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1.
Neotrop. ichthyol ; 20(1): e210153, 2022. tab, graf
Article in English | LILACS, VETINDEX | ID: biblio-1365199

ABSTRACT

Despite several difficulties in chromosomal analyses of small-sized fishes, the cytogenetics of the Lebiasinidae was largely improved in the last years, showing differential patterns in the chromosomal evolution inside the family. In this context, it has been shown that genus Lebiasina preserves its karyotypic macrostructure, composed of 2n = 36 chromosomes, whereas the other genera generally present higher 2n. This study focused on the comparative cytogenetics of three Lebiasina species, one of them analyzed here for the first time, using conventional and molecular procedures. The results reinforced the differentiated evolutionary path of the genus Lebiasina while, at the same time, highlighted the genomic particularities that have accompanied the evolution of each species. In this sense, the repetitive components of the genome played a significant role in the differentiation of each species. It is also notable that L. minuta and L. melanoguttata, the two species that occur exclusively in the Brazilian territory, show greater chromosomal similarities to each other than to the trans-Andean sister species, L. bimaculata.(AU)


Apesar das dificuldades encontradas em se realizar análises cromossômicas em peixes de pequeno porte, os estudos citogenéticos em Lebiasinidae vêm crescendo nos últimos anos e demonstrando padrões diferenciados na evolução cromossômica entre os membros da família. Nesse contexto, o gênero Lebiasina tem mostrado preservar sua macroestrutura cariotípica, composta por 2n = 36 cromossomos, enquanto os demais gêneros geralmente apresentam 2n maiores. Este estudo tem como foco a citogenética comparativa de três espécies de Lebiasina, sendo uma delas analisada pela primeira vez aqui, através do emprego de técnicas convencionais e moleculares. Os resultados obtidos reforçam a trajetória evolutiva diferenciada do gênero Lebiasina, ao mesmo tempo em que evidenciam as particularidades genômicas que acompanham a evolução de cada uma das espécies. Neste contexto, os componentes repetitivos do genoma tiveram um papel importante na caracterização particular de cada uma das espécies. Também, é notável que L. minuta e L. melanoguttata, duas espécies que ocorrem exclusivamente no território brasileiro, apresentam maior proximidade citogenética entre elas do que com a espécie irmã transandina, L. bimaculata.(AU)


Subject(s)
Animals , Chromosomes , Genome , Cytogenetics , Characiformes/genetics , Hybridization, Genetic
2.
MedUNAB ; 24(3): 365-374, 202112.
Article in Spanish | LILACS | ID: biblio-1353572

ABSTRACT

Introducción. El carcinoma de endometrio es una patología heterogénea a nivel patogénico, histopatológico y molecular. En los últimos años se han sumado esfuerzos para esclarecer y aumentar el conocimiento de las bases moleculares, logrando así dividir las pacientes en cuatro subgrupos descritos por el Atlas del Genoma del Cáncer (TCGA, por sus siglas en inglés), obteniéndose valiosa información que afecta el diagnóstico, tratamiento y pronóstico de las pacientes con esta enfermedad. El objetivo de la siguiente revisión es exponer la nueva clasificación molecular del carcinoma de endometrio, así como discutir las ventajas que esta trae a la hora de estratificar a las pacientes y tomar decisiones terapéuticas. División de los temas tratados. Se realizó una búsqueda bibliográfica no sistemática en las bases de datos PubMed, Cochrane y Medline desde el año 2014 hasta el 2020 sobre el carcinoma de endometrio y su clasificación molecular. Se expone de manera concreta y actualizada el contexto histórico, los diferentes subgrupos moleculares y cómo estos impactan en el manejo de las pacientes. Conclusiones. El carcinoma de endometrio es una enfermedad heterogénea a nivel histopatológico, clínico y molecular. Con la nueva clasificación y los estudios prospectivos se podrán crear nuevas estrategias que permitan brindar mejores protocolos diagnósticos y terapéuticos.


