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1.
Ann Lab Med ; 42(1): 24-35, 2022 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-34374346

RESUMEN

Background: Laboratory parameter abnormalities are commonly observed in COVID-19 patients; however, their clinical significance remains controversial. We assessed the prevalence, characteristics, and clinical impact of laboratory parameters in COVID-19 patients hospitalized in Daegu, Korea. Methods: We investigated the clinical and laboratory parameters of 1,952 COVID-19 patients on admission in nine hospitals in Daegu, Korea. The average patient age was 58.1 years, and 700 (35.9%) patients were men. The patients were classified into mild (N=1,612), moderate (N=294), and severe (N=46) disease groups based on clinical severity scores. We used chi-square test, multiple comparison analysis, and multinomial logistic regression to evaluate the correlation between laboratory parameters and disease severity. Results: Laboratory parameters on admission in the three disease groups were significantly different in terms of hematologic (Hb, Hct, white blood cell count, lymphocyte%, and platelet count), coagulation (prothrombin time and activated partial thromboplastin time), biochemical (albumin, aspartate aminotransferase, alanine aminotransferase, lactate, blood urea nitrogen, creatinine, and electrolytes), inflammatory (C-reactive protein and procalcitonin), cardiac (creatinine kinase MB isoenzyme and troponin I), and molecular virologic (Ct value of SARS-CoV-2 RdRP gene) parameters. Relative lymphopenia, prothrombin time prolongation, and hypoalbuminemia were significant indicators of COVID-19 severity. Patients with both hypoalbuminemia and lymphopenia had a higher risk of severe COVID-19. Conclusions: Laboratory parameter abnormalities on admission are common, are significantly associated with clinical severity, and can serve as independent predictors of COVID-19 severity. Monitoring the laboratory parameters, including albumin and lymphocyte count, is crucial for timely treatment of COVID-19.


Asunto(s)
COVID-19 , Análisis de Datos , Humanos , Laboratorios , Masculino , Persona de Mediana Edad , República de Corea/epidemiología , Estudios Retrospectivos , SARS-CoV-2
2.
Int J Mol Sci ; 22(13)2021 Jun 23.
Artículo en Inglés | MEDLINE | ID: mdl-34201749

RESUMEN

Plant abiotic stress responses are tightly regulated by different players at multiple levels. At transcriptional or post-transcriptional levels, several RNA binding proteins (RBPs) regulate stress response genes through RNA metabolism. They are increasingly recognized as critical modulators of a myriad of biological processes, including stress responses. Plant RBPs are heterogeneous with one or more conservative RNA motifs that constitute canonical/novel RNA binding domains (RBDs), which can bind to target RNAs to determine their regulation as per the plant requirements at given environmental conditions. Given its biological significance and possible consideration as a potential tool in genetic manipulation programs to improve key agronomic traits amidst frequent episodes of climate anomalies, studies concerning the identification and functional characterization of RBP candidate genes are steadily mounting. This paper presents a comprehensive overview of canonical and novel RBPs and their functions in major abiotic stresses including drought, heat, salt, and cold stress conditions. To some extent, we also briefly describe the basic motif structure of RBPs that would be useful in forthcoming studies. Additionally, we also collected RBP genes that were modulated by stress, but that lacked functional characterization, providing an impetus to conduct further research.


Asunto(s)
Proteínas de Plantas/química , Proteínas de Plantas/fisiología , Proteínas de Unión al ARN/química , Proteínas de Unión al ARN/fisiología , Estrés Fisiológico/fisiología , Respuesta al Choque por Frío/fisiología , Sequías , Respuesta al Choque Térmico/fisiología , Dominios Proteicos , Salinidad , Estrés Salino/fisiología
3.
Sci Rep ; 6: 29681, 2016 07 14.
Artículo en Inglés | MEDLINE | ID: mdl-27411898

RESUMEN

Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-generation sequencing technologies have facilitated the elucidation of the microbial community composition with higher accuracy and greater throughput than was previously achievable; however, the short sequencing reads often limit the microbial composition analysis at the species level due to the high similarity of 16S rRNA amplicon sequences. To overcome this limitation, we used the nanopore sequencing platform to sequence full-length 16S rRNA amplicon libraries prepared from the mouse gut microbiota. A comparison of the nanopore and short-read sequencing data showed that there were no significant differences in major taxonomic units (89%) except one phylotype and three taxonomic units. Moreover, both sequencing data were highly similar at all taxonomic resolutions except the species level. At the species level, nanopore sequencing allowed identification of more species than short-read sequencing, facilitating the accurate classification of the bacterial community composition. Therefore, this method of full-length 16S rRNA amplicon sequencing will be useful for rapid, accurate and efficient detection of microbial diversity in various biological and clinical samples.


