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1.
Stud Health Technol Inform ; 316: 1243-1247, 2024 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-39176606

RESUMO

GA4GH has proposed the Beacon architecture as an interface to retrieve genomic information which also protects the privacy of the individuals. In this paper, we propose to adapt the Beacon Reference Implementation to the use case of a study comparing the susceptibility to the carcinogenic effects of tobacco. This analysis compares the germline of heavy smokers who have either never developed lung cancer or, on the contrary, have developed it at a young age. To adapt the Beacon Reference Implementation to the use case, we have added filtering capabilities and a new grouping of information allowing to retrieve the data by affected gene.


Assuntos
Genômica , Neoplasias Pulmonares , Humanos , Neoplasias Pulmonares/genética , Predisposição Genética para Doença , Fumar/genética , Armazenamento e Recuperação da Informação
2.
J Exp Bot ; 75(1): 168-179, 2024 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-37798132

RESUMO

Submergence is a major constraint on rice production in South and Southeast Asia. In this study, we determined that a gene of the Sub1A-binding protein family, SAB23, encodes a plant homeodomain (PHD)-type transcription factor that has a novel function of negatively regulating submergence tolerance in rice. The T-DNA insertion mutant sab23 displayed reduced plant height, delayed seed maturation, and lower percentage seed set. Importantly, this mutant also exhibited enhanced submergence tolerance. In addition, CRISPR/Cas9 knock out of SAB23 resulted in a significant reduction in the content of the gibberellin GA4 and a dramatic increase in the content of GA1 in the plants. SAB23 binds to the promoter of CYTOCHROME P450 714B2 (CYP714B2), which encodes a GA13-oxidase that catalyses the conversion of GA53 to GA19. Disruption of SAB23 function led to increased CYP714B2 transcription, and overexpression of CYP714B2 produced phenotypes similar to those of the SAB23-knockout plants. Taken together, our results reveal that SAB23 negatively regulates rice submergence tolerance by modulating CYP714B2 expression, which has significant potential for use in future breeding.


Assuntos
Oryza , Fatores de Transcrição , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Oryza/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Melhoramento Vegetal , Sistema Enzimático do Citocromo P-450/metabolismo , Mutação
3.
Cell Genom ; 3(10): 100386, 2023 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-37868041

RESUMO

A lack of diversity in genomics for health continues to hinder equitable leadership and access to precision medicine approaches for underrepresented populations. To avoid perpetuating biases within the genomics workforce and genomic data collection practices, equity, diversity, and inclusion (EDI) must be addressed. This paper documents the journey taken by the Global Alliance for Genomics and Health (a genomics-based standard-setting and policy-framing organization) to create a more equitable, diverse, and inclusive environment for its standards and members. Initial steps include the creation of two groups: the Equity, Diversity, and Inclusion Advisory Group and the Regulatory and Ethics Diversity Group. Following a framework that we call "Reflected in our Teams, Reflected in our Standards," both groups address EDI at different stages in their policy development process.

4.
Molecules ; 28(2)2023 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-36677612

RESUMO

A branch of graph theory that makes use of a molecular graph is called chemical graph theory. Chemical graph theory is used to depict a chemical molecule. A graph is connected if there is an edge between every pair of vertices. A topological index is a numerical value related to the chemical structure that claims to show a relationship between chemical structure and various physicochemical attributes, chemical reactivity, or, you could say, biological activity. In this article, we examined the topological properties of a planar octahedron network of m dimensions and computed the total eccentricity, average eccentricity, Zagreb eccentricity, geometric arithmetic eccentricity, and atom bond connectivity eccentricity indices, which are used to determine the distance between the vertices of a planar octahedron network.

