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1.
Iran J Kidney Dis ; 14(3): 167-172, 2020 05.
Artigo em Inglês | MEDLINE | ID: covidwho-170321

RESUMO

Coronaviruses primarily cause zoonotic infections, however in the past few decades several interspecies transmissions have occurred, the last one by SARS-CoV-2, causing COVID-19 pandemic, posing serious threat to global health. The SARS-CoV-2 spike (S) protein plays an important role in viral attachment, fusion and entry. However, other structural and non-structural SARS-CoV-2 proteins are potential influencers in virus pathogenicity. Among these proteins; Orf3, Orf8, and Orf10 show the least homology to SARSCoV proteins and therefore should be further studied for their abilities to modulate antiviral and inflammatory responses. Here, we discuss how SARS-COV-2 interacts with our immune system.


Assuntos
Betacoronavirus , Infecções por Coronavirus/imunologia , Infecções por Coronavirus/virologia , Genoma Viral/genética , Sistema Imunitário/virologia , Pneumonia Viral/imunologia , Pneumonia Viral/virologia , Proteínas Virais/genética , Proteínas Virais/metabolismo , Animais , Betacoronavirus/genética , Betacoronavirus/imunologia , Ordem dos Genes , Humanos , Pandemias , Vírus da SARS/genética , Vírus da SARS/imunologia , Glicoproteína da Espícula de Coronavírus/genética , Glicoproteína da Espícula de Coronavírus/metabolismo , Estruturas Virais/genética , Internalização do Vírus
2.
J Med Microbiol ; 69(5): 739-747, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32368998

RESUMO

Introduction. Imipenemase (IMP) carbapenemase genes are relatively rare among Enterobacterales in the UK. Emergence in multiple hospitals, in different strains and species, prompted an investigation into their genetic context.Aim. Our goal was to identify and describe the elements carrying bla IMP genes in a variety of Enterobacterales from five hospitals in the UK.Methodology. Long-read nanopore sequencing was carried out on 18 IMP-positive isolates belonging to 6 species. The locations of the bla IMP genes and other associated genetic elements were identified.Results. Ten out of 18 isolates carried bla IMP-1 on an IncN3 plasmid (52-57 kb) in an In1763 class 1 integron. These plasmids also contained genes encoding type IV secretion and conjugal transfer proteins. Five out of 18 isolates carried bla IMP-1 in the same In1763 integron in much larger IncHI2 plasmids. A further isolate carried the In1763 integron in a chromosomally located plasmid fragment. Two isolates carried bla IMP-4 in IncHI2 plasmids. The isolates included three representatives of sequence type 20 of Klebsiella pneumoniae, with one carrying a distinct plasmid from the other two.Conclusion. Highly similar IncN3 plasmids were found in a range of Enterobacterales, mostly K. pneumoniae and the Enterobacter cloacae complex, from three of four London hospitals, with the same In1763 integron carrying bla IMP-1 also being found in IncHI2 plasmids and chromosomally. These plasmids carried multiple elements facilitating self-transmission. Strain typing alone was not sufficient to investigate cross-infection among this set of isolates, many of which appeared to be unrelated until plasmid analysis was undertaken, and vice versa.


Assuntos
Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Infecções por Enterobacteriaceae/microbiologia , Integrons/genética , Plasmídeos/genética , beta-Lactamases/genética , Antibacterianos/farmacologia , Enterobacteriáceas Resistentes a Carbapenêmicos/efeitos dos fármacos , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Infecção Hospitalar , Infecções por Enterobacteriaceae/epidemiologia , Ordem dos Genes , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Testes de Sensibilidade Microbiana
3.
Iran J Kidney Dis ; 14(3): 167-172, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32361692

RESUMO

Coronaviruses primarily cause zoonotic infections, however in the past few decades several interspecies transmissions have occurred, the last one by SARS-CoV-2, causing COVID-19 pandemic, posing serious threat to global health. The SARS-CoV-2 spike (S) protein plays an important role in viral attachment, fusion and entry. However, other structural and non-structural SARS-CoV-2 proteins are potential influencers in virus pathogenicity. Among these proteins; Orf3, Orf8, and Orf10 show the least homology to SARSCoV proteins and therefore should be further studied for their abilities to modulate antiviral and inflammatory responses. Here, we discuss how SARS-COV-2 interacts with our immune system.