Introduction. Endometrial carcinoma is a heterogeneous pathology in pathologenic, histopathological, and molecular terms. Over the last years, efforts have been made to clarify and increase knowledge of molecular bases, as such dividing patients into four subgroups described by the The Cancer Genome Atlas (TCGA), obtaining valuable information that affects the diagnosis, treatment, and prognosis of patients with this disease. The objective of this review is to exhibit the new molecular classification of endometrial carcinoma, and to discuss its advantages when stratifying patients and making therapeutic decisions. Division of Covered Topics. A non-systematic bibliographical search was carried out in the PubMed, Cochrane, and Medline databases from 2014 to 2020, on endometrial carcinoma and its molecular classification. The historical context, different molecular subgroups and how these impact patient handling are shown in a concrete and updated way. Conclusions. Endometrial carcinoma is a heterogeneous disease in histopathological, clinical, and molecular terms. With the new classification and the prospective studies, new strategies can be created to provide better diagnostic and therapeutic protocols.


Introdução. O carcinoma de endométrio é uma patologia heterogênea no nível patogênico, histopatológico e molecular. Nos últimos anos, foram feitos esforços para esclarecer e aumentar o conhecimento das bases moleculares, conseguindo dividir as pacientes em quatro subgrupos descritos pelo Atlas do Genoma do Câncer (TCGA, por suas siglas em inglês), obtendo informações valiosas que afetam o diagnóstico, o tratamento e o prognóstico das pacientes com esta doença. O objetivo da seguinte revisão é apresentar a nova classificação molecular do carcinoma de endométrio, bem como discutir as vantagens que ela traz no momento de estratificar as pacientes e tomar decisões terapêuticas. Divisão dos tópicos abordados. Uma pesquisa bibliográfica não sistemática foi realizada nas bases de dados PubMed, Cochrane e Medline de 2014 a 2020 sobre o carcinoma de endométrio e sua classificação molecular. São apresentados de forma concreta e atualizada o contexto histórico, os diferentes subgrupos moleculares e como esses têm impacto no tratamento das pacientes. Conclusões. O carcinoma de endométrio é uma doença heterogênea no nível histopatológico, clínico e molecular. Com a nova classificação e estudos prospectivos, novas estratégias podem ser desenvolvidas para fornecer melhores protocolos diagnósticos e terapêuticos.


Subject(s)
Endometrial Neoplasms , Prognosis , Immunohistochemistry , Carcinoma , Genome , Endometrium
3.
Electron J Biotechnol ; 49: 1-4, Jan. 2021. tab, ilus
Article in Spanish | LILACS | ID: biblio-1291931

ABSTRACT

BACKGROUND: Brucella canis is the etiological agent of canine brucellosis, a worldwide neglected zoonosis that constitutes one of the major infectious causes of infertility and reproductive failure in dogs. Although genomic information available for this pathogen has increased in recent years, here we report the first genome sequencing of a B. canis strain in Chile, and the differences in virulence genes with other B. canis strains. RESULTS: Genome assembly produced a total length of 3,289,216 bp, N50 of 95,163 and GC% of 57.27, organized in 54 contigs in chromosome I, and 21 contigs in chromosome II. The genome annotation identified a total of 1981 CDS, 3 rRNA and 36 tRNA in chromosome I, and 1113 CDS and 10 tRNA in chromosome II. There is little variation between the different strains and the SCL isolate. Phylogenetic analysis showed that the Chilean SCL strain is closely related to B. canis and B. suis strains. Small differences were found when compared to the Serbian isolate, but all strains shared the same recent common ancestor. Finally, changes in the sequence of some virulence factors showed that the SCL strain is similar to other South American B. canis strains. CONCLUSIONS: This work sequenced and characterized the complete genome of B. canis strain SCL, evidencing the complete presence of all the genes of the virB operon, and minor changes in outer membrane proteins and in the urease operon. Our data suggest that B. canis was introduced from North America and then spread throughout the South American continent.


