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1.
Drug Test Anal ; 2024 Jul 11.
Article in English | MEDLINE | ID: mdl-38992930

ABSTRACT

Due to the presumed lipolytic and anabolic properties, the misuse of human growth hormone (hGH) and its synthetic analogs in sports is prohibited both in- and out-of-competition. Within this research project, the detectability of somatrogon, a recombinant fusion glycoprotein of 22 kDa hGH and the C-terminal peptide (CTP) of the human chorionic gonadotropin (hCG) ß-subunit, with current WADA-approved doping control assays for hGH and hCG was investigated. For that purpose, cross-reactivity tests and a somatrogon administration study were conducted, and only "Kit 2" of the GH isoform differential immunoassays proved applicable to the detection of somatrogon administration in serum. In urine, the immunoassay specific for total hCG yielded presumptively positive findings for several post-administration samples, which can probably be attributed to the presence of an immunoreactive fragment of the hCG ß-subunit. As the detectability of somatrogon with these approaches was found to be limited, a highly specific detection assay (LOD: 10 ng/mL) for the drug in serum samples was developed by using affinity purification with GH receptor (GHR)-conjugated magnetic beads, proteolytic digestion, and liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS). Following optimization, the approach was comprehensively characterized, and authentic post-administration serum samples were successfully analyzed as proof-of-concept, indicating a detection window of at least 96 h. Consequently, the presented method can be employed to confirm the presence of somatrogon in serum samples, where only "Kit 2" of the currently used immunoassay kits yielded an abnormally high Rec/Pit ratio.

2.
Microbiol Resour Announc ; 13(8): e0047624, 2024 Aug 13.
Article in English | MEDLINE | ID: mdl-38953663

ABSTRACT

Mycobacterium montefiorense, a nontuberculous mycobacterium, is a causative agent of mycobacteriosis in aquatic animals, its type strain M. montefiorense ATCC BAA-256 being isolated from a moray eel. In this study, we report the complete ATCC BAA-256 genome sequence with a 5,693,452-bp-containing circular chromosome, 65.2% GC content, and 5,407 coding sequences.

3.
Drug Test Anal ; 2024 Mar 23.
Article in English | MEDLINE | ID: mdl-38520227

ABSTRACT

Testosterone, nandrolone, and boldenone, which are listed as doping substances on the World Anti-Doping Agency Prohibited List, are mostly available commercially in esterified forms. Isotope ratio mass spectrometry (IRMS) represents a key tool for identifying these substances, as they are hydrolyzed and discharged in the urine as pseudo-endogenous substances. However, IRMS, which comprises a complicated process, cannot achieve the direct detection of steroid esters in blood samples. These substances can be detected using dried blood spots (DBSs), reducing the impact of esterase hydrolysis. Here, a simultaneous liquid chromatography-tandem mass spectrometry method for detecting 28 steroid (13 testosterone, nine nandrolone, and six boldenone) esters was developed using three DBS types of samples, including a cellulose paper and polymer. The substances were first derivatized with methyloxime to increase their sensitivities (the limits of detection were <0.1-0.4, <0.1-0.9, and <0.1-0.9 ng/mL for the testosterone, nandrolone, and boldenone esters, respectively). Further, the DBS absorbents were verified since the effect of interferences depended on it. Next, a study involving seven participants was conducted to detect intramuscularly administered testosterone enanthate (100 mg). Polymer and cellulose papers were used to collect blood from their upper arms and fingertips, respectively, and testosterone enanthate was identified and detectable at both blood-collection sites for up to 144 and 216 h, respectively. Furthermore, testosterone enanthate was detectable in the DBS samples stored under refrigeration after 6 months, indicating the stable nature of DBS.