Assuntos
Betacoronavirus , Infecções por Coronavirus/imunologia , Infecções por Coronavirus/virologia , Genoma Viral/genética , Sistema Imunitário/virologia , Pneumonia Viral/imunologia , Pneumonia Viral/virologia , Proteínas Virais/genética , Proteínas Virais/metabolismo , Animais , Betacoronavirus/genética , Betacoronavirus/imunologia , Ordem dos Genes , Humanos , Pandemias , Vírus da SARS/genética , Vírus da SARS/imunologia , Glicoproteína da Espícula de Coronavírus/genética , Glicoproteína da Espícula de Coronavírus/metabolismo , Estruturas Virais/genética , Internalização do Vírus
4.
Arch Virol ; 165(5): 1245-1248, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32227308

RESUMO

The complete genomic sequence of a putative novel member of the family Secoviridae was determined by high-throughput sequencing of a pineapple accession obtained from the National Plant Germplasm Repository in Hilo, Hawaii. The predicted genome of the putative virus was composed of two RNA molecules of 6,128 and 4,161 nucleotides in length, excluding the poly-A tails. Each genome segment contained one large open reading frame (ORF) that shares homology and phylogenetic identity with members of the family Secoviridae. The presence of this new virus in pineapple was confirmed using RT-PCR and Sanger sequencing from six samples collected in Oahu, Hawaii. The name "pineapple secovirus A" (PSVA) is proposed for this putative new sadwavirus.


Assuntos
Ananas/virologia , Genoma Viral , Secoviridae/classificação , Secoviridae/isolamento & purificação , Análise de Sequência de DNA , Biologia Computacional , Ordem dos Genes , Hawaii , Sequenciamento de Nucleotídeos em Larga Escala , Fases de Leitura Aberta , Filogenia , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Secoviridae/genética
5.
PLoS One ; 15(4): e0225233, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32324729

RESUMO

The Assam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The present study decodes the first complete mitochondrial genome of P. sylhetensis (16,568 bp) by using next-generation sequencing. The assembly encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. All PCGs start with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5), which both start with GTG codon. The study also found the typical cloverleaf secondary structures in most of the predicted tRNA structures, except for serine (trnS1) which lacks of conventional DHU arm and loop. Both Bayesian and maximum-likelihood phylogenetic inference using 13 concatenated PCGs demonstrated strong support for the monophyly of all 52 Testudines species within their respective families and revealed Batagur trivittata as the nearest neighbor of P. sylhetensis. The mitogenomic phylogeny with other amniotes is congruent with previous research, supporting the sister relationship of Testudines and Archosaurians (birds and crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated plesiomorphy with the typical vertebrate GO in most of the Testudines species.


Assuntos
Espécies em Perigo de Extinção , Genoma Mitocondrial , Tartarugas/genética , Animais , Ordem dos Genes , Filogenia , RNA Ribossômico/genética , RNA de Transferência/genética , Proteínas de Répteis/genética
6.
PLoS Genet ; 16(3): e1008615, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32130223

RESUMO

The relative linear order of most genes on bacterial chromosomes is not conserved over evolutionary timescales. One explanation is that selection is weak, allowing recombination to randomize gene order by genetic drift. However, most chromosomal rearrangements are deleterious to fitness. In contrast, we propose the hypothesis that rearrangements in gene order are more likely the result of selection during niche adaptation (SNAP). Partial chromosomal duplications occur very frequently by recombination between direct repeat sequences. Duplicated regions may contain tens to hundreds of genes and segregate quickly unless maintained by selection. Bacteria exposed to non-lethal selections (for example, a requirement to grow on a poor nutrient) can adapt by maintaining a duplication that includes a gene that improves relative fitness. Further improvements in fitness result from the loss or inactivation of non-selected genes within each copy of the duplication. When genes that are essential in single copy are lost from different copies of the duplication, segregation is prevented even if the original selection is lifted. Functional gene loss continues until a new genetic equilibrium is reached. The outcome is a rearranged gene order. Mathematical modelling shows that this process of positive selection to adapt to a new niche can rapidly drive rearrangements in gene order to fixation. Signature features (duplication formation and divergence) of the SNAP model were identified in natural isolates from multiple species showing that the initial two steps in the SNAP process can occur with a remarkably high frequency. Further bioinformatic and experimental analyses are required to test if and to which extend the SNAP process acts on bacterial genomes.


