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1.
Antonie Van Leeuwenhoek ; 117(1): 69, 2024 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-38647727

RESUMO

A novel bacterial symbiont, strain A19T, was previously isolated from a root-nodule of Aeschynomene indica and assigned to a new lineage in the photosynthetic clade of the genus Bradyrhizobium. Here data are presented for the detailed genomic and taxonomic analyses of novel strain A19T. Emphasis is placed on the analysis of genes of practical or ecological significance (photosynthesis, nitrous oxide reductase and nitrogen fixation genes). Phylogenomic analysis of whole genome sequences as well as 50 single-copy core gene sequences placed A19T in a highly supported lineage distinct from described Bradyrhizobium species with B. oligotrophicum as the closest relative. The digital DNA-DNA hybridization and average nucleotide identity values for A19T in pair-wise comparisons with close relatives were far lower than the respective threshold values of 70% and ~ 96% for definition of species boundaries. The complete genome of A19T consists of a single 8.44 Mbp chromosome and contains a photosynthesis gene cluster, nitrogen-fixation genes and genes encoding a complete denitrifying enzyme system including nitrous oxide reductase implicated in the reduction of N2O, a potent greenhouse gas, to inert dinitrogen. Nodulation and type III secretion system genes, needed for nodulation by most rhizobia, were not detected. Data for multiple phenotypic tests complemented the sequence-based analyses. Strain A19T elicits nitrogen-fixing nodules on stems and roots of A. indica plants but not on soybeans or Macroptilium atropurpureum. Based on the data presented, a new species named Bradyrhizobium ontarionense sp. nov. is proposed with strain A19T (= LMG 32638T = HAMBI 3761T) as the type strain.


Assuntos
Bradyrhizobium , Genoma Bacteriano , Fixação de Nitrogênio , Oxirredutases , Fotossíntese , Filogenia , Simbiose , Bradyrhizobium/genética , Bradyrhizobium/classificação , Bradyrhizobium/metabolismo , Bradyrhizobium/isolamento & purificação , Oxirredutases/genética , Oxirredutases/metabolismo , DNA Bacteriano/genética , RNA Ribossômico 16S/genética , Nódulos Radiculares de Plantas/microbiologia
2.
Artigo em Inglês | MEDLINE | ID: mdl-34106824

RESUMO

Six bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soil of legumes native to Canada were previously characterized and 1) placed in two novel lineages within the genus Bradyrhizobium and 2) assigned to symbiovar septentrionale. Here we verified the taxonomic status of these strains using genomic and phenotypic analyses. Phylogenetic analyses of five protein encoding partial gene sequences as well as 52 full length ribosome protein subunit gene sequences confirmed placement of the novel strains in two highly supported lineages distinct from named Bradyrhizobium species. The highest average nucleotide identity values of strains representing these two lineages relative to type strains of closest relatives were 90.7 and 92.3% which is well below the threshold value for bacterial species circumscription. The genomes of representative strains 1S1T, 162S2 and 66S1MBT have sizes of 10598256, 10733150 and 9032145 bp with DNA G+C contents of 63.5, 63.4 and 63.8 mol%, respectively. These strains possess between one and three plasmids based on copy number of plasmid replication and segregation (repABC) genes. Novel strains also possess numerous insertion sequences, and, relative to reference strain Bradyrhizobium diazoefficiens USDA110T, exhibit inversion and fragmentation of nodulation (nod) and nitrogen-fixation (nif) gene clusters. Phylogenetic analyses of nodC and nifH gene sequences confirmed placement of novel strains in a distinct lineage corresponding to symbiovar septentrionale. Data for morphological, physiological and symbiotic characteristics complement the sequence-based results. The data presented here support the description of two new species for which the names Bradyrhizobium septentrionale sp. nov. (sv. septentrionale) and Bradyrhizobium quebecense sp. nov. (sv. septentrionale) are proposed, with 1S1T (=LMG 29930T=HAMBI 3676T) and 66S1MBT (=LMG 31547T=HAMBI 3720T) as type strains, respectively.


