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Johnson JA, Athrey G, Anderson CM, Bell DA, Dixon A, Kumazawa Y, Maechtle T, Meeks GW, Mindell D, Nakajima K, Novak B, Talbot S, White C, Zhan X. Whole-genome survey reveals extensive variation in genetic diversity and inbreeding levels among peregrine falcon subspecies. Ecol Evol 2023; 13:e10347. [PMID: 37484928 PMCID: PMC10361364 DOI: 10.1002/ece3.10347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023] Open
Abstract
In efforts to prevent extinction, resource managers are often tasked with increasing genetic diversity in a population of concern to prevent inbreeding depression or improve adaptive potential in a changing environment. The assumption that all small populations require measures to increase their genetic diversity may be unwarranted, and limited resources for conservation may be better utilized elsewhere. We test this assumption in a case study focused on the peregrine falcon (Falco peregrinus), a cosmopolitan circumpolar species with 19 named subspecies. We used whole-genome resequencing to generate over two million single nucleotide polymorphisms (SNPs) from multiple individuals of all peregrine falcon subspecies. Our analyses revealed extensive variation among subspecies, with many island-restricted and nonmigratory populations possessing lower overall genomic diversity, elevated inbreeding coefficients (F ROH)-among the highest reported, and extensive runs of homozygosity (ROH) compared to mainland and migratory populations. Similarly, the majority of subspecies that are either nonmigratory or restricted to islands show a much longer history of low effective population size (N e). While mutational load analyses indicated an increased proportion of homozygous-derived deleterious variants (i.e., drift load) among nonmigrant and island populations compared to those that are migrant or reside on the mainland, no significant differences in the proportion of heterozygous deleterious variants (i.e., inbreeding load) was observed. Our results provide evidence that high levels of inbreeding may not be an existential threat for some populations or taxa. Additional factors such as the timing and severity of population declines are important to consider in management decisions about extinction potential.
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Xiaokaiti X, Hashiguchi Y, Ota H, Kumazawa Y. Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae. Genes (Basel) 2022; 13:genes13081470. [PMID: 36011381 PMCID: PMC9407768 DOI: 10.3390/genes13081470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem repeats in these genomes. This led us to show that major noncoding regions in the mitochondrial genomes of those three sea snakes contain considerably long tandem duplications, unlike the mitochondrial genomes previously reported for same and other sea snake species. We also found a transposition of the light-strand replication origin within a tRNA gene cluster for the three sea snakes. This change can be explained by the Tandem Duplication—Random Loss model, which was further supported by remnant intervening sequences between tRNA genes. Mitochondrial genomes of true snakes (Alethinophidia) have been shown to contain duplicate major noncoding regions, each of which includes the control region necessary for regulating the heavy-strand replication and transcription from both strands. However, the control region completely disappeared from one of the two major noncoding regions for two Hydrophis sea snakes, posing evolutionary questions on the roles of duplicate control regions in snake mitochondrial genomes. The timing and molecular mechanisms for these changes are discussed based on the elapid phylogeny.
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Shirasawa H, Kumazawa Y, Sato W, Togashi K, Ono N, Fujishima A, Terada Y. P-346 First comparison of the egg freezing and storage cost between medical adaptation and social adaptation of Japan fertility hospitals and clinics based on institution's websites. Hum Reprod 2022. [DOI: 10.1093/humrep/deac107.329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Study question
In Japan, how much of freezing cost and the yearly storage cost of medical and social egg freezing for fertility preservation is clearly disclosed on the institution's website?
Summary answer
Of the 621 infertility treatment institutions, 146 listed egg freezing on their websites, 46 specified the freezing cost, and 71 specified the yearly storage cost.
What is known already
In Japan, from April 2022, standard assisted reproductive technology will be covered by insurance, but medical and social egg freezing will continue to be privately funded. Therefore, it is unclear how many facilities in Japan perform egg freezing. Furthermore, while the cost of freezing and yearly storage varies significantly from facility to facility, there has been no data comparing egg freezing among facilities in Japan or other countries. Therefore, we extracted data about freezing and storage cost from each institution's website and compared them for the first time.
Study design, size, duration
This study is a web-based survey in which a single board-certified specialist by Japan Society for Reproductive Medicine exhaustively browsed the websites of all 621 fertility treatment institutions in Japan in October 2021 and analyzed the implementation of egg freezing, freezing costs, and yearly storage costs of egg are clearly stated on the websites. The costs of drugs used for egg retrieval and ovarian stimulation were excluded.