Assuntos
Aclimatação/genética , Cromossomos Bacterianos/genética , Duplicação Gênica/genética , Rearranjo Gênico/genética , Seleção Genética/genética , Aberrações Cromossômicas , Evolução Molecular , Frequência do Gene/genética , Ordem dos Genes/genética , Genoma Bacteriano/genética , Modelos Teóricos , Filogenia
7.
Exp Appl Acarol ; 80(4): 521-530, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32162137

RESUMO

In this study, we de novo sequenced and analyzed the circular mitochondrial genome (mitogenome) of Tyrophagus putrescentiae. It was 14,156 bp long and contained a complete set of 37 genes, contrary to the initial published sequences; it included 22 tRNA sequences and the largest non-coding region. The mtDNA gene order of T. putrescentiae was found to be identical to that of Aleuroglyphus ovatus, Caloglyphus berlesei, and Rhizoglyphus robini (all Acaroidea). Most tRNAs of T. putrescentiae lack at least a D-arm or T-arm. Tyrophagus putrescentiae tRNAs also shared considerable structural and sequence similarity with the tRNAs of other reported Acaroidea species that have the full set of tRNAs. The largest non-coding region was located between trnF and trnS1, and it contained a microsatellite-like (AT)n sequence, short palindromic sequences, and several hairpin loops, as observed in other reported Acaroidea species (excepting Tyrophagus longior).


Assuntos
Acaridae/genética , Genoma Mitocondrial , Animais , DNA Mitocondrial/genética , Ordem dos Genes , RNA de Transferência/genética
8.
Plasmid ; 108: 102490, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32004577

RESUMO

In this study, a cryptic plasmid from Aeromonas hydrophila (pAhX22) was cloned and characterized. pAhX22 was 2523 bp long, had a GC content of 59.9%, and contained two putative open reading frames (ORFs). orf1 and orf2 encoded putative proteins of 458 amino acids and 88 amino acids, respectively; these putative proteins might be involved in plasmid replication. An Escherichia coli-A. hydrophila shuttle vector, pAEsv-1 (4587 bp, KanR), was constructed using in-fusion cloning, combining pAhX22 with the kanamycin-resistance gene and the origin of replication from E. coli expression vector pET-28a. The transformation efficiency of pAEsv-1 in A. hydrophila strains ranged from 2.2 × 106 to 1.0 × 107 CFU/µg DNA, while transformation efficiency in E. coli DH5α was about 1.6 × 106 CFU/µg DNA. pAEsv-1 was segregationally and structurally stable in A. hydrophila in the absence of selective pressure. A green fluorescent protein gene (gfp) from pHT315-gfp was successfully cloned and expressed in A. hydrophila strain X2 using pAEsv-1, and 82.3% ± 2.5% of cells maintained the recombinant plasmid after one week in liquid culture without kanamycin. These results suggested that pAEsv-1 might potentially be used as a stable cloning vector for A. hydrophila, which might facilitate genetic studies of A. hydrophila.


Assuntos
Aeromonas hydrophila/genética , Clonagem Molecular , Vetores Genéticos/genética , Plasmídeos/genética , Expressão Gênica , Ordem dos Genes , Genes Reporter , Engenharia Genética , Análise de Sequência de DNA
9.
BMC Evol Biol ; 20(1): 22, 2020 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-32024460

