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1.
Int J Mol Sci ; 22(2)2021 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-33440692

RESUMO

The early vascular plants in the genus Selaginella, which is the sole genus of the Selaginellaceae family, have an important place in evolutionary history, along with ferns, as such plants are valuable resources for deciphering plant evolution. In this study, we sequenced and assembled the plastid genome (plastome) sequences of two Selaginella tamariscina individuals, as well as Selaginella stauntoniana and Selaginella involvens. Unlike the inverted repeat (IR) structures typically found in plant plastomes, Selaginella species had direct repeat (DR) structures, which were confirmed by Oxford Nanopore long-read sequence assembly. Comparative analyses of 19 lycophytes, including two Huperzia and one Isoetes species, revealed unique phylogenetic relationships between Selaginella species and related lycophytes, reflected by structural rearrangements involving two rounds of large inversions that resulted in dynamic changes between IR and DR blocks in the plastome sequence. Furthermore, we present other uncommon characteristics, including a small genome size, drastic reductions in gene and intron numbers, a high GC content, and extensive RNA editing. Although the 16 Selaginella species examined may not fully represent the genus, our findings suggest that Selaginella plastomes have undergone unique evolutionary events yielding genomic features unparalleled in other lycophytes, ferns, or seed plants.

2.
J Fungi (Basel) ; 6(4)2020 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-33207581

RESUMO

In eukaryotes, the MAP kinase signaling pathway plays pivotal roles in regulating the expression of genes required for growth, development, and stress response. Here, we deleted the mpkB gene (AFLA_034170), an ortholog of the Saccharomyces cerevisiae FUS3 gene, to characterize its function in Aspergillus flavus, a cosmopolitan, pathogenic, and aflatoxin-producing fungus. Previous studies revealed that MpkB positively regulates sexual and asexual differentiation in Aspergillus nidulans. In A. flavus, mpkB deletion resulted in an approximately 60% reduction in conidia production compared to the wild type without mycelial growth defects. Moreover, the mutant produced immature and abnormal conidiophores exhibiting vesicular dome-immaturity in the conidiophore head, decreased phialide numbers, and very short stalks. Interestingly, the ΔmpkB mutant could not produce sclerotia but produced aflatoxin B1 normally. Taken together, these results suggest that the A. flavus MpkB MAP kinase positively regulates conidiation and sclerotia formation but is not involved in the production of secondary metabolites such as aflatoxin B1.

3.
Artigo em Inglês | MEDLINE | ID: mdl-33119482

RESUMO

A Gram-stain-negative, non-pigmented, non-spore-forming, motile, strictly aerobic bacterial strain, designated CAU 1492T, was isolated from a coastal sand dune and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1492T grew optimally at 30 °C, pH 7.0 and in 3 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence of CAU 1492T showed that it formed a distinct lineage within the family Rhodobacteraceae as a separate deep branch, with 96.8 % or lower sequence similarity values to representatives of the genera Marivita, Donghicola, Sulfitobacter, Marinovum, Phaeobacter, Primorskyibacter, Roseovarius and Aestuariihabitans. Strain CAU 1492T was closely related to Marivita geojedonensis DPG-138T (96.8 %), Donghicola eburneus SW-277T (96.7 %), Sulfitobacter porphyrae SCM-1T (96.7 %), Marinovum algicola FF3T (96.6 %) and Aestuariihabitans beolgyonensis BB-MW15T (96.4 %) based on 16S rRNA gene sequences. The major cellular fatty acids of strain CAU 1492T were cyclo-C19 : 0 ω8c and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The polar lipid pattern was composed of phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified aminolipid. The strain contained Q-10 as the sole respiratory quinone. The draft genome of strain CAU 1492T was 4.63 Mb with a DNA G+C content of 63.1 mol%. The genome includes 4292 protein-coding genes and a five rRNA operons. On the basis of the phenotypic, chemotaxonomic and genomic data, strain CAU 1492T represents a novel genus in the family Rhodobacteraceae for which the name Arenibacterium halophilum gen. nov., sp. nov. is proposed. The type strain of Arenibacterium halophilum is CAU 1492T (=KCTC 62998T=NBRC 113696T).

