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1.
BMC Genomics ; 25(1): 593, 2024 Jun 12.
Artículo en Inglés | MEDLINE | ID: mdl-38867153

RESUMEN

BACKGROUND: Terpenes are important components of plant aromas, and terpene synthases (TPSs) are the key enzymes driving terpene diversification. In this study, we characterized the volatile terpenes in five different Chrysanthemum nankingense tissues. In addition, genome-wide identification and expression analysis of TPS genes was conducted utilizing an improved chromosome-scale genome assembly and tissue-specific transcriptomes. The biochemical functions of three representative TPSs were also investigated. RESULTS: We identified tissue-specific volatile organic compound (VOC) and volatile terpene profiles. The improved Chrysanthemum nankingense genome assembly was high-quality, including a larger assembled size (3.26 Gb) and a better contig N50 length (3.18 Mb) compared to the old version. A total of 140 CnTPS genes were identified, with the majority representing the TPS-a and TPS-b subfamilies. The chromosomal distribution of these TPS genes was uneven, and 26 genes were included in biosynthetic gene clusters. Closely-related Chrysanthemum taxa were also found to contain diverse TPS genes, and the expression profiles of most CnTPSs were tissue-specific. The three investigated CnTPS enzymes exhibited versatile activities, suggesting multifunctionality. CONCLUSIONS: We systematically characterized the structure and diversity of TPS genes across the Chrysanthemum nankingense genome, as well as the potential biochemical functions of representative genes. Our results provide a basis for future studies of terpene biosynthesis in chrysanthemums, as well as for the breeding of improved chrysanthemum varieties.


Asunto(s)
Transferasas Alquil y Aril , Chrysanthemum , Genoma de Planta , Familia de Multigenes , Terpenos , Transferasas Alquil y Aril/genética , Transferasas Alquil y Aril/metabolismo , Chrysanthemum/genética , Chrysanthemum/enzimología , Terpenos/metabolismo , Filogenia , Compuestos Orgánicos Volátiles/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Transcriptoma
2.
Mol Biol Evol ; 40(12)2023 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-38069902

RESUMEN

Rumpless chickens exhibit an abnormality in their tail development. The genetics and biology of this trait has been studied for decades to illustrate a broad variation in both the types of inheritance and the severity in the developmental defects of the tail. In this study, we created a backcross pedigree by intercrossing Piao (rumpless) with Xianju (normal) to investigate the genetic mechanisms and molecular basis of the rumpless trait in Piao chicken. Through genome-wide association and linkage analyses, the candidate region was fine-mapped to 798.5 kb (chromosome 2: 86.9 to 87.7 Mb). Whole-genome sequencing analyses identified a single variant, a 4.2 kb deletion, which was completely associated with the rumpless phenotype. Explorations of the expression data identified a novel causative gene, Rum, that produced a long, intronless transcript across the deletion. The expression of Rum is embryo-specific, and it regulates the expression of MSGN1, a key factor in regulating T-box transcription factors required for mesoderm formation and differentiation. These results provide genetic and molecular experimental evidence for a novel mechanism regulating tail development in chicken and report the likely causal mutation for the tail abnormity in the Piao chicken. The novel regulatory gene, Rum, will, due to its role in fundamental embryo development, be of interest for further explorations of a potential role in tail and skeletal development also in other vertebrates.


Asunto(s)
Pollos , Estudio de Asociación del Genoma Completo , Animales , Pollos/genética , Mutación con Pérdida de Función , Mutación , Fenotipo , Polimorfismo de Nucleótido Simple
3.
Small ; : e2401426, 2024 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-38686686