Asunto(s)
Bacterias/genética , Microbioma Gastrointestinal/genética , ARN Ribosómico 16S/genética , Animales , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Masculino , Metagenoma/genética , Ratones , Ratones Endogámicos C57BL , Nanoporos , Análisis de Secuencia de ADN/métodos
4.
J Nanosci Nanotechnol ; 15(5): 3852-61, 2015 May.
Artículo en Inglés | MEDLINE | ID: mdl-26505015

RESUMEN

Clostridium aceticum is an anaerobic homoacetogen, able to reduce CO2 to multi-carbon products using the reductive acetyl-CoA pathway. This unique ability to use CO2 or CO makes the microbe a potential platform for the biotech industry. However, the development of genetically engineered homoacetogen for the large-scale production of commodity chemicals is hampered by the limited amount of their genetic and metabolic information. Here we exploited next-generation sequencing to reveal C. aceticum genome. The short-read sequencing produced 44,871,196 high quality reads with an average length of 248 bases. Following sequence trimming step, 30,256,976 reads were assembled into 12,563 contigs with 168-fold coverage and 1,971 bases in length using de Bruijn graph algorithm. Since the k-mer hash length in the algorithm is an important factor for the quality of output contigs, a window of k-mers (k-51 to k-201) was tested to obtain high quality contigs. In addition to the assembly metrics, the functional annotation of the contigs was investigated to select the k-mer optimum. Metabolic pathway mapping using the functional annotation identified the majority of central metabolic pathways, such as the glycolysis and TCA cycle. Further, these analyses elucidated the enzymes consisting of Wood-Ljungdahl pathway, in which CO2 is fixed into acetyl-CoA. Thus, the metabolic reconstruction based on the draft genome assembly provides a foundation for the functional genomics required to engineer C. aceticum.


Asunto(s)
Clostridium/genética , Genoma Bacteriano/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Redes y Vías Metabólicas/genética , Análisis de Secuencia de ADN/métodos , Secuencia de Aminoácidos , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Clostridium/metabolismo , ADN Bacteriano/análisis , ADN Bacteriano/genética , Datos de Secuencia Molecular , Alineación de Secuencia
5.
J Control Release ; 175: 10-6, 2014 Feb 10.
Artículo en Inglés | MEDLINE | ID: mdl-24333627

RESUMEN

Cell-based drug delivery systems (DDSs) have been increasingly exploited because cells can be utilized as a continuous drug delivering system to produce therapeutic molecules over a more extended period compared to the simple drug carriers. Although hydrogels have many advantages for this application, their mechanical properties are generally not desirable to structurally protect implanted cells. Here, we present a three-dimensional (3D) hybrid scaffold with a combination of a 3D framework and a hydrogel to enhance the mechanical properties without chemically altering the transport properties of the hydrogel. Based on the 3D Ormocomp scaffold (framework) fabricated by projection-based microstereolithography with defined parameters, we developed a 3D hybrid scaffold by injection of the mixture of cells and the alginate gel into the internal space of the framework. This hybrid scaffold showed the improved mechanical strength and the framework in the scaffold played the role of an adhesion site for the encapsulated cells during the culture period. Additionally, we confirmed its protection of exogenous human cells from acute immune rejection in a mouse model. Eventually, we demonstrated the feasibility of applying this hybrid scaffold to the treatment of Parkinson's disease as a cell-based DDS. Dopamine released from the 3D hybrid scaffolds encapsulating dopamine-secreting cells for 8weeks suggested its clinical applicability. Further study on its long-term efficacy is necessary for the clinical applicability of this 3D hybrid scaffold for the treatment of Parkinson's disease.