4.
Arch Microbiol ; 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-33057911

RESUMO

A Gram-stain-negative, slightly curved, rod-shaped bacterial strain CAU 1517T was isolated from marine sediment in Busan, the Republic of Korea. The taxonomic position of strain CAU 1517T was investigated via a polyphasic approach comprising phenotypic, chemotaxonomic and phylogenetic properties. Strain CAU 1517T grew optimally at 30 °C, pH 7.5 and in the presence of 7% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain CAU 1517T belongs to the genus Halarcobacter and is most closely related to Halarcobacter bivalviorum LMG 26154T (96.5% similarity). The average nucleotide identity and digital DNA-DNA hybridization values between strain CAU 1517T and members of genus Halarcobacter ranged from were 76.7-78.0% and 19.5-21.2%, respectively. The strain contained menaquinone-6 (MK-6) as the only respiratory quinone, and C16:0, summed feature 3 (C16:1 ω7c/C16:1 ω6c), and summed feature 8 (C18:1ω7c/C18:1ω6c) as the major fatty acids. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified aminophospholipids. The G+C content was 28.2 mol%. Therefore, it has been demonstrated that the isolate represents a novel species of the genus Halarcobacter, for which the name Halarcobacter arenosus sp. nov., is proposed. The type strain is CAU 1517T (=KCTC 72232T =NBRC 113955T).

5.
Medicine (Baltimore) ; 99(40): e22641, 2020 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-33019489

RESUMO

RATIONALE: Rotavirus is routinely diagnosed by the detection of antigens or the viral genome. However, these tests have limitations, in that they do not detect all rotavirus strains. PATIENT CONCERNS: We present a case of a 27-month-old girl who was hospitalized for 4 days with severe gastroenteritis, including high fever, vomiting, diarrhea, mild dehydration, and periumbilical pain. Notably, the patient previously received the Rotarix vaccine. DIAGNOSES: The laboratory tests were negative for rotavirus, astrovirus, adenovirus, and norovirus as well as common diarrhea-causing bacteria. Human-bovine recombinant rotavirus was detected by MinION sequencing. INTERVENTIONS: To investigate the cause agents from the unexplained severe gastroenteritis infant, the stool sample was prepared by random amplification for Nanopore MinION sequencing. OUTCOMES: Treatment through the administration of ORS solution and galtase powder with probiotics was successful after the diagnosis of unusual rotavirus infection. LESSONS: This case report is the first detection of an unusual human-bovine recombinant rotavirus in an idiopathic gastroenteritis using Nanopore MinION sequencing.


Assuntos
Gastroenterite/virologia , Sequenciamento por Nanoporos/métodos , Infecções por Rotavirus/diagnóstico , Vacinas contra Rotavirus/efeitos adversos , Rotavirus/genética , Dor Abdominal , Doença Aguda , Pré-Escolar , Desidratação/etiologia , Diarreia/etiologia , Fezes/virologia , Feminino , Febre/etiologia , Hidratação/métodos , Gastroenterite/patologia , Gastroenterite/terapia , Humanos , Probióticos/uso terapêutico , Rotavirus/isolamento & purificação , Infecções por Rotavirus/complicações , Infecções por Rotavirus/virologia , Índice de Gravidade de Doença , Resultado do Tratamento , Vacinação/efeitos adversos , Vacinas Atenuadas/efeitos adversos , Vômito/etiologia
6.
J Korean Med Sci ; 35(34): e281, 2020 Aug 31.
Artigo em Inglês | MEDLINE | ID: mdl-32864904

RESUMO

On October 4, 2018, an outbreak of gastroenteritis associated with sapovirus occurred among elementary school students in Gyeonggi-do, Korea. Epidemiologic studies were conducted in a retrospective cohort approach. Using self-administered questionnaires, we collected information on symptoms and food items consumed. Of the 999 subjects, 17 developed patients that met the case definition. The main symptom was vomiting (100%), and the symptomatic age was 6-12 years. Positive samples were identified by conventional reverse transcription polymerase chain reaction for sequencing. They were classified into genotype GI.3 by phylogenetic analysis. This is the first report of an outbreak associated with sapovirus GI.3 in Korea.