RESUMO

BACKGROUND: Polyplacophora, or chitons, have long fascinated malacologists for their distinct and rather conserved morphology and lifestyle compared to other mollusk classes. However, key aspects of their phylogeny and evolution remain unclear due to the few morphological, molecular, or combined phylogenetic analyses, particularly those addressing the relationships among the major chiton lineages. RESULTS: Here, we present a mitogenomic phylogeny of chitons based on 13 newly sequenced mitochondrial genomes along with eight available ones and RNAseq-derived mitochondrial sequences from four additional species. Reconstructed phylogenies largely agreed with the latest advances in chiton systematics and integrative taxonomy but we identified some conflicts that call for taxonomic revisions. Despite an overall conserved gene order in chiton mitogenomes, we described three new rearrangements that might have taxonomic utility and reconstructed the most likely scenario of gene order change in this group. Our phylogeny was time-calibrated using various fossils and relaxed molecular clocks, and the robustness of these analyses was assessed with several sensitivity analyses. The inferred ages largely agreed with previous molecular clock estimates and the fossil record, but we also noted that the ambiguities inherent to the chiton fossil record might confound molecular clock analyses. CONCLUSIONS: In light of the reconstructed time-calibrated framework, we discuss the evolution of key morphological features and call for a continued effort towards clarifying the phylogeny and evolution of chitons.


Assuntos
Genoma Mitocondrial , Poliplacóforos/classificação , Poliplacóforos/genética , Animais , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Evolução Molecular , Fósseis , Ordem dos Genes , Genoma Mitocondrial/genética , Moluscos/classificação , Moluscos/genética , Filogenia , Análise de Sequência de DNA/métodos
10.
BMC Genomics ; 21(1): 45, 2020 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-31937237

RESUMO

BACKGROUND: Clostridium perfringens is a Gram-positive anaerobic pathogen that causes multiple diseases in humans and animals. C. perfringens lack flagella but have type IV pili (TFP) and can glide on agar surfaces. When C. perfringens bacteria are placed on surfaces, they become elongated, flexible and have TFP on their surface, traits not seen in liquid-grown cells. In addition, the main pilin in C. perfringens TFP, PilA2, undergoes differential post-translational modification when grown in liquid or on plates. To understand the mechanisms underlying these phenotypes, bacteria were grown in three types of liquid media and on agar plates with the same medium to compare gene expression using RNA-Seq. RESULTS: Hundreds of genes were differentially expressed, including transcriptional regulatory protein-encoding genes and genes associated with TFP functions, which were higher on plates than in liquid. Transcript levels of TFP genes reflected the proportion of each protein predicted to reside in a TFP assembly complex. To measure differences in rates of translation, the Escherichia coli reporter gene gusA gene (encoding ß-glucuronidase) was inserted into the chromosome downstream of TFP promoters and in-frame with the first gene of the operon. ß-glucuronidase expression was then measured in cells grown in liquid or on plates. ß-glucuronidase activity was proportional to mRNA levels in liquid-grown cells, but not plate-grown cells, suggesting significant levels of post-transcriptional regulation of these TFP-associated genes occurs when cells are grown on surfaces. CONCLUSIONS: This study reveals insights into how a non-flagellated pathogenic rod-shaped bacterium senses and responds to growth on surfaces, including inducing transcriptional regulators and activating multiple post-transcriptional regulatory mechanisms associated with TFP functions.


Assuntos
Clostridium perfringens/fisiologia , Proteínas de Fímbrias/genética , Regulação Bacteriana da Expressão Gênica , Animais , Aderência Bacteriana , Toxinas Bacterianas/genética , Sequência de Bases , Perfilação da Expressão Gênica , Ordem dos Genes , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Camundongos , Mioblastos/virologia , Óperon , Regiões Promotoras Genéticas , Temperatura , Transcriptoma
11.
mBio ; 11(1)2020 01 28.
Artigo em Inglês | MEDLINE | ID: mdl-31992628