RESUMEN

The current high-capacity lithium-ion batteries (LIBs), reliant on flammable liquid electrolytes (LEs) and nickel-rich cathodes, are plagued by safety hazards, especially the risk of hazardous gas release stemming from internal side reactions. To address these safety concerns, an electron beam (E-beam)-induced gel polymer electrolyte (E-Gel) is introduced, employing dipentaerythritol hexaacrylate (DPH) as a bi-functional cross-linkable additive (CIA). The dual roles of DPH are exploited through a strategically designed E-beam irradiation process. Applying E-beam irradiation on the pre-cycled cells allows DPH to function as an additive during the initial cycle, establishing a protective layer on the surface of the anode and cathode and as a cross-linker during the E-beam irradiation step, forming a polymer framework. The prepared E-Gel with CIA has superior interfacial compatibility, facilitating lithium-ion diffusion at the electrode/E-Gel interface. The electrochemical assessment of 1.2 Ah pouch cells demonstrates that E-Gel substantially reduces gas release by 2.5 times compared to commercial LEs during the initial formation stage and ensures superior reversible capacity retention even after prolonged cycling at 55 °C. The research underscores the synergy of bifunctional CIA with E-beam technology, paving the way for large-scale production of safe, high-capacity, and commercially viable LIBs.

4.
Bioorg Med Chem Lett ; : 129862, 2024 Jun 27.
Artículo en Inglés | MEDLINE | ID: mdl-38944398

RESUMEN

Chronic pain is a common and challenging clinical problem that significantly impacts patients' quality of life. The sodium channel Nav1.8 plays a crucial role in the occurrence and development of chronic pain, making it one of the key targets for treating chronic pain. In this article, we combined virtual screening with cell membrane chromatography techniques to establish a novel method for rapid high-throughput screening of selective Nav1.8 inhibitors. Using this approach, we identified a small molecule compound 6, which not only demonstrated high affinity and inhibitory activity against Nav1.8 but also exhibited significant inhibitory effects on CFA-induced chronic inflammatory pain. Compared to the positive drug VX-150, compound 6 showed a more prolonged analgesic effect making it a promising candidate as a Nav1.8 inhibitor with potential clinical applications. This discovery provides a new therapeutic option for the treatment of chronic pain.

5.
J Clin Pediatr Dent ; 48(1): 128-137, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38239165

RESUMEN

To investigate the role of a fully digital process in the surgical treatment of mandibular fractures in children. We analyzed a complete dataset from 22 children with mandibular fractures treated with digital surgical assistance. The patient's treatment process included preoperative thin layer CT (Computed Tomography) scanning, computer-aided design (3D reconstruction, virtual reduction, and internal fixation device determination and shaping), and 3D printing (jaw model, bite plate). We used occlusal and shaping plates during surgery to assist in fracture reduction and fixation. During the follow-up, we observed the occurrence of fracture healing, occlusal relationships, opening degrees, and complications in pediatric patients after surgery. Next, we used the 3D overlay function of MIMICS software to compare the preoperative surgical design with postoperative jaw imaging data to evaluate the overall surgical effect. The postoperative imaging data showed good fracture healing, normal occlusion during follow-up, and significant improvement in opening degrees. The mean preoperative opening degree was 23.59 ± 2.89 mm, and the mean postoperative opening degree was 29.82 ± 1.79 mm; there was a significant difference between these two parameters (p < 0.05). There were no complications such as tooth germ injury, nerve injury or fracture block displacement. The postoperative mandibular imaging data was imported into MIMICS software for 3D overlay visualization, and the postoperative mandibular morphology recovery was well-matched with the preoperative design. We measured the average upper deviation (0.65 ± 0.09) mm and the average lower deviation (-0.57 ± 0.14) mm. The fully digital process has a precise, minimally invasive, and safe effect in the surgical treatment of mandibular fractures in children, and the clinical effect is satisfactory.


Asunto(s)
Fracturas Mandibulares , Humanos , Niño , Fracturas Mandibulares/diagnóstico por imagen , Fracturas Mandibulares/cirugía , Fijación Interna de Fracturas/métodos , Curación de Fractura , Impresión Tridimensional , Diseño Asistido por Computadora
6.
Small ; 19(48): e2305416, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37528714