Subject(s)
Animals , Dogs , Brucellosis/epidemiology , Brucella canis/genetics , Brucella canis/pathogenicity , Urease/genetics , Brucellosis/transmission , Zoonoses , Chile , Genome
4.
Braz. j. med. biol. res ; 54(3): e9571, 2021. tab, graf
Article in English | LILACS | ID: biblio-1153526

ABSTRACT

Cancer cell lines are widely used as in vitro models of tumorigenesis, facilitating fundamental discoveries in cancer biology and translational medicine. Currently, there are few options for glioblastoma (GBM) treatment and limited in vitro models with accurate genomic and transcriptomic characterization. Here, a detailed characterization of a new GBM cell line, namely AHOL1, was conducted in order to fully characterize its molecular composition based on its karyotype, copy number alteration (CNA), and transcriptome profiling, followed by the validation of key elements associated with GBM tumorigenesis. Large numbers of CNAs and differentially expressed genes (DEGs) were identified. CNAs were distributed throughout the genome, including gains at Xq11.1-q28, Xp22.33-p11.1, Xq21.1-q21.33, 4p15.1-p14, 8q23.2-q23.3 and losses at Yq11.21-q12, Yp11.31-p11.2, and 15q11.1-q11.2 positions. Nine druggable genes were identified, including HCRTR2, ETV1, PTPRD, PRKX, STS, RPS6KA6, ZFY, USP9Y, and KDM5D. By integrating DEGs and CNAs, we identified 57 overlapping genes enriched in fourteen pathways. Altered expression of several cancer-related candidates found in the DEGs-CNA dataset was confirmed by RT-qPCR. Taken together, this first comprehensive genomic and transcriptomic landscape of AHOL1 provides unique resources for further studies and identifies several druggable targets that may be useful for therapeutics and biologic and molecular investigation of GBM.


Subject(s)
Humans , Glioblastoma/genetics , Gene Expression Regulation, Neoplastic , Minor Histocompatibility Antigens , Genome , Genomics , Cell Line, Tumor , Histone Demethylases , Transcriptome
5.
Science ; 372(6544): 1-7, 2021. graf
Article in English | ColecionaSUS, LILACS, ColecionaSUS, SES-SP, CONASS, SESSP-IALPROD, SES-SP | ID: biblio-1247888

ABSTRACT

Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.


Subject(s)
Angiotensins , Genome , Betacoronavirus
6.
Chinese Journal of Biotechnology ; (12): 1526-1540, 2021.
Article in Chinese | WPRIM | ID: wpr-878653

ABSTRACT

Genome-scale metabolic network model (GSMM) is becoming an important tool for studying cellular metabolic characteristics, and remarkable advances in relevant theories and methods have been made. Recently, various constraint-based GSMMs that integrated genomic, transcriptomic, proteomic, and thermodynamic data have been developed. These developments, together with the theoretical breakthroughs, have greatly contributed to identification of target genes, systems metabolic engineering, drug discovery, understanding disease mechanism, and many others. This review summarizes how to incorporate transcriptomic, proteomic, and thermodynamic-constraints into GSMM, and illustrates the shortcomings and challenges of applying each of these methods. Finally, we illustrate how to develop and refine a fully integrated GSMM by incorporating transcriptomic, proteomic, and thermodynamic constraints, and discuss future perspectives of constraint-based GSMM.


Subject(s)
Genome/genetics , Metabolic Engineering , Metabolic Networks and Pathways/genetics , Models, Biological , Proteomics
7.
Chinese Journal of Biotechnology ; (12): 1821-1826, 2021.
Article in Chinese | WPRIM | ID: wpr-887765

ABSTRACT

Natural products, important sources of innovative drugs, food, spices and daily chemicals, are closely related to people's healthy life. With the development and integration of modern biological and chemical technologies of natural products, the researches on biosynthesis of natural products have made great progresses in recent years. The biosynthetic pathways of a number of natural products have been analyzed. Many pathway enzymes and modifying enzymes involved in the biosynthesis of natural products have been mined and functionally characterized. Furthermore, genes encoding pathway enzymes have been introduced into chassis to construct cell factories producing natural products through synthetic biology technologies. Also, other biotechnologies including genome editing and genome mining, have been used in the biosynthesis of natural products. In order to further promote the development of researches on biosynthesis of natural products, we edited a Special Issue on the topic of "biosynthesis of natural products", focusing on the researches progress in three aspects: the analysis of biosynthetic pathways of natural products, genome-wide mining and functional characterization of genes encoding tool enzymes, and the scale preparation of natural products by biosynthetic technology. Also included in this Special Issue was the prospect of the biosynthesis of natural products. This Special Issue can provide reference and guidance for the further development of natural product biosynthesis.