RESUMO

The intracellular pathogen Legionella pneumophila utilizes the Icm/Dot type IV secretion system to translocate >300 effector proteins into host cells during infection. The regulation of some of these effector-encoding genes was previously shown to be coordinated by several global regulators, including three two-component systems (TCSs) found in all the Legionella species examined. Here, we describe the first Legionella genomic island encoding a single Icm/Dot effector and a dedicated TCS, which regulates its expression. This genomic island, which we named Lci, undergoes horizontal gene transfer in the Legionella genus, and the TCS encoded from this island (LciRS) is homologous to TCSs that control the expression of various metal resistance systems found in other bacteria. We found that the L. pneumophila sensor histidine kinase LciS is specifically activated by copper via a unique, small periplasmic sensing domain. Upon activation by LciS, the response regulator LciR directly binds to a conserved regulatory element and activates the expression of the adjacently located lciE effector-encoding gene. Thus, LciR represents the first local regulator of effectors identified in L. pneumophila Moreover, we found that the expression of the lciRS operon is repressed by the Fis1 and Fis3 regulators, leading to Fis-mediated effects on copper induction of LciE and silencing of the expression of this genomic island in the absence of copper. This island represents a novel type of effector regulation in Legionella, shedding new light on the ways by which the Legionella pathogenesis system evolves its effector repertoire and expands its activating signals.IMPORTANCE Legionella pneumophila is an intracellular human pathogen that utilizes amoebae as its environmental host. The adaptation of L. pneumophila to the intracellular environment requires coordination of expression of its multicomponent pathogenesis system, which is composed of a secretion system and effector proteins. However, the regulatory factors controlling the expression of this pathogenesis system are only partially uncovered. Here, we discovered a novel regulatory system that is activated by copper and controls the expression of a single effector protein. The genes encoding both the regulatory system and the effector protein are located on a genomic island that undergoes horizontal gene transfer within the Legionella genus. This regulator-effector genomic island represents the first reported case of local regulation of effectors in Legionella The discovery of this regulatory mechanism is an important step forward in the understanding of how the regulatory network of effectors functions and evolves in the Legionella genus.


Assuntos
Proteínas de Bactérias/genética , Cobre/metabolismo , Regulação Bacteriana da Expressão Gênica , Genoma Bacteriano , Ilhas Genômicas , Legionella/genética , Legionella/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Ordem dos Genes , Transferência Genética Horizontal , Legionella/classificação , Legionella pneumophila/classificação , Legionella pneumophila/genética , Legionella pneumophila/metabolismo , Filogenia , Ligação Proteica , Transcrição Genética
12.
Sci Rep ; 10(1): 1329, 2020 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-31992772

RESUMO

The genome of Rhodothermus marinus DSM 4253 encodes six glycoside hydrolases (GH) classified under GH family 3 (GH3): RmBgl3A, RmBgl3B, RmBgl3C, RmXyl3A, RmXyl3B and RmNag3. The biochemical function, modelled 3D-structure, gene cluster and evolutionary relationships of each of these enzymes were studied. The six enzymes were clustered into three major evolutionary lineages of GH3: ß-N-acetyl-glucosaminidases, ß-1,4-glucosidases/ß-xylosidases and macrolide ß-glucosidases. The RmNag3 with additional ß-lactamase domain clustered with the deepest rooted GH3-lineage of ß-N-acetyl-glucosaminidases and was active on acetyl-chitooligosaccharides. RmBgl3B displayed ß-1,4-glucosidase activity and was the only representative of the lineage clustered with macrolide ß-glucosidases from Actinomycetes. The ß-xylosidases, RmXyl3A and RmXyl3B, and the ß-glucosidases RmBgl3A and RmBgl3C clustered within the major ß-glucosidases/ß-xylosidases evolutionary lineage. RmXyl3A and RmXyl3B showed ß-xylosidase activity with different specificities for para-nitrophenyl (pNP)-linked substrates and xylooligosaccharides. RmBgl3A displayed ß-1,4-glucosidase/ß-xylosidase activity while RmBgl3C was active on pNP-ß-Glc and ß-1,3-1,4-linked glucosyl disaccharides. Putative polysaccharide utilization gene clusters were also investigated for both R. marinus DSM 4253 and DSM 4252T (homolog strain). The analysis showed that in the homolog strain DSM 4252T Rmar_1080 (RmXyl3A) and Rmar_1081 (RmXyl3B) are parts of a putative polysaccharide utilization locus (PUL) for xylan utilization.