5.
Am J Med Genet C Semin Med Genet ; 190(2): 231-242, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35872606

RESUMO

Technological advances in both genome sequencing and prenatal imaging are increasing our ability to accurately recognize and diagnose Mendelian conditions prenatally. Phenotype-driven early genetic diagnosis of fetal genetic disease can help to strategize treatment options and clinical preventive measures during the perinatal period, to plan in utero therapies, and to inform parental decision-making. Fetal phenotypes of genetic diseases are often unique and at present are not well understood; more comprehensive knowledge about prenatal phenotypes and computational resources have an enormous potential to improve diagnostics and translational research. The Human Phenotype Ontology (HPO) has been widely used to support diagnostics and translational research in human genetics. To better support prenatal usage, the HPO consortium conducted a series of workshops with a group of domain experts in a variety of medical specialties, diagnostic techniques, as well as diseases and phenotypes related to prenatal medicine, including perinatal pathology, musculoskeletal anomalies, neurology, medical genetics, hydrops fetalis, craniofacial malformations, cardiology, neonatal-perinatal medicine, fetal medicine, placental pathology, prenatal imaging, and bioinformatics. We expanded the representation of prenatal phenotypes in HPO by adding 95 new phenotype terms under the Abnormality of prenatal development or birth (HP:0001197) grouping term, and revised definitions, synonyms, and disease annotations for most of the 152 terms that existed before the beginning of this effort. The expansion of prenatal phenotypes in HPO will support phenotype-driven prenatal exome and genome sequencing for precision genetic diagnostics of rare diseases to support prenatal care.


Assuntos
Biologia Computacional , Placenta , Recém-Nascido , Humanos , Feminino , Gravidez , Biologia Computacional/métodos , Fenótipo , Doenças Raras , Sequenciamento do Exoma
6.
Hum Mutat ; 43(6): 659-667, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35537081

RESUMO

The Matchmaker Exchange (MME) was launched in 2015 to provide a robust mechanism to discover novel disease-gene relationships. It operates as a federated network connecting databases holding relevant data using a common application programming interface, where two or more users are looking for a match for the same gene (two-sided matchmaking). Seven years from its launch, it is clear that the MME is making outstanding contributions to understanding the morbid anatomy of the genome. The number of unique genes present across the MME has steadily increased over time; there are currently >13,520 unique genes (~68% of all protein-coding genes) connected across the MME's eight genomic matchmaking nodes, GeneMatcher, DECIPHER, PhenomeCentral, MyGene2, seqr, Initiative on Rare and Undiagnosed Disease, PatientMatcher, and the RD-Connect Genome-Phenome Analysis Platform. The collective data set accessible across the MME currently includes more than 120,000 cases from over 12,000 contributors in 98 countries. The discovery of potential new disease-gene relationships is happening daily and international collaborative teams are moving these advances forward to publication, now numbering well over 500. Expansion of data sharing into routine clinical practice by clinicians, genetic counselors, and clinical laboratories has ensured access to discovery for even more individuals with undiagnosed rare genetic diseases. Tens of thousands of patients and their family members have been directly or indirectly impacted by the discoveries facilitated by two-sided genomic matchmaking. MME supports further connections to the literature (PubCaseFinder) and to human and model organism resources (Monarch Initiative) and scientists (ModelMatcher). Efforts are now underway to explore additional approaches to matchmaking at the gene or variant level where there is only one querier (one-sided matchmaking). Genomic matchmaking has proven its utility over the past 7 years and will continue to facilitate discoveries in the years to come.


Assuntos
Bases de Dados Genéticas , Predisposição Genética para Doença , Genômica , Humanos , Disseminação de Informação , Fenótipo , Doenças Raras/genética
7.
Hum Mutat ; 43(6): 791-799, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35297548

RESUMO

Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human genomic data, through providing simple "yes" or "no" responses to queries about the presence of a given variant in datasets hosted by Beacon providers. The popularity of this concept has fostered the design of a version 2, that better serves real-world requirements and addresses the needs of clinical genomics research and healthcare, as assessed by several contributing projects and organizations. Particularly, rare disease genetics and cancer research will benefit from new case level and genomic variant level requests and the enabling of richer phenotype and clinical queries as well as support for fuzzy searches. Beacon is designed as a "lingua franca" to bridge data collections hosted in software solutions with different and rich interfaces. Beacon version 2 works alongside popular standards like Phenopackets, OMOP, or FHIR, allowing implementing consortia to return matches in beacon responses and provide a handover to their preferred data exchange format. The protocol is being explored by other research domains and is being tested in several international projects.