Subject(s)
Biological Products , Biosynthetic Pathways/genetics , Biotechnology , Genome , Synthetic Biology
8.
Chinese Journal of Biotechnology ; (12): 980-990, 2021.
Article in Chinese | WPRIM | ID: wpr-878608

ABSTRACT

Aspergillus niger is a vital industrial workhouse widely used for the production of organic acids and industrial enzymes. This fungus is a crucial cell factory due to its innate tolerance to a diverse range of abiotic conditions, high production titres, robust growth during industrial scale fermentation, and status as a generally recognized as safe (GRAS) organism. Rapid development of synthetic biology and systems biology not only offer powerful approaches to unveil the molecular mechanisms of A. niger productivity, but also provide more new strategies to construct and optimize the A. niger cell factory. As a new generation of genome editing technology, the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR associated (Cas) system brings a revolutionary breakthrough in targeted genome modification for A. niger. In this review, we focus on current advances to the CRISPR/Cas genome editing toolbox, its application on gene modification and gene expression regulation in this fungal. Moreover, the future directions of CRISPR/Cas genome editing in A. niger are highlighted.


Subject(s)
Aspergillus niger/genetics , CRISPR-Cas Systems/genetics , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , Gene Editing , Genome
9.
Gac. méd. boliv ; 43(2): 179-183, dic. 2020. ilus
Article in Spanish | LILACS | ID: biblio-1249981

ABSTRACT

El artículo se centra en la utilización de la nueva herramienta, CRISPR (repeticiones palindrómicas cortas agrupadas a intervalos regulares), la cual permite editar los genomas de los seres vivos de manera más precisa que otras técnicas; a lo largo del artículo se mencionan trabajos relacionados con la detención de la angiogénesis, cáncer, Sarcoma de Kaposi en inmunodeficiencias, Parkinson, regeneración y modificación genética en humanos, todas estas investigaciones tiene en común la utilización de la herramienta CRISPR. También se comenta las complicaciones éticas que conlleva utilizar esta tecnología en el ADN de células embrionarias humanas, que según diferentes criterios, podrían llevar a generar seres humanos “mejorados”, es decir no solo sin susceptibilidad a enfermedades degenerativas o incurables, sino también modificados en aspectos físicos que no necesariamente estarían ligados a alguna patología.


The article focuses on the use of the new tool, CRISPR (short palindromic repetitions grouped at regular intervals), which allows editing the genomes of living beings more accurately than other techniques; Throughout the article, works related to the arrest of angiogenesis, cancer, Kaposi’s sarcoma in immunodeficiencies, Parkinson’s, regeneration and genetic modification in humans are mentioned, all these investigations have in common the use of the CRISPR tool. You can also comment on the ethical complications that involve using this technology in the DNA of human embryonic cells, which according to different criteria, carry out improved human beings, that is not only without susceptibility to degenerative or incurable diseases, but also modified in physical aspects that are not linked to any pathology.


Subject(s)
DNA , Clustered Regularly Interspaced Short Palindromic Repeats , Sarcoma, Kaposi , Cells , Genome , Genetics , Neoplasms
10.
Electron. j. biotechnol ; 44: 25-32, Mar. 2020. graf, tab, ilus
Article in English | LILACS | ID: biblio-1087637

ABSTRACT

BACKGROUND: Cultivated peanut (Arachis hypogaea. L) represents one of the most important oil crops in the world. Although much effort has been expended to characterize microsatellites or Simple Sequence Repeats (SSRs) in peanut, the quantity and quality of the markers in breeding applications remain limited. Here, genome-wide SSR characterization and marker development were performed using the recently assembled genome of the cultivar Tifrunner. RESULTS: In total, 512,900 microsatellites were identified from 2556.9-Mb genomic sequences. Based on the flanking sequences of the identified microsatellites, 7757 primer pairs (markers) were designed, and further evaluated in the assembled genomic sequences of the tetraploid Arachis cultivars, Tifrunner and Shitouqi, and the diploid ancestral species, A. duranensis and A. ipaensis. In silico PCR analysis showed that the SSR markers had high amplification efficiency and polymorphism in four Arachis genotypes. Notably, nearly 60% of these markers were single-locus SSRs in tetraploid Arachis species, indicating they are more specific in distinguishing the alleles of the A and B sub-genomes of peanut. In addition, two markers closely related with purple testa color and 27 markers near to FAD2 genes were identified, which could be used for breeding varieties with purple testa and high-oleic acid content, respectively. Moreover, the potential application of these SSR markers in tracking introgressions from Arachis wild relatives was discussed. CONCLUSIONS: This study reported the development of genomic SSRs from assembled genomic sequences of the tetraploid Arachis Tifrunner, which will be useful for diversity analysis, genetic mapping and functional genomics studies in peanut