Participants/materials, setting, methods
Of the 621 institutions, 88 institutions that clearly stated on their websites that they offer egg freezing for medical reasons were divided into a medical group, and 58 institutions that clearly stated that they offer egg freezing for only social reasons were divided into social group for statistical analysis. We compared the freezing and the yearly storage cost, respectively, whether it varies depending on the number of eggs or whether it is a fixed cost.
Main results and the role of chance
Of the 621 institutions, 146 (23.5%), 88 in the medical group and 58 in the social group, specified that they offer egg freezing. The percentages of clarification for freezing cost and yearly storage cost on the website were 27.3% and 30.7% in the medical group, 72.4%, and 75.9% in the social group, so the social group was higher in both cases (p < 0.01). The percentage of fixed costs for egg freezing was significantly lower in the social group (6/42, 14.3%) than in the medical group (9/24, 37.5%) (p < 0.05). The percentage of fixed costs for yearly storage cost was samely significantly lower in the social group (30/44, 68.2%) than in the medical group (25/27, 92.6%) (p < 0.05). The mean freezing cost/yearly storage cost was as follows for 1, 5, and 10 eggs. The medical group was (JPY45,527/JPY22,327, JPY65,179/JPY22,530, JPY90,311/JPY22,770), and the social group was (JPY56,822/JPY40,178, JPY88,429/JPY56,502, JPY136,550/JPY79,090), so the social group had the significantly highest amount of costs in each case. Note that JPY 10,000 is about EUR77.7. The most expensive clinic to store ten eggs was JPY500,000 (EUR3,883) per year, and the least university hospital was JPY 4,600 (EUR35.7) per year.
Limitations, reasons for caution
This survey was conducted by carefully browsing the facility's website, but since we did not confirm the information through questionnaires or e-mail, there is the possibility that the information may have been updated. Another limitation is that less than half of the medical groups list cost details on their websites.
Wider implications of the findings
This is the first report to analyze the cost of egg freezing in Japan using the institution's website. The rate of cost disclosure on the website is still low. Moreover, the costs of social freezing are significantly higher than medical reasons, but this may change with the insurance of ART.
Trial registration number
not applicable
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Hirakawa T, Goto M, Takahashi K, Iwasawa T, Fujishima A, Makino K, Shirasawa H, Sato W, Sato T, Kumazawa Y, Terada Y. Na+/K+ ATPase α1 and β3 subunits are localized to the basolateral membrane of trophectoderm cells in human blastocysts. Hum Reprod 2022; 37:1423-1430. [PMID: 35640043 PMCID: PMC9247425 DOI: 10.1093/humrep/deac124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/09/2022] [Indexed: 11/25/2022] Open
Abstract
STUDY QUESTION Is there a relation between specific Na+/K+ ATPase isoform expression and localization in human blastocysts and the developmental behavior of the embryo? SUMMARY ANSWER Na+/K+ ATPase α1, β1 and β3 are the main isoforms expressed in human blastocysts and no association was found between the expression level of their respective mRNAs and the rate of blastocyst expansion. WHAT IS KNOWN ALREADY In mouse embryos, Na+/K+ ATPase α1 and β1 are expressed in the basolateral membrane of trophectoderm (TE) cells and are believed to be involved in blastocoel formation (cavitation). STUDY DESIGN, SIZE, DURATION A total of 20 surplus embryos from 11 patients who underwent IVF and embryo transfer at a university hospital between 2009 and 2018 were analyzed. PARTICIPANTS/MATERIALS, SETTING, METHODS After freezing and thawing Day 5 human blastocysts, their developmental behavior was observed for 24 h using time-lapse imaging, and the expression of Na+/K+ ATPase isoforms was examined using quantitative RT-PCR (RT-qPCR). The expressed isoforms were then localized in blastocysts using fluorescent immunostaining. MAIN RESULTS AND THE ROLE OF CHANCE RT-qPCR results demonstrated the expression of Na+/K+ ATPase α1, β1 and β3 isoforms in human blastocysts. Isoforms α1 and β3 were localized to the basolateral membrane of TE cells, and β1 was localized between TE cells. A high level of β3 mRNA expression correlated with easier hatching (P = 0.0261). LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION The expression of mRNA and the localization of proteins of interest were verified, but we have not been able to perform functional analysis. WIDER IMPLICATIONS OF THE FINDINGS Of the various Na+/K+ ATPase isoforms, expression levels of the α1, β1 and β3 mRNAs were clearly higher than other isoforms in human blastocysts. Since α1 and β3 were localized to the basolateral membrane via fluorescent immunostaining, we believe that these subunits contribute to the dilation of the blastocoel. The β1 isoform is localized between TE cells and may be involved in tight junction formation, as previously reported in mouse embryos. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the JSPS KAKENHI (https://www.jsps.go.jp/english/index.html), grant number 17K11215. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors have no conflicts of interest.
