The Experts below are selected from a list of 1221 Experts worldwide ranked by ideXlab platform
Thomas D Kocher - One of the best experts on this subject based on the ideXlab platform.
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The genetic relationships of two subspecies of striped field mice, Apodemus Agrarius coreae and Apodemus Agrarius chejuensis
Heredity, 2000Co-Authors: Thomas D KocherAbstract:We obtained 282 base pairs of sequence for the mitochondrial control region of 70 individuals of Korean striped field mice Apodemus Agrarius coreae and Apodemus Agrarius chejuensis to determine the levels of genetic divergence between these morphologically distinct taxa. The DNA sequences showed more genetic diversity ( π ) in A. Agrarius coreae (2.98%) than in A. Agrarius chejuensis (1.86%). Our data do not support the current concept that the two morphotypes are different species, but phylogenetic analysis indicates that animals of A. Agrarius coreae with large body size from Wan Island cluster with the large-bodied A. Agrarius chejuensis , and should be included in that taxon. As currently accepted A. Agrarius coreae is not strictly monophyletic, because the large-bodied samples cluster within the range of mitochondrial variation of A. Agrarius chejuensis . The fact that the two morphotypes do not share mitochondrial haplotypes ( χ ^2=66, P < 0.001) suggests that there is little gene flow between them. A molecular clock estimate suggests that the two subspecies might have been isolated at the time of separation of the islands from the mainland.
Chongsoon Kim - One of the best experts on this subject based on the ideXlab platform.
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potential of dark striped field mice Apodemus Agrarius coreae for use as a biological radiation dosimeter for human environments
Integrated Environmental Assessment and Management, 2006Co-Authors: Hee Sun Kim, Yoshikazu Nishimura, Chongsoon KimAbstract:This study examined the possibility of using striped field mice as a biological dosimeter or indicator for surveillance of the ecological effects of boundary radiation emitted by nuclear power plants. For this study, the external morphological characteristics and isoenzymic electrophoretypes of Korean domestic dark-striped field mice were studied after they were captured, controlled for reproduction, and their exact species were identified. In terms of morphological external characteristics, the dark-brown coat, dark back stripe, head-to-tail length, tail length, and ear length matched the taxonomical characteristics of dark-striped field mice. In terms of isoenzymic electrophoretypes, the analyses on l-lactate dehydrogenase, aspartate aminotransferase, and malate dehydrogenase revealed that one species of dark-striped field mice, called Apodemus Agrarius coreae, was scattered throughout a wide range of habitats. On the other hand, after irradiating the A. a. coreae (0, 0.5, 1, 3, 5, and 7 gray [Gy]) to analyze their survival rate and frequency of micronuclei in peripheral polychromatic erythrocytes, their LD50/30 was approximately 5 Gy. Also, the mice that contained 1 or 3 Gy gained weight compared with those that contained 0.5 Gy. Moreover, those with 0.5 Gy and higher showed an increase in white blood cells and platelets as well as in sodium and creatinine. However, decreased concentrations of alkaline phosphatase, alanine animotransferase, calcium, phosphorus, and globulin were observed in the A. a. coreae after irradiation. The results of the study reveal that wild A. a. coreae mice have high potential as a biological monitoring system to determine radiation effects in human environments such as those within the vicinity of nuclear power plants.
Seung-ho Lee - One of the best experts on this subject based on the ideXlab platform.
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novel paju Apodemus paramyxovirus 1 and 2 harbored by Apodemus Agrarius in the republic of korea
Virology, 2021Co-Authors: Seung-ho Lee, Kijin Kim, Shailesh Budhathoki, Kyungmin Park, Geumyoung Lee, Seungchan Cho, Bonghyun Kim, Seunghee Cho, Jongwoo Kim, Jingyeong LeeAbstract:Abstract Paramyxoviruses harbored by multiple natural reservoirs pose a potential threat to public health. Jeilongvirus has been proposed as a novel paramyxovirus genus found in rodents, bats, and cats. Paramyxovirus RNA was detected in 108/824 (13.1%) Apodemus Agrarius captured at 14 trapping sites in the Republic of Korea. We first present two genetically distinct novel paramyxoviruses, Paju Apodemus paramyxovirus 1 (PAPV-1) and 2 (PAPV-2). The disparity between PAPV-1 (19,716 nucleotides) and -2 (17,475 nucleotides) revealed the presence of the SH gene and length of the G gene in the genome organization. The phylogeny of PAPV-1 and -2 belonged to distinct genetic lineages of Jeilongvirus, respectively, even though these viruses were originated from A. Agrarius. PAPV-1 infected human epithelial and endothelial cells, facilitating the induction of type I/III interferons, interferon-stimulated genes, and pro-inflammatory cytokines. Therefore, this study provides insights into the molecular epidemiology, genetic diversity, and virus-host interactions of novel rodent-borne paramyxoviruses.