4.
Mol Phylogenet Evol ; 190: 107960, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37918683

ABSTRACT

The cycad genus Ceratozamia comprises 40 species from Mexico, Guatemala, Belize, and Honduras, where cycads occur throughout climatically varied montane habitats. Ceratozamia has the potential to reveal the history and processes of species diversification across diverse Neotropical habitats in this region. However, the species relationships within Ceratozamia and the ecological trends during its evolution remain unclear. Here, we aimed to clarify the phylogenetic relationships, the timing of clade and species divergences, and the niche evolution throughout the phylogenetic history of Ceratozamia. Genome-wide DNA sequences were obtained with MIG-seq, and multiple data-filtering steps were used to optimize the dataset used to construct an ultrametric species tree. Divergence times among branches and ancestral niches were estimated. The niche variation among species was evaluated, summarized into two principal components, and their ancestral states were reconstructed to test whether niche shifts among branches can be explained by random processes, under a Brownian Motion model. Ceratozamia comprises three main clades, and most species relationships within the clades were resolved. Ceratozamia has diversified since the Oligocene, with major branching events occurring during the Miocene. This timing is consistent with fossil evidence, the timing estimated for other Neotropical plant groups, and the major geological events that shaped the topographic and climatic variation in Mexico. Patterns of niche evolution in the genus do not accord with the Brownian Motion model. Rather, non-random evolution with shifts towards more seasonal environments at high latitudes, or shifts towards humid or dry environments at low latitudes explain the diversification of Ceratozamia. We present a comprehensive phylogenetic reconstruction for Ceratozamia and identify for the first time the environmental factors involved in clade and species diversification within the genus. This study alleviates the controversies regarding the species relationships in the genus and provides the first evidence that latitude-associated environmental factors may influence processes of niche evolution in cycads.


Subject(s)
Zamiaceae , Phylogeny , Zamiaceae/genetics , Phylogeography , Ecosystem , Time Factors
5.
Sci Rep ; 13(1): 21940, 2023 12 19.
Article in English | MEDLINE | ID: mdl-38114661

ABSTRACT

Seasonal environmental change is one of the most rapid and striking environmental variables. Although relatively rapid adaptation to environmental changes over several years or several decades has been described in many taxa, rapid responses to seasonal environments are delicate, and therefore, the detection of the evolutionary responses requires sensitive methods. In this study, we examined seasonal changes in phenotypes related to thermal tolerance and morphological traits of Drosophila lutescens collected at the spring and autumn periods from a single location. We first demonstrated that flies in the two seasonal periods were almost genetically identical using double-digest restriction site-associated DNA sequencing and analysis. Using an experimental design to eliminate the effect of possible confounding factors that influence phenotypes (i.e., maternal effects and the environmental conditions in which each phenotype was analyzed), we showed that the heat tolerance of D. lutescens was significantly higher in the autumn population than in the spring population. Furthermore, cold tolerance was slightly higher in the spring population than in the autumn one. Although wing length and thorax length did not change significantly between seasons, the ratio of wing length to thorax length changed significantly between them. These results suggest that seasonal environmental heterogeneity induces rapid phenotypic changes within a year. Finally, we discuss the possibility of rapid evolutionary responses to seasonal changes.


Subject(s)
Drosophila , Animals , Drosophila/genetics , Seasons , Phenotype
6.
DNA Res ; 30(5)2023 Oct 01.
Article in English | MEDLINE | ID: mdl-37943179

ABSTRACT

Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32,337, and 30,889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production.


Subject(s)
Echinochloa , Oryza , Telomere/genetics , Oryza/genetics , Phenotype , Tetraploidy
7.
Sci Rep ; 13(1): 17674, 2023 10 17.
Article in English | MEDLINE | ID: mdl-37848466

ABSTRACT

Recently, many new cultivars have been taken abroad illegally, which is now considered an international issue. Botanical evidence found at a crime scene provides valuable information about the origin of the sample. However, botanical resources for forensic evidence remain underutilized because molecular markers, such as microsatellites, are not available without a limited set of species. Multiplexed intersimple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and its analysis method, identification of not applicable (iD-NA), have been used to determine several genome-wide genetic markers, making them applicable to all plant species, including those with limited available genetic information. Camellia cultivars are popular worldwide and are often planted in many gardens and bred to make new cultivars. In this study, we aimed to analyze Camellia cultivars/species through MIG-seq. MIG-seq could discriminate similar samples, such as bud mutants and closely related samples that could not be distinguished based on morphological features. This discrimination was consistent with that of a previous study that classified cultivars based on short tandem repeat (STR) markers, indicating that MIG-seq has the same or higher discrimination ability as STR markers. Furthermore, we observed unknown phylogenetic relationships. Because MIG-seq can be applied to unlimited species and low-quality DNA, it may be useful in various scientific fields.


