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Durian is one of the important fruit crops in Southeast Asia with its unique flavor and important economic benefits. Breeding programs have produced hundreds of different cultivars of durian. These cultivars are classified mainly by fruit and flower characteristics, which cannot be observed at the vegetative stage. Therefore, molecular biology is a powerful tool to approach and explore the genetic characteristics of durians. Many studies based on barcoded DNA and molecular markers have been conducted and valuable data have been exploited. Thanks to the advancement of sequencing technology, the plastid genome and the whole genome were sequenced in some durian cultivars. The data revealed reliable data on the structure and function of several genes. This review aims to update recent studies on the durian genome attributes and potential applications in the conservation of germplasm, authentication, and exploration of the gene structure and function of this specialty plant.
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Abstract The resources and platforms available on the internet for collecting and sharing information and performing genomic sequence analysis have made it possible to follow closely the evolution the evolution of SARS-CoV-2. However, the current monkeypox outbreak in the world brings us back to the need to use these resources to appraise the extent of this outbreak. The objective of this work was an analysis of the information presented so far in the genomic database GISAID EpiPox™, using various tools available on the web. The results indicate that the monkeypox outbreak is referred as MPXV clade II B.1 lineage and sub-lineages, isolated from male patients mainly from the European and American continents. In the current scenario, the access to genomic sequences, epidemiological information, and tools available to the scientific community is of great importance for global public health in order to follow the evolution of pathogens.
Resumen Los recursos y plataformas disponibles en Internet para recopilar, compartir información y realizar análisis de secuencias genómicas han permitido seguir de cerca la evolución del SARS-CoV-2. El actual brote global de viruela del mono en el mundo, requiere de nuevo utilizar estos recursos para conocer el alcance de este brote. El objetivo de este trabajo fue un análisis de la información presentada hasta el momento en la base de datos genómica EpiPox™ de GISAID, utilizando diversas herramientas disponibles en la web. Los resultados indican que el brote de la viruela del mono o símica está referido al linaje y sub-linajes B.1 del clado II de MPXV, aislado principalmente de pacientes hombres de Europa y América. En el escenario actual, el acceso a las secuencias genómicas, la información epidemiológica, y las herramientas disponibles para la comunidad científica son de gran importancia para la salud pública mundial con el fin de seguir la evolución de los patógenos.
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OBJECTIVE@#AP2/ERF (APETALA2/ethylene-responsive factor) superfamily is one of the largest gene families in plants and has been reported to participate in various biological processes, such as the regulation of biosynthesis of active lignan. However, few studies have investigated the genome-wide role of the AP2/ERF superfamily in Isatis indigotica. This study establishes a complete picture of the AP2/ERF superfamily in I. indigotica and contributes valuable information for further functional characterization of IiAP2/ERF genes and supports further metabolic engineering.@*METHODS@#To identify the IiAP2/ERF superfamily genes, the AP2/ERF sequences from Arabidopsis thaliana and Brassica rapa were used as query sequences in the basic local alignment search tool. Bioinformatic analyses were conducted to investigate the protein structure, motif composition, chromosome location, phylogenetic relationship, and interaction network of the IiAP2/ERF superfamily genes. The accuracy of omics data was verified by quantitative polymerase chain reaction and heatmap analyses.@*RESULTS@#One hundred and twenty-six putative IiAP2/ERF genes in total were identified from the I. indigotica genome database in this study. By sequence alignment and phylogenetic analysis, the IiAP2/ERF genes were classified into 5 groups including AP2, ERF, DREB (dehydration-responsive element-binding factor), Soloist and RAV (related to abscisic acid insensitive 3/viviparous 1) subfamilies. Among which, 122 members were unevenly distributed across seven chromosomes. Sequence alignment showed that I. indigotica and A. thaliana had 30 pairs of orthologous genes, and we constructed their interaction network. The comprehensive analysis of gene expression pattern in different tissues suggested that these genes may play a significant role in organ growth and development of I. indigotica. Members that may regulate lignan biosynthesis in roots were also preliminarily identified. Ribonucleic acid sequencing analysis revealed that the expression of 76 IiAP2/ERF genes were up- or down-regulated under salt or drought treatment, among which, 33 IiAP2/ERF genes were regulated by both stresses.@*CONCLUSION@#This study undertook a genome-wide characterization of the AP2/ERF superfamily in I. indigotica, providing valuable information for further functional characterization of IiAP2/ERF genes and discovery of genetic targets for metabolic engineering.