RESUMEN

Flexible lithium-ion batteries (LIBs) have attracted significant attention owing to their ever-increasing use in flexible and wearable electronic devices. However, the practical application of flexible LIBs in devices has been plagued by the challenge of simultaneously achieving high energy density and high flexibility. Herein, a hierarchical 3D electrode (H3DE) is introduced with high mass loading that can construct highly flexible LIBs with ultrahigh energy density. The H3DE features a bicontinuous structure and the active materials along with conductive agents are uniformly distributed on the 3D framework regardless of the active material type. The bicontinuous electrode/electrolyte integration enables a rapid ion/electron transport, thereby improving the redox kinetics and lowering the internal cell resistance. Moreover, the H3DE exhibits exceptional structural integrity and flexibility during repeated mechanical deformations. Benefiting from the remarkable physicochemical properties, pouch-type flexible LIBs using H3DE demonstrate stable cycling under various bending states, achieving a record-high energy density (438.6 Wh kg-1 and 20.4 mWh cm-2 ), and areal capacity (5.6 mAh cm-2 ), outperforming all previously reported flexible LIBs. This study provides a feasible solution for the preparation of high-energy-density flexible LIBs for various energy storage devices.

7.
J Appl Commun Res ; 51(3): 320-339, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37287935

RESUMEN

Participatory interventions enable active user engagement, but research is needed to examine the longitudinal mechanisms through which engagement may generate outcomes. This study investigated the social processes following a web-based participatory media literacy intervention. In this program, young women were asked to create a digital counter message against the media content that promotes risk behavior. The effects of the message production were assessed at an immediate post-test and three- and six-month follow-ups. Message production increased collective efficacy at immediate post-test, which then stimulated the sharing of self-generated messages and interpersonal conversation at three-month follow-up. These sharing behaviors, in turn, led to critical media use and negative attitude toward risk behavior at six months. Collective efficacy and sharing behavior sequentially mediated the effects of message production on outcomes. Theoretical and pragmatic implications are discussed.

8.
Bioinformatics ; 37(18): 3026-3028, 2021 09 29.
Artículo en Inglés | MEDLINE | ID: mdl-33714997

RESUMEN

SUMMARY: In this article, we introduce a hierarchical clustering and Gaussian mixture model with expectation-maximization (EM) algorithm for detecting copy number variants (CNVs) using whole exome sequencing (WES) data. The R shiny package 'HCMMCNVs' is also developed for processing user-provided bam files, running CNVs detection algorithm and conducting visualization. Through applying our approach to 325 cancer cell lines in 22 tumor types from Cancer Cell Line Encyclopedia (CCLE), we show that our algorithm is competitive with other existing methods and feasible in using multiple cancer cell lines for CNVs estimation. In addition, by applying our approach to WES data of 120 oral squamous cell carcinoma (OSCC) samples, our algorithm, using the tumor sample only, exhibits more power in detecting CNVs as compared with the methods using both tumors and matched normal counterparts. AVAILABILITY AND IMPLEMENTATION: HCMMCNVs R shiny software is freely available at github repository https://github.com/lunching/HCMM_CNVs.and Zenodo https://doi.org/10.5281/zenodo.4593371. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Carcinoma de Células Escamosas , Neoplasias de la Boca , Humanos , Secuenciación del Exoma , Variaciones en el Número de Copia de ADN , Neoplasias de la Boca/genética , Programas Informáticos , Algoritmos , Análisis por Conglomerados
9.
Opt Express ; 30(15): 27539-27559, 2022 Jul 18.
Artículo en Inglés | MEDLINE | ID: mdl-36236923

RESUMEN

Accurate three-dimensional (3D) morphological computational models of cells are important in a number of biological studies. This study proposes a precise depth-varying point spread function (PDV-PSF) method for reconstructing 3D computational models of suspended cells from two-dimensional (2D) confocal image stacks. Our approach deblurs the 2D images in horizontal plane and corrects the deformation in vertical direction to overcome the refractive index mismatch problem caused by suspended cells imaging through stratified media. Standard fluorescent polystyrene spheres and Jurkat T-lymphocytes are selected to evaluate the validity and accuracy of this PDV-PSF method. Qualitative and quantitative results demonstrate that our approach has superior performance in 3D morphological computational models reconstruction of suspended cells.