Assuntos
Bradyrhizobium/genética , Bradyrhizobium/fisiologia , Fabaceae/microbiologia , Rearranjo Gênico , Mutagênese Insercional/genética , Simbiose/genética , Composição de Bases , Sequência de Bases , Teorema de Bayes , Bradyrhizobium/classificação , Canadá , Fenótipo , Filogenia , Nodulação/genética , RNA Ribossômico 16S/genética , Subunidades Ribossômicas/genética , Nódulos Radiculares de Plantas/microbiologia
3.
Int J Syst Evol Microbiol ; 70(9): 5063-5074, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32804606

RESUMO

The taxonomic status of two previously characterized Bradyrhizobium strains (58S1T and S23321) isolated from contrasting habitats in Canada and Japan was verified by genomic and phenotypic analyses. Phylogenetic analyses of five and 27 concatenated protein-encoding core gene sequences placed both strains in a highly supported lineage distinct from named species in the genus Bradyrhizobium with Bradyrhizobium betae as the closest relative. Average nucleotide identity values of genome sequences between the test and reference strains were between 84.5 and 94.2 %, which is below the threshold value for bacterial species circumscription. The complete genomes of strains 58S1T and S23321 consist of single chromosomes of 7.30 and 7.23 Mbp, respectively, and do not have symbiosis islands. The genomes of both strains have a G+C content of 64.3 mol%. Present in the genome of these strains is a photosynthesis gene cluster (PGC) containing key photosynthesis genes. A tRNA gene and its partial tandem duplication were found at the boundaries of the PGC region in both strains, which is likely the hallmark of genomic island insertion. Key nitrogen-fixation genes were detected in the genomes of both strains, but nodulation and type III secretion system genes were not found. Sequence analysis of the nitrogen fixation gene, nifH, placed 58S1T and S23321 in a novel lineage distinct from described Bradyrhizobium species. Data for phenotypic tests, including growth characteristics and carbon source utilization, supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium cosmicum sp. nov. is proposed with 58S1T (=LMG 31545T=HAMBI 3725T) as the type strain.


Assuntos
Bradyrhizobium/classificação , Ilhas Genômicas , Glycine max/microbiologia , Fotossíntese/genética , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , Bradyrhizobium/isolamento & purificação , Canadá , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Japão , Família Multigênica , Fixação de Nitrogênio/genética , RNA Ribossômico 16S/genética , Nódulos Radiculares de Plantas/microbiologia , Análise de Sequência de DNA , Simbiose/genética
4.
Int J Syst Evol Microbiol ; 70(1): 442-449, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31626586

RESUMO

Four bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soil of either Amphicarpaea bracteata (Hog Peanut) or Desmodium canadense (Showy Tick Trefoil) growing in Canada, were previously characterized and placed in a novel lineage within the genus Bradyrhizobium. The taxonomic status of the novel strains was verified by genomic and phenotypic analyses. Phylogenetic analyses of individual and concatenated housekeeping gene sequences (atp D, gln II, rec A, gyr B and rpo B) placed all novel strains in a highly supported lineage distinct from named Bradyrhizobium species. Data for sequence similarities of concatenated housekeeping genes of novel strains relative to type strains of named species were consistent with the phylogenetic data. Average nucleotide identity values of genome sequences (84.5-93.7 %) were below the threshold value of 95-96 % for bacterial species circumscription. Close relatives to the novel strains are Bradyrhizobium amphicarpaeae, Bradyrhizobium ottawaense and Bradyrhizobium shewense. The complete genomes of strains 85S1MBT and 65S1MB consist of single chromosomes of size 7.04 and 7.13 Mbp, respectively. The genomes of both strains have a G+C content of 64.3 mol%. These strains lack a symbiosis island as well as key nodulation, nitrogen-fixation and photosystem genes. Data from various phenotypic tests including growth characteristics and carbon source utilization supported the sequence-based analyses. Based on the data presented here, the four strains represent a novel species for which the name B radyrhizobium symbiodeficiens sp. nov., is proposed, with 85S1MBT (=LMG 29937T=HAMBI 3684T) as the type strain.


Assuntos
Bradyrhizobium/classificação , Fabaceae/microbiologia , Filogenia , Nódulos Radiculares de Plantas/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Sequência de Bases , Bradyrhizobium/isolamento & purificação , Canadá , DNA Bacteriano/genética , Genes Bacterianos , Genoma Bacteriano , Fixação de Nitrogênio , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Glycine max/microbiologia , Simbiose
5.
Int J Syst Evol Microbiol ; 69(9): 2841-2848, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31251718