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Kambayashi C, Kakehashi R, Sato Y, Mizuno H, Tanabe H, Rakotoarison A, Künzel S, Furuno N, Ohshima K, Kumazawa Y, Nagy ZT, Mori A, Allison A, Donnellan SC, Ota H, Hoso M, Yanagida T, Sato H, Vences M, Kurabayashi A. Geography-Dependent Horizontal Gene Transfer from Vertebrate Predators to Their Prey. Mol Biol Evol 2022; 39:6563207. [PMID: 35417559 PMCID: PMC9007160 DOI: 10.1093/molbev/msac052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Horizontal transfer (HT) of genes between multicellular animals, once thought to be extremely rare, is being more commonly detected, but its global geographic trend and transfer mechanism have not been investigated. We discovered a unique HT pattern of Bovine-B (BovB) LINE retrotransposons in vertebrates, with a bizarre transfer direction from predators (snakes) to their prey (frogs). At least 54 instances of BovB HT were detected, which we estimate to have occurred across time between 85 and 1.3 Ma. Using comprehensive transcontinental sampling, our study demonstrates that BovB HT is highly prevalent in one geographical region, Madagascar, suggesting important regional differences in the occurrence of HTs. We discovered parasite vectors that may plausibly transmit BovB and found that the proportion of BovB-positive parasites is also high in Madagascar where BovB thus might be physically transported by parasites to diverse vertebrates, potentially including humans. Remarkably, in two frog lineages, BovB HT occurred after migration from a non-HT area (Africa) to the HT hotspot (Madagascar). These results provide a novel perspective on how the prevalence of parasites influences the occurrence of HT in a region, similar to pathogens and their vectors in some endemic diseases.
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Maeda E, Jwa SC, Kumazawa Y, Saito K, Iba A, Yanagisawa A, Kuwahara A, Saito H, Terada Y, Fukuda T, Ishihara O, Kobayashi Y. P–721 Probability of receiving assisted reproductive technology treatment through out-of-pocket payment and household income: A discrete choice experiment in Japan. Hum Reprod 2021. [DOI: 10.1093/humrep/deab130.720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Study question
What is the probability that patients will receive assisted reproductive technology (ART) treatment based on their out-of-pocket payment and income class?
Summary answer
Higher-income patients opted for ART even at a higher cost, whereas an out-of-pocket payment was the most influential determinant in all income groups.
What is known already
Economic disparities affect access to ART treatment in many countries. At the time of this survey, Japan provided partial reimbursement for ART treatment exclusively for those in low- or middle-income classes due to limited governmental budgets. However, the optimal financial support by income class is unknown.
Study design, size, duration
We conducted a discrete choice experiment (DCE) in Japan in January 2020 including 824 women with fertility problems who were recruited via an online social research panel.
Participants/materials, setting, methods
Participants included women aged 25–44 years undergoing fertility diagnosis or treatment. They completed a DCE questionnaire including 16 hypothetical scenarios, created by orthogonal design, to measure six relevant ART attributes (pregnancy rate, risk of adverse effects, number of visits to outpatient clinics, consultation hours, kindness of staff, and out-of-pocket expense) and their relation to treatment choice. We used mixed-effect logistic regression models to estimate the probability of receiving ART treatment for each attribute.
Main results and the role of chance
Of the 1,247 eligible women recruited, 824 completed the survey (66% participation rate). All six attributes significantly influenced treatment preference, with participants valuing out-of-pocket payment the most, followed by pregnancy rates and kindness of staff. The odds ratios of each attribute to receiving ART treatment were 0.58 (95% confidence interval [CI]: 0.57 − 0.59) for out-of-pocket payments per additional 100,000 Japanese yen (JPY; i.e., 800 euros), 1.47 (95% CI: 1.43 − 1.53) for pregnancy rates per additional 5%, and 4.16 (95% CI: 3.73 − 4.64) for kindness of staff, after adjusting for clinical and socioeconomic factors. Significant interactions occurred between high household income (≥8 million JPY) and high out-of-pocket payment (≥500,000 JPY). However, the mean predicted probability of the highest-income patients (i.e., ≥10 million JPY) to receive ART treatment at the average cost without public funding (i.e., 400,000 JPY) was 47% (interquartile range: 18%−76%), whereas that of middle-income patients (i.e., 6–8 million JPY) to receive ART at the average subsidized cost (i.e., 100,000 JPY) was 60% (interquartile range: 33%–88%).
Limitations, reasons for caution
Other attributes not included in our DCE scenarios might be relevant in real-life settings. Choices made in a DCE would not wholly match the actual treatment choices.
