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1.
Article in English | WPRIM | ID: wpr-1010586

ABSTRACT

With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides (miPs), a kind of small polypeptides. Although miPs are difficult to analyze and identify, a number of studies have begun to focus on them. More and more miPs have been revealed as essential for energy metabolism homeostasis, immune regulation, and tumor growth and development. Many reports have shown that miPs are especially essential for regulating glucose and lipid metabolism and regulating mitochondrial function. MiPs are also involved in the progression of related diseases. This paper reviews the sources and identification of miPs, as well as the functional significance of miPs for metabolism-related diseases, with the aim of revealing their potential clinical applications.


Subject(s)
Humans , Open Reading Frames , Peptides , Glucose , Genome , Metabolic Diseases
2.
Rev. ecuat. pediatr ; 23(3): 239-248, 12 de Diciembre del 2022.
Article in Spanish | LILACS | ID: biblio-1411268

ABSTRACT

Introducción: Las dificultades del aprendizaje son las alteraciones de mayor presencia en las aulas escolares y sus indicadores pueden diagnosticarse y prevenirse desde edades tempranas. El objetivo de esta investigación fue validar el Test para la detección temprana de las dificultades en el aprendizaje de la lectura y escritura. Métodos: El enfoque de la investigación fue cuantitativo, descriptivo y de corte transversal. Se utilizó la validez de constructo acorde con la propuesta original del test y de fiabilidad a través del Alpha de Cronbach en una muestra de 501 niños ecuatorianos de cuatro años. Resultados: La validación del instrumento evidencia una moderada correlación entre las sub-tareas y alta correlación entre las sub-tareas y el puntaje total. La fiabilidad es buena, α= 0.71, muy próxima a la de la población española α= 0.73. Por lo que, la prueba puede ser utilizada en el contexto ecuatoriano en su versión original, adecuando en las instrucciones dos palabras a la realidad lingüística del país y para la calificación los puntos de corte de dificultad. Conclusión: Considerando su valor y fácil aplicación se recomienda el uso de la prueba de lectura en contextos educativos y de salud.


Introduction: Learning difficulties are the alterations with the most significant presence in school classrooms, and their indicators can be diagnosed and prevented early. This research aimed to validate the test for the early detection of difficulties in learning to read and write. Methods: The research approach was quantitative, descriptive, and cross-sectional. Construct validity was used according to the original proposal of the test and reliability through Cronbach's alpha in a sample of 501 four-year-old Ecuadorian children. Results: The validation of the instrument shows a moderate correlation between the subtasks and a high correlation between the subtasks and the total score. The reliability is good, α = 0.71, very close to that of the Spanish population α = 0.73. Therefore, the test can be used in the Ecuadorian context in its original version, adapting two words in the instructions to the linguistic reality of the country and for the qualification of the cutoff points of difficulty. Conclusion: With the easy application of the "test of reading" in 4-year-old children, the authors recommended its application for the identification of dyslexia and phonological processing deficits in school children in Ecuador. The reading test's validity allows its application at a regional level.


Subject(s)
Humans , Child, Preschool , Articulation Disorders , Reading , Comprehension , Open Reading Frames , Reading Frames , Dyslexia
3.
Chinese Journal of Biotechnology ; (12): 1953-1964, 2022.
Article in Chinese | WPRIM | ID: wpr-927830