RESUMO

A bacterial strain, designated 39S1MBT, isolated from a root nodule of a soybean plant that had been inoculated with root-zone soil of Amphicarpaea bracteata (hog peanut) growing in Canada, was previously characterized and placed in a novel lineage within the genus Bradyrhizobium. The taxonomic status of strain 39S1MBT was verified by genomic and phenotypic analyses. Phylogenetic analyses of individual and concatenated protein-encoding gene sequences (atpD, glnII, recA, gyrB and rpoB) placed 39S1MBT in a lineage distinct from named species. Data for sequence similarities of concatenated genes relative to type strains of named species supported the phylogenetic data. Average nucleotide identity values of genome sequences (84.5-91.7 %) were well below the threshold value for bacterial species circumscription. Based on these data, Bradyrhizobium ottawaense OO99T and Bradyrhizobium shewense ERR11T are close relatives of 39S1MBT. The complete genome of 39S1MBT consists of a single 7.04 Mbp chromosome without a symbiosis island; G+C content is 64.7 mol%. Present in the genome are key photosystem and nitrogen-fixation genes, but not nodulation and type III secretion system genes. Sequence analysis of the nitrogen fixation gene, nifH, placed 39S1MBT in a novel lineage distinct from named Bradyrhizobium species. Data for phenotypic tests including growth characteristics and carbon source utilization supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium amphicarpaeae sp. nov. is proposed with 39S1MBT (=LMG 29934T=HAMBI 3680T) as the type strain.


Assuntos
Bradyrhizobium/classificação , Bradyrhizobium/genética , Genoma Bacteriano , Glycine max/microbiologia , Filogenia , Nódulos Radiculares de Plantas/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Canadá , DNA Bacteriano/genética , Fabaceae/microbiologia , Ácidos Graxos/química , Genes Bacterianos , Nitrogênio , Fixação de Nitrogênio/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vigna/microbiologia , Sequenciamento Completo do Genoma
6.
J Chem Phys ; 148(2): 021101, 2018 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-29331144

RESUMO

This work demonstrates that selective excision of hydrogen atoms at a particular site of the DNA base adenine can be achieved in collisions with electronegative atoms by controlling the impact energy. The result is based on analysing the time-of-flight mass spectra yields of potassium collisions with a series of labeled adenine derivatives. The production of dehydrogenated parent anions is consistent with neutral H loss either from selective breaking of C-H or N-H bonds. These unprecedented results open up a new methodology in charge transfer collisions that can initiate selective reactivity as a key process in chemical reactions that are dominant in different areas of science and technology.


Assuntos
Adenina/química , Transporte de Elétrons , Hidrogênio/química , Espectrometria de Massas , Conformação de Ácido Nucleico
7.
J Chem Phys ; 148(13): 134301, 2018 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-29626890

RESUMO

We report on a combined experimental and theoretical study of electron-transfer-induced decomposition of adenine (Ad) and a selection of analog molecules in collisions with potassium (K) atoms. Time-of-flight negative ion mass spectra have been obtained in a wide collision energy range (6-68 eV in the centre-of-mass frame), providing a comprehensive investigation of the fragmentation patterns of purine (Pu), adenine (Ad), 9-methyl adenine (9-mAd), 6-dimethyl adenine (6-dimAd), and 2-D adenine (2-DAd). Following our recent communication about selective hydrogen loss from the transient negative ions (TNIs) produced in these collisions [T. Cunha et al., J. Chem. Phys. 148, 021101 (2018)], this work focuses on the production of smaller fragment anions. In the low-energy part of the present range, several dissociation channels that are accessible in free electron attachment experiments are absent from the present mass spectra, notably NH2 loss from adenine and 9-methyl adenine. This can be understood in terms of a relatively long transit time of the K+ cation in the vicinity of the TNI tending to enhance the likelihood of intramolecular electron transfer. In this case, the excess energy can be redistributed through the available degrees of freedom inhibiting fragmentation pathways. Ab initio theoretical calculations were performed for 9-methyl adenine (9-mAd) and adenine (Ad) in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process.