Subject(s)
Camellia , Camellia/genetics , Phylogeny , Plant Breeding , Genome , Genetic Markers/genetics , Microsatellite Repeats/genetics
8.
Sci Adv ; 9(42): eabq3542, 2023 10 20.
Article in English | MEDLINE | ID: mdl-37862418

ABSTRACT

Prevalence of impervious surface and resulting higher temperatures in urban areas, known as urban heat islands, comprises prominent characteristics in global cities. However, it is not known whether and how urban plants adapt to such heat stress. This study focused on Oxalis corniculata, which has intraspecific polymorphism in leaf color (green and red) and examined whether the leaf color variation is associated with urban heat stress. Field observations revealed that green-leaved plants were dominant in green habitats, and red-leaved individuals were dominant in urban habitats, at local (<500 meters), landscape (<50 kilometers), and global scales. Growth and photosynthesis experiments demonstrated that red-leaved individuals performed better under heat stress, while green-leaved individuals performed better under nonstressful conditions. Genome-wide SNP analysis suggests that the red leaf may have evolved multiple times from the ancestral green leaf. Overall, the results suggest that the red leaves of O. corniculata observed in cities worldwide are evidence of plant adaptive evolution due to urban heat islands.


Subject(s)
Hot Temperature , Photosynthesis , Humans , Cities , Photosynthesis/genetics , Plants , Plant Leaves/genetics , Heat-Shock Response , Color
9.
Ecol Evol ; 13(7): e10319, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37456070

ABSTRACT

The genus Symplocarpus in basal Araceae includes both thermogenic and non/slightly thermogenic species that prefer cold environments. If floral thermogenesis of Symplocarpus contributes to cold adaptation, it would be expected that thermogenic species have a larger habitat than non/slightly thermogenic species during an ice age, leading to increased genetic diversity in the current population. To address this question, potential distribution in past environment predicted by ecological niche modeling (ENM), genetic diversity, and population structure of chloroplast and genome-wide single nucleotide polymorphisms were compared between thermogenic Symplocarpus renifolius and non/slightly thermogenic Symplocarpus nipponicus. ENM revealed that the distribution of S. nipponicus decreased, whereas that of S. renifolius expanded in the Last Glacial Maximum. Phylogeographic analyses have shown that the population structures of the two species were genetically segmented and that the genetic diversity of S. renifolius was higher than that of S. nipponicus. The phylogenetic relationship between chloroplast and nuclear DNA is topologically different in the two species, which may be due to the asymmetric gene flow ubiquitously observed in plants. The results of this study imply that floral thermogenesis of Symplocarpus contributes to expanding the distribution during an ice age, resulting in increased genetic diversity due to cold adaptation.

