-CoV-2-infected lung tissues. We identified significant differentially expressed proteins involved in a variety of fundamental biological processes including cellular metabolism, blood coagulation, immune response, angiogenesis, and cell microenvironment regulation. Several inflammatory factors were upregulated, which was possibly caused by the activation of NF-κB signaling. Extensive dysregulation of the lung proteome in response to SARS-CoV-2 infection was discovered. Our results systematically outlined the molecular pathological features in terms of the lung response to SARS-CoV-2 infection, and provided the scientific basis for the therapeutic target that is urgently needed to control the COVID-19 pandemic.


Asunto(s)
Betacoronavirus/patogenicidad , Infecciones por Coronavirus/genética , Lesión Pulmonar/genética , Neumonía Viral/genética , Proteoma/genética , Proteómica/métodos , Síndrome Respiratorio Agudo Grave/genética , Anciano , Autopsia , Infecciones por Coronavirus/metabolismo , Infecciones por Coronavirus/patología , Infecciones por Coronavirus/virología , Citocinas/genética , Citocinas/metabolismo , Femenino , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Ontología de Genes , Humanos , Pulmón/metabolismo , Pulmón/patología , Pulmón/virología , Lesión Pulmonar/metabolismo , Lesión Pulmonar/patología , Lesión Pulmonar/virología , Masculino , Redes y Vías Metabólicas , Anotación de Secuencia Molecular , FN-kappa B/genética , FN-kappa B/metabolismo , Pandemias , Neumonía Viral/metabolismo , Neumonía Viral/patología , Neumonía Viral/virología , Proteoma/metabolismo , Síndrome Respiratorio Agudo Grave/metabolismo , Síndrome Respiratorio Agudo Grave/patología , Síndrome Respiratorio Agudo Grave/virología , Índice de Severidad de la Enfermedad , Transducción de Señal
17.
Viruses ; 12(10)2020 10 16.
Artículo en Inglés | MEDLINE | ID: mdl-33081421

RESUMEN

To address the expression pattern of the SARS-CoV-2 receptor ACE2 and the viral priming protease TMPRSS2 in the respiratory tract, this study investigated RNA sequencing transcriptome profiling of samples of airway and oral mucosa. As shown, ACE2 has medium levels of expression in both small airway epithelium and masticatory mucosa, and high levels of expression in nasal epithelium. The expression of ACE2 is low in mucosal-associated invariant T (MAIT) cells and cannot be detected in alveolar macrophages. TMPRSS2 is highly expressed in small airway epithelium and nasal epithelium and has lower expression in masticatory mucosa. Our results provide the molecular basis that the nasal mucosa is the most susceptible locus in the respiratory tract for SARS-CoV-2 infection and consequently for subsequent droplet transmission and should be the focus for protection against SARS-CoV-2 infection.


Asunto(s)
Betacoronavirus/fisiología , Infecciones por Coronavirus/genética , Peptidil-Dipeptidasa A/biosíntesis , Neumonía Viral/genética , Serina Endopeptidasas/biosíntesis , Internalización del Virus , Infecciones por Coronavirus/metabolismo , Infecciones por Coronavirus/virología , Epitelio/metabolismo , Epitelio/virología , Expresión Génica , Perfilación de la Expresión Génica , Humanos , Mucosa Nasal/metabolismo , Mucosa Nasal/virología , Pandemias , Peptidil-Dipeptidasa A/genética , Neumonía Viral/metabolismo , Neumonía Viral/virología , Sistema Respiratorio/metabolismo , Sistema Respiratorio/virología , Serina Endopeptidasas/genética
19.
Nat Commun ; 11(1): 5332, 2020 10 21.
Artículo en Inglés | MEDLINE | ID: mdl-33087697

RESUMEN

Cytotoxic T lymphocyte (CTL)-based cancer immunotherapies have shown great promise for inducing clinical regressions by targeting tumor-associated antigens (TAA). To expand the TAA landscape of pancreatic ductal adenocarcinoma (PDAC), we performed tandem mass spectrometry analysis of HLA class I-bound peptides from 35 PDAC patient tumors. This identified a shared HLA-A*0101 restricted peptide derived from co-transcriptional activator Vestigial-like 1 (VGLL1) as a putative TAA demonstrating overexpression in multiple tumor types and low or absent expression in essential normal tissues. Here we show that VGLL1-specific CTLs expanded from the blood of a PDAC patient could recognize and kill in an antigen-specific manner a majority of HLA-A*0101 allogeneic tumor cell lines derived not only from PDAC, but also bladder, ovarian, gastric, lung, and basal-like breast cancers. Gene expression profiling reveals VGLL1 as a member of a unique group of cancer-placenta antigens (CPA) that may constitute immunotherapeutic targets for patients with multiple cancer types.