Wider implications of the findings: The present DCE suggested that out-of-pocket payment was the primary determinant in patients’ ART decisions. High-income patients were more likely to receive ART treatment even at a high cost, but their ineligibility for government financial support due to their high income might discourage them from receiving treatment.
Trial registration number
NA
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Nasu K, Yokoyama Y, Sun Y, Suzuki-Matsubara M, Teramoto T, Moriyama A, Kawase M, Kumazawa Y. Mitochondrial genome of Cipangopaludina japonica (Gastropoda: Viviparidae) with a tRNA gene rearrangement. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1735269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Matsubara K, Kumazawa Y, Ota H, Nishida C, Matsuda Y. Karyotype Analysis of Four Blind Snake Species (Reptilia: Squamata: Scolecophidia) and Karyotypic Changes in Serpentes. Cytogenet Genome Res 2019; 157:98-106. [PMID: 30754040 DOI: 10.1159/000496554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The suborder Serpentes is divided into 2 infraorders, Scolecophidia and Alethinophidia, which diverged at an early stage of snake diversification. In this study, we examined karyotypes of 4 scolecophidian species (Letheobia simonii, Xerotyphlops vermicularis, Indotyphlops braminus, and Myriopholis macrorhyncha) and performed FISH with 18S-28S rDNA as well as microchromosomal and Z chromosome-linked genes of Elaphe quadrivirgata (Alethinophidia) to investigate the karyotype evolution in the scolecophidian lineage. Diploid chromosome numbers of X. vermicularis and L. simonii were 30 (16 macrochromosomes and 14 microchromosomes) and 32 (16 macrochromosomes and 16 microchromosomes), respectively. The karyotype of a female M. macrorhyncha consisted of 15 macrochromosomes and 19 microchromosomes, including a heterochromatic microchromosome, indicating the presence of a heteromorphic chromosome pair. E. quadrivirgata Z-linked genes mapped to chromosome 4 of M. macrorhyncha, not to the heteromorphic pair. Therefore, M. macrorhyncha may have differentiated ZW sex chromosomes which are not homologous to those of E. quadrivirgata. One of the E. quadrivirgata microchromosomal genes mapped to the terminal region of chromosome 4q in X. vermicularis, suggesting that fusions between microchromosomes and macrochromosomes occurred in this species. rDNA was localized in different macrochromosomal pairs in the 2 diploid scolecophidian snakes examined here, whereas the gene location in a microchromosomal pair was conserved in 5 alethinophidian species examined. These results might imply the occurrence of chromosome fusions in the scolecophidian lineages. In I. braminus, a unique parthenogenetic snake with a triploid karyotype (21 macrochromosomes and 21 microchromosomes), morphological heteromorphisms were identified in chromosomes 1 and 7. Such heteromorphisms in 2 chromosomes were also observed in individuals from distant locations in the broad distribution range of this species, suggesting that the heteromorphisms were fixed in the genome at an early stage of its speciation.
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Atminarso D, Wibowo A, Kusuma WE, Prianto E, Ahnelt H, Vasemägi A, Kumazawa Y. The complete mitochondrial DNA sequence of Pectenocypris sp. (Actinopterygii: Cyprinidae) from Serkap River, Sumatra, Indonesia. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:122-124. [PMID: 33474089 PMCID: PMC7799607 DOI: 10.1080/23802359.2018.1424585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The whole mitochondrial genome of a small cyprinid freshwater fish Pectenocypris sp. collected from Serkap River, Central Sumatra, Indonesia was sequenced. This mitochondrial genome consisted of 16,589 bp and included 37 genes in the same order as in many other vertebrates including the human. Phylogenetic analysis suggested that this taxon clusters with Boraras maculatus among several Rasbora species.
