• Asian-Australasian Journal of Animal Sciences
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• v.19 no.7
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• pp.953-957
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• 2006

The eukaryotic elongation factor 1 A (EEF1A) participates in protein synthesis by forming the eEF1A GTP tRNA complex to deliver aminoacyl-tRNA to the A site of ribosomes. This study described cDNA sequences and partial genomic structure of porcine EEF1A1. The porcine EEF1A1 gene encoded a protein with 462 amino acids, which shared complete homology with human, chimpanzee and dog. The temporal expression pattern showed the diversity of EEF1A1 level in mRNA was relatively minor in prenatal embryo skeletal muscle, however, the expression decreased during aging after birth in skeletal muscle of the Chinese Tongcheng pig. The spatial expression patterns indicated that the gene expressed in skeletal muscle, heart, lung, liver, kidney, fat and spleen. In addition, we assigned the gene to porcine chromosome 1 using a radiation hybrid panel.

• Korean Journal of Soil Science and Fertilizer
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• v.44 no.1
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• pp.127-145
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• 2011

Various environmental ecosystems are valuable sources for microbial ecology studies, and their analyses using recently developed molecular ecological approaches have drawn significant attention within the scientific community. Changes in the microbial community structures due to various anthropogenic activities can be evaluated by various culture-independent methods e.g. ARISA, DGGE, SSCP, T-RFLP, clone library, pyrosequencing, etc. Direct amplification of total community DNA and amplification of most conserved region (16S rRNA) are common initial steps, followed by either fingerprinting or sequencing analysis. Fingerprinting methods are relatively quicker than sequencing analysis in evaluating the changes in the microbial community. Being an efficient, sensitive and time- and cost effective method, T-RFLP is regularly used by many researchers to access the microbial diversity. Among various fingerprinting methods T-RFLP became an important tool in studying the microbial community structure because of its sensitivity and reproducibility. In this present review, we will discuss the important developments in T-RFLP methodology to distinguish the total microbial diversity and community composition in the various ecosystems.

• The Plant Pathology Journal
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• v.20 no.3
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• pp.212-219
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• 2004

Three isolates of Cucumber mosaic virus (CMV) from lily plants showing mosaic and distortion symptoms were detected by reverse-transcriptase polymerase chain reaction (RT-PCR) using primers specific to Cucumovirus genus namely, LK-CMV, LK4-CMV, and LKS-CMV. Restriction enzymes patterns of the RT-PCR products revealed that the lily isolates belonged to subgroup IA of CMV. In terms of biological properties, the lily isolates have highly similar but distinct pathogenicity as reported in other lily strains and ordinary strains of CMV. To characterize the molecular properties, cDNAs containing coat protein (CP) gene and 3' non-coding region (NCR) of RNA3 for the isolates were cloned and their nucleotide sequences were determined. The CP similarity (218 amino acids) was highly homologous (>97％) with that of subgroup I CMV strains. However, an additional 20-nulcleotide long segment was only present in 3' NCR of lily isolates, which form an additional stem-loop RNA structure. By using chimeric construct exchange cDNA containing 3'NCR of LK-CMV into the full-length cDNA clone of RNA3 of Fny-CMV, this additional segment may prove to be significant in the identification and fitness of the virus in lily plants. The pathology of zucchini squash infected by F1F2L3-CMV, a pseudorecombinant virus was showed to change drastically the severe mosaic and stunting symptom into a mild chlorotic spot on systemic leave, compared with Fny-CMV. To delimit the sequence of RNA3 affected the pathology, various RNA3 chimeras were constructed between two strains of CMV. The symptom determinants of F1F2L3-CMV were mapped to the positions amino acid 234, 239, and 250 in 3a movement protein (MP). RNA3 chimeras changed the sequences encoding three amino acids were resulted in alteration of systemic symptom.

• Journal of fish pathology
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• v.17 no.2
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• pp.91-98
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• 2004

This study was performed for the identification of Streptococcus sp. from cultured flounders (Paralichthys olivaceus) showing streptococcosis in the Jeju island. We isolated 10 strains of Streptococcus iniae from the cultured olive flounders with streptococcosis. Isolated strains were identified in S. iniae since they have formed the expected band through performing PCR assay using specific primers, Sin-1 (5'-CTAGAGTACACATGTACT(AGCT)AAG-3') and Sin-2 (5'-GGATTTTCCACTCCCATTAC-3'). In addition to 16S-23S rRNA intergenic spacers (ISR), operon structure of isolated strains showed that all strains had three 16S-23S rRNA ISR band patterns. The 16S-23S rRNA ISR sequence of isolated strains showed 96% sequence identity with S. iniae (GenBank accession number AF 048773). This paper is the first report that S. iniae is associated with streptococcosis of Olive flounder in Korea.

• Genomics & Informatics
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• v.12 no.4
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• pp.261-267
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• 2014

MicroRNAs (miRNAs) are known for their role in mRNA silencing via interference pathways. Repetitive elements (REs) share several characteristics with endogenous precursor miRNAs. In this study, 406 previously identified and 1,494 novel RE-derived miRNAs were sorted from the GENCODE v.19 database using the RepeatMasker program. They were divided into six major types, based on their genomic structure. More novel RE-derived miRNAs were confirmed than identified as RE-derived miRNAs. In conclusion, many miRNAs have not yet been identified, most of which are derived from REs.