Asunto(s)
Imagenología Tridimensional , Poliestirenos , Algoritmos , Simulación por Computador , Imagenología Tridimensional/métodos
10.
Med Care ; 60(5): 375-380, 2022 05 01.
Artículo en Inglés | MEDLINE | ID: mdl-35250021

RESUMEN

BACKGROUND: Commercial health plans establish networks and require much higher cost sharing for out-of-network (OON) care. Yet, the adequacy of health plan networks for access to pediatric specialists, especially for children with medical complexity, is largely unknown. OBJECTIVE: To examine differences in OON care and associated cost-sharing payments for commercially insured children with different levels of medical complexity. DESIGN: Cross-sectional study using a nationwide commercial claims database. SUBJECTS: Enrollees 0-18 years old in employer-sponsored insurance plans. The Pediatric Medical Complexity Algorithm was used to classify individuals into 3 levels of medical complexity: children with no chronic disease, children with non-complex chronic diseases, and children with complex chronic diseases. MAIN OUTCOMES: OON care rates, cost-sharing payments for OON care and in-network care, OON cost sharing as a proportion of total health care spending, and OON cost sharing as a proportion of total cost sharing. RESULTS: The study sample included 6,399,006 individuals with no chronic disease, 1,674,450 with noncomplex chronic diseases, and 603,237 with complex chronic diseases. Children with noncomplex chronic diseases were more likely to encounter OON care by 6.77 percentage points with higher cost-sharing by $288 for OON care, relative to those with no chronic disease. For those with complex chronic diseases, these differences rose to 16.08 percentage points and $599, respectively. Among children who saw behavioral health providers, rates of OON care were especially high. CONCLUSIONS: Commercially insured children with medical complexity experience higher rates of OON care with higher OON cost-sharing payments compared with those with no chronic disease.


Asunto(s)
Seguro de Costos Compartidos , Seguro de Salud , Adolescente , Niño , Preescolar , Enfermedad Crónica , Estudios Transversales , Bases de Datos Factuales , Humanos , Lactante , Recién Nacido , Estados Unidos
11.
Int J Mol Sci ; 23(6)2022 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-35328716

RESUMEN

Morphologically tunable copper oxide-based nanomaterials on Cu wire have been synthesized through a one-step alkali-assisted surface oxidation process for non-enzymatic glucose sensing. Subsequently, copper oxide-based nanomaterials on Cu wire as a supporting matrix to deposit manganese oxide for the construction of heterostructured Mn-Cu bimetallic oxide architectures through spontaneous redox reaction in the KMnO4 solution for supercapacitors. Field emission scanning electron microscopy (FESEM), field emission transmission electron microscopy (FETEM), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) confirmed that morphological and phase transformation from Cu(OH)2 to CuO occurred in copper oxide-based nanomaterials on Cu wire with different degrees of growth reaction. In non-enzymatic glucose sensing, morphologically tunable copper oxide-based nanomaterials owned the high tunability of electrocatalytically active sites and intrinsic catalytic activity to meet efficient glucose electrooxidation for obtaining promoted non-enzymatic glucose sensing performances (sensitivity of 2331 µA mM-1 cm-2 and the limit of detection of 0.02 mM). In the supercapacitor, heterostructured Mn-Cu bimetallic oxide-based nanomaterials delivered abundant redox-active sites and continuous conductive network to optimize the synergistic effect of Mn and Cu redox species for boosting the pseudo-capacitance performance (areal capacitance value of 79.4 mF cm-2 at 0.2 mA cm-2 current density and capacitance retention of 74.9% after 1000 cycles). It concluded that morphologically tunable copper oxide-based nanomaterials on Cu wire with/without deposition of manganese oxide could be good candidates for the future design of synergistic multifunctional materials in electrochemical techniques.