Asunto(s)
Dopaminérgicos/administración & dosificación , Dopamina/administración & dosificación , Sistemas de Liberación de Medicamentos/métodos , Hidrogel de Polietilenoglicol-Dimetacrilato/química , Andamios del Tejido/química , Alginatos/química , Animales , Células Cultivadas , Femenino , Ácido Glucurónico/química , Ácidos Hexurónicos/química , Humanos , Ratones , Ratones Endogámicos C57BL , Enfermedad de Parkinson/tratamiento farmacológico
6.
Genomics Inform ; 11(2): 76-82, 2013 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-23843773

RESUMEN

Over the past decade or so, dramatic developments in our ability to experimentally determine the content and function of genomes have taken place. In particular, next-generation sequencing technologies are now inspiring a new understanding of bacterial transcriptomes on a global scale. In bacterial cells, whole-transcriptome studies have not received attention, owing to the general view that bacterial genomes are simple. However, several recent RNA sequencing results are revealing unexpected levels of complexity in bacterial transcriptomes, indicating that the transcribed regions of genomes are much larger and complex than previously anticipated. In particular, these data show a wide array of small RNAs, antisense RNAs, and alternative transcripts. Here, we review how current transcriptomics are now revolutionizing our understanding of the complexity and regulation of bacterial transcriptomes.

7.
Games Health J ; 1(1): 69-73, 2012 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-26196435

RESUMEN

With the advent of the Apple iPad(®), learning applications (apps) have enabled children with special needs to have easy access to the technological benefits of computer-based learning. As the iPad was introduced into therapy for these children, we at Project Injini saw the potential for extending early intervention to therapeutic play at home. We developed the Injini Child Development Game Suite with specific guidelines in mind to design an app appropriate for children's abilities and needs. We field-tested Injini at schools and centers for disabilities to receive feedback. This article describes the initial results of these efforts.

8.
Genome Biol ; 11(9): R94, 2010.
Artículo en Inglés | MEDLINE | ID: mdl-20875114

RESUMEN

BACKGROUND: The species Brassica rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species. RESULTS: We have determined and analyzed the sequence of B. rapa chromosome A3. We obtained 31.9 Mb of sequences, organized into nine contigs, which incorporated 348 overlapping BAC clones. Annotation revealed 7,058 protein-coding genes, with an average gene density of 4.6 kb per gene. Analysis of chromosome collinearity with the A. thaliana genome identified conserved synteny blocks encompassing the whole of the B. rapa chromosome A3 and sections of four A. thaliana chromosomes. The frequency of tandem duplication of genes differed between the conserved genome segments in B. rapa and A. thaliana, indicating differential rates of occurrence/retention of such duplicate copies of genes. Analysis of 'ancestral karyotype' genome building blocks enabled the development of a hypothetical model for the derivation of the B. rapa chromosome A3. CONCLUSIONS: We report the near-complete chromosome sequence from a dicotyledonous crop species. This provides an example of the complexity of genome evolution following polyploidy. The high degree of contiguity afforded by the clone-by-clone approach provides a benchmark for the performance of whole genome shotgun approaches presently being applied in B. rapa and other species with complex genomes.


Asunto(s)
Brassica rapa/genética , Cromosomas de las Plantas , Secuencia Conservada , Análisis de Secuencia de ADN , Sintenía , Arabidopsis/genética , Secuencia de Bases , Mapeo Cromosómico , Estructuras Cromosómicas , Cromosomas Artificiales Bacterianos , Mapeo Contig , ADN de Plantas/genética , Evolución Molecular , Duplicación de Gen , Reordenamiento Génico , Genoma de Planta , Cariotipificación , Anotación de Secuencia Molecular , Poliploidía
9.
Genome Biol ; 10(10): R111, 2009.
Artículo en Inglés | MEDLINE | ID: mdl-19821981

RESUMEN

BACKGROUND: Brassica rapa is one of the most economically important vegetable crops worldwide. Owing to its agronomic importance and phylogenetic position, B. rapa provides a crucial reference to understand polyploidy-related crop genome evolution. The high degree of sequence identity and remarkably conserved genome structure between Arabidopsis and Brassica genomes enables comparative tiling sequencing using Arabidopsis sequences as references to select the counterpart regions in B. rapa, which is a strong challenge of structural and comparative crop genomics. RESULTS: We assembled 65.8 megabase-pairs of non-redundant euchromatic sequence of B. rapa and compared this sequence to the Arabidopsis genome to investigate chromosomal relationships, macrosynteny blocks, and microsynteny within blocks. The triplicated B. rapa genome contains only approximately twice the number of genes as in Arabidopsis because of genome shrinkage. Genome comparisons suggest that B. rapa has a distinct organization of ancestral genome blocks as a result of recent whole genome triplication followed by a unique diploidization process. A lack of the most recent whole genome duplication (3R) event in the B. rapa genome, atypical of other Brassica genomes, may account for the emergence of B. rapa from the Brassica progenitor around 8 million years ago. CONCLUSIONS: This work demonstrates the potential of using comparative tiling sequencing for genome analysis of crop species. Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.