7.
J Dairy Sci ; 103(11): 9803-9814, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32896398

RESUMO

Obesity, which has become a major public health problem, can arise from complex dyslipidemia, insulin resistance, and immune responses, among other mechanisms. Some Lactobacillus strains effectively ameliorate obesity; however, the beneficial effects of Lactococcus spp., which are often used as dairy starters, remain unclear. In the present study, we evaluated the efficacy of Lactococcus chungangensis CAU 28 using the 3T3-L1 cell line and obese mice fed a high-fat diet. Overall, administration of Lc. chungangensis CAU 28 effectively resolved obesity associated with weight gain and lipid accumulation. In differentiated 3T3-L1 cells, Lc. chungangensis CAU 28 treatment significantly diminished the total lipid quantity, inhibited triglyceride formation, and prevented the proliferation of adipogenic transcription factors (fatty acid synthase, adiponectin, peroxisome proliferator-activated receptor-gamma, and CCAAT-enhancer-binding protein-α) associated with lipid accumulation. In the obesity mouse model, wherein the intake of Lc. chungangensis CAU 28 effectively reduced body weight gain, along with fat differentiation and accumulation (white fat; abdominal and subcutaneous). Furthermore, Lc. chungangensis CAU 28 increased serum adiponectin levels, decreased serum leptin levels, and effectively regulated adipokine secretion. It also increased the high-density lipoprotein:cholesterol ratio, reduced total cholesterol and triglyceride levels, reduced the low-density lipoprotein:cholesterol ratio, and affected obesity-regulated inflammatory cytokines IL-6, tumor necrosis factor-α, IFN-γ, and IL-1ß. Additionally, Lc. chungangensis CAU 28 was associated with an increase in the CD3+CD4+CD8- phenotype among obese mice. Thus, the administration of Lc. chungangensis CAU 28 induced antiobesity effects, suggesting potential applications of this species as a supplement for obesity mitigation.

8.
Medicine (Baltimore) ; 99(38): e22192, 2020 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-32957348

RESUMO

BACKGROUND: Rotavirus is one of the most common causes of infantile enteritis. In common enterocolitis, probiotic organisms, including Lactobacilli, are effective in treating diarrhea. A new species, Lactobacillus plantarum (LRCC5310), which was shown to inhibit the adherence and proliferation of rotavirus in the small intestine through animal experiments, was investigated for the efficacy and safety of patients with rotaviral enteritis. METHODS: LRCC5310 (Group I) and control (Group II) groups consisting of children who were hospitalized for rotaviral enteritis were compared, and the medical records of patients (Group III) who were hospitalized for rotaviral enteritis during the same study period were retrospectively analyzed. Clinical symptoms were compared and stool samples were collected to compare changes in virus multiplication between Groups I and II. RESULTS: Groups I, II, and III comprised 15, 8, and 27 children, respectively. There were no differences in clinical information among the groups at admission. In Group I, a statistically significant improvement was noted in the number of patients with diarrhea, number of defecation events on Day 3, and total diarrhea period as opposed to Group II (P = .033, P = .003, and P = .012, respectively). The improvement of Vesikari score in Group I was greater than that in the other groups (P = .076, P = .061, and P = .036, respectively). Among rotavirus genotypes, 9 (22.5%) strains and 8 (20.0%) strains belonged to the G9P8 and G1P8 genotypes, respectively. The virus reduction effect, as confirmed via stool specimens, was also greater in Group I. No significant side effects were noted in infants. CONCLUSION: LRCC5310 improved clinical symptoms, including diarrhea and Vesikari score, and inhibited viral proliferation in rotaviral gastroenteritis.