ABSTRACT

Reynoutria japonica Houtt., belonging to Polygoneae of Polygonaceae, is a Chinese medicinal herb with the functions of draining dampness and relieving jaundice, clearing heat and detoxifying, dispersing blood stasis and relieving pain, and relieving cough and resolving phlegm. In this study, we carried out high-throughput sequencing for the chloroplast genome sequences of five cultivars of R. japonica and analyzed the genome structure and variations. The chloroplast genomes of the five R. japonica cultivars had two sizes (163 376 bp and 163 371 bp) and a typical circular tetrad structure composed of a large single-copy (LSC) region of 85 784 bp, a small single-copy (SSC) region of 18 616 bp, and a pair of inverted repeat (IR) regions (IRa/IRb) which are spaced apart. A total of 161 genes were obtained by annotation, which consisted of 106 protein-coding genes, 10 rRNA-coding genes, and 45 tRNA-coding genes. The total GC content was 36.7%. Specifically, the GC content in the LSC, SSC, and IR regions were 34.8%, 30.7%, and 42.7%, respectively. Comparison of the whole chloroplast genome among the five cultivars showed that trnk-UUU, rpoC1, petD, rpl16, ndhA, and rpl12 in coding regions had sequence variations. In the phylogenetic tree constructed for the 11 samples of Polygoneae, the five cultivars of R. japonica clustered into one clade near the root and was a sister group of Fallopia multiflora (Thunb.).


Subject(s)
Base Composition , Genome, Chloroplast/genetics , Open Reading Frames , Phylogeny , Reynoutria
4.
Article in English | WPRIM | ID: wpr-927668

ABSTRACT

Objective@#This study aimed to identify internal ribosome entry sites (IRESs) in the open reading frame (ORF) of the Coxsackievirus B3 (CVB3) genome.@*Methods@#The sequences of P1, P2, or P3 of the CVB3 genome or the truncated sequences from each antithymocyte globulin (ATG) to the end of the P1, P2, or P3 gene were inserted into the pEGFP-N1 vector. After transfection, possible IRES-dependent green fluorescent protein (GFP)-fused proteins were detected by anti-GFP western blotting. The sequences of possible IRESs were inserted into specific Fluc/Rluc bicistronic vectors, in which the potential IRESs were determined according to the Fluc/Rluc activity ratio. Expression of Fluc and Rluc mRNA of the bicistronic vector was detected by RT-qPCR.@*Results@#After transfection of full length or truncated sequences of the P1, P2, or P3 plasmids, six GFP-fused protein bands in P1, six bands in P2 and nine bands in P3 were detected through western blotting. Two IRESs in VP2 (1461-1646 nt) and VP1 (2784-2983 nt) of P1; one IRES in 2C (4119-4564 nt) of P2; and two IRESs in 3C (5634-5834 nt) and 3D (6870-7087 nt) of P3 were identified according to Fluc/Rluc activity ratio. The cryptic promoter was also excluded by RT-qPCR.@*Conclusion@#Five IRESs are present in the CVB3 coding region.


Subject(s)
Internal Ribosome Entry Sites/genetics , Open Reading Frames , RNA, Messenger/genetics
5.
Chinese Journal of Biotechnology ; (12): 772-781, 2020.
Article in Chinese | WPRIM | ID: wpr-826899

ABSTRACT

Rhus chinensis is an important economic species, which could provide raw materials for pharmaceutical and industrial dyes. Rhus chinensis is famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. We report here Rhus chinensis chloroplast genomes by de novo sequencing. The results show that the length of Rhus chinensis was 159 082 bp, exhibiting a typical four-part structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The length of LSC and SSC was 85 394 bp and 18 663 bp, respectively. The genomes contained 126 genes, including 88 protein encoding genes, 8 rRNA and 30 tRNA genes. In the chloroplast genome, 61.97% of the sequence were gene coding region. In the sequence of gene encoding region, the vast majority of sequences were protein encoding region, accounting for 86.65%, followed by rRNA (10 620 bp, 10.77%) and tRNA (2 540 bp, 2.58%). In Rhus chinensis chloroplast genome, only 8 genes contain introns, all containing 1 intron except ycf3 gene (2 introns). The Rhus chinensis chloroplast genome contains 755 SSR locies. SSR mainly consists of dinucleotide and mononucleotide, accounting for 60% (453) and 28.74% (217) respectively. The clustering results show that Anacardiaceae were closest to Rhus chinensis, followed by Aceraceae and Sapindaceae. This study provides a molecular basis for the classification of Rhus chinensis.