Assuntos
Genômica , Disseminação de Informação , Humanos , Disseminação de Informação/métodos , Fenótipo , Doenças Raras , Software
8.
Cell Genom ; 1(2): None, 2021 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-34820659

RESUMO

Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset's allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers' discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide.

9.
Front Plant Sci ; 12: 713514, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34646285

RESUMO

Gibberellin (GA) plays a key role in the release of bud dormancy and the GA receptor GID1 (GIBBERELLIN INSENSITIVE DWARF1) and DELLA protein are the GA signaling parts, but the molecular mechanism of GA-GID1-DELLA module regulating leaf bud dormancy in peach (Prunus persica) is still not very clear. In this study, we isolated and characterized the GID1 gene PpGID1c from the peach cultivar "Zhong you No.4." Overexpressing PpGID1c in Arabidopsis promoted seed germination, which indicated that PpGID1c has an important function in dormancy. The expression level of PpGID1c in peach leaf buds during endodormancy release was higher than that during ecodormancy and was positively correlated with GA4 levels. Our study also found that GA4 had the most obvious effect on promoting the bud break, indicating that GA4 may be the key gibberellin to promoting peach leaf bud endodormancy release. Moreover, a quantitative real-time PCR (qRT-PCR) found that GA4 could increase the expression of the gibberellin signaling gene PpDELLA2. A yeast two-hybrid (Y2H) assay suggested that the PpGID1c interaction with the PpDELLA1 protein was not dependent on gibberellin, while the PpGID1c interaction with PpDELLA2 required GA4 or another gibberellin. These findings suggested that the GA4-GID1c-DELLA2 module regulates peach leaf bud endodormancy release, with this finding significantly enhancing our comprehensive understanding of bud endodormancy release and revealing a new mechanism for regulating leaf bud endodormancy release in peach.

10.
EJNMMI Res ; 11(1): 114, 2021 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-34718888

RESUMO

BACKGROUND: Imaging diagnosis of inflammation has been challenging for many years. Inflammation imaging agents commonly used in nuclear medicine, such as [67Ga]Ga-citrate and 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG) showed some limitations. The identification of a radiotracer with high specificity and low radiation dose is clinically important. With the commercialization of 68Ge/68Ga generators and the high 68Ga cyclotron production capacity, the study of 68Ga-based tracer for inflammation has increased and shown good potential. In the present work, we report the synthesis of 4HMSA, a new acyclic chelator, and its first investigation for 68Ga complexation and as a new positron emission tomography (PET) imaging agent of inflammation in comparison to [68Ga]Ga-citrate. RESULTS: The present experimental studies have shown that the novel [68Ga]Ga-4HMSA is stable allowing imaging of inflammation in a preclinical model of adjuvant- and pathogen-based inflammation involving intraplantar injection of complete Freund's adjuvant (CFA). We also found that [68Ga]Ga-4HMSA displayed similar uptakes in the inflamed paw than [68Ga]Ga-citrate, which are superior compared to those of contralateral (non-injected) paws at days 1-3 from PET imaging. [68Ga]Ga-citrate accumulated in the upper body of the animal such as the liver, lungs and the heart, whereas the [68Ga]Ga-4HMSA revealed low uptakes in the majority of the organs and was cleared relatively rapidly from blood circulation through the kidneys and bladder. CONCLUSION: The results highlight the potential of [68Ga]Ga-4HMSA as an interesting alternative to [68Ga]Ga-citrate for inflammation imaging by PET. The new PET tracer also offers additional advantages than [68Ga]Ga-citrate in term of dosimetry and lower overall background activity.