Assuntos
Enterite/terapia , Lactobacillus plantarum , Probióticos/uso terapêutico , Infecções por Rotavirus/terapia , Criança , Pré-Escolar , Enterite/epidemiologia , Enterite/virologia , Fezes/virologia , Feminino , Humanos , Lactente , Masculino , República da Coreia/epidemiologia , Estudos Retrospectivos , Infecções por Rotavirus/epidemiologia
9.
Sci Rep ; 10(1): 15836, 2020 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-32985574

RESUMO

Rotavirus is the leading cause of acute gastroenteritis among young children worldwide. However, agents specifically designed to treat rotavirus infection have not been developed yet. In this study, the anti-rotavirus and anti-inflammatory effects of genipin, a chemical compound found in the fruit of Gardenia jasminoides, were evaluated. Genipin had an antiviral effect against the human rotavirus Wa and SA-11 strains in vitro, and it inhibited two distinct stages of the viral replication cycle: attachment and penetration (early stage) in pre-treatment and assembly and release (late stage) in post-treatment. Additionally, genipin downregulated nitric oxide synthase and pro-inflammatory cytokines in lipopolysaccharide-stimulated RAW264.7 cells and rotavirus-infected Caco-2 cells. Oral administration of genipin before and after viral infection with the murine rotavirus epidemic diarrhea of infant mice strain led to a reduced duration of diarrhea and faecal viral shedding and to decreased destruction of the enteric epithelium. Genipin could have potential as a natural compound with preventive and therapeutic effects against infection and colitis caused by rotavirus.

10.
Arch Microbiol ; 202(10): 2655-2661, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32715322

RESUMO

A Gram stain-negative, aerobic, non-motile, short, rod-shaped bacterial strain CAU 1482T was isolated from coal mine wastewater in Hongcheon, Korea. It grew well at 30 °C, pH 8.5, 2% NaCl (w/v). 16S rRNA-based phylogeny indicated that CAU 1482T forms a distinct lineage within Aureimonas with high similarity to Aureimonas frigidaquae CW5T (98.2%), Aureimonas altamirensis S21BT (98.0%), and Aureimonas glaciei B5-2T (96.3%). The predominant cellular fatty acids were C18:1 2-OH, C16:0, C18:1 ω7c, and/or C18:1 ω6c (summed feature 8), with Q-10 as the major isoprenoid quinone. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified aminolipids, and three unidentified lipids. The 3.9-Mb genome included 8 contigs and 3599 protein-coding genes with a 56.7 mol% G + C content. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CAU 1482T and closely related strains of A. frigidaquae CW5T and A. altamirensis S21BT were 72.2‒72.4% and 18.7‒18.8%, respectively. These phenotypic, chemotaxonomic, and phylogenetic data support CAU 1482T as a novel Aureimonas species, for which the name Aureimonas fodinaquatilis sp. nov. is proposed. The type strain is CAU 1482T (= KCTC 62995T = NBRC 113692T).


Assuntos
Alphaproteobacteria/classificação , Filogenia , Águas Residuárias/microbiologia , Alphaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Composição de Bases , Carvão Mineral , Ácidos Graxos/análise , Genoma Bacteriano/genética , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Especificidade da Espécie
11.
ACS Appl Mater Interfaces ; 12(31): 35098-35104, 2020 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-32648732