Subject(s)
Genome, Chloroplast , Genetics , Open Reading Frames , Phylogeny , Rhus , Classification , Genetics , Sequence Analysis, DNA
6.
Article in Chinese | WPRIM | ID: wpr-828311

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a patient featuring multiple carboxylase deficiency (MCD).@*METHODS@#PCR and Sanger sequencing were used to detect variant in the coding region of BT and HLCS genes in the patient. Suspected variants were verified in her parents and 80 unrelated healthy controls by a PCR-restriction fragment length polymorphism (PCR-RFLP) method.@*RESULTS@#The patient was found to carry compound heterozygous variants of the HLCS gene, namely c.286delG (p.Val96Leufs*162) and c.1648G>A (p.Val550Met). The c.286delG (p.Val96Leufs*162) was verified to be novel variant based on the result of PCR-RFLP analysis. No variant was found in the coding regions of BT gene in the patient.@*CONCLUSION@#The compound c.286delG (p.Val96Leufs*162) and c.1648G>A (p.Val550Met) variants probably underlie the MCD disorder in this patient. Above results have enriched the variant spectrum of MCA.


Subject(s)
Female , Humans , Carbon-Nitrogen Ligases , Genetics , Exons , Multiple Carboxylase Deficiency , Genetics , Mutation , Open Reading Frames , Polymerase Chain Reaction , Polymorphism, Restriction Fragment Length , Sequence Analysis, DNA
7.
Electron. j. biotechnol ; 40: 65-70, July. 2019. ilus
Article in English | LILACS | ID: biblio-1053486

ABSTRACT

Background: In Saccharomyces cerevisiae, Msn2, which acts as a key transcription factor downstream the MAPKHOG cascade pathway, also regulates the expression of genes related to stress responses. However, little is known about the regulation mechanisms of the transcription factor in Setosphaeria turcica. Results: In this study, a zinc finger DNA-binding protein, designated as StMSN2, was cloned from S. turcica. Sequencing results showed that StMSN2 had a 1752 bp open reading frame (ORF), which was interrupted by an intron (135 bp) and encoded a putative 538-amino acid protein. Phylogenetic analysis further revealed that StMsn2 was more closely related to Msn2 of Aspergillus parasiticus. StMSN2 was cloned into the pET-28a vector with His (Histidine) tags and induced with 1 mM IPTG (isopropyl-ß-D-thiogalactoside) at 37°C. The recombinant His-tagged StMsn2 was purified, and a band of size approximately 58.8 kDa was obtained. The high specificity of the polyclonal antibody Msn2-2 was detected with the StMsn2 protein from S. turcica and prokaryotic expression system, respectively. Conclusions: A new gene, named StMSN2, with 1617 bp ORF was cloned from S. turcica and characterized using bioinformatics methods. StMsn2 was expressed and purified in a prokaryotic system. A polyclonal antibody, named Msn2-2, against StMsn2 with high specificity was identified.


Subject(s)
Plant Diseases , Ascomycota/genetics , Ascomycota/pathogenicity , Transcription Factors/isolation & purification , Ascomycota/metabolism , Stress, Physiological , Transcription Factors/genetics , Transcription Factors/metabolism , Carrier Proteins , Gene Expression , Blotting, Western , Open Reading Frames , Zinc Fingers , Cloning, Molecular , Zea mays , Escherichia coli , Helminthosporium , Epitopes
8.
Article in English | WPRIM | ID: wpr-1010499

ABSTRACT

Noncoding RNAs (ncRNAs) have played a critical role in cellular biological functions. Recently, some peptides or proteins originating from annotated ncRNAs were identified in organism development and various diseases. Here, we briefly review several novel peptides translated by annotated ncRNAs and related key functions. In addition, we summarize the potential mechanism of bifunctional ncRNAs and propose a specific "switch" triggering the transformation from the noncoding to the coding state under certain stimuli or cellular stress. The coding properties of ncRNAs and their peptide products may provide a novel horizon in proteomic research and can be regarded as a potential therapeutic target for the treatment of various diseases.