Assuntos
Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/metabolismo , Família Multigênica , Rhodothermus/enzimologia , Rhodothermus/genética , Ativação Enzimática , Ordem dos Genes , Genes Bacterianos , Loci Gênicos , Glicosídeo Hidrolases/química , Glicosídeo Hidrolases/classificação , Concentração de Íons de Hidrogênio , Hidrólise , Cinética , Modelos Moleculares , Conformação Proteica , Relação Estrutura-Atividade , Temperatura
13.
Stem Cell Reports ; 14(1): 154-166, 2020 01 14.
Artigo em Inglês | MEDLINE | ID: mdl-31902707

RESUMO

Rat embryonic stem cells (rESCs) are capable of contributing to all differentiated tissues, including the germ line in chimeric animals, and represent a unique, authentic alternative to mouse embryonic stem cells for studying stem cell pluripotency and self-renewal. Here, we describe an EGFP reporter transgene that tracks expression of the benchmark naive pluripotency marker gene Rex1 (Zfp42) in the rat. Insertion of the EGFP reporter gene downstream of the Rex1 promoter disrupted Rex1 expression, but REX1-deficient rESCs and rats were viable and apparently normal, validating this targeted knockin transgene as a neutral reporter. The Rex1-EGFP gene responded to self-renewal/differentiation factors and validated the critical role of ß-catenin/LEF1 signaling. The stem cell reporter also allowed the identification of functionally distinct sub-populations of cells within rESC cultures, thus demonstrating its utility in discriminating between cell states in rat stem cell cultures, as well as providing a tool for tracking Rex1 expression in the rat.


Assuntos
Diferenciação Celular , Autorrenovação Celular/genética , Células-Tronco Embrionárias/citologia , Células-Tronco Embrionárias/metabolismo , Genes Reporter , Células-Tronco Pluripotentes/citologia , Células-Tronco Pluripotentes/metabolismo , Animais , Biomarcadores , Diferenciação Celular/genética , Células Cultivadas , Imunofluorescência , Expressão Gênica , Ordem dos Genes , Vetores Genéticos/genética , Imunofenotipagem , Ratos
14.
Arch Virol ; 165(2): 483-486, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31781858

RESUMO

Ornithogalum thyrsoides, commonly known as chincherinchee, is an indigenous ornamental plant widely cultivated in South Africa. It is commercially valued as a flowering pot plant and for the production of cut flowers. Virus infections resulting in the development of severe necrotic mosaic symptoms threaten the success of commercial cultivation. The virome of an O. thyrsoides plant displaying necrotic mosaic symptoms was determined using high-throughput sequencing (HTS). In this plant, ornithogalum mosaic virus and ornithogalum virus 3 were identified, as well as a previously unknown virus. The full genome sequence of this virus was confirmed by Sanger sequencing using overlapping amplicons combined with rapid amplification of cDNA ends (RACE). Based on genome organisation and phylogenetic analysis, this novel virus can be classified as a polerovirus.


Assuntos
Genoma Viral , Luteoviridae/genética , Ornithogalum/virologia , Doenças das Plantas/virologia , Sequenciamento Completo do Genoma , Biologia Computacional , Ordem dos Genes , Sequenciamento de Nucleotídeos em Larga Escala , Luteoviridae/classificação , Luteoviridae/isolamento & purificação , Filogenia , África do Sul
15.
Arch Virol ; 165(2): 479-482, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31776676

RESUMO

Screening of apple samples using a high-throughput sequencing (HTS) approach led to the discovery of a novel virus, tentatively named "Malus domestica virus A" (MdoVA). Its genomic organisation and phylogenetic relationship showed relatedness to viruses of the genus Velarivirus in the family Closteroviridae. It is not clear whether MdoVA has any impact on its host, as the analysed apple tree contained other viruses and a viroid.


Assuntos
Closteroviridae/classificação , Closteroviridae/genética , Genoma Viral , Malus/virologia , Filogenia , Doenças das Plantas/virologia , Sequenciamento Completo do Genoma , Closteroviridae/isolamento & purificação , Biologia Computacional , Ordem dos Genes
16.
Mol Phylogenet Evol ; 143: 106669, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31698050

RESUMO

We present here a combined mitogenome gene order dataset totalling 62% of the known genera of East Asian potamiscine freshwater crabs that includes first-time mitogenome data for 14 species and gene order data from 37 other species of potamiscines. A surprisingly high number of mitogenome gene order rearrangements were found in the taxa studied (comprising nine different rearrangements and seven major patterns, one of which has two sub-arrangements). Our phylogenetic reconstructions indicate that the mitogenome gene order rearrangements are associated with the evolutionary history of potamiscine lineages. We also used a new Event-based Maximum Parsimony method to reconstruct ancestral gene orders, which takes into consideration gene duplication, pseudogeneticization, and tandem duplication random loss. Furthermore, shared mitogenome gene order patterns were used to inform the taxonomic placement of Sinopotamon parvum, and the cryptic diversity in Potamiscus. The remarkably frequent mitogenome rearrangements in potamiscine freshwater crabs have great potential to contribute to our understanding of the evolutionary history of these highly diverse decapods in East Asia.