9.
Int J Syst Evol Microbiol ; 67(4): 889-895, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-27902304

RESUMO

The bacterial strain 2-92T, isolated from a field plot under long-term (>40 years) mineral fertilization, exhibited in vitro antagonistic properties against fungal pathogens. A polyphasic approach was undertaken to verify its taxonomic status. Strain 2-92T was Gram-reaction-negative, aerobic, non-spore-forming, motile by one or more flagella, and oxidase-, catalase- and urease-positive. The optimal growth temperature of strain 2-92T was 30 °C. 16S rRNA gene sequence analysis demonstrated that the strain is related to species of the genus Pseudomonas. Phylogenetic analysis of six housekeeping genes (dnaA, gyrB, recA, recF, rpoB and rpoD) revealed that strain 2-92T clustered as a distinct and well separated lineage with Pseudomonassimiae as the most closely related species. Polar lipid and fatty acid compositions corroborated the taxonomic position of strain 2-92T in the genus Pseudomonas. Phenotypic characteristics from carbon utilization tests could be used to differentiate strain 2-92T from closely related species of the genus Pseudomonas. DNA-DNA hybridization values (wet laboratory and genome-based) and average nucleotide identity data confirmed that this strain represents a novel species. On the basis of phenotypic and genotypic characteristics, it is concluded that this strain represents a separate novel species for which the name Pseudomonas canadensis sp. nov. is proposed, with type strain 2-92T (=LMG 28499T=DOAB 798T). The DNA G+C content is 60.30 mol%.


Assuntos
Agentes de Controle Biológico/isolamento & purificação , Filogenia , Pseudomonas/classificação , Microbiologia do Solo , Agricultura , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fertilizantes , Genes Bacterianos , Minerais , Hibridização de Ácido Nucleico , Ontário , Pseudomonas/genética , Pseudomonas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
10.
Evid Based Med ; 22(4): 123-131, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28735276

RESUMO

The effectiveness of a continuing education programme in paediatric psychopharmacology designed for primary healthcare providers was objectively measured based on the assumption that training would lead to measurable changes in referral patterns and established clinical measures of referred patients. Using established, valid and reliable measures of clinical urgency embedded in to a regional healthcare system since 2002, the referrals to child and adolescent psychiatric services of physicians who participated in the training (n=99) were compared pretraining and post-training, and to non-participating/untrained referring physicians (n=7753) making referrals over the same time period. Referrals were analysed for evidence of change based on frequencies and measures of clinical urgency. Participants of the training programme also completed standardised baseline and outcome self-evaluations. Congruent with participants self-reported evaluative reports of improved knowledge and practice, analysis of referral frequency and the clinical urgency of referrals to paediatric psychiatric services over the study period indicated that trained physicians made more appropriate referrals (clinically more severe) and reduced referrals to emergency services. Quantitative clinical differences as completed by intake clinicians blind to referrals from the study group designations were observed within the trained physician group pretraining and post-training, and between the trained physician group and the unexposed physician group. The results illustrate a novel model for objectively measuring change among physicians based on training in paediatric mental health management.


Assuntos
Serviços de Saúde do Adolescente , Serviços de Saúde da Criança , Educação Médica Continuada , Serviços de Saúde Mental , Médicos de Atenção Primária/educação , Padrões de Prática Médica , Encaminhamento e Consulta , Adolescente , Criança , Humanos , Autorrelato
11.
Int J Obes (Lond) ; 40(4): 646-53, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26563815

RESUMO

BACKGROUND/OBJECTIVES: Pregnancy is accompanied by fat gain and insulin resistance. Changes in adipose tissue morphology and function during pregnancy and factors contributing to gestational insulin resistance are incompletely known. We sought to characterize adipose tissue in trimesters 1 and 3 (T1/T3) in normal weight (NW) and obese pregnant women, and identify adipose tissue-related factors associated with gestational insulin resistance. SUBJECTS/METHODS: Twenty-two NW and 11 obese women were recruited early in pregnancy for the Pregnancy Obesity Nutrition and Child Health study. Examinations and sampling of blood and abdominal adipose tissue were performed longitudinally in T1/T3 to determine fat mass (air-displacement plethysmography); insulin resistance (homeostasis model assessment of insulin resistance, HOMA-IR); size, number and lipolytic activity of adipocytes; and adipokine release and density of immune cells and blood vessels in adipose tissue. RESULTS: Fat mass and HOMA-IR increased similarly between T1 and T3 in the groups; all remained normoglycemic. Adipocyte size increased in NW women. Adipocyte number was not influenced, but proportions of small and large adipocytes changed oppositely in the groups. Lipolytic activity and circulating adipocyte fatty acid-binding protein increased in both groups. Adiponectin release was reduced in NW women. Fat mass and the proportion of very large adipocytes were most strongly associated with T3 HOMA-IR by multivariable linear regression (R(2)=0.751, P<0.001). CONCLUSIONS: During pregnancy, adipose tissue morphology and function change comprehensively. NW women accumulated fat in existing adipocytes, accompanied by reduced adiponectin release. In comparison with the NW group, obese women had signs of adipocyte recruitment and maintained adiponectin levels. Body fat and large adipocytes may contribute significantly to gestational insulin resistance.


