• Molecules and Cells
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• v.27 no.4
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• pp.429-441
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• 2009

We have determined the complete mitochondrial genome of the yellow-spotted long horned beetle, Psacothea hilaris (Coleoptera: Cerambycidae), an endangered insect species in Korea. The 15,856-bp long P. hilaris mitogenome harbors gene content typical of the animal mitogenome and a gene arrangement identical to the most common type found in insect mitogenomes. As with all other sequenced coleopteran species, the 5-bp long TAGTA motif was also detected in the intergenic space sequence located between $tRNA^{Ser}$(UCN) and ND1 of P. hilaris. The 1,190-bp long non-coding A+T-rich region harbors an unusual series of seven identical repeat sequences of 57-bp in length and several stretches of sequences with the potential to form stem-and-loop structures. Furthermore, it contains one $tRNA^{Arg}$-like sequence and one $tRNA^{Lys}$-like sequence. Phylogenetic analysis among available coleopteran mitogenomes using the concatenated amino acid sequences of PCGs appear to support the sister group relationship of the suborder Polyphaga to all remaining suborders, including Adephaga, Myxophaga, and Archostemata. Among the two available infraorders in Polyphaga, a monophyletic Cucujiformia was confirmed, with the placement of Cleroidea as the basal lineage for Cucujiformia. On the other hand, the infraorder Elateriformia was not identified as monophyletic, thereby indicating that Scirtoidea and Buprestoidea are the basal lineages for Cucujiformia and the remaining Elateriformia.

• Animal Systematics, Evolution and Diversity
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• v.36 no.4
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• pp.336-346
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• 2020

Mitochondrial genome is an important molecule for systematic and evolutionary studies in metazoans. The development of next-generation sequencing (NGS) technique has rapidly increased the number of mitogenome sequences. The process of generating mitochondrial genome based on NGS includes different steps, from DNA preparation, sequencing, assembly, and annotation. Despite the effort to improve sequencing, assembly, and annotation methods of mitogenome, the low quality and/or quantity sequence in the final map can still be generated through the work. Therefore, it is necessary to check and curate mitochondrial genome sequence after annotation for proofreading and feedback. In this study, we introduce the pipeline for sequencing and curation for mitogenome based on NGS. For this purpose, two mitogenome sequences of Dermatobranchus otome were sequenced by Illumina Miseq system with different amount of raw read data. Generated reads were targeted for assembly and annotation with commonly used programs. As abnormal repeat regions present in the mitogenomes after annotation, primers covering these regions were designed and conventional PCR followed by Sanger sequencing were performed to curate the mitogenome sequences. The obtained sequences were used to replace the abnormal region. Following the replacement, each mitochondrial genome was compared with the other as well as the sequences of close species available on the Genbank for confirmation. After curation, two mitogenomes of D. otome showed a typically circular molecule with 14,559 bp in size and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes. The phylogenetic tree revealed a close relationship between D. otome and Tritonia diomea. The finding of this study indicated the importance of caution and curation for the generation of mitogenome from NGS.

• Biomolecules & Therapeutics
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• v.29 no.5
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• pp.483-491
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• 2021

Parkinson's disease (PD) is a neurodegenerative disorder that involves the loss of dopaminergic neurons in the substantia nigra (SN). Matrix metalloproteinases-8 (MMP-8), neutrophil collagenase, is a functional player in the progressive pathology of various inflammatory disorders. In this study, we administered an MMP-8 inhibitor (MMP-8i) in Leucine-rich repeat kinase 2 (LRRK2) G2019S transgenic mice, to determine the effects of MMP-8i on PD pathology. We observed a significant increase of ionized calcium-binding adapter molecule 1 (Iba1)-positive activated microglia in the striatum of LRRK2 G2019S mice compared to normal control mice, indicating enhanced neuro-inflammatory responses. The increased number of Iba1-positive activated microglia in LRRK2 G2019S PD mice was down-regulated by systemic administration of MMP-8i. Interestingly, this LRRK2 G2019S PD mice showed significantly reduced size of cell body area of tyrosine hydroxylase (TH) positive neurons in SN region and MMP-8i significantly recovered cellular atrophy shown in PD model indicating distinct neuro-protective effects of MMP-8i. Furthermore, MMP-8i administration markedly improved behavioral abnormalities of motor balancing coordination in rota-rod test in LRRK2 G2019S mice. These data suggest that MMP-8i attenuates the pathological symptoms of PD through anti-inflammatory processes.