11.
Planta ; 254(3): 59, 2021 Aug 24.
Artigo em Inglês | MEDLINE | ID: mdl-34427790

RESUMO

MAIN CONCLUSION: Through combined analysis of the transcriptome and targeted metabolome of lily bulbs, the possible molecular mechanism of dormancy release was revealed. Regulation of bulb dormancy is critical for ensuring annual production and high-quality cultivation. The application of low temperatures is the most effective method for breaking bulb dormancy, but the molecular mechanism underlying this response is unclear. Herein, targeted metabolome and transcriptome analyses were performed on Lilium davidii var. unicolor bulbs stored for 0, 50, and 100 days at 4 °C. Dormancy release mainly depended on the accumulation of gibberellins GA4 and GA7, which are synthesized by the non-13-hydroxylation pathway, rather than GA3, and ABA was degraded in the process. The contents of nonbioactive GA9, GA15, and GA24, the precursors of GA4 synthesis, increased with bulb dormancy release. Altogether, 113,252 unique transcripts were de novo assembled through high-throughput transcriptome sequences, and 639 genes were continuously differentially expressed. Energy sources during carbohydrate metabolism mainly depend on glycolysis and the pentose phosphate pathway. Screening of transcription factor families involved in bulb dormancy release showed that MYB, WRKY, NAC, and TCP members were significantly correlated with the targeted metabolome. Coexpression analysis further confirmed that ABI5, PYL8, PYL4, and PP2C, which are vital ABA signaling elements, regulated GA3ox and GA20ox in the GA4 biosynthesis pathway, and XERICO may be involved in the regulation of ABA and GA4 signaling through the ubiquitination pathway. WRKY32, WRKY71, DAM14, NAC8, ICE1, bHLH93, and TCP15 also participated in the ABA/GA4 regulatory network, and ICE1 may be the key factor linking temperature signals and hormone metabolism. These results will help to reveal the bulb dormancy molecular mechanism and develop new strategies for high-quality bulb production.


Assuntos
Lilium , Regulação da Expressão Gênica de Plantas , Lilium/genética , Metabolômica , Dormência de Plantas , Sementes , Transcriptoma
12.
BMC Plant Biol ; 21(1): 292, 2021 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-34167472

RESUMO

BACKGROUND: Parthenocarpy results in traits attractive to both consumers and breeders, and it overcomes the obstacle of self-incompatibility in the fruit set of horticultural crops, including pear (Pyrus bretshneider). However, there is limited knowledge regarding the genetic and molecular mechanisms that regulate parthenogenesis. RESULTS: Here, in a transcriptional comparison between pollination-dependent fruit and GA4-induced parthenocarpy, PbCYP78A6 was identified and proposed as a candidate gene involved in parthenocarpy. PbCYP78A6 is similar to Arabidopsis thaliana CYP78A6 and highly expressed in pear hypanthia. The increased PbCYP78A6 expression, as assessed by RT-qPCR, was induced by pollination and GA4 exposure. The ectopic overexpression of PbCYP78A6 contributed to parthenocarpic fruit production in tomato. The PbCYP78A6 expression coincided with fertilized and parthenocarpic fruitlets development and the expression of fruit development-related genes as assessed by cytological observations and RT-qPCR, respectively. PbCYP78A6 RNA interference and overexpression in pear calli revealed that the gene is an upstream regulator of specific fruit development-related genes in pear. CONCLUSIONS: Our findings indicate that PbCYP78A6 plays a critical role in fruit formation and provide insights into controlling parthenocarpy.