Subject(s)
Abscisic Acid , Isatis/genetics , Multigene Family , Phylogeny , Homeodomain Proteins/genetics , Genome, PlantABSTRACT
In recent years, the incidence of single-gene nephrolithiasis has been increasing year by year. With the application of whole-genome analysis and whole-exome sequencing technology, the etiology of single-gene mutations leading to the development of urinary calculi has been extensively verified. Therefore, this article reviews the research on urinary calculi-related genetic diseases at home and abroad, and introduces transport proteins and channels; ions, protons and amino acids. The role of urinary calculi in the majority of clinicians realizes the significance of genetic testing in such diseases, thereby increasing the understanding of genetically related urinary calculi and improving the level of clinical diagnosis and treatment.
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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.
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Genetic manipulation of bacteria is a procedure necessary to obtain new strains that express peculiar and defined genetic determinants or to introduce genetic variants responsible for phenotypic modifications. This procedure can be applied to explore the biotechnological potential associated with environmental bacteria and to utilize the functional properties of specific genes when inserted into an appropriate host. In the past years, marine bacteria have received increasing attention because they represent a fascinating reservoir of genetic and functional diversity that can be utilized to fuel the bioeconomy sector. However, there is an urgent need for an in-depth investigation and improvement of the genetic manipulation tools applicable to marine strains because of the paucity of knowledge regarding this. This review aims to describe the genetic manipulation methods hitherto used in marine bacteria, thus highlighting the limiting factors of the different techniques available today to increase manipulation efficiency. In particular, we focus on methods of natural and artificial transformations (especially electroporation) and conjugation because they have been successfully applied to several marine strains. Finally, we emphasize that, to avoid failure, future work should be carried out to establish tailored methodologies for marine bacteria.
Subject(s)
Seawater/microbiology , Bacteria/genetics , Genetic Engineering , Transformation, Bacterial , Genome , Electroporation , Conjugation, Genetic , Metagenomics , Single-Cell Analysis , Genetic VectorsABSTRACT
Porcine deltacoronavirus (PDCoV) has emerged in several pig-raising countries and has been a causative pathogen associated with diarrheal diseases in South Korea since 2014. In the present study, we were able to isolate and cultivate a Korean PDCoV strain (KNU16-07) in cell culture and investigate its pathogenicity. PDCoV-inoculated piglets showed watery diarrhea accompanied by acute enteritis in the natural host. Sequencing analysis demonstrated the genetic stability of KNU16-07 for at least thirty serial passages.
Subject(s)
Cell Culture Techniques , Diarrhea , Enteritis , Korea , Serial Passage , VirulenceABSTRACT
<b>Objective: </b>Owing to the recent advances in genetic analysis technology, its application in drug development is expected to increase, although there are concerns regarding the leakage of personal information. This study aimed to assess the attitudes of community citizens toward genetic analysis studies associated with clinical trials planned by the pharmaceutical industry.<br><b>Methods: </b>A questionnaire survey was conducted after an educational seminar on drug development at a university campus festival. Answers were obtained from 47 citizens (16 males and 31 females, ages ranging from teens to fifties).<br><b>Results: </b>Attitudes toward providing genome samples were assessed using a 100-mm visual analogue scale, and the data revealed significant differences in the conditions of sample use (A, limited to specific genes during the trial, 89±14 mm; B, limited to genes related to the test drug or target disease, 81±23 mm; C, unlimited, 71±33 mm, <i>p</i><0.01). Twenty-seven citizens (57%) consistently expressed acceptance toward all three conditions. The remaining 38% (<i>n</i>=18) expressed denial as the analysis targets widened. Regarding the acceptable period for sample storage, 17 citizens (36%) allowed “indefinite storage” but 14 citizens (30%) requested “immediate disposal after analysis.” A feedback on the accidental findings of abnormalities was requested by 43 citizens (91%).<br><b>Conclusion: </b>The results demonstrated a wide variety of attitudes toward providing samples. On the other hand, most citizens requested a feedback on the findings of abnormalities for disease-related genes. These results suggest that it is necessary to improve the study protocol to reflect these fears and expectations.
