Displaying publications 21 - 36 of 36 in total

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  1. Fulltext Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches
    Makita Y, Kawashima M, Lau NS, Othman AS, Matsui M
    BMC Genomics, 2018 01 19;19(Suppl 1):922.
    PMID: 29363422 DOI: 10.1186/s12864-017-4333-y
    BACKGROUND: Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-generation sequencing (NGS) technologies brought draft genomes of three rubber cultivars and a variety of RNA sequencing (RNA-seq) data. However, no current genome or transcriptome databases (DB) are organized by gene.

    RESULTS: A gene-oriented database is a valuable support for rubber research. Based on our original draft genome sequence of H. brasiliensis RRIM600, we constructed a rubber tree genome and transcriptome DB. Our DB provides genome information including gene functional annotations and multi-transcriptome data of RNA-seq, full-length cDNAs including PacBio Isoform sequencing (Iso-Seq), ESTs and genome wide transcription start sites (TSSs) derived from CAGE technology. Using our original and publically available RNA-seq data, we calculated co-expressed genes for identifying functionally related gene sets and/or genes regulated by the same transcription factor (TF). Users can access multi-transcriptome data through both a gene-oriented web page and a genome browser. For the gene searching system, we provide keyword search, sequence homology search and gene expression search; users can also select their expression threshold easily.

    CONCLUSION: The rubber genome and transcriptome DB provides rubber tree genome sequence and multi-transcriptomics data. This DB is useful for comprehensive understanding of the rubber transcriptome. This will assist both industrial and academic researchers for rubber and economically important close relatives such as R. communis, M. esculenta and J. curcas. The Rubber Transcriptome DB release 2017.03 is accessible at http://matsui-lab.riken.jp/rubber/ .

  2. Chemical-Induced Inhibition of Blue Light-Mediated Seedling Development Caused by Disruption of Upstream Signal Transduction Involving Cryptochromes in Arabidopsis thaliana
    Ong WD, Okubo-Kurihara E, Kurihara Y, Shimada S, Makita Y, Kawashima M, et al.
    Plant Cell Physiol, 2017 01 01;58(1):95-105.
    PMID: 28011868 DOI: 10.1093/pcp/pcw181
    Plants have a remarkable ability to perceive and respond to various wavelengths of light and initiate regulation of different cascades of light signaling and molecular components. While the perception of red light and the mechanisms of its signaling involving phytochromes are largely known, knowledge of the mechanisms of blue light signaling is still limited. Chemical genetics involves the use of diverse small active or synthetic molecules to evaluate biological processes. By combining chemicals and analyzing the effects they have on plant morphology, we identified a chemical, 3-bromo-7-nitroindazole (3B7N), that promotes hypocotyl elongation of wild-type Arabidopsis only under continuous blue light. Further evaluation with loss-of-function mutants confirmed that 3B7N inhibits photomorphogenesis through cryptochrome-mediated light signaling. Microarray analysis demonstrated that the effect of 3B7N treatment on gene expression in cry1cry2 is considerably smaller than that in the wild type, indicating that 3B7N specifically interrupts cryptochrome function in the control of seedling development in a light-dependent manner. We demonstrated that 3B7N directly binds to CRY1 protein using an in vitro binding assay. These results suggest that 3B7N is a novel chemical that directly inhibits plant cryptochrome function by physical binding. The application of 3B7N can be used on other plants to study further the blue light mechanism and the genetic control of cryptochromes in the growth and development of plant species.
  3. Fulltext Awareness and preparedness of healthcare workers against the first wave of the COVID-19 pandemic: A cross-sectional survey across 57 countries
    Huy NT, Chico RM, Huan VT, Shaikhkhalil HW, Uyen VNT, Qarawi ATA, et al.
    PLoS One, 2021;16(12):e0258348.
    PMID: 34936646 DOI: 10.1371/journal.pone.0258348
    BACKGROUND: Since the COVID-19 pandemic began, there have been concerns related to the preparedness of healthcare workers (HCWs). This study aimed to describe the level of awareness and preparedness of hospital HCWs at the time of the first wave.