Assuntos
Ciclo Celular , Sistema Enzimático do Citocromo P-450/genética , Genes de Plantas/genética , Partenogênese , Proteínas de Plantas/genética , Pyrus/metabolismo , Ciclo Celular/genética , Ciclo Celular/fisiologia , Sistema Enzimático do Citocromo P-450/fisiologia , Perfilação da Expressão Gênica , Genes de Plantas/fisiologia , Partenogênese/genética , Partenogênese/fisiologia , Filogenia , Proteínas de Plantas/fisiologia , Polinização , Pyrus/genética , Pyrus/crescimento & desenvolvimento , Pyrus/fisiologia
13.
Plant Mol Biol ; 105(1-2): 83-97, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32926248

RESUMO

KEY MESSAGE: This study is the first to demonstrate that GA4-induced dormancy release is associated with the NF-Y complex, which interacts with gibberellin inhibitor RGL2 in Japanese apricot. Seasonal dormancy is not only vital for the survival in cold winter but also affects flowering of temperate fruit trees and the dormancy release depends on the accumulation of the cold temperatures (Chilling requirement-CR). To understand the mechanism of dormancy release in deciduous fruit crops, we compared miRNA sequencing data during the transition stage from paradormancy to dormancy release in the Japanese apricot and found that the miR169 family showed significant differentially up-regulated expression during dormancy induction and was down-regulated during the dormancy release periods. The 5' RACE assay and RT-qPCR validated its target gene NUCLEAR FACTOR-Y subunit A (NF-YA), which exhibited the opposite expression pattern. Further study showed that exogenous GA4 could inhibit the expression of the gibberellic acid (GA) signal transduction suppressor PmRGL2 (RGA-LIKE 2) and promote the expression of NF-Y. Moreover, the interaction between the NF-Y family and GA inhibitor PmRGL2 was verified by the yeast-two-hybrid (Y2H) system and a bimolecular fluorescence complementarity (BiFC) experiment. These results suggest that synergistic regulation of the NF-Y and PmRGL2 complex leads to the activation of dormancy release induced by GA4. These findings will help to elucidate the functional and regulatory roles of miR169 and NF-Y complex in seasonal bud dormancy induced by GA in Japanese apricot and provide new insights for the discovery of dormancy release mechanisms in woody plants.


Assuntos
Fator de Ligação a CCAAT/metabolismo , MicroRNAs/metabolismo , Dormência de Plantas/fisiologia , Proteínas de Plantas/metabolismo , Prunus/metabolismo , Fatores de Transcrição/metabolismo , Fator de Ligação a CCAAT/genética , Temperatura Baixa , Flores/genética , Flores/crescimento & desenvolvimento , Flores/metabolismo , Frutas/metabolismo , Regulação da Expressão Gênica de Plantas , Giberelinas/metabolismo , Giberelinas/farmacologia , MicroRNAs/genética , Dormência de Plantas/efeitos dos fármacos , Dormência de Plantas/genética , Proteínas de Plantas/genética , Prunus/genética , Análise de Sequência de RNA , Fatores de Transcrição/genética , Transcriptoma
14.
Cell Genom ; 1(2): 100031, 2021 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-36778584

RESUMO

The current paradigm for data use oversight of biomedical datasets is onerous, extending the timescale and resources needed to obtain access for secondary analyses, thus hindering scientific discovery. For a researcher to utilize a controlled-access dataset, a data access committee must review her research plans to determine whether they are consistent with the data use limitations (DULs) specified by the informed consent form. The newly created GA4GH data use ontology (DUO) holds the potential to streamline this process by making data use oversight computable. Here, we describe an open-source software platform, the Data Use Oversight System (DUOS), that connects with DUO terminology to enable automated data use oversight. We analyze dbGaP data acquired since 2006, finding an exponential increase in data access requests, which will not be sustainable with current manual oversight review. We perform an empirical evaluation of DUOS and DUO on selected datasets from the Broad Institute's data repository. We were able to structure 118/123 of the evaluated DULs (96%) and 52/52 (100%) of research proposals using DUO terminology, and we find that DUOS' automated data access adjudication in all cases agreed with the DAC manual review. This first empirical evaluation of the feasibility of automated data use oversight demonstrates comparable accuracy to human-based data access oversight in real-world data governance.