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The gram-positive, mesophilic and non-motile coccus Streptococcus gordonii is an important causativeagent of infective endocarditis (IE). This pioneer species of dental plaque also causes bacteraemiain immune-supressed patients. In this study, we analysed the genome of a representative strain,Streptococcus gordonii SK12 that was originally isolated from the oral cavity. To gain a better understandingof the biology, virulence and phylogeny, of this potentially pathogenic organism, high-throughput IlluminaHiSeq technology and different bioinformatics approaches were performed. Genome assembly of SK12was performed using CLC Genomic Workbench 5.1.5 while RAST annotation revealed the key genomicfeatures. The assembled draft genome of Streptococcus gordonii SK12 consists of 27 contigs, with agenome size of 2,145,851 bp and a G+C content of 40.63%. Phylogenetic inferences have confirmedthat SK12 is closely related to the widely studied strain Streptococcus gordonii Challis. Interestingly, wepredicted 118 potential virulence genes in SK12 genome which may contribute to bacterial pathogenicityin infective endocarditis. We also discovered an intact prophage which might be recently integratedinto the SK12 genome. Examination of genes present in genomic islands revealed that this oral strainmight has potential to acquire new phenotypes/traits including strong defence system, bacitracinresistance and collateral detergent sensitivity. This detailed analysis of S. gordonii SK12 further improvesour understanding of the genetic make-up of S. gordonii as a whole and may help to elucidate howthis species is able to transition between living as an oral commensal and potentially causing the lifethreateningcondition infective endocarditis.
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Mutations in Bruton's tyrosine kinase (BTK) gene are responsible for X-linked agammaglobulinemia (XLA), which is characterized by recurrent bacterial infections, profound hypogammaglobulinemia, and decreased numbers of mature B cells in peripheral blood. We evaluated 5 male Brazilian patients, ranging from 3 to 10 years of age, from unrelated families, whose diagnosis was based on recurrent infections, markedly reduced levels of IgM, IgG and IgA, and circulating B cell numbers <2 percent. BTK gene analysis was carried out using PCR-SSCP followed by sequencing. We detected three novel (Ala347fsX55, I355T, and Thr324fsX24) and two previously reported mutations (Q196X and E441X). Flow cytometry revealed a reduced expression of BTK protein in patients and a mosaic pattern of BTK expression was obtained from mothers, indicating that they were XLA carriers.
Subject(s)
Child , Child, Preschool , Humans , Male , Agammaglobulinemia/genetics , Genetic Diseases, X-Linked/genetics , Mutation/genetics , Protein-Tyrosine Kinases/genetics , Agammaglobulinemia/enzymology , Flow Cytometry , Genetic Diseases, X-Linked/enzymology , Polymerase Chain Reaction , Polymorphism, Single-Stranded ConformationalABSTRACT
Helicobacter pylori is a causative agent of type B gastritis and plays a central role in the pathogenesis of gastroduodenal ulcer and gastric cancer. To elucidate the host-parasite relationship of the H. pylori infection on the basis of molecular biology, we tried to evaluate the genomic diversity of H. pylori. An ordered overlapping bacterial artificial chromosome (BAC) library of a Korean isolate, H, pylori 51 was constructed to set up a genomic map. A circular physical map was constructed by aligning ApaI, Notl and SfiI-digested chromosomal DNA. When the physical map of H. pylori 51 was compared to that of unrelated strain, H. pylori 26695, completely different restriction patterns were shown. Fifteen known genes were mapped on the chromosome of H. pylori 51 and the genetic map was compared with those of strain 26695 and J99, of which the entire genomic sequences were reported. There were some variability in the gene location as well as gene order among three strains. For further analysis on the genomic diversity of H. pylori, when comparing the genomic structure of 150 H. pylori Korean isolates with one another, genomic macrodiversity of H. pylori was characterized by several features: whether or not susceptible to restriction digestion of the chromsome, variation in chromosomal restriction fingerprint and/or high frequency of gene rearrangement. We also examined the extent of allelic variation in nucleotide or deduced amino acid sequences at the individual gene level. fucT, cagA and vacA were confirmed to carry regions of high variation in nucleotide sequence among strains. The plasticity zone and strain-specific genes of H. pylori 51 were analyzed and compared with the former two genomic sequences. It should be noted that the H. pylori 51-specific sequences were dispersed on the chromosome, not congregated in the plasticity zone unlike J99- or 26695-specific genes, suggesting the high frequency of gene rearrangement in H. pylori genome. The genomc of H. pylori 51 shows differences in the overall genomic organization, gene order, and even in the nucleotide sequences among the H. pylori strains, which are far greater than the differences reported on the genomic. diversity of H. pylori.