Assuntos
Braquiúros/classificação , Braquiúros/genética , Genoma Mitocondrial , Animais , Evolução Molecular , Extremo Oriente , Água Doce , Duplicação Gênica , Ordem dos Genes , Filogenia
17.
Diagn Microbiol Infect Dis ; 96(2): 114900, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31859023

RESUMO

This study used whole-genome sequencing (WGS) and PFGE to analysis KPC-2-producing Klebsiella pneumoniae strains from clinical specimens collected in Brazilian hospitals. The study identifies the emergence of a novel small IncX3 plasmid (pKPB11), 12,757-bp in length, in a high-risk K. pneumoniae ST11/CG258 lineage, a successful clonal group in Brazil, carrying the blaKPC-2 gene on a non-Tn4401 genetic element (NTEKPC-Ic). Comparative analysis of the pKPB11 showed that this plasmid reduced its size, losing part of its conjugation apparatus. The pKPB11 was also compared to another strain sequenced in this study (KPC89) that had the hybrid IncX3-IncU plasmid (pKP89), of approximately 45 kb in length, similarly carrying the blaKPC-2 gene on NTEKPC-Ic. To the best of our knowledge, pKPB11 is the first example of small IncX3 plasmid found in a high-risk KPC-2-producing K. pneumoniae ST11/CG258.


Assuntos
Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/classificação , Klebsiella pneumoniae/genética , Plasmídeos/genética , beta-Lactamases/genética , Brasil/epidemiologia , Ordem dos Genes , Genoma Bacteriano , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Infecções por Klebsiella/epidemiologia , Tipagem de Sequências Multilocus
18.
Plasmid ; 108: 102477, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31870701

RESUMO

OBJECTIVES: Systematic comparison of multiple plasmids remains challenging. We aimed to develop a new method for phylogenetic analysis of plasmids, open reading frame (ORF)-based binarized structure network analysis of plasmids (OSNAp). METHODS: With the OSNAp, the genetic structures of plasmids in a given plasmid group are expressed as binary sequences based on the presence or absence of ORFs regardless of their positions or directions. As a proof-of-concept, ORFs were collected from 101 complete I1 plasmid sequences, and their corresponding binary sequences were generated. A tree was generated using the neighbor-net, an algorithm for constructing phylogenetic networks based on distance between taxa, to visualize the plasmid phylogeny drawn from binary sequences. The results were compared with those of plasmid sequence types (pSTs) defined by plasmid multilocus sequence typing (pMLST). RESULTS: All I1 plasmids were placed on the phylogenetic tree constructed from the binary sequences. Most plasmids belonging to the same pSTs had Dice indices of ≥0.95 and were placed in the same OSNAp split. On the other hand, pST12 plasmids were distributed on separate splits due to differences in ORFs not used in pMLST, suggesting improved differentiation of the plasmids with OSNAp compared with pMLST. CONCLUSION: OSNAp is a novel holistic approach to assess relatedness of a population of plasmids in a given plasmid group based on nucleotide sequence data. It provides higher discrimination than pMLST, which may prove useful in tracing bacteria that harbor plasmids of shared origins.