Subject(s)
Animals , Humans , Calcium/metabolism , Open Reading Frames , Protein Biosynthesis , RNA, Messenger/genetics , RNA, Untranslated/physiology
9.
Article in English | WPRIM | ID: wpr-1010481

ABSTRACT

Fowl adenovirus serotype 4 (FAdV-4) strain SD1511 was isolated from chickens with severe inclusion body hepatitis and hydropericardium syndrome in Shandong Province, China. The isolate was cultured in primary chicken embryo kidney cells. A study of pathogenicity indicated that SD1511 readily infected 7-35-d-old chickens by intramuscular injection and intranasal and oral routes, causing 50%-100% mortality. The 35-d-old chickens suffered more severe infection than 7- and 21-d-old chickens with mortality highest in the intramuscular injection group. The serum from surviving chickens showed potent viral neutralizing capability. The complete genome of SD1511 was sequenced and analyzed. The strain was found to belong to the FAdV-4 cluster with more than 99% identity with the virulent FAdV-4 strains isolated in China in recent years except for some distinct variations, including deletions of open reading frame 27 (ORF27), ORF48, and part of ORF19. Our findings suggest that SD1511 might be used as a prototype strain for the study of pathogenesis and vaccine development.


Subject(s)
Animals , Antibodies, Neutralizing , Aviadenovirus/pathogenicity , Cell Line , Chick Embryo/virology , Chickens/virology , China , Gene Deletion , Genetic Variation , Genome , Genome, Viral , Genomics , Kidney/virology , Liver/virology , Open Reading Frames , Poultry Diseases/virology , Serogroup , Viral Load , Virulence , Virus Diseases/virology
10.
Article in Chinese | WPRIM | ID: wpr-771402

ABSTRACT

A novel protein encoded by the open reading frame 4 (ORF4) was recently discovered in porcine circovirus type 2 (PCV2). However, little is known about the interaction proteins of ORF4 which hindered better understanding the biological functions of ORF4 in the life cycle of PCV2. In the present study, the ORF4 was inserted into the multiple cloning site of pCMV-N-Flag-GST, yielding recombinant plasmid pCMV-N-Flag-GST-ORF4. The recombinant plasmid was transfected into 293T cells and the intracellular interaction complex of ORF4 were enriched and separated by GST pull-down and SDS-PAGE, sequentially. The potential interacting proteins of PCV2 ORF4 were stained with silver and identified by mass spectrometry (MS). Finally, five candidate ORF4-interacting proteins, including Serine/threonine-protein phosphatase 6 catalytic subunit, alpha cardiac muscle 1, actin, SEC14-like protein 5 and myosin 9 were identified. These results would benefit a better understanding of the biological function of ORF4 in PCV2 infected cells.


Subject(s)
Animals , Humans , Circoviridae Infections , Circovirus , HEK293 Cells , Mass Spectrometry , Open Reading Frames , Swine , Viral Proteins
11.
Article in English | WPRIM | ID: wpr-758906

ABSTRACT

The 4a and 4b proteins of the Middle East respiratory syndrome coronavirus (MERS-CoV) have been described for their antagonism on host innate immunity. However, unlike clustering patterns of the complete gene sequences of human and camel MERS-CoVs, the 4a and 4b protein coding regions did not constitute species-specific phylogenetic groups. Moreover, given the estimated evolutionary rates of the complete, 4a, and 4b gene sequences, the 4a and 4b proteins might be less affected by species-specific innate immune pressures. These results suggest that the 4a and 4b proteins of MERS-CoV may function against host innate immunity in a manner independent of host species and/or evolutionary clustering patterns.