Asunto(s)
Brassica rapa/genética , Duplicación de Gen , Genes Duplicados/genética , Genoma de Planta/genética , Arabidopsis/genética , Secuencia de Bases , Cromosomas Artificiales Bacterianos/genética , Cromosomas de las Plantas/genética , Biología Computacional , Secuencia Conservada , Mapeo Contig , Evolución Molecular , Reordenamiento Génico/genética , Cariotipificación , Sistemas de Lectura Abierta/genética , Filogenia , Poliploidía , Secuencias Repetitivas de Ácidos Nucleicos/genética , Sintenía/genética
10.
FEBS J ; 276(13): 3559-74, 2009 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-19456863

RESUMEN

Glucosinolates play important roles in plant defense against herbivores and microbes, as well as in human nutrition. Some glucosinolate-derived isothiocyanate and nitrile compounds have been clinically proven for their anticarcinogenic activity. To better understand glucosinolate biosynthesis in Brassica rapa, we conducted a comparative genomics study with Arabidopsis thaliana and identified total 56 putative biosynthetic and regulator genes. This established a high colinearity in the glucosinolate biosynthesis pathway between Arabidopsis and B. rapa. Glucosinolate genes in B. rapa share 72-94% nucleotide sequence identity with the Arabidopsis orthologs and exist in different copy numbers. The exon/intron split pattern of B. rapa is almost identical to that of Arabidopsis, although inversion, insertion, deletion and intron size variations commonly occur. Four genes appear to be nonfunctional as a result of the presence of a frame shift mutation and retrotransposon insertion. At least 12 paralogs of desulfoglucosinolate sulfotransferase were found in B. rapa, whereas only three were found in Arabidopsis. The expression of those paralogs was not tissue-specific but varied greatly depending on B. rapa tissue types. Expression was also developmentally regulated in some paralogs but not in other paralogs. Most of the regulator genes are present as triple copies. Accordingly, glucosinolate synthesis and regulation in B. rapa appears to be more complex than that of Arabidopsis. With the isolation and further characterization of the endogenous genes, health-beneficial vegetables or desirable animal feed crops could be developed by metabolically engineering the glucosinolate pathway.


Asunto(s)
Brassica rapa , Genoma de Planta , Glucosinolatos/biosíntesis , Proteínas de Plantas/genética , Sulfotransferasas/genética , Animales , Arabidopsis/genética , Evolución Biológica , Brassica rapa/genética , Brassica rapa/metabolismo , Mapeo Cromosómico , Cromosomas de las Plantas , Regulación de la Expresión Génica de las Plantas , Biblioteca de Genes , Humanos , Datos de Secuencia Molecular , Filogenia , Proteínas de Plantas/clasificación , Proteínas de Plantas/metabolismo , Sulfotransferasas/clasificación , Sulfotransferasas/metabolismo
11.
Mol Cells ; 26(6): 595-605, 2008 Dec 31.
Artículo en Inglés | MEDLINE | ID: mdl-18797175

RESUMEN

Genome wide transcription analysis in response to stresses is essential to provide the basis of effective engineering strategies to improve stress tolerance in crop plants. In order to perform transcriptome analysis in Brassica rapa, we constructed a B. rapa oligo microarray, KBGP-24K, using sequence information from approximately 24,000 unigenes and analyzed cold (4 degrees C), salt (250 mM NaCl), and drought (air-dry) treated B. rapa plants. Among the B. rapa unigenes represented on the microarray, 417 (1.7%), 202 (0.8%), and 738 (3.1%) were identified as responsive genes that were differently expressed 5-fold or more at least once during a 48-h treatment with cold, salt, and drought, respectively. These results were confirmed by RT-PCR analysis. In the abiotic stress responsive genes identified, we found 56 transcription factor genes and 60 commonly responsive genes. It suggests that various transcriptional regulatory mechanisms and common signaling pathway are working together under the abiotic stresses in B. rapa. In conclusion, our new developed 24K oligo microarray will be a useful tool for transcriptome profiling and this work will provide valuable insight in the response to abiotic stress in B. rapa.


Asunto(s)
Brassica rapa/genética , Perfilación de la Expresión Génica , Estrés Fisiológico/genética , Frío , Sequías , Regulación de la Expresión Génica de las Plantas , Genes de Plantas , Análisis de Secuencia por Matrices de Oligonucleótidos , Proteínas de Plantas/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Cloruro de Sodio/farmacología
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