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Sun Y, Kurisaki M, Hashiguchi Y, Kumazawa Y. Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing. BMC Genomics 2017; 18:665. [PMID: 28851277 PMCID: PMC5576253 DOI: 10.1186/s12864-017-4080-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/21/2017] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Genes encoded in vertebrate mitochondrial DNAs are transcribed as a polycistronic transcript for both strands, which is later processed into individual mRNAs, rRNAs and tRNAs, followed by modifications, such as polyadenylation at the 3' end of mRNAs. Although mechanisms of the mitochondrial transcription and RNA processing have been extensively studied using some model organisms, structural variability of mitochondrial mRNAs across different groups of vertebrates is poorly understood. We conducted the high-throughput RNA sequencing to identify major polyadenylation sites for mitochondrial mRNAs in the Japanese grass lizard, Takydromus tachydromoides and compared the polyadenylation profiles with those identified similarly for 23 tetrapod species, featuring sauropsid taxa (reptiles and birds). RESULTS As compared to the human, a major polyadenylation site for the NADH dehydrogenase subunit 5 mRNA of the grass lizard was located much closer to its stop codon, resulting in considerable truncation of the 3' untranslated region for the mRNA. Among the other sauropsid taxa, several distinct polyadenylation profiles from the human counterpart were found for different mRNAs. They included various truncations of the 3' untranslated region for NADH dehydrogenase subunit 5 mRNA in four taxa, bird-specific polyadenylation of the light-strand-transcribed NADH dehydrogenase subunit 6 mRNA, and the combination of the ATP synthase subunit 8/6 mRNA with a neighboring mRNA into a tricistronic mRNA in the side-necked turtle Pelusios castaneus. In the last case of P. castaneus, as well as another example for NADH dehydrogenase subunit 1 mRNAs of some birds, the association between the polyadenylation site change and the gene overlap was highlighted. The variations in the polyadenylation profile were suggested to have arisen repeatedly in diverse sauropsid lineages. Some of them likely occurred in response to gene rearrangements in the mitochondrial DNA but the others not. CONCLUSIONS These results demonstrate structural variability of mitochondrial mRNAs in sauropsids. The efficient and comprehensive characterization of the mitochondrial mRNAs will contribute to broaden our understanding of their structural and functional evolution.
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Kusuma WE, Samuel PD, Wiadnya DGR, Hariati AM, Kumazawa Y. Complete mitogenome sequence of Rasbora argyrotaenia (Actinopterygii: Cyprinidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:373-374. [PMID: 33473832 PMCID: PMC7800954 DOI: 10.1080/23802359.2017.1347835] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The mitochondrial genome of a small freshwater fish Rasbora argyrotaenia from Java Island, Indonesia, was completely sequenced. This mitochondrial genome had 16,740 bp in length and consisted of 37 genes in the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis showed that R. argyrotaenia is more closely related to R. borapetensis than to other Javanese rasboras, R. aprotaenia and R. lateristriata.
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Morita H, Hasunuma R, Hoshino M, Fujihara M, Tanaka S, Yamamoto S, Kumazawa Y. Difference in clearance of exogenously administered smooth-form LPS following host responses among normal, sensitized and LPS-tolerant mice. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/096805199700400605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Clearance of exogenously administered Salmonella abortus equi LPS from the circulation following induction of host responses, e.g. release of soluble CD14 (sCD14) and TNFα production, were investigated. The endotoxin unit of administered LPS in plasma was monitored by a combined method. After 1 h, more than 80% of injected LPS disappeared from the circulation of normal mice at all doses except a 100 μg dose, but sCD14 in plasma could not yet be detected by Western blotting. Release of sCD14 reached a peak 9 h after LPS injection. According to pretreatment with either Propionibacterium acnes or silver nitrate, the clearance rates of exogenously added LPS from the circulation were accelerated in comparison with the rate in normal mice, but plasma TNF levels were the opposite. In LPS-tolerant mice, LPS clearance and production of TNF and sCD14 was reduced. Pretreatment with anti-CD14 mAb reduced LPS-induced TNF production but did not influence the clearance rates. Taken together, in vivo, sCD14 may not play a critical role for early LPS clearance.
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Morita H, Hasunuma R, Fujihara M, Tanaka S, Galanos C, Freudenberg M, Morrison D, Kumazawa Y. Measurement of different types of endotoxin in murine plasma by pretreatment with alkaline reagent and kinetic chromogenic Limulus test. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/096805199700400505] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Using a combined pretreatment methodology employing an alkaline reagent and a kinetic chromogenic Limulus test using Endospecy®, different types of endotoxins in murine plasma were able to be measured quantitatively. The detection of smooth (S)-form Salmonella abortus equi LPS (S-LPS) was approximately twice as sensitive as Helicobacter pylori LPS in aqueous solution. S-LPS added to whole mouse blood was recovered quantitatively from plasma, but the rough (R)-form S. minnesota LPS was not. The rates of clearance of S-LPS from the circulation following intravenous injection were shown to be different among BALB/c, C3H/HeN and B10Sn mice. Infection of mice with Salmonella typhimurium 3 days earlier resulted in accelerated clearance of subsequently injected LPS from the circulation. Significantly higher amounts of free non-microbe-associated LPS were detected in the blood of mice 1 h after infection with Escherichia coli O111:B4 followed by immediate treatment with ceftazidime, in comparison with non-antibiotic-treated but infected mice.