• Journal of Plant Biotechnology
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• v.47 no.4
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• pp.298-308
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• 2020

Genetic diversity among Thaumatococcus daniellii populations in the southwestern region of Nigeria were assessed using morphometric and molecular markers to determine the population structure and existing genetic relationship for its improvement, conservation and sustainable utilisation. Populations from five locations in each of the six states were used for the study. Morphometric data were collected on folia characters and analysed for variability. Genome DNA was isolated from the plant leaf and amplified by polymerase chain reaction with inter-simple sequence repeat markers (ISSR) to determine the allelic polymorphism, marker effectiveness and genetic relationship of the population. The results showed significant variations in petiole length and leaf dimensions of the populations within and across the states. These morphometric traits are the major parameters that delimit the populations and they correlated significantly at P≤0.05. Analysis of the electrophoregram showed that the ISSR markers are effective for the diversity study. A total of 136 loci were amplified with an average of 7.16 loci per marker, 63.2% of the loci were polymorphic. The Principal Coordinate Analysis revealed that seven factors accounted for 81.6% of the variation and the dendrogram separated the populations into two major groups at a genetic distance of 10 (about 90% similarity) with sub-groups and clusters. Most populations within the state had a high degree of similarity, nonetheless, strong genetic relationship exists among populations from different states. The close relationship between populations across the states suggests a common progenitor, which are likely separated by ecological or geographical isolation mechanisms.

• International Journal of Computer Science & Network Security
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• v.22 no.11
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• pp.157-162
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• 2022

Cerebral palsy is one of the most serious forms of disorders of the psychophysical development of children, which manifests itself in disturbances of motor functions, which are often combined with speech disorders, other complications of the formation of higher mental functions, and often with a decrease in intelligence. The article will discuss the speech disorder in children with cerebral palsy. Emphasis is placed on some important aspects, which should bear in mind, investigating the problem of specifics of speech development of children with cerebral palsy. In particular at the heart of speech disorders in the cerebral palsy is not only damage to certain structures of the brain, but also the later formation or underdevelopment of those parts of the cerebral cortex, which are of major importance in linguistic and mental activity. This is an ontogenetically young region of the cerebral cortex, which is most rapidly developing after birth (premotor, frontal, temmono-temporal). It is important to take into account, that children with cerebral palsy have disturbances of phonemic perception. Often, children do not distinguish between hearing sounds, cannot repeat component rows, allocate sounds in words. At dysarthria, there are violations of pronunciation of vowel and consonant sounds, tempo of speech, modulation of voice, breathing, phonation, as well as asynchronous breathing, alignment and articulation. As a result, we identified the main features and specifics of the speech development of children with cerebral palsy and described the conditions necessary for the full development of language. Language disturbances in children's cerebral palsy depend on the localization and severity of brain damage. Great importance in the mechanism of speech disorders has a pathology that limits the ability of movement and knowledge of the world.

• Journal of Interdisciplinary Genomics
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• v.6 no.1
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• pp.6-13
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• 2024

Background: ABO typing is crucial for ensuring safe blood transfusion and is commonly performed by examining antigen-antibody interactions. Determining ABO blood group can be difficult when dealing with ABO discrepancy and ABO subgroups. ABO genotyping may be necessary to resolve ABO discrepancy. ABO genotyping primarily involves direct sequencing, with the possibility of using other molecular methods. Methods: PCR and direct sequencing of exons 6 and 7 were performed for total 108 samples from June 2010 to December 2019. Also, other molecular methods including cloning sequencing and short tandem repeat analysis were carried out just in case. Sequencing data were compared with allele information of blood group antigen mutation databases. Results: The predominant causal allele among 108 ABO discrepant cases was cis-AB01, with 28 cases. This was followed by rare ABO alleles (B309, B306, A204, Bw29, and Ax01) with 14 cases, and blood chimera with 5 cases. Five new alleles were identified during the investigation. Conclusion: This study reaffirms that cis-AB is the most common cause of inherited ABO discrepancies, and cis-AB01 is the most prevalent cis-AB allele in the Korean population, also in the southeastern region. In addition, we discovered five new alleles and five blood chimeras by adopting sequencing analysis and additional molecular techniques to resolve ABO discrepancies, which provide regional data on rare alleles. This study presents rare and new ABO alleles and blood chimeras identified over a ten-year period at two major university hospitals in Southeastern Korea.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.68 no.3
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• pp.134-146
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• 2023

Phytophthora root rot (PRR) is a major soybean disease caused by an oomycete, Phytophthora sojae. PRR can be severe in poorly drained fields or wet soils. The disease management primarily relies on resistance genes called Rps (resistance to P. sojae). This study aimed to identify resistance loci associated with resistance to P. sojae isolate 40468 in Daepung × CheonAl recombinant inbred line (RIL) population. CheonAl is resistant to the isolate, while Daepung is generally susceptible. We genotyped the parents and RIL population via high-throughput single nucleotide polymorphism genotyping and constructed a set of genetic maps. The presence or absence of resistance to P. sojae was evaluated via hypocotyl inoculation technique, and phenotypic distribution fit to a ratio of 1:1 (R:S) (χ² = 0.57, p = 0.75), indicating single gene mediated inheritance. Single-marker association and the linkage analysis identified a highly significant genomic region of 55.9~56.4 megabase pairs on chromosome 18 that explained ~98% of phenotypic variance. Many previous studies have reported several Rps genes in this region, and also it contains nine genes that are annotated to code leucine-rich repeat or serine/threonine kinase within the approximate 500 kilobase pairs interval based on the reference genome database. CheonAl is the first domestic soybean genotype characterized for resistance against P. sojae isolate 40468. Therefore, CheonAl could be a valuable genetic source for breeding resistance to P. sojae.