    METHODS: This multinational, multicenter, cross-sectional survey was conducted among hospital HCWs from February to May 2020. We used a hierarchical logistic regression multivariate analysis to adjust the influence of variables based on awareness and preparedness. We then used association rule mining to identify relationships between HCW confidence in handling suspected COVID-19 patients and prior COVID-19 case-management training.

    RESULTS: We surveyed 24,653 HCWs from 371 hospitals across 57 countries and received 17,302 responses from 70.2% HCWs overall. The median COVID-19 preparedness score was 11.0 (interquartile range [IQR] = 6.0-14.0) and the median awareness score was 29.6 (IQR = 26.6-32.6). HCWs at COVID-19 designated facilities with previous outbreak experience, or HCWs who were trained for dealing with the SARS-CoV-2 outbreak, had significantly higher levels of preparedness and awareness (p<0.001). Association rule mining suggests that nurses and doctors who had a 'great-extent-of-confidence' in handling suspected COVID-19 patients had participated in COVID-19 training courses. Male participants (mean difference = 0.34; 95% CI = 0.22, 0.46; p<0.001) and nurses (mean difference = 0.67; 95% CI = 0.53, 0.81; p<0.001) had higher preparedness scores compared to women participants and doctors.

    INTERPRETATION: There was an unsurprising high level of awareness and preparedness among HCWs who participated in COVID-19 training courses. However, disparity existed along the lines of gender and type of HCW. It is unknown whether the difference in COVID-19 preparedness that we detected early in the pandemic may have translated into disproportionate SARS-CoV-2 burden of disease by gender or HCW type.