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Matsubara K, Nishida C, Matsuda Y, Kumazawa Y. Sex chromosome evolution in snakes inferred from divergence patterns of two gametologous genes and chromosome distribution of sex chromosome-linked repetitive sequences. ZOOLOGICAL LETTERS 2016; 2:19. [PMID: 27570632 PMCID: PMC5002183 DOI: 10.1186/s40851-016-0056-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 08/18/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND The discovery of differentially organized sex chromosome systems suggests that heteromorphic sex chromosomes evolved from a pair of homologous chromosomes. Whereas karyotypes are highly conserved in alethinophidian snakes, the degeneration status of the W chromosomes varies among species. The Z and W chromosomes are morphologically homomorphic in henophidian species, whereas in snakes belonging to caenophidian families the W chromosomes are highly degenerated. Snakes therefore are excellent animal models in which to study sex chromosome evolution. Herein, we investigated the differentiation processes for snake sex chromosomes using both coding and repetitive sequences. We analyzed phylogenetic relationships of CTNNB1 and WAC genes, localized to the centromeric and telomeric regions, respectively, of the long arms on snake sex chromosomes, and chromosome distribution of sex chromosome-linked repetitive sequences in several henophidian and caenophidian species. RESULTS Partial or full-length coding sequences of CTNNB1 and WAC were identified for Z homologs of henophidian species from Tropidophiidae, Boidae, Cylindrophiidae, Xenopeltidae, and Pythonidae, and for Z and W homologs of caenophidian species from Acrochordidae, Viperidae, Elapidae, and Colubridae. Female-specific sequences for the two genes were not found in the henophidian (boid and pythonid) species examined. Phylogenetic trees constructed using each gene showed that the Z and W homologs of the caenophidian species cluster separately. The repetitive sequence isolated from the W chromosome heterochromatin of the colubrid Elaphe quadrivirgata and a microsatellite motif (AGAT)8 were strongly hybridized with W chromosomes of the viperid and colubrid species examined. CONCLUSION Our phylogenetic analyses suggest that the cessation of recombination between the Z and W homologs of CTNNB1 and WAC predated the diversification of the caenophidian families. As the repetitive sequences on the W chromosomes were shared among viperid and colubrid species, heterochromatinization of the proto-W chromosome appears to have occurred before the splitting of these two groups. These results collectively suggest that differentiation of the proto-Z and proto-W chromosomes extended to wide regions on the sex chromosomes in the common ancestor of caenophidian families during a relatively short period.
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Matsuzawa Y, Kamezaki N, Ishihara T, Omuta K, Takeshita H, Goto K, Arata T, Honda H, Kameda K, Kashima Y, Kayo M, Kawazu I, Kodama J, Kumazawa Y, Kuroyanagi K, Mizobuchi K, Mizuno K, Oki K, Watanabe KK, Yamamoto A, Yamashita Y, Yamato T, Hamabata T, Ishizaki A, Dutton PH. Fine-scale genetic population structure of loggerhead turtles in the Northwest Pacific. ENDANGER SPECIES RES 2016. [DOI: 10.3354/esr00724] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Kusuma WE, Kumazawa Y. Complete mitochondrial genome sequences of two Indonesian rasboras (Rasbora aprotaenia and Rasbora lateristriata). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4222-4223. [PMID: 26061337 DOI: 10.3109/19401736.2015.1022749] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Complete mitochondrial genome sequences were determined for two Indonesian freshwater fishes, Rasbora aprotaenia and Rasbora lateristriata. These genomes are 16,541 bp and 16,539 bp in length, respectively and encode 37 genes in the typical vertebrate gene arrangement. Phylogenetic analyses supported a view that these species are very closely related to each other.
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Oba Y, Ôhira H, Murase Y, Moriyama A, Kumazawa Y. DNA barcoding of Japanese click beetles (Coleoptera, Elateridae). PLoS One 2015; 10:e0116612. [PMID: 25636000 PMCID: PMC4312051 DOI: 10.1371/journal.pone.0116612] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/11/2014] [Indexed: 12/05/2022] Open
Abstract
Click beetles (Coleoptera: Elateridae) represent one of the largest groups of beetle insects. Some click beetles in larval form, known as wireworms, are destructive agricultural pests. Morphological identification of click beetles is generally difficult and requires taxonomic expertise. This study reports on the DNA barcoding of Japanese click beetles to enable their rapid and accurate identification. We collected and assembled 762 cytochrome oxidase subunit I barcode sequences from 275 species, which cover approximately 75% of the common species found on the Japanese main island, Honshu. This barcode library also contains 20 out of the 21 potential pest species recorded in Japan. Our analysis shows that most morphologically identified species form distinct phylogenetic clusters separated from each other by large molecular distances. This supports the general usefulness of the DNA barcoding approach for quick and reliable identification of Japanese elaterid species for environmental impact assessment, agricultural pest control, and biodiversity analysis. On the other hand, the taxonomic boundary in dozens of species did not agree with the boundary of barcode index numbers (a criterion for sequence-based species delimitation). These findings urge taxonomic reinvestigation of these mismatched taxa.