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multiplex pcr based nanopore sequencing and epidemiological surveillance of hantaan orthohantavirus in Apodemus Agrarius republic of korea
Viruses, 2021Co-Authors: Kyungmin Park, Seung-ho Lee, Shailesh Budhathoki, Geumyoung Lee, Seungchan Cho, Jongwoo Kim, Jingyeong Lee, Kkothanahreum Park, Yu Jin KimAbstract:Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus Agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat worldwide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. Agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.
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novel paju Apodemus paramyxovirus 1 and 2 harbored by Apodemus Agrarius in the republic of korea
bioRxiv, 2021Co-Authors: Seung-ho Lee, Kijin Kim, Shailesh Budhathoki, Kyungmin Park, Geumyoung Lee, Seungchan Cho, Bonghyun Kim, Seunghee Cho, Hyeok Sun Choi, Jongwoo KimAbstract:Abstract Paramyxoviruses, negative-sense single-stranded RNA viruses, pose a potential threat to public health. Currently, 78 species and 17 genera of paramyxoviruses are classified and harbored by multiple natural reservoirs, including rodents, bats, birds, reptiles, and fish. Jeilongvirus has been proposed as a novel paramyxovirus genus containing J-, Beilong, and Tailam viruses, found in wild rodents. Using RT-PCR, 824 Apodemus Agrarius individuals were examined for the prevalence of paramyxovirus infections. Paramyxovirus RNA was detected in 108 (13.1%) rodents captured at 14 trapping sites in Korea. We first present two genetically distinct novel paramyxoviruses (genus Jeilongvirus), Paju Apodemus paramyxoviruses 1 (PAPV-1) and 2 (PAPV-2), from A. Agrarius. Six PAPV strains were completely sequenced using next-generation and Sanger sequencing. PAPV-1 genome comprised 19,716 nucleotides, with eight genes (3′-N-P/V/C-M-F-SH-TM-G-L-5′), whereas PAPV-2 genome contained 17,475 nucleotides, with seven genes (3′-N-P/V/C-M-F-TM-G-L-5′). The disparity between PAPV-1 and -2 revealed the presence of the SH gene and length of the G gene in the genome organization. The phylogenies of PAPV-1 and -2 belong to distinct genetic lineages of Jeilongvirus despite being from the same natural host. PAPV-1 clustered with Beilong and Tailam viruses, while PAPV-2 formed a genetic lineage with Mount Mabu Lophuromys virus-1. PAPV-1 infected human epithelial and endothelial cells, facilitating the induction of type I/III interferons, interferon-stimulated genes, and proinflammatory cytokines. Therefore, this study provides profound insights into the molecular epidemiology, virus-host interactions, and zoonotic potential of novel rodent-borne paramyxoviruses. Importance Paramyxoviruses are a critical public health and socio-economic burden to humans. Rodents play a crucial role in transmitting pathogens to humans. In the last decade, novel paramyxoviruses have been discovered in different rodents. Here, we found that Apodemus Agrarius harbored two distinct genotypes of the novel paramyxoviruses, Paju Apodemus paramyxovirues 1 (PAPV-1) and 2 (PAPV-2), possessing unique genome structures that are responsible for encoding TM and G proteins of different sizes. In addition, PAPV-1 infected human epithelial and endothelial cells, facilitating the induction of type I/III IFNs, ISGs, and proinflammatory cytokines. Thus, this study provides significant insights into molecular prevalence, virus-host interactions of paramyxoviruses. These observations raise the awareness of physicians and scientists about the emergence of new rodent-borne paramyxoviruses.