10.
Physiol Plant ; 175(4): e13957, 2023.
Article in English | MEDLINE | ID: mdl-37338180

ABSTRACT

In floral thermogenesis, sugars play an important role not only as energy providers but also as growth and development facilitators. Yet, the mechanisms underlying sugar translocation and transport in thermogenic plants remain to be studied. Asian skunk cabbage (Symplocarpus renifolius) is a species that can produce durable and intense heat in its reproductive organ, the spadix. Significant morphological and developmental changes in the stamen are well-characterized in this plant. In this study, we focused on the sugar transporters (STPs), SrSTP1 and SrSTP14, whose genes were identified by RNA-seq as the upregulated STPs during thermogenesis. Real-time PCR confirmed that mRNA expression of both STP genes was increased from the pre-thermogenic to the thermogenic stage in the spadix, where it is predominantly expressed in the stamen. SrSTP1 and SrSTP14 complemented the growth defects of a hexose transporter-deficient yeast strain, EBY4000, on media containing 0.02, 0.2, and 2% (w/v) glucose and galactose. Using a recently developed transient expression system in skunk cabbage leaf protoplasts, we revealed that SrSTP1 and SrSTP14-GFP fusion proteins were mainly localized to the plasma membrane. To dig further into the functional analysis of SrSTPs, tissue-specific localization of SrSTPs was investigated by in situ hybridization. Using probes for SrSTP14, mRNA expression was observed in the microspores within the developing anther at the thermogenic female stage. These results indicate that SrSTP1 and SrSTP14 transport hexoses (e.g., glucose and galactose) at the plasma membrane and suggest that SrSTP14 may play a role in pollen development through the uptake of hexoses into pollen precursor cells.


Subject(s)
Araceae , Galactose/metabolism , Pollen/genetics , Pollen/metabolism , Glucose/metabolism , Thermogenesis , RNA, Messenger/genetics , Plant Proteins/genetics , Plant Proteins/metabolism
11.
DNA Res ; 2023 Apr 25.
Article in English | MEDLINE | ID: mdl-37186136

ABSTRACT

Here, we report the first telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake), which consists of 13 sequences (spanning 161.0 Mb) and a 76 kb circular mitochondrial genome. All the 13 sequences were supported with telomeric repeats at the ends. GC-rich regions are located at the middle of the sequences and are enriched with long interspersed nuclear elements (LINEs). Repetitive sequences including long-terminal repeats (LTRs) and LINEs occupy 71.6% of the genome. A total of 21,887 potential protein-coding genes were predicted. The genomic data reported in this study served not only matsutake gene sequences but also genome structures and intergenic sequences. The information gained would be a great reference for exploring the genetics, genomics, and evolutionary study of matsutake in the future, and ultimately facilitate the conservation of this vulnerable genetic resource.

12.
Drug Test Anal ; 2022 Nov 23.
Article in English | MEDLINE | ID: mdl-36417202

ABSTRACT

Dried blood spot (DBS) analysis has been an inherent part of sports drug testing through the technological advancements of the past decade. Trimetazidine, a non-threshold banned substance, is excreted into urine after a dose of the permitted drug lomerizine. Therefore, a lomerizine-specific metabolite (M6) is analyzed to confirm the origin of trimetazidine in traditional urine analysis. Application studies were conducted to develop an analytical method for trimetazidine applicable to DBS. These studies comprise (1) the effect of different sampling sites on the detection of trimetazidine, (2) the determination of the appropriate trimetazidine level required for DBS analysis, and (3) differentiating between trimetazidine and lomerizine use. A high-resolution mass spectrometric method for detecting trimetazidine in DBS was validated. After oral administration of trimetazidine (n = 7), venous and capillary blood (fingertip and upper arm) were spotted on cellulose paper. Trimetazidine could be identified in DBS in all subjects up to 60 h after administration. The limit of detection was 0.05 ng/ml, and the limit of identification was 0.06 ng/ml, suggesting the minimum required performance level of 0.2 ng/ml. In the fingertip capillary blood, biases of 9.7% (vs. upper arm) and 13.0% (vs. vein) were observed in the trimetazidine intensity; however, there were no concerns in the qualitative analysis. After administering lomerizine (n = 10), the intact lomerizine has a strong peak intensity in blood compared to trimetazidine. Contrary to urine analysis, the M6 was less detectable in blood. Laboratories should confirm intact lomerizine whenever trimetazidine is identified in DBS.