Assuntos
Adipócitos/metabolismo , Tecido Adiposo/metabolismo , Resistência à Insulina , Obesidade/metabolismo , Complicações na Gravidez/metabolismo , Adiponectina/metabolismo , Tecido Adiposo/patologia , Adulto , Glicemia/metabolismo , Distribuição da Gordura Corporal , Índice de Massa Corporal , Proteínas de Ligação a Ácido Graxo/metabolismo , Feminino , Humanos , Imuno-Histoquímica , Insulina/sangue , Obesidade/complicações , Obesidade/patologia , Obesidade/fisiopatologia , Tamanho do Órgão , Gravidez , Complicações na Gravidez/patologia , Gordura Subcutânea/metabolismo
12.
J Phys Chem A ; 119(31): 8503-11, 2015 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-26171941

RESUMO

We present the first set of ab initio calculations (vertical energies and oscillator strengths) of the valence and Rydberg transitions of the anaesthetic compound halothane (CF3CHBrCl). These results are complemented by high-resolution vacuum ultraviolet photoabsorption measurements over the wavelength range 115-310 nm (10.8-4.0 eV). The spectrum reveals several new features that were not previously reported in the literature. Spin-orbit effects have been considered in the calculations for the lowest-lying states, allowing us to explain the broad nature of the 6.1 and 7.5 eV absorption bands assigned to σ*(C-Br) ← nBr and σ*(C-Cl) ← n(Cl) transitions. Novel absolute photoabsorption cross sections from electron scattering data were derived in the 4.0-40.0 eV range. The measured absolute photoabsorption cross sections have been used to calculate the photolysis lifetime of halothane in the upper stratosphere (20-50 km).


Assuntos
Elétrons , Halotano/química , Teoria Quântica , Raios Ultravioleta , Espectroscopia Fotoeletrônica , Síncrotrons , Vácuo
13.
Int J Syst Evol Microbiol ; 64(Pt 9): 3202-3207, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-24969302

RESUMO

Sixteen strains of symbiotic bacteria from root nodules of Glycine max grown in Ottawa, Canada, were previously characterized and placed in a novel group within the genus Bradyrhizobium. To verify their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences that were 99.79 % similar to the closest relative, Bradyrhizobium liaoningense LMG 18230(T). Phylogenetic analysis of concatenated atpD, glnII, recA, gyrB, rpoB and dnaK genes divided the 16 strains into three multilocus sequence types that were placed in a highly supported lineage distinct from named species of the genus Bradyrhizobium consistent with results of DNA-DNA hybridization. Based on analysis of symbiosis gene sequences (nodC and nifH), all novel strains were placed in a phylogenetic group with five species of the genus Bradyrhizobium that nodulate soybeans. The combination of phenotypic characteristics from several tests including carbon and nitrogen source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Novel strain OO99(T) elicits effective nodules on Glycine max, Glycine soja and Macroptilium atropurpureum, partially effective nodules on Desmodium canadense and Vigna unguiculata, and ineffective nodules on Amphicarpaea bracteata and Phaseolus vulgaris. Based on the data presented, we conclude that our strains represent a novel species for which the name Bradyrhizobium ottawaense sp. nov. is proposed, with OO99(T) ( = LMG 26739(T) = HAMBI 3284(T)) as the type strain. The DNA G+C content is 62.6 mol%.


Assuntos
Bradyrhizobium/classificação , Glycine max/microbiologia , Fixação de Nitrogênio , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , Bradyrhizobium/genética , Bradyrhizobium/isolamento & purificação , Canadá , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Nódulos Radiculares de Plantas/microbiologia , Análise de Sequência de DNA , Simbiose
14.
J Phys Chem A ; 118(4): 690-6, 2014 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-24400742

RESUMO

Time-of-flight (TOF) negative ion mass spectra have been obtained in collisions of 20-100 eV neutral potassium atoms with tetrahydrofuran (C4H8O), an analogue for the sugar unit in DNA/RNA. Major enhancements in O(-) and C2H3O(-) production were observed compared with earlier dissociative electron attachment (DEA) experiments. In further contrast with DEA, no evidence was observed for dehydrogenated parent anions, and three new fragment anions were detected: CH(-), C2(-), and C2H(-). These contrasting results for potassium impact and DEA highlight significant differences in the reaction pathways initiated by the two electron delivery processes.