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comparison of targeted next generation sequencing for whole genome sequencing of hantaan orthohantavirus in Apodemus Agrarius lung tissues
Scientific Reports, 2019Co-Authors: Won-keun Kim, Jeong-ah Kim, Seung-ho Lee, Seungchan Cho, Daesang Lee, Dong Hyun Song, Seong Tae Jeong, Michael R Wiley, Gustavo Palacios, Jin-won SongAbstract:Orthohantaviruses, negative-sense single-strand tripartite RNA viruses, are a global public health threat. In humans, orthohantavirus infection causes hemorrhagic fever with renal syndrome or hantavirus cardiopulmonary syndrome. Whole-genome sequencing of the virus helps in identification and characterization of emerging or re-emerging viruses. Next-generation sequencing (NGS) is a potent method to sequence the viral genome, using molecular enrichment methods, from clinical specimens containing low virus titers. Hence, a comparative study on the target enrichment NGS methods is required for whole-genome sequencing of orthohantavirus in clinical samples. In this study, we used the sequence-independent, single-primer amplification, target capture, and amplicon NGS for whole-genome sequencing of Hantaan orthohantavirus (HTNV) from rodent specimens. We analyzed the coverage of the HTNV genome based on the viral RNA copy number, which is quantified by real-time quantitative PCR. Target capture and amplicon NGS demonstrated a high coverage rate of HTNV in Apodemus Agrarius lung tissues containing up to 103–104 copies/μL of HTNV RNA. Furthermore, the amplicon NGS showed a 10-fold (102 copies/μL) higher sensitivity than the target capture NGS. This report provides useful insights into target enrichment NGS for whole-genome sequencing of orthohantaviruses without cultivating the viruses.
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Monthly capture rates of Apodemus Agrarius collected at Camp Humphreys and the new expansion site from 2008–2010 and 2012.
2017Co-Authors: Heung-chul Kim, Won-keun Kim, Terry A. Klein, Sung-tae Chong, Peter V. Nunn, Jeong-ah Kim, Seung-ho Lee, Jin-won SongAbstract:Monthly capture rates of Apodemus Agrarius collected at Camp Humphreys and the new expansion site from 2008–2010 and 2012.
Jingyeong Lee - One of the best experts on this subject based on the ideXlab platform.
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novel paju Apodemus paramyxovirus 1 and 2 harbored by Apodemus Agrarius in the republic of korea
Virology, 2021Co-Authors: Seung-ho Lee, Kijin Kim, Shailesh Budhathoki, Kyungmin Park, Geumyoung Lee, Seungchan Cho, Bonghyun Kim, Seunghee Cho, Jongwoo Kim, Jingyeong LeeAbstract:Abstract Paramyxoviruses harbored by multiple natural reservoirs pose a potential threat to public health. Jeilongvirus has been proposed as a novel paramyxovirus genus found in rodents, bats, and cats. Paramyxovirus RNA was detected in 108/824 (13.1%) Apodemus Agrarius captured at 14 trapping sites in the Republic of Korea. We first present two genetically distinct novel paramyxoviruses, Paju Apodemus paramyxovirus 1 (PAPV-1) and 2 (PAPV-2). The disparity between PAPV-1 (19,716 nucleotides) and -2 (17,475 nucleotides) revealed the presence of the SH gene and length of the G gene in the genome organization. The phylogeny of PAPV-1 and -2 belonged to distinct genetic lineages of Jeilongvirus, respectively, even though these viruses were originated from A. Agrarius. PAPV-1 infected human epithelial and endothelial cells, facilitating the induction of type I/III interferons, interferon-stimulated genes, and pro-inflammatory cytokines. Therefore, this study provides insights into the molecular epidemiology, genetic diversity, and virus-host interactions of novel rodent-borne paramyxoviruses.
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multiplex pcr based nanopore sequencing and epidemiological surveillance of hantaan orthohantavirus in Apodemus Agrarius republic of korea
Viruses, 2021Co-Authors: Kyungmin Park, Seung-ho Lee, Shailesh Budhathoki, Geumyoung Lee, Seungchan Cho, Jongwoo Kim, Jingyeong Lee, Kkothanahreum Park, Yu Jin KimAbstract:Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus Agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat worldwide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. Agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.
M V Pavlenko - One of the best experts on this subject based on the ideXlab platform.
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Differentiation of Continental Isolates of the Striped Field Mouse (Apodemus Agrarius Pallas, 1771) by Microsatellite Loci
Biology Bulletin Reviews, 2020Co-Authors: L. V. Frisman, I V Kartavtseva, M V Pavlenko, I N Sheremetyeva, A. S. Bogdanov, K. V. Shlufman, Yu. M. KovalskayaAbstract:Microsatellite analysis was used to examine intraspecific polymorphism in two extensive continental isolates of the striped field mouse ( Apodemus Agrarius Pallas, 1771) separated by the Baikal disjunction. Striped field mice from the western isolate (from the European and Kazakh-Siberian parts of the range) and from the eastern isolate (from the territory of the Middle Amur Region and Coastal Territory of Far East) were tested. The analysis used 180 specimens collected from 33 localities and five microsatellite loci developed earlier for the genus Apodemus . The work was carried out based on the summation of local samples in each of the aforementioned geographical regions. It was shown that allelic diversity and the number of specific alleles were higher in the eastern isolate that may be the result of the longer habitation of the striped field mouse in the eastern part of the range. The limited number of specific alleles in the western isolate as compared to the eastern one can be determined by the founder effect and may reflect the direction of the historical migration of the species from east to west. Our results demonstrate no more than a population level of differentiation within the continental isolates of the striped field mouse and indicate no more than a subspecies level of differences between these isolated forms, i.e., the relatively recent penetration of A. Agrarius to western Eurasia.