13.
Drug Test Anal ; 14(11-12): 1836-1852, 2022 Nov.
Article in English | MEDLINE | ID: mdl-36208085

ABSTRACT

The doping control analyses at the XXXII Olympic Games (July 23 to August 8, 2021) and the XVI Paralympic Games (August 24 to September 5, 2021) held in Tokyo, Japan, after a year of delay due to the COVID-19 pandemic are summarized in this paper. A new satellite facility at the existing World Anti-Doping Agency (WADA)-accredited Tokyo laboratory was established and fully operated by 278 staff, including 33 Tokyo laboratory staff, 49 international experts, and 196 Japanese temporary staff. The numbers of urine samples were 5081 (Olympics) and 1519 (Paralympics), and the numbers of blood samples were 1103 (Olympics) and 500 (Paralympics). The laboratory could prepare for analysis in advance using a paperless chain-of-custody system, allowing for faster turnaround time reporting. For the first time, a new polymerase chain reaction method for detecting erythropoietin (EPO) gene doping was used. The laboratory also analyzed blood samples for detecting steroid esters following the spotting of collected venous EDTA blood onto dried blood spot cards. Moreover, full-scan data acquisition using high-resolution mass spectrometers was performed for all urine samples, allowing for detecting traces of doping substances, which are not currently analyzed in the subsequent data processing. The presence of some prohibited substances was confirmed, resulting in 8 atypical findings (ATFs) and 11 adverse analytical findings (AAFs), including homologous blood transfusion (2 cases) and recombinant EPO in the blood (1 case), at the Olympics, whereas 2 ATFs and 10 AAFs were reported at the Paralympics.


Subject(s)
COVID-19 , Doping in Sports , Sports , Humans , Tokyo , Pandemics , COVID-19/diagnosis , COVID-19/epidemiology , Mass Spectrometry
14.
Microb Genom ; 8(3)2022 03.
Article in English | MEDLINE | ID: mdl-35315751

ABSTRACT

Serratia marcescens is an important nosocomial pathogen causing various opportunistic infections, such as urinary tract infections, bacteremia and sometimes even hospital outbreaks. The recent emergence and spread of multidrug-resistant (MDR) strains further pose serious threats to global public health. This bacterium is also ubiquitously found in natural environments, but the genomic differences between clinical and environmental isolates are not clear, including those between S. marcescens and its close relatives. In this study, we performed a large-scale genome analysis of S. marcescens and closely related species (referred to as the 'S. marcescens complex'), including more than 200 clinical and environmental strains newly sequenced here. Our analysis revealed their phylogenetic relationships and complex global population structure, comprising 14 clades, which were defined based on whole-genome average nucleotide identity. Clades 10, 11, 12 and 13 corresponded to S. nematodiphila, S. marcescens sensu stricto, S. ureilytica and S. surfactantfaciens, respectively. Several clades exhibited distinct genome sizes and GC contents and a negative correlation of these genomic parameters was observed in each clade, which was associated with the acquisition of mobile genetic elements (MGEs), but different types of MGEs, plasmids or prophages (and other integrative elements), were found to contribute to the generation of these genomic variations. Importantly, clades 1 and 2 mostly comprised clinical or hospital environment isolates and accumulated a wide range of antimicrobial resistance genes, including various extended-spectrum ß-lactamase and carbapenemase genes, and fluoroquinolone target site mutations, leading to a high proportion of MDR strains. This finding suggests that clades 1 and 2 represent hospital-adapted lineages in the S. marcescens complex although their potential virulence is currently unknown. These data provide an important genomic basis for reconsidering the classification of this group of bacteria and reveal novel insights into their evolution, biology and differential importance in clinical settings.


Subject(s)
Bacteremia , Serratia marcescens , Hospitals , Humans , Phylogeny , Plasmids , Serratia marcescens/genetics
15.
Drug Test Anal ; 14(11-12): 1995-2001, 2022 Nov.
Article in English | MEDLINE | ID: mdl-35043573