• Korean Journal of Microbiology
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• v.32 no.1
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• pp.20-27
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• 1994

An inducible ${\beta}$-lactamase gene (bla) was identified and isolated from the chromosomal DNA of multiple drug resistant strains of Staphylococcus aureus. Determined base sequence of bla and of its flanking region was compared with those of bla genes identified on the staphylococcal plasmids pPC1, pI258, pI1071, and pUB101. Base sequence of 843 base-long structural gene of our bla was same as that of pPCl-, pI258-, and pS1-bla. However, HindIII recognition site Which is found in most of the bla genes at 140 base upstream from the structural gene was moved to the site of 370 base upstream from the structural gene. And one of the two direct repeat sequence found in downstream flanking region of pI1071-bla was deleted in our bla. Amino acid sequence homology analysis of the ORF located around HindIII recognition site reveals that this 80 amino acids-long polypeptide is C-terminus of transposase of Tn4001.

• The Journal of the Korean Society for Microbiology
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• v.35 no.3
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• pp.263-271
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• 2000

A clinical isolate of Klebsiella pneumoniae K7746 produced the extended-spectrum ${\beta}$-lactamase (ESBL) SHV-12. A 6.6 kb BamHI fragment containing the $bla_{SHV-12}$ gene of K7746 strain was cloned into pCRScriptCAM vector resulting in the recombinant plasmid p7746-Cl. The restriction map of 3.6 kb inserted DNA and sequences immediately surrounding $bla_{SHV-12}$ of p7746-C1 were homologous to plasmid pMPA2a carrying $bla_{SHV-2a}$. In addition, both $bla_{SHV-12}$ and $bla_{SHV-2a}$ were expressed from a common hybrid promoter made of the -35 region derived from the left inverted repeat of IS26 and the -10 region from the $bla_{SHV}$ promoter itself. The results indicate that $bla_{SHV-12}$ and $bla_{SHV-2a}$ may have evolved from a common ancestor in the sequential order of $bla_{SHV-2a}$ first, followed by $bla_{SHV-12}$. Furthermore, by the PCR mapping method using primers corresponding to the IS26 and $bla_{SHV}$, the association between IS26 and $bla_{SHV}$ was studied in 12 clinical isolates carrying $bla_{SHV-2a}$, 27 clinical isolates carrying $bla_{SHV-12}$, and 5 reference strains carrying $bla_{SHV-1}$ to $bla_{SHV-5}$. All 39 strains carrying $bla_{SHV-2a}$ or $bla_{SHV-12}$ were positive by the PCR, providing confirmative evidence that IS26 has been involved in the evolution and dissemination of $bla_{SHV-2a}$ and $bla_{SHV-12}$. But 5 reference strains carrying $bla_{SHV-1}$ to $bla_{SHV-5}$ were negative by the PCR. Therefore, we concluded that the molecular evolutionary pathway of $bla_{SHV-2a}$ and $bla_{SHV-12}$ may be different from that of other $bla_{SHV-ESBL}$, e.g., $bla_{SHV-2}$, $bla_{SHV-3}$, $bla_{SHV-4}$, and $bla_{SHV-5}$.

• The Korean Journal of Mycology
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• v.27 no.4 s.91
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• pp.274-279
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• 1999

The internal transcribed spacer regions(ITS) of the ribosomal DNA gene repeat from Coprinus and Psathyrella spp. were amplified using polymerase chain reaction (PCR) and sequenced. Sequences from 11 species including Coprinus comatus, C. atramentarius, C. micaceus, C. cinereus, C. rhizophorus, C. radians, C. echinosporus, C. disseminatus, Psathyrella candolleana, P. spadiceogrisea and Stropharia rugosoannulata were compared. The spacer region I and II were $258{\sim}301\;bp\;and\;253{\sim}275\;bp$ in length respectively and partially contained 17S, 5.8S and 25S. The reciprocal homologies of ITS sequences among these strains were in the range of $43.9{\sim}96.0%$. According to the analysis of ITS sequences, Coprinus and Psathyrella spp. were classified into three clusters. Cluster I consisted of Coprinus lagopus, C. cinereus, C. echinosporus, C. rhizophorus, and C. atramentarius. Cluster II comprised C. micaceus, C. radians, C. disseminatus, Psathyrella candolleana, and P. spadiceogrisea. On the other hand C. comatus is in Cluster III with Stropharia rugosoannulata even though this species is belonging to the section Coprinus in morphological aspect. These results suggest that taxonomic position of Psathyrella would better be inculded in genus Coprinus. Coprinus comatus, the type species of Coprinus, gives a doubt on monophyletic evolution and is assumed to be paraphyletic or polyphyletic.