Subject(s)
Arachis/genetics , Breeding/methods , Microsatellite Repeats , Polymorphism, Genetic , Genetic Markers , Polymerase Chain Reaction , Genome , Crops, Agricultural
11.
Article in Korean | WPRIM | ID: wpr-811373

ABSTRACT

OBJECTIVES: Most cohort studies used food frequency questionnaires (FFQ) to evaluate coffee consumption as it assesses habitual dietary patterns, whereas some studies have used the 24-hour recalls (24HR) as it elicits in-depth description of foods and the amount eaten. The aim of this study was to compare FFQs and 24HR to assess the consumption of various types of coffee.METHODS: We included 25,904 participants aged 40 years or older from the Health Examinees (HEXA) Study of the Korean Genome and Epidemiologic Study (KoGES). Each participant completed one FFQ and one-day (n=11,280) or two-day 24HR (n=14,624). We classified coffee types into: black coffee, coffee with sugar and cream, and coffee with sugar alone or cream alone. We compared the proportions of nondrinkers, black coffee, and coffee with sugar and cream through FFQ and 24HR.RESULTS: Among those who completed one FFQ and one-day 24HR, 39.4% of “nondrinkers” on one-day 24HR reported that they did not drink coffee on their FFQs. Whereas among those who complete two-day 24HR, 71.2% of “nondrinkers” on two-day 24HR said that they did not drink coffee on their FFQs. Among those who completed one FFQ and oneday 24HR, 58.3% marked “black coffee” on one-day 24HR said that they drank black coffee on their FFQs. Among those who complete two-day 24HR, 58.8% marked “black coffee” on two-day 24HR said that they drank black coffee on their FFQs. The kappa coefficients and percent agreements were 0.4 and 59.6%, respectively, for the comparison of coffee intake between FFQ and one-day 24HR, and 0.6 and 72.8%, respectively, for the comparison of coffee intake between FFQ and two-day 24HR.CONCLUSIONS: We found discrepancies between FFQs and 24HR in the types of coffee consumed. Such limitations should be considered when using the 24HR data to examine the effect of coffee consumption on disease development.


Subject(s)
Coffee , Cohort Studies , Epidemiologic Studies , Genome
12.
Article in Korean | WPRIM | ID: wpr-811372

ABSTRACT

OBJECTIVES: This study examined the association of the total diet quality with the incidence risk of metabolic syndrome constituents and metabolic syndrome among Korean adults.METHODS: Based on a community-based cohort of the Korean Genome and Epidemiology Study (KoGES) from 2001 to 2014, data from a total of 5,549 subjects (2,805 men & 2,744 women) aged 40~69 years at the baseline with a total follow-up period of 38,166 person-years were analyzed. The criteria of the National Cholesterol Education Program Adult Treatment Panel was employed to define metabolic syndrome. The total diet quality was estimated using the Korean Healthy Eating Index (KHEI). Hazard ratios (HR) and 95% confidence intervals (CI) for risk of metabolic syndrome constituents and metabolic syndrome in relation to KHEI quintile groups was calculated by multivariate Cox proportional hazards regression model.RESULTS: After adjusting for age, energy intake, income, education, physical activity, smoking, and drinking, the incidence of abdominal obesity and high blood pressure was significantly lower, by approximately 29.7% (P < 0.01) and 25.2% (P < 0.01), respectively, in the fifth KHEI quintile compared to the first quintile in men. A significant decreasing trend of the metabolic syndrome incidence was observed across the improving levels of KHEI (HRq5vs.q1: 0.775, 95% CIq5vs.q1: 0.619~0.971, P for trend < 0.01). In women, the incidence of abdominal obesity and metabolic syndrome was significantly lower, by approximately 29.8% (P < 0.01) and 22.5% (P < 0.05), respectively, in the fifth KHEI quintile compared to the first quintile adjusting for multiple covariates. On the other hand, the linear trend of metabolic syndrome risk across the KHEI levels did not reach the significance level.CONCLUSIONS: A better diet quality can prevent future metabolic syndrome and its certain risk factors among Korean men and women.