RESUMO

High-Ni cathode materials with a layered structure generally suffer from structural instability induced by a highly reactive Ni component, especially at the surface. Crystalline LiNbO3, with excellent thermal stability and ionic conductivity, has the potential to considerably enhance the interfacial stability of these cathode materials. By optimizing the crystalline coating of bifunctional LiNbO3 on a high-Ni cathode material, we are able to improve cycle performance and rate capability by minimizing the direct exposure of Ni with electrolytes. Since a LiNbO3 coating layer directly affects electrochemical performance, we also focus on the correlation of LiNbO3 crystallinity with electrochemical behaviors of Li+ in the cathode materials. We show that the Li+ conducting behaviors are closely related to the crystallinity of LiNbO3. Highly crystalline LiNbO3 effectively suppresses the structural changes of the cathode materials by facilitating strain relaxation induced by repeated Li+ intercalation and deintercalation into and from the host structure. Moreover, it offers strong enhancement in mechanical and thermal stabilities at elevated temperatures above 60 °C. In this regard, this research provides a practical solution for successfully utilizing high-Ni layered cathode materials in commercial LIBs.

12.
Int J Syst Evol Microbiol ; 70(8): 4562-4568, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32618560

RESUMO

A Gram-stain-negative, yellow-pigmented, non-spore-forming, non-motile, rod-shaped, catalase-positive, strictly aerobic bacterial strain, designated CAU 1491T, was isolated from seawater and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1491T grew optimally at 30 °C, pH 7.5 and in 2.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence of CAU 1491T showed that it formed a distinct lineage within the family Flavobacteriaceae as a separate deep branch, with 97.0 % or lower sequence similarity to representatives of the genera Lacinutrix, Gaetbulibacter and Aquibacter. The major cellular fatty acids of strain CAU 1491T were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylserine, phosphatidylethanolamine and an unidentified phospholipid. The strain contained MK-6 as the sole respiratory quinone. Genome sequencing revealed that strain CAU 1491T has a genome size of 3.13 Mbp and a G+C content of 32.4 mol%. On the basis of the phenotypic, chemotaxonomic and genomic data, strain CAU 1491T represents a new genus and species in the family Flavobacteriaceae for which the name Pontimicrobium aquaticum gen. nov., sp. nov. is proposed. The type strain of Pontimicrobium aquaticum is CAU 1491T (=KCTC 72003T=NBRC 113695T).


Assuntos
Flavobacteriaceae/classificação , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
13.
Int J Biol Macromol ; 161: 1240-1246, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32526301

RESUMO

This study was conducted to investigate the degradation characteristics of kraft lignin (KL) during peracetic acid (PAA) treatment, and to produce potentially valuable polymers of low molecular weight lignin by controlling the reaction conditions. For the peracetic acid treatment, acetic acid (AA) and hydrogen peroxide (HP) were directly mixed at ratios of 4:1, 1:1, and 1:4 (v/v) and employed as reaction media. After PAA treatment of kraft lignin at 80 °C, complete dissolution of the lignin and reduction in the molecular weight were observed. When the PAA reaction was performed at high HP concentration (1:4, v/v), the aromatic lignin skeleton opened and converted to a structure containing large amounts of carboxyl groups. On the other hand, the treatment at high AA concentration (4:1, v/v) decomposed lignin while maintaining its aromatic structure. Hence, we demonstrated that the selective production of lignin-derived polymers can be controlled depending on PAA and HP concentrations.

14.
FEMS Microbiol Lett ; 367(13)2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32589213

RESUMO

A Gram stain-negative, aerobic, motile, rod-shaped bacterial strain, designated CAU 1509T, was isolated from marine sediment, and its taxonomic position was determined using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1509T formed a distinct lineage within the genus Sinimarinibacterium with the highest 16S rRNA gene sequence similarity to Sinimarinibacterium flocculans NH6-24T (97.0%). Similar to another member of Sinimarinibacterium, ubiquinone-8 (Q-8) was the predominant quinone, whereas C16:0, summed feature 3 (C16:1ω7c/ω6c) and summed feature 8 (C18:1ω7c/ω6c) were the major cellular fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, four unidentified glycolipids and three unidentified aminolipids. Strain CAU 1509T has a genome of 4.54 Mb, including 4251 coding sequences, 6 rRNAs and 50 tRNAs, with a genomic DNA G+C content of 63.2 mol%. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain CAU 1509T should be classified as a novel species of the genus Sinimarinibacterium, for which the name Sinimarinibacterium arenosum sp. nov. is proposed. The type strain is CAU 1509T (= KCTC 72000T = NBRC 113698T).