Asunto(s)
Técnicas Biosensibles , Nanoestructuras , Cobre/química , Electrodos , Glucosa/química , Compuestos de Manganeso , Óxidos
12.
Artículo en Inglés | MEDLINE | ID: mdl-33332255

RESUMEN

A Gram-stain-negative, orange-pigmented and strictly aerobic bacterium, designated strain MJ115T, was isolated from seawater in Pohang, South Korea. Cells were non-motile rods and showed positive reactions for catalase and oxidase tests. Growth of strain MJ115T was observed at 4-35 °C (optimum, 30 °C), pH 6.0-7.0 (optimum, pH 6.5) and in the presence of 0-8.0 % (w/v) NaCl (optimum, 2.0%). Strain MJ115T contained iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 1 ω9c, C17 : 0 2-OH, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) as major cellular fatty acids and menaquinone-6 as the major respiratory quinone. Phosphatidylethanolamine, two unidentified aminolipids and four unidentified lipids were detected as major polar lipids. The G+C content of the genomic DNA was 40.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ115T formed a phyletic lineage with Nonlabens marinus S1-08T, Nonlabens agnitus JC2678T and Nonlabens antarcticus AKS 622T within the genus Nonlabens. Strain MJ115T was also most closely related to N. marinus S1-08T, N. agnitus JC2678T and N. antarcticus AKS 622T with 96.5, 96.4 and 96.0 % 16S rRNA sequence similarities, respectively. Here it is proposed that strain MJ115T represents a new species of the genus Nonlabens, for which the name Nonlabens ponticola sp. nov. is proposed. The type strain is MJ115T (=KCTC 72237T=NBRC 113963T). In addition, the comparison of the whole genome sequences and phenotypic features suggested that Nonlabens tegetincola and Nonlabens sediminis belong to the same species. Therefore, it is proposed that N. sediminis is reclassified as a later heterotypic synonym of N. tegetincola.


Asunto(s)
Flavobacteriaceae/clasificación , Filogenia , Agua de Mar/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Flavobacteriaceae/aislamiento & purificación , Hibridación de Ácido Nucleico , Fosfatidiletanolaminas/química , Pigmentación , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN , Vitamina K 2/análogos & derivados , Vitamina K 2/química
13.
Environ Res ; 193: 110541, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33249041

RESUMEN

Wildland firefighters are repeatedly exposed to elevated levels of wildland fire smoke (WFS) while protecting lives and properties from wildland fires. Studies reporting personal exposure concentrations of air pollutants in WFS during fire suppression or prescribed burn activities have been geographically limited to the western and southeastern United States. The objective of this study is to characterize exposure concentrations of air pollutants in WFS emissions among wildland firefighters who conducted prescribed burns in the Midwest. Between 2016 and 2019, a total of 35 firefighters (31 males and 4 females, age of 35.63 ± 9.31 years) were recruited to participate in this study. Personal particulate matter 2.5 (PM2.5) and carbon monoxide (CO) exposure concentrations were measured during prescribed burns. The level of black carbon (BC) in WFS particulates was determined using the light transmission technique, while trace metal composition was analyzed using inductively coupled plasma mass spectrometry (ICP-MS). The results showed geometric means for PM2.5, CO, and BC concentrations were 1.43 ± 0.13 mg/m3, 7.02 ± 0.69 ppm, and 58.79 ± 5.46 µg/m3, respectively. Although no occupational exposure limits (OELs) were exceeded by 8-h time-weighted average (TWA) exposure concentration observed in the firefighters, a total of 28 personal CO exposure concentrations were above the National Institute for Occupational Safety and Health (NIOSH) Recommended Exposure Limit (REL) Ceiling (200 ppm) for CO. PM2.5 and CO concentrations were about 2-7 times higher in the Midwest than the other regions. Firefighters who performed holding had higher CO exposure concentrations compared to firefighters who performed lighting (p < 0.01), while lighters were exposed to higher level of BC in the smoke particulates (p < 0.01), possibly due to the domination of exposure by different combustion sources and stages. The levels of trace metals in WFS particulates were well below the corresponding OELs and no task-related difference was observed except for manganese. Our results suggest that wildland firefighters in the midwestern region have higher WFS exposures while working at prescribed burns compared to those western and southeastern United States.


