Biology subjects

Sakamoto, T.

Publications and source records attributed to Sakamoto, T..

58 records · Page 4Linked to original sources

bioRxiv2019

A potential genomic recombination site upstream of the rfb locus in Leptospira interrogans is associated with serogroup Serjoe and serovar Hardjo classification

Leptospirosis is a zoonotic disease caused by pathogenic spirochetes of the genus Leptospira. It has a global distribution and affects domestic animals, including cattle. In livestock production, Leptospira interrogans serogroup Sejroe serovar Hardjo is the major reproductive disease leading to economic losses. The whole-genome sequence of the first Brazilian clinical isolate classified as L. interrogans serogroup Sejroe serovar Hardjo strain Norma enabled the evaluation of its genomic features. Here, we investigated particularities of this isolate, obtained from a leptospirosis outbreak. Bioinformatic analysis using the L. interrogans serovar Hardjo str. Norma was applied as a reference for genomic evaluation and comparative analysis among L. interrogans and L. borgpetersenii serovars. Our data suggest the occurrence of genomic recombination in L. interrogans serovar Hardjo str. Norma encompassing 45 Kb located upstream of the rfb locus. A hallmark of genetic evolution was predicted through an orthologue analysis that identified that sugar enzymes associated with carbohydrate and lipid biosynthesis and metabolism composed this genetic module. Comparative genomics revealed a wide range of relatedness among the bacterial strains of serogroup Sejroe that are classified as L. interrogans and L. borgpetersenii species. Furthermore, identification of an IS3 family suggests a genetic recombination site in L. interrogans serovar Hardjo str. Norma that is distinct among L. interrogans serovars and may contribute to clarify the taxonomic classification of Leptospira spp.\n\nImpact StatementLeptospirosis remains an important neglected disease with worldwide distribution. This zoonotic disease impacts in the livestock production and the bovine infection is currently associated to species L. borgpetersenii and L. interrogans serovar Hardjo. L.interrogans serovar Hardjo infection is recognized as reproductive disease associated with abortion and economic lost. In this context, we studied a unique whole genome sequence of L. interrogans serovar Hardjo subtype Hardjo-prajitno isolated from bovine leptospirosis outbreaks in Brazilian dairy farm, one of the greatest country of milk production in world. We compared L. interrogans and L. borgpetersenii genomes with L. interrogans serogroup Sejroe serovar Hardjo subtype Hardjo-prajitno focusing on rfb locus and sugars biosynthesis. Leptospira spp. taxonomy and serology information are strictly associated with rfb locus and we found high correlation among bacterial strains classified in serogroup Sejroe. Although L. interrogans and L. borgpetersenii classified in serogroup Sejroe possess a greater genetic correlation, we uniquely identified that serovar Hardjo strains often possess identical loci carrying predicted sugar biossinthesis genes and mobile elements. The Sru (Sejroe specific Rfb Upstream locus) locus associated to rfb locus probably contribute to Leptospira spp. genetic information concerning serogroup and serovar degrees of taxonomic and serology in this microbiology field.\n\nData SummaryAll Leptospira spp. genome sequences used in this study were retrieved from National Center for Biotechnology Information (NCBI) (Table 1) with NCBI ID: NZ_CP006723.1, NZ_CP012603.1, NC_004342.2, NZ_CP011934.1, NZ_AKXA02000040.1, NZ_CP013147.1, NZ_CP012029.1, NZ_CP015048.1, NC_008508.1, GCA_000216175.3,GCA_000244115.3, NC005823.1, GCA_000244395.3, GCA_000346975.1.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@843b1eorg.highwire.dtl.DTLVardef@1453917org.highwire.dtl.DTLVardef@1a75127org.highwire.dtl.DTLVardef@1c0e185org.highwire.dtl.DTLVardef@160aa4_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1:C_FLOATNO O_TABLECAPTIONLeptospira spp. strains used in this study.\n\nC_TABLECAPTION C_TBL HighlightsO_LIThe study identified potential molecular features associated with serovar Hardjo subtype Hardjo-prajitno, present in both L. interrogans and L. borgpetersenii, by comparative genomics.\nC_LIO_LIA new potential recombinant site found upstream of the rfb locus contains proteins that correlate with serogroup taxonomy in the Leptospira genus.\nC_LIO_LIThe proteins encoded in the recombinant locus are associated with the synthesis of serological surface determinants such as carbohydrates and lipopolysaccharides.\nC_LI