15.
FEMS Microbiol Lett ; 367(13)2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32578849

RESUMO

A novel proteobacterial bacterium, designated strain CAU 1489T, was isolated from Jeju Island, Republic of Korea. Cells were strictly anaerobic, Gram stain-negative, cream-pigmented, non-spore-forming, motile and short rod-shaped. Strain CAU 1489T exhibited the highest 16S rRNA gene sequence similarity (98.2%) to Nitratireductor mangrovi SY7T. Multilocus sequence analysis of 16S rRNA and four housekeeping genes (rpoB, rpoC, gyrB and dnaK) indicated that CAU 1489T represents a distinct branch within Nitratireductor. The whole genome was 4.8 Mb with a G + C content of 64.7 mol%, including protein-coding genes related to the function terms amino acids and derivatives, nucleotides and nucleosides, protein metabolism, carbohydrates and cofactors, vitamins, prosthetic groups and pigments. The major fatty acids were 11-methyl C18:1ω7c, cyclo- C19:0ω8c, iso-C17:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c), and the predominant respiratory quinone was Q-10. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids. Digital DNA-DNA hybridization and average nucleotide identity values were 19.4-22.0% and 72.4-79.1%, respectively. On the basis of taxonomic characterization, strain CAU 1489T constitutes a novel species, for which the name Nitratireductor arenosus sp. nov. is proposed. The type strain is CAU 1489T ( = KCTC 62997T = NBRC 113694T).

16.
Genes Genomics ; 42(5): 553-570, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32200544

RESUMO

BACKGROUND: Chloroplasts are a common character in plants. The chloroplasts in each plant lineage have shaped their own genomes, plastomes, by structural changes and transferring many genes to nuclear genomes during plant evolution. Some plastid genes have introns that are mostly group II introns. OBJECTIVE: This study aimed to get genomic and evolutionary insights on the plastomes from green algae to flowering plants. METHODS: Plastomes of 115 species from green algae, bryophytes, pteridophytes (spore bearing vascular plants), gymnosperms, and angiosperms were mined from NCBI organelle genome database. Plastome structure, gene contents and GC contents were analyzed by the in-house developed Phyton code. Intronic features including presence/absence, length, intron phases were analyzed by manually in the annotated information in NCBI. RESULTS: The canonical quadripartite structures were retained in most plastomes except of a few plastomes that had lost an invert repeat (IR). Expansion or reduction or deletion of IRs resulted in the length variation of the plastomes. The number of protein coding genes ranged from 40 to 92 with an average 79.43 ± 5.84 per plastome and gene losses were apparent in specific lineages. The number of trn genes ranged from 13 to 33 with an average 21.19 ± 2.42 per plastome. Ribosomal RNA genes, rrn, were located in the IRs so that they were present in a duplicate except of the species that had lost one of the IR. GC contents were variable from 24.9 to 51.0% with an average 38.21 ± 3.27%, indicating bias to high AT contents. Plastid introns were present in 18 protein coding genes, six trn genes, and one rrn gene. Intron losses occurred among the orthologous genes in different plant lineages. The plastid introns were long compared with the nuclear introns, which might be related with the spliceosome nuclear introns and self-splicing group II plastid introns. The trnK-UUU intron contained the maturase encoding matK gene except in the chlorophyte algae and monilophyte ferns in which the trnK-UUU was lost, but matK retained. There were many annotation artefacts in the intron positions in the NCBI database. In the analysis of intron phases, phase 0 introns were more frequent than those of phase 2 and 3 introns. Phase polymorphism was observed in the introns of clpP which was derived from nucleotide insertion. Plastid trn introns were long compared to the archaeal or eukaryotic nuclear tRNA introns. Of the six plastid trn introns, one was at the D loop and other five were at the anticodon loop. The insertion sites were conserved among the trn genes in archaea, eukaryotic nuclear and plastid tRNA genes. CONCLUSIONS: Current study refurbrished the previous findings of structural variations, gene contents, and GC contents of the chloroplast genomes from green algae to flowering plants. The study also included some noble findings and discussions on the plastome introns including their length variations and phase variation. We also presented and corrected some false annotations on the introns in protein coding and tRNA genes in the genome database, which might be confirmed by the chloroplast transcriptome analysis in the future.