Asunto(s)
Contaminantes Ocupacionales del Aire , Bomberos , Incendios , Exposición Profesional , Adulto , Contaminantes Ocupacionales del Aire/análisis , Femenino , Humanos , Exposición por Inhalación/análisis , Masculino , Persona de Mediana Edad , Medio Oeste de Estados Unidos/epidemiología , Exposición Profesional/análisis , Humo/análisis , Sudeste de Estados Unidos/epidemiología , Estados Unidos
14.
Ethn Health ; 26(1): 94-109, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33059486

RESUMEN

OBJECTIVE: To investigate factors associated with the stigmatization of people of Asian descent during COVID-19 in the United States and factors that can mitigate or prevent stigmatization. DESIGN: A national sample survey of adults (N = 842) was conducted online between May 11 and May 19, 2020. Outcome variables were two dimensions of stigmatization, responsibility and persons as risk. Hierarchical regression analyses were performed. RESULTS: Racial prejudice, maladaptive coping, and biased media use each explained stigmatization. Racial prejudice, comprising stereotypical beliefs and emotion toward Asian Americans, was a stronger predictor of stigmatization than maladaptive coping or biased media use. Fear concerning the ongoing COVID-19 situation and the use of social media and partisan cable TV also predicted stigmatization. Low self-efficacy in dealing with COVID-19, when associated with high estimated harm of COVID-19, increased stigmatization. High perceived institutional efficacy in the handling of COVID-19 increased stigmatization when linked to high estimated harm of COVID-19. On the other hand, high perceived collective efficacy in coping with COVID-19 was associated with low stigmatization. More indirect contacts with Asians via the media predicted less stigmatization. CONCLUSIONS: Efforts to reduce stigmatization should address racial stereotypes and emotions, maladaptive coping, and biased media use by providing education and resources to the public. Fostering collective efficacy and media-based contacts with Asian Americans can facilitate these efforts.


Asunto(s)
Adaptación Psicológica , Asiático/psicología , COVID-19/etnología , Racismo/psicología , Medios de Comunicación Sociales/estadística & datos numéricos , Estereotipo , Femenino , Humanos , Masculino , Persona de Mediana Edad , Encuestas y Cuestionarios , Estados Unidos
15.
Comput Inform Nurs ; 39(6): 312-320, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-33214389

RESUMEN

ReLive is a nursing theory-driven and evidence-based smartphone application that aims to promote self-management among cancer survivors. It has been designed to display symptom measurement results in different traffic light colors, depending on the severity of a user's symptoms (eg, severe symptoms are presented in red). Therefore, it is easy for users to draw inferences about changes in their symptoms. Further, users can simultaneously set several physical activity goals and monitor their performance. Social support, self-efficacy, and quality of life of a user can also be monitored regularly. This study investigated the usability of this application. An iterative formative test, including a cognitive walkthrough and face-to-face interviews, was conducted. Participants were seven individuals with a diagnosis of chronic myeloid leukemia. The ease of use and understanding, acceptability, and usefulness of the application were evaluated. The results revealed that the participants had evaluated ReLive positively. This program could be used as an intervention to deliver health information and manage their performance. Further research is needed to assess the application's effects on self-management among survivors of various types of cancers.


Asunto(s)
Supervivientes de Cáncer , Neoplasias , Automanejo , Teléfono Inteligente , Humanos , Aplicaciones Móviles , Neoplasias/terapia , Calidad de Vida , Diseño Centrado en el Usuario , Interfaz Usuario-Computador
16.
Plant J ; 97(5): 841-857, 2019 03.
Artículo en Inglés | MEDLINE | ID: mdl-30444296