Subject(s)
Adult , Cholesterol , Cohort Studies , Diet , Drinking , Eating , Education , Energy Intake , Epidemiology , Female , Follow-Up Studies , Genome , Hand , Humans , Hypertension , Incidence , Male , Obesity, Abdominal , Physical Education and Training , Prospective Studies , Risk Factors , Smoke , Smoking
13.
Article in English | WPRIM | ID: wpr-811198

ABSTRACT

PURPOSE: We investigated the expression of the N-myc and STAT interactor (NMI) protein in invasive ductal carcinoma tissue and estimated its clinicopathologic significance as a prognostic factor. The expression levels and prognostic significance of NMI were also analyzed according to the molecular subgroup of breast cancers.METHODS: Human NMI detection by immunohistochemistry was performed using tissue microarrays of 382 invasive ductal carcinomas. The correlation of NMI expression with patient clinicopathological parameters and prognostic significance was analyzed and further assessed according to the molecular subgroup of breast cancers. Moreover, in vitro experiments with 13 breast cancer cell lines were carried out. We also validated NMI expression significance in The Cancer Genome Atlas cohort using the Human Protein Atlas (HPA) database.RESULTS: Low NMI expression was observed in 190 cases (49.7%). Low NMI expression was significantly associated with the “triple-negative” molecular subtype (p < 0.001), high nuclear grade (p < 0.001), high histologic grade (p < 0.001), and advanced anatomic stage (p = 0.041). Patients with low NMI expression had poorer progression-free survival (p = 0.038) than patients with high NMI expression. Low NMI expression was not significantly associated with patient prognosis in the molecular subgroup analysis. In vitro, a reduction of NMI expression was observed in 8 breast cancer cell lines, especially in the estrogen receptor-positive and basal B type of triple-negative breast cancer molecular subgroups. The HPA database showed that low NMI expression levels were associated with a lower survival probability compared with that associated with high NMI expression (p = 0.053).CONCLUSION: NMI expression could be a useful prognostic biomarker and a potential novel therapeutic target in invasive ductal carcinoma.


Subject(s)
Biomarkers, Tumor , Breast , Breast Neoplasms , Carcinoma, Ductal , Cell Line , Cohort Studies , Databases, Genetic , Disease-Free Survival , Down-Regulation , Estrogens , Genome , Humans , Immunohistochemistry , In Vitro Techniques , Prognosis , Triple Negative Breast Neoplasms
14.
Article in English | WPRIM | ID: wpr-811070

ABSTRACT

The transcriptome represents the complete set of RNA transcripts that are produced by the genome under a specific circumstance or in a specific cell. High-throughput methods, including microarray and bulk RNA sequencing, as well as recent advances in biostatistics based on machine learning approaches provides a quick and effective way of identifying novel genes and pathways related to asthma, which is a heterogeneous disease with diverse pathophysiological mechanisms. In this manuscript, we briefly review how to analyze transcriptome data and then provide a summary of recent transcriptome studies focusing on asthma pathogenesis and asthma drug responses. Studies reviewed here are classified into 2 classes based on the tissues utilized: blood and airway cells.


Subject(s)
Asthma , Biostatistics , Genetics , Genome , Machine Learning , RNA , Sequence Analysis, RNA , Transcriptome
15.
Article in English | WPRIM | ID: wpr-810955

ABSTRACT

Novel coronavirus (SARS-CoV-2) is found to cause a large outbreak started from Wuhan since December 2019 in China and SARS-CoV-2 infections have been reported with epidemiological linkage to China in 25 countries until now. We isolated SARS-CoV-2 from the oropharyngeal sample obtained from the patient with the first laboratory-confirmed SARS-CoV-2 infection in Korea. Cytopathic effects of SARS-CoV-2 in the Vero cell cultures were confluent 3 days after the first blind passage of the sample. Coronavirus was confirmed with spherical particle having a fringe reminiscent of crown on transmission electron microscopy. Phylogenetic analyses of whole genome sequences showed that it clustered with other SARS-CoV-2 reported from Wuhan.