Assuntos
Furanos/química , Potássio/química , Transporte de Elétrons , Modelos Moleculares , Conformação Molecular , Oxigênio/química
15.
J Chem Phys ; 139(24): 244311, 2013 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-24387374

RESUMO

Multi-photon ionization (MPI) of the RNA base uracil has been studied in the wavelength range 220-270 nm, coinciding with excitation to the S2(ππ*) state. A fragment ion at m/z = 84 was produced by 2-photon absorption at wavelengths ≤232 nm and assigned to C3H4N2O(+) following CO abstraction. This ion has not been observed in alternative dissociative ionization processes (notably electron impact) and its threshold is close to recent calculations of the minimum activation energy for a ring opening conical intersection to a σ(n-π)π* closed shell state. Moreover, the predicted ring opening transition leaves a CO group at one end of the isomer, apparently vulnerable to abstraction. An MPI mass spectrum of uracil-water clusters is presented for the first time and compared with an equivalent dry measurement. Hydration enhances certain fragment ion pathways (particularly C3H3NO(+)) but represses C3H4N2O(+) production. This indicates that hydrogen bonding to water stabilizes uracil with respect to neutral excited-state ring opening.


Assuntos
Conformação Molecular , Processos Fotoquímicos , Fótons , Uracila/química , Água/química
16.
Nat Genet ; 22(2): 203-6, 1999 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-10369268

RESUMO

DNA in somatic tissue is characterized by a bimodal pattern of methylation, which is established in the animal through a series of developmental events. In the mouse blastula, most DNA is unmethylated, but after implantation a wave of de novo methylation modifies most of the genome, excluding the majority of CpG islands, which are mainly associated with housekeeping genes. This genomic methylation pattern is broadly maintained during the life of the organism by maintenance methylation, and generally correlates with gene expression. Experiments both in vitro and in vivo indicate that methylation inhibits transcription. It has not yet been possible, however, to determine the role of DNA methylation on specific sequences during normal development. Cis-acting regulatory elements and trans-acting factors appear to be involved in both stage- and tissue-specific demethylation processes. Sp1-like elements have a key role in protecting the CpG island of Aprt (encoding adenine phosphoribosyltransferase) from de novo methylation, and when these elements are specifically mutated, the Aprt CpG island becomes methylated in transgenic mice. We have now characterized an embryo-specific element from the CpG island sequence upstream of Aprt that can protect itself from de novo methylation in transgenic mice as well as reduce methylation of flanking sequences. We placed this element on a removable cassette adjacent to a human HBB (encoding beta-globin) reporter and generated a transgene whose methylation pattern can be switched in vivo. Analysis of globin transcription in this system showed that methylation in cis inhibits gene expression in a variety of tissues, indicating that DNA modification may serve as a global genomic repressor.


Assuntos
Adenina Fosforribosiltransferase/genética , Metilação de DNA , Regulação da Expressão Gênica no Desenvolvimento , Globinas/genética , Transcrição Gênica , Animais , Sequência de Bases , Fosfatos de Dinucleosídeos/genética , Embrião de Mamíferos , Genes Reporter , Humanos , Camundongos , Camundongos Transgênicos , Dados de Sequência Molecular , Mutagênese Insercional , Mapeamento por Restrição , Reação em Cadeia da Polimerase Via Transcriptase Reversa
17.
Front Microbiol ; 14: 1195755, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37389331