RESUMEN

Andrographis paniculata is a herbaceous dicot plant widely used for its anti-inflammatory and anti-viral properties across its distribution in China, India and other Southeast Asian countries. A. paniculata was used as a crucial therapeutic treatment during the influenza epidemic of 1919 in India, and is still used for the treatment of infectious disease in China. A. paniculata produces large quantities of the anti-inflammatory diterpenoid lactones andrographolide and neoandrographolide, and their analogs, which are touted to be the next generation of natural anti-inflammatory medicines for lung diseases, hepatitis, neurodegenerative disorders, autoimmune disorders and inflammatory skin diseases. Here, we report a chromosome-scale A. paniculata genome sequence of 269 Mb that was assembled by Illumina short reads, PacBio long reads and high-confidence (Hi-C) data. Gene annotation predicted 25 428 protein-coding genes. In order to decipher the genetic underpinning of diterpenoid biosynthesis, transcriptome data from seedlings elicited with methyl jasmonate were also obtained, which enabled the identification of genes encoding diterpenoid synthases, cytochrome P450 monooxygenases, 2-oxoglutarate-dependent dioxygenases and UDP-dependent glycosyltransferases potentially involved in diterpenoid lactone biosynthesis. We further carried out functional characterization of pairs of class-I and -II diterpene synthases, revealing the ability to produce diversified labdane-related diterpene scaffolds. In addition, a glycosyltransferase able to catalyze O-linked glucosylation of andrograpanin, yielding the major active product neoandrographolide, was also identified. Thus, our results demonstrate the utility of the combined genomic and transcriptomic data set generated here for the investigation of the production of the bioactive diterpenoid lactone constituents of the important medicinal herb A. paniculata.


Asunto(s)
Andrographis/genética , Diterpenos/metabolismo , Genoma de Planta/genética , Glucósidos/biosíntesis , Fitoquímicos/biosíntesis , Proteínas de Plantas/metabolismo , Andrographis/química , Andrographis/enzimología , Glucosiltransferasas/genética , Glucosiltransferasas/metabolismo , Proteínas de Plantas/genética , Plantas Medicinales/química , Plantas Medicinales/enzimología , Plantas Medicinales/genética , Tetrahidronaftalenos
17.
Anal Chem ; 92(7): 4829-4837, 2020 04 07.
Artículo en Inglés | MEDLINE | ID: mdl-32125145

RESUMEN

A large proportion of the complexity and redundancy of LC-MS metabolomics data comes from adduct formation. To reduce such redundancy, many tools have been developed to recognize and annotate adduct ions. These tools rely on predefined adduct lists that are generated empirically from reversed-phase LC-MS studies. In addition, hydrophilic interaction chromatography (HILIC) is gaining popularity in metabolomics studies due to its enhanced performance over other methods for polar compounds. HILIC methods typically use high concentrations of buffer salts to improve chromatographic performance. Therefore, it is necessary to analyze adduct formation in HILIC metabolomics. To this end, we developed covariant ion analysis (COVINA) to investigate metabolite adduct formation. Using this tool, we completely annotated 201 adduct and fragment ions from 10 metabolites. Many of the metabolite adduct ions were found to contain cluster ions corresponding to mobile phase additives. We further utilized COVINA to find the major ionized forms of metabolites. Our results show that for some metabolites, the adduct ion signals can be >200-fold higher than the signals from the deprotonated form, offering better sensitivity for targeted metabolomics analysis. Finally, we developed an in-source CID ramping (InCIDR) method to analyze the intensity changes of the adduct and fragment ions from metabolites. Our analysis demonstrates a promising method to distinguish the protonated and deprotonated ions of metabolites from the adduct and fragment ions.


Asunto(s)
Metabolómica , Línea Celular Tumoral , Cromatografía Líquida de Alta Presión , Humanos , Interacciones Hidrofóbicas e Hidrofílicas , Espectrometría de Masas
18.
Bioinformatics ; 35(9): 1597-1599, 2019 05 01.
Artículo en Inglés | MEDLINE | ID: mdl-30304367