15.
J Law Med ; 27(4): 829-838, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32880401

RESUMO

As the rush to understand and find solutions to the coronavirus disease 2019 pandemic continues, it is timely to re-examine the legal, social and ethical drivers for sharing health-related data from individuals around the globe. International collaboration and data sharing will be essential to the research effort. This raises the question of whether the urgent imperative to find therapies and vaccines may justify some temporary rebalancing of existing ethical and regulatory standards. The Global Alliance for Genomic Health is playing a leading role in collecting information about national approaches to these challenging questions. In this section, we examine some of the initiatives being taken in Australia against this global backdrop.


Assuntos
Infecções por Coronavirus , Disseminação de Informação , Pandemias , Pneumonia Viral , Austrália , Betacoronavirus , COVID-19 , Humanos , SARS-CoV-2
16.
Plants (Basel) ; 9(8)2020 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-32752115

RESUMO

Dense plant cultivation is an efficient approach to improve maize production by maximizing the utilization of energy and nutrients. However, dense plant populations may aggravate the abortion rate of young grains, resulting in fewer kernels per ear. The rate and duration of grain-filling play decisive roles in maize grain yield. Therefore, to increase plant density, enhancing the grain-filling rate, extending the growth period of individual maize plants and regulating crop senescence would be the first priority. In this study, we examined the regulatory effects of GA4+7 under two application methods: shanks and silks were moistened by cotton full with GA4+7 solution at concentrations of 0, 10, 60, and 120 mg L-1. The results showed that GA4+7 improved the grain-filling rate by increasing the content of auxin, gibberellin, zeatin, and abscisic acid in grains compared to control plants. In addition, the auxin, gibberellin, and zeatin contents in the grains were positively and significantly correlated with the maximum grain weight and the maximum and mean grain-filling rates. Moreover, GA4+7 increased the activities of superoxide dismutases, catalases, and peroxidases and reduced the malondialdehyde content in leaves compared with untreated plants. At the concentration of 60 mg L-1, GA4+7 showed the greatest effect on shank and silk applications (Sh-60 and Si-60) followed by 10 mg L-1 (Sh-10) for shank treatment and 120 mg L-1 (Si-120) for silk treatment. Our results suggest that a concentration of 60 mg L-1 GA4+7 for shank and silk application may be efficiently used for changing the level of hormones in grains and antioxidant enzymes in ear leaves, which may be useful for enhancing grain-filling rate and delaying leaf senescence, resulting in an increase in maize grain yield.

17.
ACS Appl Bio Mater ; 3(1): 477-485, 2020 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-35019464

RESUMO

The spontaneous electron transfer between GaAs and ionic gold through the galvanic displacement reaction results in the formation of gold nanoparticles and a Au9Ga4 alloy. We investigated this process for decorating Legionella pneumophila and Escherichia coli, aiming at enhanced imaging of these bacteria. The surface of bacteria was modified with gold ions through the electrostatic linkage of ionic liquids with phosphate units of the bacterial cell wall. The modified bacteria were further incubated with an antibody-functionalized GaAs substrate. Due to a large gap in the reduction potential of gold and gallium ions, the induced reaction involving bacteria resulted in a reduction of the gold ions to gold nanoparticles and oxidation of GaAs to Ga2O3 and a Au9Ga4 alloy. The bacteria covered with a Au/AuGa nanoshell, if excited at 377 nm, show a bright emission at 447 nm originating from Au/Au9Ga4. This approach offers a simple and potentially less expensive method for high-contrast imaging of bacteria in comparison to the conventional methods of staining with different dyes or by conjugating green fluorescent proteins.