Subject(s)
Humans , Camelus , Clinical Coding , Coronavirus Infections , Evolution, Molecular , Immunity, Innate , Middle East Respiratory Syndrome Coronavirus , Middle East , Open Reading Frames , Phylogeny , Zoonoses
12.
Article in Chinese | WPRIM | ID: wpr-773131

ABSTRACT

The family of flavonoid 3-O-glucosyltransferase catalyzes the modification of anthocyanin from unstable-structure to stable-structure. In this study,based on homology cloning and transcriptome library,we isolated the full-length c DNA of UDP-glucose: flavonoid 3-O-glucosyltransferase( named SmUF3GT) from the flower tissues of S. miltiorrhiza. This gene was consisted of 1 353 bp open reading frames( ORF) encoding 450 amino acids. And the SmUF3GT protein was performed for the bioinformatic analysis. Our results showed that the protein was preliminary localized in the Golgi and peroxisome of cytosol,as well as plasma membrane and cell nuclear.QRT-PCR analyses indicated that SmUF3GT expressed differently in all tissues and organs but roots of S. miltiorrhiza and S. miltiorrhiza f.alba. During floral development,the expression of SmUF3GT showed a trend of rising fist and then down in purple-flower Danshen,whereas decreasing sharply fist and then slowly in white-flower Danshen. The present study provides basic information for further research on the network of synthesis and accumulation of flavonoids in S.miltiorrhiza.


Subject(s)
Cloning, Molecular , Flowers , Gene Expression Regulation, Plant , Glucosyltransferases , Genetics , Open Reading Frames , Plant Proteins , Genetics , Salvia miltiorrhiza , Genetics
13.
Article in Chinese | WPRIM | ID: wpr-776758

ABSTRACT

OBJECTIVE@#To detect the disease-causing mutation in a family with hereditary spherocytosis type Ⅰ.@*METHODS@#Genomic DNA was extracted from peripheral blood samples of the proband and his relatives. Next-generation sequencing was used to detect the mutations of relevant genes. Suspected pathogenic mutation was verified by Sanger sequencing.@*RESULTS@#The proband was found to harbor a novel frameshifting mutation in the coding region of ANK1 gene, which has resulted in abnormal structure or function of the protein. The mutation was confirmed by Sanger sequencing, with both his father and brother found to have carried the same mutation.@*CONCLUSION@#The c.247delG mutation of proband hereditary spherocytosis typeⅠin this family due to mutation of the ANK1 gene..


Subject(s)
Humans , Male , Ankyrins , Genetics , High-Throughput Nucleotide Sequencing , Mutation , Open Reading Frames , Spherocytosis, Hereditary , Genetics
14.
Braz. j. microbiol ; 49(4): 777-784, Oct.-Dec. 2018. tab, graf
Article in English | LILACS | ID: biblio-974285

ABSTRACT

ABSTRACT The aim of this study was to perform the molecular characterization of conserved and variable regions of feline calicivirus capsid genome in order to investigate the molecular diversity of variants in Brazilian cat population. Twenty-six conjunctival samples from cats living in five public short-term animal shelters and three multicat life-long households were analyzed. Fifteen cats had conjunctivitis, three had oral ulceration, eight had respiratory signs (cough, sneeze and nasal discharge) and nine were asymptomatic. Feline calicivirus were isolated in CRFK cells and characterized by reverse transcription PCR target to both conserved and variable regions of open reading frame 2. The amplicons obtained were sequenced. A phylogenetic analysis along with most of the prototypes available in GenBank database and an amino acid analysis were performed. Phylogenetic analysis based on both conserved and variable region revealed two clusters with an aLTR value of 1.00 and 0.98 respectively and the variants from this study belong to feline calicivirus genogroup I. No association between geographical distribution and/or clinical signs and clustering in phylogenetic tree was observed. The variants circulating in public short-term animal shelter demonstrated a high variability because of the relatively rapid turnover of carrier cats constantly introduced of multiple viruses into this location over time.