• Biomedical Science Letters
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• v.4 no.2
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• pp.129-135
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• 1998

We have carried out polymerase chain reaction (PCR) to investigate if retropseudogene for CYP2El is present in human genome. PCR primers were designed based on the structure of functional CYP2El gene and used to amplify both functional gene and retropseudogene in one reaction. From the repeated experiments we were able to amplify a previously unidentified CYP2El retropseudogene that was present in human genome. Its detailed structure was confirmed by Southern blotting and DNA sequencing. Nucleotide sequence of this retropseudogene was completely matched up to human liver CYP2El mRNA suggesting that the development of this retropseudogene might be a relatively recent event.

• Molecules and Cells
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• v.37 no.12
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• pp.851-856
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• 2014

ATAD2, a remarkably conserved, yet poorly characterized factor is found upregulated and associated with poor prognosis in a variety of independent cancers in human. Studies conducted on the yeast Saccharomyces cerevisiae ATAD2 homologue, Yta7, are now indicating that the members of this family may primarily be regulators of chromatin dynamics and that their action on gene expression could only be one facet of their general activity. In this review, we present an overview of the literature on Yta7 and discuss the possibility of translating these findings into other organisms to further define the involvement of ATAD2 and other members of its family in regulating chromatin structure and function both in normal and pathological situations.

• Genomics & Informatics
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• v.19 no.4
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• pp.47.1-47.12
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• 2021

Kaposi's sarcoma-associated herpesvirus (KSHV) is one of the few human oncogenic viruses, which causes a variety of malignancies, including Kaposi's sarcoma, multicentric Castleman disease, and primary effusion lymphoma, particularly in human immunodeficiency virus patients. The currently available treatment options cannot always prevent the invasion and dissemination of this virus. In recent times, siRNA-based therapeutics are gaining prominence over conventional medications as siRNA can be designed to target almost any gene of interest. The ORF57 is a crucial regulatory protein for lytic gene expression of KSHV. Disruption of this gene translation will inevitably inhibit the replication of the virus in the host cell. Therefore, the ORF57 of KSHV could be a potential target for designing siRNA-based therapeutics. Considering both sequence preferences and target site accessibility, several online tools (i-SCORE Designer, Sfold web server) had been utilized to predict the siRNA guide strand against the ORF57. Subsequently, off-target filtration (BLAST), conservancy test (fuzznuc), and thermodynamics analysis (RNAcofold, RNAalifold, and RNA Structure web server) were also performed to select the most suitable siRNA sequences. Finally, two siRNAs were identified that passed all of the filtration phases and fulfilled the thermodynamic criteria. We hope that the siRNAs predicted in this study would be helpful for the development of new effective therapeutics against KSHV.

• ALGAE
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• v.37 no.1
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• pp.1-14
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• 2022

Cyanobacteria are distributed worldwide, and many new cyanobacterial species are discovered in tropical region. The Nostoc-like genus Amazonocrinis has been separated from the genus Nostoc based on polyphasic methods. However, species diversity within this genus remains poorly understood systematically because only one species (Amazonocrinis nigriterrae) has been described. In this study, two novel strains (NUACC02 and NUACC03) were isolated from moist rice field soil in Thailand. These two strains were characterized using a polyphasic approach, based on morphology, 16S rRNA phylogenetic analysis, internal transcribed spacer secondary structure and ecology. Phylogenetic analyses based on 16S rRNA gene sequences confirmed that the two novel strains formed a monophyletic clade related to the genus Amazonocrinis and were distant from the type species A. nigriterrae. The 16S rRNA gene sequence similarity (<98.1%) between novel strains and all other closely related taxa including the Amazonocrinis members exceeded the cutoff for species delimitation in bacteriology, reinforcing the presence of a new Amazonocrinis species. Furthermore, the novel strains possessed unique phenotypic characteristics such as the presence of the sheath, necridia-like cells, larger cell dimension and akinete cell arrangement in long-chains and the singularity of D1-D1', Box-B, V2, and V3 secondary structures that distinguished them from other Amazonocrinis members. Considering all the results, we described our two strains as Amazonocrinis thailandica sp. nov. in accordance with the International Code of Nomenclature for Algae, Fungi and Plants.

• The Plant Pathology Journal
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• v.34 no.2
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• pp.150-156
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• 2018

The genome sequences of two novel monopartite RNA viruses were identified in a common eelgrass (Zostera marina) transcriptome dataset. Sequence comparison and phylogenetic analyses revealed that these two novel viruses belong to the genus Amalgavirus in the family Amalgaviridae. They were named Zostera marina amalgavirus 1 (ZmAV1) and Zostera marina amalgavirus 2 (ZmAV2). Genomes of both ZmAV1 and ZmAV2 contain two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. The fusion protein (ORF1+2) of ORF1 and ORF2, which mediates RNA replication, was produced using the +1 programmed ribosomal frameshifting (PRF) mechanism. The +1 PRF motif sequence, UUU_CGN, which is highly conserved among known amalgaviruses, was also found in ZmAV1 and ZmAV2. Multiple sequence alignment of the ORF1+2 fusion proteins from 24 amalgaviruses revealed that +1 PRF occurred only at three different positions within the 13-amino acid-long segment, which was surrounded by highly conserved regions on both sides. This suggested that the +1 PRF may be constrained by the structure of fusion proteins. Genome sequences of ZmAV1 and ZmAV2, which are the first viruses to be identified in common eelgrass, will serve as useful resources for studying evolution and diversity of amalgaviruses.