18.
Gigascience ; 8(5)2019 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-31077313

RESUMO

BACKGROUND: The study of genetic variations is the basis of many research domains in biology. From genome structure to population dynamics, many applications involve the use of genetic variants. The advent of next-generation sequencing technologies led to such a flood of data that the daily work of scientists is often more focused on data management than data analysis. This mass of genotyping data poses several computational challenges in terms of storage, search, sharing, analysis, and visualization. While existing tools try to solve these challenges, few of them offer a comprehensive and scalable solution. RESULTS: Gigwa v2 is an easy-to-use, species-agnostic web application for managing and exploring high-density genotyping data. It can handle multiple databases and may be installed on a local computer or deployed as an online data portal. It supports various standard import and export formats, provides advanced filtering options, and offers means to visualize density charts or push selected data into various stand-alone or online tools. It implements 2 standard RESTful application programming interfaces, GA4GH, which is health-oriented, and BrAPI, which is breeding-oriented, thus offering wide possibilities of interaction with third-party applications. The project home page provides a list of live instances allowing users to test the system on public data (or reasonably sized user-provided data). CONCLUSIONS: This new version of Gigwa provides a more intuitive and more powerful way to explore large amounts of genotyping data by offering a scalable solution to search for genotype patterns, functional annotations, or more complex filtering. Furthermore, its user-friendliness and interoperability make it widely accessible to the life science community.


Assuntos
Biologia Computacional , Genômica , Genótipo , Software , Bases de Dados Genéticas , Variação Genética/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Internet , Polimorfismo de Nucleotídeo Único/genética , Interface Usuário-Computador
19.
Plant Mol Biol ; 99(4-5): 461-476, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30710225

RESUMO

KEY MESSAGE: ABA/GA4 ratio, stress resistance, carbon and nitrogen metabolism, and chromatin structure play important roles in vigour differences of seeds located at different maize ear positions. Seed vigour, which ensures rapid and uniform field emergence across diverse environments, differs at different maize ear positions. However, little is known regarding the associated mechanisms. In this study, we determined that seed vigour, stress resistance, and carbon and nitrogen metabolism were higher in seeds from middle and bottom section of the ear, while the ABA/GA4 ratio in the embryos was significantly lower. Compared with the seeds subjected to repeated pollination during silking, less variation in seed vigour and the ABA/GA4 ratio in the embryos was observed in seeds at different ear positions subjected to single pollination after complete silking. This indicated that single pollination can reduce, but not eliminate, the differences in seed vigour at different ear positions. RNA-seq analysis indicated that the seed vigour differences at the different locations of the maize ears of the single pollinated treatment were related to carbon and nitrogen metabolism. In contrast, the differences in seed vigour under repeated pollination were related to chromatin structure. The present study contributes to our understanding of the mechanisms underlying differences in seed vigour at different positions on the maize ear.


Assuntos
Adaptação Fisiológica , Reguladores de Crescimento de Plantas/metabolismo , Sementes/metabolismo , Análise de Sequência de RNA , Estresse Fisiológico , Zea mays/metabolismo , Ácido Abscísico/genética , Ácido Abscísico/metabolismo , Carbono/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Giberelinas/genética , Giberelinas/metabolismo , Nitrogênio/metabolismo , Reguladores de Crescimento de Plantas/genética , Polinização , RNA de Plantas/análise , Sementes/genética , Zea mays/genética
20.
ACS Appl Mater Interfaces ; 10(48): 41512-41524, 2018 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-30379517

RESUMO

The increasing interest in the development of ratiometric optical thermal sensors has led to a wide variety of new systems with promising properties. Among them, singly-doped ratiometric thermometers were recently demonstrated to be particularly reliable. With the aim to discuss the development of an ideal optical thermal sensor, a combined experimental and theoretical insight into the spectroscopy of the Bi2Ga4O9:Cr3+ system is reported showing the importance of an insightful analysis in a wide temperature range. Low-temperature photoluminescence analysis (from 10 K) and the temperature dependence of the lifetime investigation, together with the crystal field analysis and the modeling of the thermal quenching process, allow the estimation of key parameters such as the Debye temperature (cutoff frequency), the Huang-Rhys parameter, and the energy barrier between 2Eg and 4T2g. Additionally, by considering the reliable class of singly-doped ratiometric thermometers based on a couple of excited states obeying the Boltzmann law, the important role played by the absolute sensitivity was discussed and the great potential of Cr3+ singly-activated systems was demonstrated. The results may provide new guidelines for the design of reliable optical thermometers with outstanding and robust performances.

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