Subject(s)
Animals , Cats , Cat Diseases/virology , Calicivirus, Feline/isolation & purification , Calicivirus, Feline/genetics , Caliciviridae Infections/veterinary , Pets/virology , Phylogeny , Brazil , Open Reading Frames , Genome, Viral , Calicivirus, Feline/classification , Caliciviridae Infections/virology , Capsid Proteins/genetics
15.
Braz. j. microbiol ; 49(3): 575-583, July-Sept. 2018. tab, graf
Article in English | LILACS | ID: biblio-951799

ABSTRACT

Abstract Mamastrovirus 5 (MAstV5), belonging to the Astroviridae (AstV) family, previously known as canine astrovirus or astrovirus-like particles, has been reported in several countries to be associated with viral enteric disease in dogs since the 1980s. Astroviruses have been detected in fecal samples from a wide variety of mammals and birds that are associated with gastroenteritis and extra enteric manifestations. In the present study, RT-PCR was used to investigate the presence of MAstV5 in 269 dog fecal samples. MAstV5 was detected in 26% (71/269) of the samples. Interestingly, all MAstV5-positive samples derived from dogs displaying clinical signs suggestive of gastroenteritis, other enteric viruses were simultaneously detected (canine parvovirus, canine distemper virus, canine coronavirus, canine adenovirus and canine rotavirus). Based on genomic sequence analysis of MAstV5 a novel classification of the species into four genotypes, MAstV5a-MAstV5d, is proposed. Phylogenetic analyses based on the ORF2 amino acid sequences, samples described herein grouped into the putative genotype 'a' closed related with Chinese samples. Other studies are required to attempt the clinical and antigenic implications of these astrovirus genotypes in dogs.


Subject(s)
Animals , Dogs , Mamastrovirus/isolation & purification , Mamastrovirus/genetics , Astroviridae Infections/veterinary , Dog Diseases/virology , Gastroenteritis/veterinary , Phylogeny , Mamastrovirus/classification , Open Reading Frames , Astroviridae Infections/virology , Feces/virology , Gastroenteritis/virology , Genotype
16.
Braz. j. microbiol ; 49(supl.1): 260-261, 2018. graf
Article in English | LILACS | ID: biblio-974329

ABSTRACT

ABSTRACT Rio Negro virophage (RNV) was co-isolated with a strain of mimivirus named sambavirus, from Brazilian Amazon. We report the near complete genome sequence of RNV, the first virophage isolated in Brazil. We also present new microscopical data demonstrating that RNV particles have similar dimensions to that described to sputnik virophages.


Subject(s)
Togaviridae/genetics , Acanthamoeba/virology , Genome, Viral , Virophages/genetics , Phylogeny , Togaviridae/isolation & purification , Togaviridae/ultrastructure , Brazil , Open Reading Frames , Microscopy, Electron, Transmission , Virophages/isolation & purification , Virophages/ultrastructure
17.
Article in English | WPRIM | ID: wpr-1010387

ABSTRACT

We report the recovery of a 7068-nt viral sequence from the "viral fossils" embedded in the genome of Alhagi sparsifolia, a typical desert plant. Although the full viral genome remains to be completed, the putative genome structure, the deduced amino acids and phylogenetic analysis unambiguously demonstrate that this viral sequence represents a novel species of the genus Badnavirus. The putative virus is tentatively termed Alhagi bacilliform virus (ABV). Southern blotting and inverse polymerase chain reaction (PCR) data indicate that the ABV-related sequence is integrated into the A. sparsifolia genome, and probably does not give rise to functional episomal virus. Molecular evidence that the ABV sequence exists widely in A. sparsifolia is also presented. To our knowledge, this is the first endogenous badnavirus identified from plants in the Gobi desert, and may provide new clues on the evolution, geographical distribution as well as the host range of the badnaviruses.


Subject(s)
Badnavirus/genetics , Biological Evolution , Desert Climate , Fabaceae/virology , Genes, Plant , Genetic Variation , Genome, Viral , Geography , Open Reading Frames , Phylogeny , Plant Diseases/virology , Plasmids , Sequence Analysis, RNA
18.
Genomics & Informatics ; : 22-29, 2018.
Article in English | WPRIM | ID: wpr-714916