RESUMEN

SUMMARY: The rapid advances of omics technologies have generated abundant genomic data in public repositories and effective analytical approaches are critical to fully decipher biological knowledge inside these data. Meta-analysis combines multiple studies of a related hypothesis to improve statistical power, accuracy and reproducibility beyond individual study analysis. To date, many transcriptomic meta-analysis methods have been developed, yet few thoughtful guidelines exist. Here, we introduce a comprehensive analytical pipeline and browser-based software suite, called MetaOmics, to meta-analyze multiple transcriptomic studies for various biological purposes, including quality control, differential expression analysis, pathway enrichment analysis, differential co-expression network analysis, prediction, clustering and dimension reduction. The pipeline includes many public as well as >10 in-house transcriptomic meta-analytic methods with data-driven and biological-aim-driven strategies, hands-on protocols, an intuitive user interface and step-by-step instructions. AVAILABILITY AND IMPLEMENTATION: MetaOmics is freely available at https://github.com/metaOmics/metaOmics. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Programas Informáticos , Transcriptoma , Perfilación de la Expresión Génica , Genómica , Reproducibilidad de los Resultados
19.
Occup Environ Med ; 2020 Nov 02.
Artículo en Inglés | MEDLINE | ID: mdl-33139344

RESUMEN

OBJECTIVE: Wildland firefighters (WLFFs) experience repeated exposures to wildland fire smoke (WFS). However, studies about WLFFs remain regionally limited. The objective of this study was to assess the effect of WFS exposure on urinary mutagenicity and cell oxidation among WLFFs who work at prescribed burns in the Midwestern USA. METHODS: A total of 120 spot urine samples was collected from 19 firefighters right before (pre-shift), immediately after (post-shift), and the morning (next-morning) following work shifts on prescribed burn days (burn days) and regular workdays (non-burn days). The levels of urinary mutagenicity, 8-isoprostane, malondialdehyde and oxidised guanine species (Ox-GS) were measured. Linear mixed-effect models were used to determine the difference of cross-shift changes in the concentrations of urinary biomarkers. RESULTS: Post-shift levels of creatinine-corrected urinary mutagenicity and 8-isoprostane were non-significantly higher than pre-shift levels (1.16× and 1.64×; p=0.09 and 0.07) on burn days. Creatinine-corrected Ox-GS levels increased significantly in next-morning samples following WFS exposure (1.62×, p=0.03). A significant difference in cross-shift changes between burn and non-burn days was observed in 8-isoprostane (2.64×, p=0.03) and Ox-GS (3.00×, p=0.02). WLFFs who contained the fire (performed holding tasks) had a higher pre-morning to next-morning change in urinary mutagenicity compared with those who were lighting fires during the prescribed burns (1.56×, p=0.03). CONCLUSIONS: Compared with the other regions, WLFFs who worked in Midwestern forests had an elevated urinary mutagenicity and systemic oxidative changes associated with WFS exposure at prescribed burns.

20.
Environ Res ; 185: 109414, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-32234599

RESUMEN

A series of biomass cellulose-derived carbon nanofibers (CCNF) were prepared at different pyrolysis temperatures in this study. Subsequently, this CCNF was combined with bismuth oxybromide (BiOBr) to form BiOBr/CCNF composite. The feasibility of BiOBr/CCNF as photocatalyst was investigated for the treatment against organic dye, rhodamine B (RhB) and inorganic metal ion, hexavalent chromium (Cr(VI)). The effect of the pyrolysis temperature on the properties (e.g., crystalline structure, functional group distribution, and graphitization degree) of the prepared CCNF was investigated in relation to its photocatalytic performance. A pyrolysis temperature over 800 °C resulted in CCNF with higher degrees of graphitization which was accompanied by a better photocatalytic performance of its composite against RhB and Cr(VI). Their reaction kinetic rates were estimated as 8.15 × 10-2 and 0.21 mmol/g/h, respectively (at the initial concentration of 10 mg/L), while their quantum yield values were 1.56 × 10-6 and 3.83 × 10-6 molecules per photon, respectively. BiOBr/CCNF catalysts were efficient enough to simultaneously remove RhB and Cr(VI) through the generation of active oxidative and reductive oxygen species, respectively. The strategies used in this study offer a new pathway for preparing cost-effective photocatalysts with biomass derived carbonaceous materials for the efficient removal of multicomponent contaminants in water.


Asunto(s)
Nanofibras , Contaminantes Químicos del Agua , Bismuto , Carbono , Celulosa , Cromo , Pirólisis , Rodaminas , Temperatura , Agua , Contaminantes Químicos del Agua/análisis
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