  4. Fulltext Author Correction: Ongoing declines for the world's amphibians in the face of emerging threats
    Luedtke JA, Chanson J, Neam K, Hobin L, Maciel AO, Catenazzi A, et al.
    Nature, 2024 Jan;625(7993):E2.
    PMID: 38040869 DOI: 10.1038/s41586-023-06851-6
  5. A new species of Rock Gecko genus Cnemaspis (Squamata: Gekkonidae) from Western Sarawak, Malaysia
    Kurita T, Nishikawa K, Matsui M, Hikida T
    Zootaxa, 2017 05 03;4258(6):525-538.
    PMID: 28609895 DOI: 10.11646/zootaxa.4258.6.2
    A new species of Asian rock gecko, genus Cnemaspis, is described from Padawan, western Sarawak, Malaysian Borneo. The new species forms a clade with C. paripari and C. nigridia of the C. nigridia group in a mitochondrial DNA phylogeny and is similar to them morphologically in some characters such as caudal scalation. It differs from the other Asian Cnemaspis species in its unique combination of snout-vent length (up to 62.7 mm), 4-9 precloacal pores in males, keeled subcaudals with an enlarged, smooth, median row, presence of ventrolateral caudal tubercles, and coloration (head and upper flanks dark-yellow; anterior portion of tail black; posterior portion of tail white with black, paravertebral blob). Phylogenetic relationships within the C. nigridia group and the distributional ranges of species within the group suggest allopatric speciation by geographic isolation.
  6. A new species of Philautus (Amphibia, Anura, Rhacophoridae) from the lowland of Sarawak, western Borneo
    Matsui M
    Zoolog Sci, 2009 Jun;26(6):437-42.
    PMID: 19583504 DOI: 10.2108/zsj.26.437
    A new species in the rhacophorid genus Philautus is described on the basis of five male specimens collected from the Matang Range, a herpetologically well-surveyed area of the lowland of Sarawak, western Borneo. The species possesses a cutaneous pectoris muscle but lacks vomerine teeth, and is assigned to the aurifasciatus group of Philautus. It is superficially similar to some other species of the same group, but can be differentiated from them by a combination of several morphological characters, including lack of a nuptial pad and lingual papilla, and more significantly, by a distinct advertisement call. This discovery underscores the immediate necessity for detailed surveys in the already well-explored lowlands of Borneo.
  7. A new species of Meristogenys (Amphibia, Anura, Ranidae) from Sabah, Borneo
    Matsui M, Shimada T, Sudin A
    Zoolog Sci, 2010 Jan;27(1):61-6.
    PMID: 20064010 DOI: 10.2108/zsj.27.61
    We describe a new species of torrent-dwelling ranid frog of the genus Meristogenys from the Crocker Range, western Sabah, northern Borneo. The new species, Meristogenys maryatiae, differs from congeners by the combination of: small body, males 31-37 mm and females 65-66 mm in snout-vent length; head narrower than long; eyes moderate, diameter subequal to snout; iris unicolored; legs long; ventral surface of tibia without heavy pigmentation; rear of thigh blotched dark brown and cream; toes fully webbed; outer metatarsal tubercle present; larval dental formula 7(4-7)/6(1).
  8. A new species of Leptolalax from Sarawak, Western Borneo (Anura: Megophryidae)
    Matsui M, Zainudin R, Nishikawa K
    Zoolog Sci, 2014 Nov;31(11):773-9.
    PMID: 25366161 DOI: 10.2108/zs140137
    A new megophryid species is described from southwestern Sarawak, Malaysian Borneo. In appearance, Leptolalax marmoratus sp. nov. is most similar to L. hamidi also from southwestern Sarawak, but differs from it by mtDNA sequence, larger body size, and higher dominant frequency of advertisement call. The assumption that more than one species of Leptolalax coexist at one locality in Borneo is supported. The finding of the new species raises the species number of Leptolalax known from Borneo to nine, and the island is thought to be one of the diversification centers of the genus.
  9. A new species of Leptolalax (Anura: Megophryidae) from Gunung Mulu National Park, Sarawak, East Malaysia (Borneo)
    Dehling JM, Matsui M
    Zootaxa, 2013;3670:33-44.
    PMID: 26438919
    We describe a new species of Leptolalax from Gunung Mulu National Park in eastern Sarawak, Malaysian Borneo. The new species had been assigned to Leptolalax dringi and Leptolalax gracilis in the past. It is shown to differ from both these species and from all other species of the genus by a unique combination of morphological characters including large body size, rounded snout, interorbital distance being smaller than width of upper eyelid, bipartite subgular vocal sac in males, basal toe webbing, shagreened skin with tiny tubercles on dorsum and dorsal side of head, angled supratympanic fold, small pectoral glands, absence of supraaxillary glands and ventrolateral glandular ridges, spotted venter, advertisement call consisting of long series of 8-289 notes, each composed of three or four pulses, and dominant frequency at 7225-9190 Hz, with prominent frequency modulation.
  10. A new species of Leptolalax (Amphibia, Anura, Megophryidae) from Peninsular Malaysia
    Matsui M, Belabut DM, Ahmad N, Yong HS
    Zoolog Sci, 2009 Mar;26(3):243-7.
    PMID: 19341347 DOI: 10.2108/zsj.26.243