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Kumazawa Y, Miura S, Yamada C, Hashiguchi Y. Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes. BMC Genomics 2014; 15:930. [PMID: 25344428 PMCID: PMC4223735 DOI: 10.1186/1471-2164-15-930] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 10/13/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Vertebrate mitochondrial genomes (mitogenomes) are 16-18 kbp double-stranded circular DNAs that encode a set of 37 genes. The arrangement of these genes and the major noncoding region is relatively conserved through evolution although gene rearrangements have been described for diverse lineages. The tandem duplication-random loss model has been invoked to explain the mechanisms of most mitochondrial gene rearrangements. Previously reported mitogenomic sequences for geckos rarely included gene rearrangements, which we explore in the present study. RESULTS We determined seven new mitogenomic sequences from Gekkonidae using a high-throughput sequencing method. The Tropiocolotes tripolitanus mitogenome involves a tandem duplication of the gene block: tRNAArg, NADH dehydrogenase subunit 4L, and NADH dehydrogenase subunit 4. One of the duplicate copies for each protein-coding gene may be pseudogenized. A duplicate copy of the tRNAArg gene appears to have been converted to a tRNAGln gene by a C to T base substitution at the second anticodon position, although this gene may not be fully functional in protein synthesis. The Stenodactylus petrii mitogenome includes several tandem duplications of tRNALeu genes, as well as a translocation of the tRNAAla gene and a putative origin of light-strand replication within a tRNA gene cluster. Finally, the Uroplatus fimbriatus and U. ebenaui mitogenomes feature the apparent loss of the tRNAGlu gene from its original position. Uroplatus fimbriatus appears to retain a translocated tRNAGlu gene adjacent to the 5' end of the major noncoding region. CONCLUSIONS The present study describes several new mitochondrial gene rearrangements from Gekkonidae. The loss and reassignment of tRNA genes is not very common in vertebrate mitogenomes and our findings raise new questions as to how missing tRNAs are supplied and if the reassigned tRNA gene is fully functional. These new examples of mitochondrial gene rearrangements in geckos should broaden our understanding of the evolution of mitochondrial gene arrangements.
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Baba S, Takanoha S, Ishiyama A, Komaki H, Takeshita E, Imaizumi H, Abe Y, Kobayashi M, Kumazawa Y, Sasaki M. G.P.179. Neuromuscul Disord 2014. [DOI: 10.1016/j.nmd.2014.06.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ratmuangkhwang S, Musikasinthorn P, Kumazawa Y. Molecular phylogeny and biogeography of air sac catfishes of the Heteropneustes fossilis species complex (Siluriformes: Heteropneustidae). Mol Phylogenet Evol 2014; 79:82-91. [PMID: 24875251 DOI: 10.1016/j.ympev.2014.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 03/17/2014] [Accepted: 05/06/2014] [Indexed: 10/25/2022]
Abstract
The air sac catfish, Heteropneustes fossilis (Siluriformes: Heteropneustidae), is widely distributed in freshwaters of the Indian subcontinent and mainland southeast Asia. No comprehensive molecular studies that cover the broad distributional areas have been carried out to date. Here, we conducted molecular phylogenetic analyses using both mitochondrial and nuclear gene sequences to suggest that the Heteropneustes fossilis species complex consists of three clades that may potentially be separate species with distinct geographical distribution (southeast Asia, northeastern India, and southwestern India). The first and second clades are more closely related to each other than they are to the third clade. Within the first clade there is a basal divergence of a subclade consisting of individuals from the Upper Irrawaddy River basin of Myanmar, which share some morphological traits with members of the Indian clades. Our molecular and morphological data are congruent with hypotheses that the Early-Middle Miocene disconnection between the paleo-Tsangpo River and the Irrawaddy River caused the vicariant divergence between southeast Asian and northeastern Indian clades, and that the southeast Asian Heteropneustes originated from the Upper Irrawaddy.