genomics↗

bioRxiv2019

Synergic Interaction between Permethrin and Bt toxins discovered using RNA-seq

Acting against the development of resistance to antibiotics and insecticides, involving negatively correlated cross-resistance (NCR) is an alternative to use- and-discard approach. It is termed NCR that toxic chemicals interact with each other and resistance of target organisms to one chemical is sometimes associated with increased susceptibility to a second chemical when; an allele confers resistance to one toxic chemical and hyper-susceptibility to another, NCR occurs. However, only 11 toxin pairs have been revealed to cause NCR in insects. Finding novel NCRs is needed for integrated pest management. We analyzed permethrin, an insecticide, induced transcriptomes of cultured fat bodies of the silkworm Bombyx mori, a lepidopteran model insect. Differentially expressed gene analyses suggested Bacillus thuringiensis (Bt) toxin was an NCR toxin of permethrin. NCR to permethrin and Bt toxins in Thysanoplusia intermixta, the agricultural pest moth, was examined; the children of permethrin survivor T. intermixta had increased susceptibility to Bt toxin. A novel NCR toxin pair, permethrin and Bt toxin, was discovered. The screening and developmental method for negatively correlated cross-resistance toxins established in this study was effective, in vitro screening using model organisms and in vivo verification using agricultural pests.

zoology↗

bioRxiv2019

Theoretical Expression for the Evolution of Genomic Island of Speciation: From Its Birth to Preservation

Ecological speciation could be driven by divergent selection that works to maintain phenotypes that are adaptive to each niche. In its early stages, genetic divergence (or FST) can be maintained around the target sites of divergent selection, while in other regions, genetic variation can be mixed by gene flow or migration. Such regions of elevated genetic divergence are called genomic islands of speciation. In this work, we theoretically consider the evolutionary process of a genomic island of speciation, from its birth to stable preservation. Under a simple two-population model, we use a diffusion approach to obtain analytical expressions for the probability of initial establishment of a locally adaptive allele, the reduction of genetic variation due to the spread of the adaptive allele, and the process to the development of a sharp peak of divergence. Our result would be useful to understand how genomes evolve through ecological speciation with gene flow.

evolutionary biology↗

bioRxiv2018

Changes choroidal area following trabeculectomy: long-term effect of intraocular pressure reduction

PurposeTo investigate the long-term effects of intraocular pressure (IOP) changes after trabeculectomy on the macular and peripapillary choroidal areas.\n\nMethodsThis prospective longitudinal study examined 30 eyes of 30 patients with glaucoma that was uncontrolled by medical therapy. At 1 day before and at 1 year after the trabeculectomy surgery, macular and peripapillary choroidal images were recorded by enhanced depth imaging optical coherence tomography (EDI-OCT). Luminal and interstitial areas were converted to binary images using the Niblack method. Factors influencing the macular choroidal and peripapillary area were examined by multivariate analysis.\n\nResultsAfter trabeculectomy, the mean IOP was 10.8{+/-}3.2 mmHg compared to 17.8{+/-}7.2 mmHg at baseline (P < 0.001). The total macular choroidal area after the surgery increased from 317,735{+/-}77,380 to 338,120{+/-}90,700 m2, while the interstitial area increased from 108,598{+/-}24,502 to 119,172{+/-}31,495 m2 (all P < 0.05). The total peripapillary choroidal area after the surgery also increased from 1,557,487{+/-}431,798 to 1,650,253{+/-}466,672 m2, while the interstitial area increased from 689,891{+/-}149,476 to 751,816{+/-}162,457 m2 (all P < 0.05). However, there were no significant differences observed in the luminal area before and after the surgery. A decrease in the IOP was among the factors associated with the changes in the peripapillary choroidal area.\n\nConclusionsIOP reductions after trabeculectomy led to increases in the macular and peripapillary choroidal areas for at least 1 year postoperative. Increases in the interstitial areas were the primary reason for observed changes in the choroidal area after trabeculectomy.

pathology↗