    A new megophryid species, Leptolalax kecil, is described from the Cameron Highlands of Peninsular Malaysia on the basis of acoustic and morphological characteristics. It has an advertisement call dissimilar to that of other, congeneric species, and is the smallest of the known Leptolalax. It is similar to L. pluvialis from Vietnam in small body size, but differs from it in ventral color, and in the size and color of the pectoral gland. The distributional pattern of the new species Is discussed.
  11. A new species of Kalophrynus with a unique male humeral spine from Peninsular Malaysia (Amphibia, Anura, Microhylidae)
    Matsui M
    Zoolog Sci, 2009 Aug;26(8):579-85.
    PMID: 19719411 DOI: 10.2108/zsj.26.579
    A new microhylid, Kalophrynus yongi, Is described from the Cameron Highlands of Peninsular Malaysia. Morphologically, the new species differs from all known congeners by having a very stout forelimb with a humeral spine in males. Acoustically, it resembles K. baluensis and K. heterochirus and sharply differs from K. interlineatus, K. pleurostigma, K. palmatissimus, and K. nubicola.
  12. A new cascade frog of the subgenus Odorrana from peninsular Malaysia
    Matsui M, Jaafar I
    Zoolog Sci, 2006 Jul;23(7):647-51.
    PMID: 16908965
    We describe a new species of cascade frog of the genus Rana, from west Malaysia. Rana monjerai, new species is a medium-sized frog of the subgenus Odorrana (SVL of males, 38-43 mm; of one female, 75 mm), and is distinguished from all other members of this subgenus by the combination of: white lip stripe, dorsolateral fold, full web on the fourth toe, vomerine teeth, gular vocal pouch and relatively large tympanum in males, no dorsal marking, no clear light spots on rear of thigh, first finger subequal to second, finely tuberculated dorsum, and unpigmented ova. The significance of finding this species from peninsular Malaysia is discussed.
  13. A new Occidozyga from Sarawak, Malaysian Borneo (Anura: Dicroglossidae)
    Matsui M, Nishikawa K, Eto K, Hamidy A, Hossman Y, Fukuyama I
    Zootaxa, 2021 Feb 10;4926(4):zootaxa.4926.4.4.
    PMID: 33756730 DOI: 10.11646/zootaxa.4926.4.4
    We found a uniquely colored dicroglossid frog of the genus Occidozyga from western Sarawak, East Malaysia. It is divergent from other congeners in morphology and mtDNA sequences. In a molecular phylogeny, this species is the sister lineage to the continental species O. lima and O. martensii with weak support. The species is small with SVL 16-18 mm in males and 18-19 mm in females, without dorsolateral fold but with transverse wrinkles on dorsum, tips of fingers lacking disks but of toes with disks, only first and second toes webbed to disks, and orange-brown dorsum with dark brown band. We thus describe it as a new species.
  14. A new Leptolalax from the mountains of Sabah, Borneo (Amphibia, Anura, Megophryidae)
    Matsui M, Nishikawa K, Yambun P
    Zootaxa, 2014;3753:440-52.
    PMID: 24869507 DOI: 10.11646/zootaxa.3753.5.3
    A new species of Leptolalax is described from Kinabalu National Park in western Sabah, Malaysian Borneo. The new species had been assigned to L. dringi, L. gracilis, or L. fritinniens in the past. It differs from all congeners, including these species, by a unique combination of morphological characters, including small body size, rounded snout, narrower interorbital than upper eyelid, basal toe webbing, smooth skin with tiny tubercles on dorsum and dorsal side of head, small pectoral glands, absence of supraaxillary glands and ventrolateral glandular ridges, spotted venter, advertisement call consisting of long series of 1-149 notes, each composed of three or four pulses, and dominant frequency at 6.90-7.35 kHz, without prominent frequency modulation.
  15. A New Species of Pelophryne from Western Sarawak, Malaysian Borneo (Anura, Bufonidae)
    Matsui M, Nishikawa K, Eto K, Hossman MYB
    Zoolog Sci, 2017 Aug;34(4):345-350.
    PMID: 28770684 DOI: 10.2108/zs170008
    A new small, semi-arboreal toad of the genus Pelophryne is described from western Sarawak, Malaysian Borneo, on the basis of molecular and morphological evidence. Of the two morphotypes recognized in the genus, the new species belongs to the one in which the tips of the fingers are expanded into truncate discs. Among the species in the morphotype, the new species is most similar to P. murudensis, but differs from it by body size, relative hindlimb length, and dorsal coloration. The new species is currently known only from a limited area on Gunung (= Mt.) Penrissen, and future measures of its habitat conservation are necessary.
  16. A New Species of Meristogenys (Anura: Ranidae) from Sarawak, Borneo
    Shimada T, Matsui M, Nishikawa K, Eto K
    Zoolog Sci, 2015 Oct;32(5):474-84.
    PMID: 26428726 DOI: 10.2108/zs140289
    A cryptic Bornean torrent frog of the genus Meristogenys, which is divergent genetically and morphologically from all known congeners, is described from mountain streams of western Sarawak, East Malaysia (Borneo). The species occurs sympatrically with the type species of the genus, M. jerboa, but apparently differs from it in adult coloration and larval morphology, such as keratodont formulae and glands in tail fins. Females of the new species possess much larger and fewer eggs than in sympatric M. jerboa, suggesting significantly different reproductive traits between these species. A key to larvae of known species of the genus is provided.
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