ABSTRACT

Bazedoxifene, a selective estrogen receptor modulator, has been explicitly included in the prohibited list issued by the World Anti-Doping Agency (WADA) since January 2020. A high-resolution liquid chromatography-tandem mass spectrometric detection method was developed to identify bazedoxifene and its metabolites in human urine and to quantify bazedoxifene (free plus glucuronide) for doping control purposes. Bazedoxifene acetate (20 mg) was orally administered to seven male volunteers, and the urine samples collected were analyzed using the developed method. The linearity ranged from 0.5 to 200 ng/ml, and the limit of detection was <0.2 ng/ml. The interday precision (2.2% to 3.6%) and the interday accuracy (-10.0% to 1.9%) were adequate. Bazedoxifene, bazedoxifene-N-oxide, and bazedoxifene glucoconjugates were identified in the urine samples. The profiles of the urinary excretion indicated the presence of small amounts of free bazedoxifene and bazedoxifene-N-oxide, whereas bazedoxifene glucuronide was the predominant metabolite. The cumulative excretion amount of bazedoxifene (free form plus glucuronide conjugate) within 78 h after the administration was 0.7% to 1.3% of the total dose. In all subjects, bazedoxifene (free plus glucuronide) could be detected in urine up to 78 h after administration.


Subject(s)
Doping in Sports , Tandem Mass Spectrometry , Humans , Male , Tandem Mass Spectrometry/methods , Selective Estrogen Receptor Modulators , Glucuronides , Substance Abuse Detection/methods , Chromatography, Liquid/methods , Oxides
16.
Plant Cell Rep ; 41(1): 263-275, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34704119

ABSTRACT

KEY MESSAGE: Floral thermogenesis is an important reproductive strategy for attracting pollinators. We developed essential biological tools for studying floral thermogenesis using two species of thermogenic aroids, Symplocarpus renifolius and Alocasia odora. Aroids contain many species with intense heat-producing abilities in their inflorescences. Several genes have been proposed to be involved in thermogenesis of these species, but biological tools for gene functional analyses are lacking. In this study, we aimed to develop a protoplast-based transient expression (PTE) system for the study of thermogenic aroids. Initially, we focused on skunk cabbage (Symplocarpus renifolius) because of its ability to produce intense as well as durable heat. In this plant, leaf protoplasts were isolated from potted and shoot tip-cultured plants with high efficiency (ca. 1.0 × 105/g fresh weight), and more than half of these protoplasts were successfully transfected. Using this PTE system, we determined the protein localization of three mitochondrial energy-dissipating proteins, SrAOX, SrUCPA, and SrNDA1, fused to green fluorescent protein (GFP). These three GFP-fused proteins were localized in MitoTracker-stained mitochondria in leaf protoplasts, although the green fluorescent particles in protoplasts expressing SrUCPA-GFP were significantly enlarged. Finally, to assess whether the PTE system established in the leaves of S. renifolius is applicable for floral tissues of thermogenic aroids, inflorescences of S. renifolius and another thermogenic aroid (Alocasia odora) were used. Although protoplasts were successfully isolated from several tissues of the inflorescences, PTE systems worked well only for the protoplasts isolated from the female parts (slightly thermogenic or nonthermogenic) of A. odora inflorescences. Our developed system has a potential to be widely used in inflorescences as well as leaves in thermogenic aroids and therefore may be a useful biological tool for investigating floral thermogenesis.


Subject(s)
Alocasia/physiology , Araceae/physiology , Botany/methods , Flowers/physiology , Protoplasts/metabolism , Thermogenesis
17.
Genome Res ; 31(6): 1060-1068, 2021 06.
Article in English | MEDLINE | ID: mdl-34006571

ABSTRACT

DNA methylation is an important factor regulating gene expression in organisms. However, whether DNA methylation plays a key role in adaptive evolution is unknown. Here, we show evidence of naturally selected DNA methylation in Arabidopsis thaliana In comparison with single nucleotide polymorphisms, three types of methylation-methylated CGs (mCGs), mCHGs, and mCHHs-contributed highly to variable gene expression levels among an A thaliana population. Such variably expressed genes largely affect a large variation of specialized metabolic quantities. Among the three types of methylations, only mCGs located in promoter regions of genes associated with specialized metabolites show a selective sweep signature in the A thaliana population. Thus, naturally selected mCGs appear to be key mutations that cause the expressional diversity associated with specialized metabolites during plant evolution.