Assuntos
Biologia Computacional/métodos , Fases de Leitura Aberta , Filogenia , Plasmídeos/classificação , Plasmídeos/genética , Ordem dos Genes , Tipagem de Sequências Multilocus
19.
Genomics ; 112(1): 82-91, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31863840

RESUMO

Grapsoidea and Ocypodoidea, two of the most abundant and economically important groups in Brachyura, are of great commercial value to fisheries and aquaculture. However, the taxonomy of Ocypodoidea and Grapsoidea has long been highly disputed. Previous studies have investigated this problem through phylogenetic analysis based on limited taxonomic sampling, with different reports proposing either monophyly or paraphyly, but no definitive conclusion has been reached. In this study, the complete mitogenome of Macrophthalmus pacificus (Ocypodoidea, Macrophthalmidae) is reported on and the relationship between Ocypodoidea and Grapsoidea is further investigated. Sequencing the M. pacificus mitogenome, which is a closed circular molecule containing a typical 37 genes, preliminarily determined the ancestral gene order of Macrophthalmidae, which is consistent with previous studies. Comparative analyses of gene order among Ocypodoidea and Grapsoidea revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) have the same rearrangement, which confirms previous research. Larger data analysis revealed that these two families (Varunidae and Macrophthalmidae) cluster into a monophyletic clade as sister groups. Rearrangement and phylogeny lines of evidence is concluded that Varunidae and Macrophthalmidae may be of common origin. Furthermore, the remaining Ocypodoidea and Grapsoidea families mix paraphyletically in the phylogenetic tree. Therefore, both gene rearrangement and phylogenetic analysis support the paraphyly of Ocypodoidea and Grapsoidea, which reinforces this view. These findings provide important information regarding Brachyura's phylogenetic relationships, which demonstrates the advantage of mitogenome sequence data in phylogenetic studies.


Assuntos
Braquiúros/genética , Genoma Mitocondrial , Animais , Composição de Bases , Braquiúros/classificação , Uso do Códon , DNA Mitocondrial/química , Ordem dos Genes , Genes de RNAr , Genômica , Proteínas Mitocondriais/genética , Filogenia , RNA de Transferência/química , RNA de Transferência/genética
20.
Antiviral Res ; 173: 104652, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31751590

RESUMO

Both classical swine fever (CSF) and pseudorabies are highly contagious, economically significant diseases of swine in China. Although vaccination with the C-strain against classical swine fever virus (CSFV) is widely carried out and severe outbreaks of CSF seldom occur in China, CSF is sporadic in many pig herds and novel sub-subgenotypes of CSFV endlessly emerge. Thus, new measures are needed to eradicate CSFV from Chinese farms. The emergence of a pseudorabies virus (PRV) variant also posed a new challenge for the control of swine pseudorabies. Here, the recombinant PRV strain JS-2012-ΔgE/gI-E2 expressing E2 protein of CSFV was developed by inserting the E2 expression cassette into the intergenic region between the gG and gD genes of the gE/gI-deletion PRV variant strain JS-2012-ΔgE/gI. The recombinant virus was stable when passaged in vitro. A single vaccination of JS-2012-ΔgE/gI-E2 via intramuscular injection fully protected against lethal challenges of PRV and CSFV. Vaccination of piglets with the recombinant JS-2012-ΔgE/gI-E2 in the presence of high levels of maternally derived antibodies (Abs) to PRV can provide partial protection against lethal challenge of CSFV. Vaccination of the recombinant PRV JS-2012-ΔgE/gI-E2 strain did not induce the production of Abs to the gE protein of PRV or to the CSFV proteins other than E2. Thus, JS-2012-ΔgE/gI-E2 appears to be a promising recombinant marker vaccine candidate against PRV and CSFV for the control and eradication of the PRV variant and CSFV.


Assuntos
Peste Suína Clássica/prevenção & controle , Expressão Gênica , Vetores Genéticos/genética , Herpesvirus Suídeo 1/genética , Herpesvirus Suídeo 1/imunologia , Pseudorraiva/prevenção & controle , Proteínas do Envelope Viral/genética , Proteínas do Envelope Viral/imunologia , Animais , Anticorpos Antivirais/imunologia , Peste Suína Clássica/imunologia , Peste Suína Clássica/patologia , Vírus da Febre Suína Clássica/genética , Vírus da Febre Suína Clássica/imunologia , Ordem dos Genes , Herpesvirus Suídeo 1/patogenicidade , Pseudorraiva/imunologia , Pseudorraiva/patologia , Proteínas Recombinantes/genética , Proteínas Recombinantes/imunologia , Suínos , Doenças dos Suínos/prevenção & controle , Vacinação , Vacinas Virais/genética , Vacinas Virais/imunologia
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