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morphological and genetic variability in small island populations of the striped field mouse Apodemus Agrarius pallas 1771
Biology Bulletin, 2017Co-Authors: I N Sheremetyeva, I V Kartavtseva, M V Pavlenko, V A Kostenko, I S Sheremetyev, I O Katin, M E KosoyAbstract:Morphological (craniometrical characteristics and variations of cusp t3 on the second upper molar (M2)) and genetic (polymorphism of chromosomes and blood proteins) variability was analyzed in small island populations of the striped field mouse Apodemus Agrarius Pallas, 1771 from the Peter the Great Bay (Sea of Japan). It was found that the absence of t3 on M2 is not a specific trait for A. Agrarius. It was demonstrated that the population of field mice on the Bolshoy Pelis Island significantly differs from the populations from other islands and from the mainland according to the craniometrical parameters, teeth phenes, and variants of blood transferrin. The possible age of establishment of the island populations of the striped field mouse is discussed.
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Current distribution of the striped field mouse (Apodemus Agrarius Pallas, 1771) in Eastern Transbaikalia: New findings in the disjunction area
Russian Journal of Biological Invasions, 2015Co-Authors: Yu. A. Bazhenov, M V Pavlenko, V. P. Korablev, A. I. KardashAbstract:Materials on the new findings of the striped field mouse ( Apodemus Agrarius ) in Transbaikalia, within an earlier disjunction area in the habitat of this species (in the basins of the Onon and Ingoda rivers), are presented. Possible causes of the expansion of the species range are discussed. It is most probable that the species was introduced from the basin of the Argun River with a cargo of agricultural products to the lower reaches of the Onon River or the upper reaches of the Shilka River. Currently, the striped field mouse is a common species inhabiting a floodplain shrub biotope in the lower reaches of the Ingoda and Onon rivers.
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Diversity of the mitochondrial DNA cytochrome b gene of the field mouse Apodemus Agrarius Pallas, 1771 in the south of the Russian Far East
Biology Bulletin, 2014Co-Authors: V. V. Pereverzeva, M V PavlenkoAbstract:We studied the variability of a fragment of the cytochrome b gene and the corresponding amino acid sequence of the field mouse Apodemus Agrarius (Pallas, 1771) in the South of Primorskii krai (Far East of Russia). A significant polymorphism of these traits was detected. High indices of molecular diversity were obtained. The topology of the phylogenetic tree and the median networks suggest that the population of field mice in the south of Primorskii krai originated from three maternal lines. It was noted that clustering of haplotypes on a territorial basis is absent, and the field mouse population in southern Primorskii krai can be considered as one of the key points in maintaining a high genetic diversity of the species.
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chromosome variation in the striped field mouse Apodemus Agrarius rodentia muridae
2000Co-Authors: I V Kartavtseva, M V PavlenkoAbstract:Chromosome sets of 114 Apodemus Agrarius mice from 29 localities in Moldova, Ukraine, Siberia, and the Far East were studied by means of G-, C-, and NOR-banding. In all populations studied, the Y chromo- some was shown to be a medium-size acrocentric chromosome consisting of heterochromatin. Chromosome polymorphism observed in populations from Primorskii krai concerned (1) the morphology of the first two autosome pairs (variants A/A, A/ST, and ST/ST), (2) the number of metacentric chromosomes (from 6 to 8), and (3) heterochromatin localization in the pericentromeric regions of two metacentric chromosome pairs. A karyotype with an additional heterochromatic microchromosome found in all the metaphases studied was described in one mouse from a locality of western Primorye that has not been studied previously. In the karyo- type of 15 mice from four populations of Primorye, the pool of nucleolus organizer regions is distributed over three autosome pairs rather than over four, as is the case in A. Agrarius from Europe. Based on the analysis of literature sources and our own data, the problem of chromosome polymorphism in the field mouse is discussed.