Subject(s)
China , Coronavirus , Crowns , Genome , Humans , Korea , Microscopy, Electron , Microscopy, Electron, Transmission , Phylogeny , Vero Cells
18.
Chinese Journal of Biotechnology ; (12): 2791-2812, 2020.
Article in Chinese | WPRIM | ID: wpr-878530

ABSTRACT

Three-dimensional (3D) genomics is an emerging discipline that studies the 3D spatial structure and function of genomes, focusing on the 3D spatial conformation of genome sequences in the nucleus and its biological effects on biological processes such as DNA replication, DNA recombination and gene expression regulation. The invention of chromosome conformation capture (3C) technology speeds up the research on 3D genomics and its related fields. Furthermore, the development of 3C-based technologies, such as the genome-wide chromosome conformation capture (Hi-C) and chromatin interaction analysis using paired-end tag sequencing (ChIA-PET), help scientists get insight into the 3D genomes of various species. Aims of 3D genomics are to reveal the spatial genome organization, chromosomal interaction patterns, mechanisms underlying the transcriptional regulation and formation of biological traits of microorganism, plant, animal. Additionally, the identification of key genes and signaling pathways associated with biological processes and disease via chromosome 3C technology boosts the rapid development of agricultural science, life science and medical science. This paper reviews the research progress of 3D genomics, mainly in the concept of 3D genomics, the development of chromosome 3C technologies and their applications in agricultural science, life science and medical science, specifically in the field of tumor.


Subject(s)
Animals , Cell Nucleus , Chromatin/genetics , Chromosomes/genetics , Genome , Genomics
19.
Chinese Journal of Biotechnology ; (12): 2040-2050, 2020.
Article in Chinese | WPRIM | ID: wpr-878464

ABSTRACT

Linear chromatin is compacted into eukaryotic nucleus through a complex and multi-layered architecture. Consequently, chromatin conformation in a local or long-distance manner is strongly correlated with gene expression. Chromosome conformation capture (3C) technology, together with its variants like 4C/5C/Hi-C, has been well developed to study chromatin looping and whole genome structure. In this review, we introduce new technologies including chromosome capture combined with immunoprecipitation, nuclei acid-based hybridization, single cell and genome sequencing, as well as their application.


Subject(s)
Cell Nucleus , Chromatin/genetics , Chromosomes/genetics , Genetic Techniques , Genome/genetics
20.
Article in Korean | WPRIM | ID: wpr-816642

ABSTRACT

The 2019 novel coronavirus disease (COVID-19) outbreaks that emerged in Wuhan city, Hubei province, have led to a formidable number of confirmed cases that resulted in >5,700 deaths globally, including 143 countries in all 6 continents. The World Health Organization declared a Public Health Emergency of International Concern with a very high level of global risk assessment. Severe acute respiratory syndrome (SARS)-coronavirus-2 (SARS-CoV-2), the agent of COVID-19, has >79% nucleotide sequence homology to SARS-CoV; therefore, both belong to the genus betacoronavirus and subgenus sarbecovirus. The S1 domains of the two appeared to share the cellular receptor ACE2, but revealed a much higher S1-ACE2 binding affinity. As seen in many other human coronaviruses, SARS-CoV-2 also shows respiratory infection, but the basic reproductive number (R₀) in transmission and the clinical latency are quite dissimilar from those of SARS- or MERS-CoVs. Many scientists infer that the time point of cross-barrier transfer from bats to mediate animals or to humans should be a rather recent event based on the full-length genome analyses obtained from the very first patients. Copy-choice polymerization, which often leads to a significant genome recombination rate in most coronaviruses, predicts the continued emergence of novel coronaviruses.


Subject(s)
Animals , Base Sequence , Chiroptera , Coronavirus , Disease Outbreaks , Emergencies , Genome , Humans , Middle East Respiratory Syndrome Coronavirus , Molecular Biology , Polymerization , Polymers , Public Health , Recombination, Genetic , Risk Assessment , SARS Virus , Severe Acute Respiratory Syndrome , World Health Organization
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