Subject(s)
Arabidopsis , Epigenomics , Genome, Plant , Arabidopsis/genetics , Arabidopsis/metabolism , DNA Methylation , Epigenesis, Genetic , Gene Expression Regulation, Plant , Mutation
18.
J Genomics ; 8: 37-42, 2020.
Article in English | MEDLINE | ID: mdl-32328204

ABSTRACT

Bifidobacterium species are well recognized as probiotics and colonized in various parts of the human body. Here, we report the draft genome sequences of Bifidobacterium animalis isolated from two healthy Japanese volunteers, one of which was sampled twice before and after a 10-year interval. A core genome phylogeny analysis indicated that the strains isolated from the same volunteer were closely related. This paper is the first report of multiple draft genome sequences of B. animalis independently isolated from the same individual and provides insight into the probiotic potential of a member of this species.

19.
Microb Genom ; 6(1)2020 01.
Article in English | MEDLINE | ID: mdl-31935184

ABSTRACT

Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are usually fragmented, limiting our understanding of their dynamics. Here, we performed a systematic analysis of 239 draft genomes and 7 complete genomes of Shiga toxin (Stx)-producing Escherichia coli O145:H28, the major virulence factors of which are encoded by prophages (PPs) or plasmids. The results indicated that PPs are more stably maintained than plasmids. A set of ancestrally acquired PPs was well conserved, while various PPs, including Stx phages, were acquired by multiple sublineages. In contrast, gains and losses of a wide range of plasmids have frequently occurred across the O145:H28 lineage, and only the virulence plasmid was well conserved. The different dynamics of PPs and plasmids have differentially impacted the pangenome of O145:H28, with high proportions of PP- and plasmid-associated genes in the variably present and rare gene fractions, respectively. The dynamics of PPs and plasmids have also strongly impacted virulence gene repertoires, such as the highly variable distribution of stx genes and the high conservation of a set of type III secretion effectors, which probably represents the core effectors of O145:H28 and the genes on the virulence plasmid in the entire O145:H28 population. These results provide detailed insights into the dynamics of PPs and plasmids, and show the application of genomic analyses using a large set of draft genomes and appropriately selected complete genomes.


Subject(s)
Genome, Bacterial , Plasmids , Prophages , Shiga-Toxigenic Escherichia coli/genetics , Siphoviridae , Virulence Factors/genetics , Phylogeny , Polymorphism, Single Nucleotide
20.
Drug Test Anal ; 11(11-12): 1724-1730, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31664780

ABSTRACT

Tretoquinol (trimetoquinol), a ß2-agonist, has been explicitly listed on the World Anti-Doping Agency Prohibited List 2019 since January 2019; however, it has been distributed as an antiasthmatic on the medical market. This study aimed to develop a liquid chromatography-tandem mass spectrometric method for the quantification of tretoquinol (free form plus glucuronide) in human urine for doping control purposes. An excretion study (n = 6) of tretoquinol hydrochloride hydrate (6 mg) was performed, and urine samples were collected prior to oral administration and during the first 48 h, along with spot urine samples at 7 and 14 days after administration. All the urine samples were analysed using the developed method. The limit of detection for the developed method was 0.03 ng/mL. The inter-day precision for the target analyte was excellent (2.7% to 9.2%), and the inter-day accuracy of target analyte was -0.6% to -3.6%. In all subjects, tretoquinol (free form plus glucuronide conjugate) was identified up to 48 h after administration. The maximum concentrations were in the range of 12.4-78.8 ng/mL and the mean concentration was 55.3 ng/mL. The metabolites O-methylated tretoquinol, tretoquinol sulphate and O-methylated tretoquinol sulphate could be also identified in human urine after administration. The longest-lasting urinary metabolite of tretoquinol currently known, O-methylated tretoquinol, is also likely to be a useful marker in doping controls.


Subject(s)
Adrenergic beta-Agonists/urine , Tandem Mass Spectrometry/methods , Tretoquinol/urine , Adrenergic beta-Agonists/metabolism , Adult , Chromatography, High Pressure Liquid/methods , Doping in Sports , Female , Humans , Limit of Detection , Male , Substance Abuse Detection/methods , Tretoquinol/metabolism , Young Adult
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