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Matsubara K, Kuraku S, Tarui H, Nishimura O, Nishida C, Agata K, Kumazawa Y, Matsuda Y. Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC(3) profiling in snake. BMC Genomics 2012; 13:604. [PMID: 23140509 PMCID: PMC3549455 DOI: 10.1186/1471-2164-13-604] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 10/24/2012] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Extant sauropsids (reptiles and birds) are divided into two major lineages, the lineage of Testudines (turtles) and Archosauria (crocodilians and birds) and the lineage of Lepidosauria (tuatara, lizards, worm lizards and snakes). Karyotypes of these sauropsidan groups generally consist of macrochromosomes and microchromosomes. In chicken, microchromosomes exhibit a higher GC-content than macrochromosomes. To examine the pattern of intra-genomic GC heterogeneity in lepidosaurian genomes, we constructed a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 183 cDNA clones by fluorescence in situ hybridization, and examined the correlation between the GC-content of exonic third codon positions (GC3) of the genes and the size of chromosomes on which the genes were localized. RESULTS Although GC3 distribution of snake genes was relatively homogeneous compared with those of the other amniotes, microchromosomal genes showed significantly higher GC3 than macrochromosomal genes as in chicken. Our snake cytogenetic map also identified several conserved segments between the snake macrochromosomes and the chicken microchromosomes. Cross-species comparisons revealed that GC3 of most snake orthologs in such macrochromosomal segments were GC-poor (GC3 < 50%) whereas those of chicken orthologs in microchromosomes were relatively GC-rich (GC3 ≥ 50%). CONCLUSION Our results suggest that the chromosome size-dependent GC heterogeneity had already occurred before the lepidosaur-archosaur split, 275 million years ago. This character was probably present in the common ancestor of lepidosaurs and but lost in the lineage leading to Anolis during the diversification of lepidosaurs. We also identified several genes whose GC-content might have been influenced by the size of the chromosomes on which they were harbored over the course of sauropsid evolution.
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Calenic B, Yaegaki K, Ishkitiev N, Kumazawa Y, Imai T, Tanaka T. p53-Pathway activity and apoptosis in hydrogen sulfide-exposed stem cells separated from human gingival epithelium. J Periodontal Res 2012; 48:322-30. [DOI: 10.1111/jre.12011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2012] [Indexed: 12/13/2022]
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Jonniaux P, Hashiguchi Y, Kumazawa Y. Mitochondrial genomes of two African geckos of genus Hemitheconyx (Squamata: Eublepharidae). ACTA ACUST UNITED AC 2012; 23:278-9. [PMID: 22708855 DOI: 10.3109/19401736.2012.668898] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitochondrial genomes of two eyelid geckos (Hemitheconyx caudicinctus and Hemitheconyx taylori) were sequenced. Although these genomes conserve a typical vertebrate gene organization, tRNA(Gln) gene of the former appears to have been pseudogenized. A very extensive RNA editing may restore its function in the RNA level or a functional tRNA(Gln) encoded in the nuclear chromosome may be imported into mitochondria.
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Dehara Y, Hashiguchi Y, Matsubara K, Yanai T, Kubo M, Kumazawa Y. Characterization of squamate olfactory receptor genes and their transcripts by the high-throughput sequencing approach. Genome Biol Evol 2012; 4:602-16. [PMID: 22511035 PMCID: PMC3342882 DOI: 10.1093/gbe/evs041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The olfactory receptor (OR) genes represent the largest multigene family in the genome of terrestrial vertebrates. Here, the high-throughput next-generation sequencing (NGS) approach was applied to characterization of OR gene repertoires in the green anole lizard Anolis carolinensis and the Japanese four-lined ratsnake Elaphe quadrivirgata. Tagged polymerase chain reaction (PCR) products amplified from either genomic DNA or cDNA of the two species were used for parallel pyrosequencing, assembling, and screening for errors in PCR and pyrosequencing. Starting from the lizard genomic DNA, we accurately identified 56 of 136 OR genes that were identified from its draft genome sequence. These recovered genes were broadly distributed in the phylogenetic tree of vertebrate OR genes without severe biases toward particular OR families. Ninety-six OR genes were identified from the ratsnake genomic DNA, implying that the snake has more OR gene loci than the anole lizard in response to an increased need for the acuity of olfaction. This view is supported by the estimated number of OR genes in the Burmese python's draft genome (∼280), although squamates may generally have fewer OR genes than terrestrial mammals and amphibians. The OR gene repertoire of the python seems unique in that many class I OR genes are retained. The NGS approach also allowed us to identify candidates of highly expressed and silent OR gene copies in the lizard's olfactory epithelium. The approach will facilitate efficient and parallel characterization of considerable unbiased proportions of multigene family members and their transcripts from nonmodel organisms.
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Marzulli G, Magrone T, Kawaguchi K, Kumazawa Y, Jirillo E. Fermented Grape Marc (FGM): Immunomodulating Properties and its Potential Exploitation in the Treatment of Neurodegenerative Diseases. Curr Pharm Des 2012; 18:43-50. [DOI: 10.2174/138161212798919011] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 10/13/2011] [Indexed: 11/22/2022]
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