Asunto(s)
Antígenos de Neoplasias/inmunología , Neoplasias de la Mama/inmunología , Proteínas de Unión al ADN/inmunología , Neoplasias Pancreáticas/inmunología , Factores de Transcripción/inmunología , Antígenos de Neoplasias/genética , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/inmunología , Neoplasias de la Mama/genética , Carcinoma Ductal Pancreático/genética , Carcinoma Ductal Pancreático/inmunología , Carcinoma Ductal Pancreático/terapia , Línea Celular Tumoral , Citotoxicidad Inmunológica , Proteínas de Unión al ADN/genética , Femenino , Perfilación de la Expresión Génica , Antígeno HLA-A1/inmunología , Humanos , Inmunoterapia Adoptiva , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/terapia , Placenta/inmunología , Embarazo , Pronóstico , Linfocitos T Citotóxicos/inmunología , Factores de Transcripción/genética
20.
Medicine (Baltimore) ; 99(42): e22434, 2020 Oct 16.
Artículo en Inglés | MEDLINE | ID: mdl-33080677

RESUMEN

BACKGROUND: Hypopharyngeal and esophageal squamous cell carcinoma (ESCC) are the most common double primary tumors with poor prognosis. Intensive work has been made to illuminate the etiology, but the common carcinogenic mechanism remains unclear. Thus, we conducted the study to seek to find the common gene signatures and key functional pathways associated with oncogenesis and treatment in hypopharyngeal squamous cell carcinoma (HSCC) and ESCC by bioinformatic analysis. METHODS: Three independent datasets (GSE2379, GSE20347, and GSE75241) were screened out from the Gene Expression Omnibus (GEO) database and the overlapping differentially expressed genes (DEGs) were identified using GEO2R online platform. Subsequently, the Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis of DEGs were conducted using database for annotation, visualization and integrated discovery (DAVID). Meanwhile, the protein-protein interaction network (PPI) constructed by search tool for the retrieval of interacting genes (STRING) was visualized using Cytoscape. Afterwards, the most key module and hub genes were extracted from the PPI network using the Molecular Complex Detection plugin. Moreover, the gene expression profiling interactive analysis (GEPIA) was applied to verify the expression differences and conduct the survival analyses of hub genes. Finally, the interaction network of miRNAs and hub genes constructed by encyclopedia of RNA interactomes (ENCORI) was visualized using Cytoscape. RESULTS: A total of 43 DEGs were identified, comprising 25 upregulated genes and 18 downregulated genes, which were mainly involved in the extracellular matrix-receptor interaction, collagen metabolic, epidermis development, cell adhesion, and PI3K/Akt signaling pathways. Subsequently, 12 hub genes were obtained and survival analysis demonstrated SERPINE1 and SPP1 were closely related to poor prognosis of patients with HSCC and ESCC. Finally, hsa-miR-29c-3p, hsa-miR-29a-3p, and hsa-miR-29b-3p were confirmed as the top 3 interactive miRNAs that target the most hub genes according to the interaction network of miRNAs and hub genes. CONCLUSION: The common gene signatures and functional pathways identified in the study may contribute to understanding the molecular mechanisms involved in the carcinogenesis and progression of HSCC and ESCC, and provide potential diagnostic and therapeutic targets.


Asunto(s)
Carcinoma de Células Escamosas/genética , Neoplasias Esofágicas/genética , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Ontología de Genes , Neoplasias Faríngeas/genética , Biomarcadores de Tumor/genética , Biología Computacional , Bases de Datos Genéticas , Humanos , Pronóstico
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