RESUMO

A bacterial strain, designated T173T, was previously isolated from a root-nodule of a Melilotus albus plant growing in Canada and identified as a novel Ensifer lineage that shared a clade with the non-symbiotic species, Ensifer adhaerens. Strain T173T was also previously found to harbour a symbiosis plasmid and to elicit root-nodules on Medicago and Melilotus species but not fix nitrogen. Here we present data for the genomic and taxonomic description of strain T173T. Phylogenetic analyses including the analysis of whole genome sequences and multiple locus sequence analysis (MLSA) of 53 concatenated ribosome protein subunit (rps) gene sequences confirmed placement of strain T173T in a highly supported lineage distinct from named Ensifer species with E. morelensis Lc04T as the closest relative. The highest digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of genome sequences of strain T173T compared with closest relatives (35.7 and 87.9%, respectively) are well below the respective threshold values of 70% and 95-96% for bacterial species circumscription. The genome of strain T173T has a size of 8,094,229 bp with a DNA G + C content of 61.0 mol%. Six replicons were detected: a chromosome (4,051,102 bp) and five plasmids harbouring plasmid replication and segregation (repABC) genes. These plasmids were also found to possess five apparent conjugation systems based on analysis of TraA (relaxase), TrbE/VirB4 (part of the Type IV secretion system (T4SS)) and TraG/VirD4 (coupling protein). Ribosomal RNA operons encoding 16S, 23S, and 5S rRNAs that are usually restricted to bacterial chromosomes were detected on plasmids pT173d and pT173e (946,878 and 1,913,930 bp, respectively) as well as on the chromosome of strain T173T. Moreover, plasmid pT173b (204,278 bp) was found to harbour T4SS and symbiosis genes, including nodulation (nod, noe, nol) and nitrogen fixation (nif, fix) genes that were apparently acquired from E. medicae by horizontal transfer. Data for morphological, physiological and symbiotic characteristics complement the sequence-based characterization of strain T173T. The data presented support the description of a new species for which the name Ensifer canadensis sp. nov. is proposed with strain T173T (= LMG 32374T = HAMBI 3766T) as the species type strain.

18.
Spectrochim Acta A Mol Biomol Spectrosc ; 289: 122237, 2023 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-36535224

RESUMO

Absolute cross-section values are reported from high-resolution vacuum ultraviolet (VUV) photoabsorption measurements of gas-phase formic acid (HCOOH) in the photon energy range 4.7-10.8 eV (265-115 nm), together with quantum chemical calculations to provide vertical energies and oscillator strengths. The combination of experimental and theoretical methods has allowed a comprehensive assignment of the electronic transitions. The VUV spectrum reveals various vibronic features not previously reported in the literature, notably associated with (3pa'←10a'), (3p'a'←10a'), (3sa'←2a″) and (3pa'←2a″) Rydberg transitions. The assignment of vibrational features in the absorption bands reveal that the C=O stretching, v3'a', the H'-O-C' deformation, v5'a', the C-O stretching, v6'a', and the O=C-O' deformation, v7'a' modes are mainly active. The measured absolute photoabsorption cross sections have also been used to estimate the photolysis lifetime of HCOOH in the upper stratosphere (30-50 km), showing that solar photolysis is an important sink at altitudes above 30 km but not in the troposphere. Potential energy curves for the lowest-lying electronic excited states, as a function of the C=O coordinate, are obtained employing time dependent density functional theory (TD-DFT). These calculations have shown the relevance of internal conversion from Rydberg to valence character governing the nuclear dynamics, yielding clear evidence of the rather complex multidimensional nature of the potential energy surfaces involved.

19.
Front Mol Biosci ; 9: 887763, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35712354

RESUMO

The rapid development of multidrug-resistant pathogens against conventional antibiotics is a global public health problem. The irrational use of antibiotics has promoted therapeutic limitations against different infections, making research of new molecules that can be applied to treat infections necessary. Antimicrobial peptides (AMPs) are a class of promising antibiotic molecules as they present broad action spectrum, potent activity, and do not easily induce resistance. Several AMPs from scorpion venoms have been described as a potential source for the development of new drugs; however, some limitations to their application are also observed. Here, we describe strategies used in several approaches to optimize scorpion AMPs, addressing their primary sequence, biotechnological potential, and characteristics that should be considered when developing an AMP derived from scorpion venoms. In addition, this review may contribute towards improving the understanding of rationally designing new molecules, targeting functional AMPs that may have a therapeutic application.

20.
Phys Chem Chem Phys ; 13(34): 15657-65, 2011 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-21796297

RESUMO

Ion-pair formation has been studied in hyperthermal (30-100 eV) neutral potassium collisions with gas phase thymine (C(5)H(6)N(2)O(2)) and uracil (C(4)H(4)N(2)O(2)). Negative ions formed by electron transfer from the alkali atom to the target molecule were analysed by time-of-flight (TOF) mass spectrometry. The most abundant product anions are assigned to CNO(-) and (U-H)(-)/(T-H)(-) and the associated electron transfer mechanisms are discussed. Special emphasis is given to the enhancement of ring breaking pathways in the present experiments, notably CNO(-) formation, compared with free electron attachment measurements.


Assuntos
Timina/química , Uracila/química , Transporte de Elétrons , Espectrometria de Massas , Potássio/química
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