ABSTRACT

Incorporation of unique barcodes into fission yeast gene deletion collections has enabled the identification of gene functions by growth fitness analysis. For fine tuning, it is important to examine barcode sequences, because mutations arise during strain construction. Out of 8,708 barcodes (4,354 strains) covering 88.5% of all 4,919 open reading frames, 7,734 barcodes (88.8%) were validated as high-fidelity to be inserted at the correct positions by Sanger sequencing. Sequence examination of the 7,734 high-fidelity barcodes revealed that 1,039 barcodes (13.4%) deviated from the original design. In total, 1,284 mutations (mutation rate of 16.6%) exist within the 1,039 mutated barcodes, which is comparable to budding yeast (18%). When the type of mutation was considered, substitutions accounted for 845 mutations (10.9%), deletions accounted for 319 mutations (4.1%), and insertions accounted for 121 mutations (1.6%). Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (~28%) and well above the predicted error of Sanger sequencing (~2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. When the mutation rate was analyzed by position within 20-mer barcodes using the 1,284 mutations from the 7,734 sequenced barcodes, there was no significant difference between up-tags and down-tags at a given position. The mutation frequency at a given position was similar at most positions, ranging from 0.4% (32/7,734) to 1.1% (82/7,734), except at position 1, which was highest (3.1%), as in budding yeast. Together, well-defined barcode sequences, combined with the next-generation sequencing platform, promise to make the fission yeast gene deletion library a powerful tool for understanding gene function.


Subject(s)
DNA , Gene Deletion , Mutation Rate , Open Reading Frames , Polymerase Chain Reaction , Saccharomycetales , Schizosaccharomyces
19.
Mycobiology ; : 429-439, 2018.
Article in English | WPRIM | ID: wpr-729732

ABSTRACT

To develop a convenient promoter analysis system for fungi, a null-pigment mutant (NPG) of Aspergillus nidulans was used with the 4′-phosphopantetheinyl transferase (PPTase) gene, npgA, which restores the normal pigmentation in A. nidulans, as a new reporter gene. The functional organization of serially deleted promoter regions of the A. nidulans trpC gene and the Cryphonectria parasitica crp gene in filamentous fungi was representatively investigated to establish a novel fungal promoter assay system that depends on color complementation of the NPG mutant with the PPTase npgA gene. Several promoter regions of the trpC and crp genes were fused to the npgA gene containing the 1,034-bp open reading frame and the 966-bp 3’ downstream region from the TAA, and the constructed fusions were introduced into the NPG mutant in A. nidulans to evaluate color recovery due to the transcriptional activity of the sequence elements. Serial deletion of the trpC and crp promoter regions in this PPTase reporter assay system reaffirmed results in previous reports by using the fungal transformation step without a laborious verification process. This approach suggests a more rapid and convenient system than conventional analyses for fungal gene expression studies.


Subject(s)
Aspergillus nidulans , Aspergillus , Complement System Proteins , Fungi , Genes, Fungal , Genes, Reporter , Open Reading Frames , Pigmentation , Promoter Regions, Genetic , Transferases
20.
Article in Korean | WPRIM | ID: wpr-718758

ABSTRACT

Human cytomegalovirus (HCMV) is a ubiquitous human pathogen and contains double stranded DNA genome with approximately 230 kbp. Molecular genomic studies of HCMV have been attempted in order to understand the pathogenesis and evolution of HCMV. However, studies on HCMV strains of Asian origin are limited. In this study, it was attempted to understand the genomics of HCMV isolated from Korea. Clinical strain LCW isolated from Korean patient was passaged in vitro cell culture, and subjected to next-generation sequencing. Complete genome sequence was obtained and compared with other HCMV strains. The LCW genome was found to contain 170 open reading frames (ORFs) and two ORF (RL5A and RL13) of the strain LCW were found to be truncated due to early stop codon. Phylogenetic analysis suggested that the strain LCW was closely related with Asian strains such as HCMV strains JHC and HAN. Common nucleotide sequences among the 3 Asian strains distinguishable from other strains were detected at 197 sites including 104 sites in ORFs.


Subject(s)
Animals , Humans , Asian People , Base Sequence , Cell Culture Techniques , Codon, Terminator , Cytomegalovirus , DNA , Ecthyma, Contagious , Genome , Genomics , In Vitro Techniques , Korea , Open Reading Frames
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