17.
Int J Syst Evol Microbiol ; 70(5): 3055-3061, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32195650

RESUMO

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strain, designated CAU 1488T, was isolated from tidal flat sediment, and its taxonomic position was investigated using a polyphasic approach. The organism grew optimally at a temperature of 30 °C, at pH 7.0-7.5 and in the presence of 0-6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1488T forms a lineage distinct from Ruegeria marisrubri ZGT 118T (97.9 %), Ruegeria marina ZH17T (97.6 %), Ruegeria lacuscaerulensis ITI 1157T (97.5 %), Ruegeria pomeroyi DSS-3T (97.1 %), Ruegeria profundi ZGT108T (97.0 %), Ruegeria intermedia CC-GIMAT-2T (96.8 %), Ruegeria atlantica CECT 4292T (96.7 %) and Ruegeria kandeliae J95T (95.9 %). Genome sequencing revealed that CAU 1488T had a genome size of 4.23 Mbp and a G+C content of 63.2 mol%. Overall genome related indexes including average nucleotide identity and digital DNA-DNA hybridization values were 75.0-83.0 % and 26.2 %, which are below the cutoffs of 95 and 70 %, respectively, indicating that strain CAU 1488T represents a distinct species from the members of the genus Ruegeria. The predominant quinone was ubiquinone-10 (Q-10). The major fatty acids were summed feature 8 (C18 : 1 ω7c/ω6c; 60.7 %) and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and unidentified aminolipids. On the basis of phenotypic, chemotaxonomic and genomic data, strain CAU 1488T constitutes a novel species of the genus Ruegeria, for which the name Ruegeria sediminis sp. nov. is proposed. The type strain is CAU 1488T (=KCTC 62996T=NBRC 113693T).


Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Rhodobacteraceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Rhodobacteraceae/isolamento & purificação , Água do Mar/microbiologia , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
18.
Genomics Inform ; 17(3): e27, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31610623

RESUMO

Supernumerary B chromosomes were found in Lilium amabile (2n = 2x = 24), an endemic Korean lily that grows in the wild throughout the Korean Peninsula. The extra B chromosomes do not affect the host-plant morphology; therefore, whole transcriptome analysis was performed in 0B and 1B plants to identify differentially expressed genes. A total of 154,810 transcripts were obtained from over 10 Gbp data by de novo assembly. By mapping the raw reads to the de novo transcripts, we identified 7,852 differentially expressed genes (log2FC > |10|), in which 4,059 and 3,794 were up- and down-regulated, respectively, in 1B plants compared to 0B plants. Functional enrichment analysis revealed that various differentially expressed genes were involved in cellular processes including the cell cycle, chromosome breakage and repair, and microtubule formation; all of which may be related to the occurrence and maintenance of B chromosomes. Our data provide insight into transcriptomic changes and evolution of plant B chromosomes and deliver an informative database for future study of B chromosome transcriptomes in the Korean lily.

19.
J Dairy Sci ; 102(12): 10737-10747, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31521345

RESUMO

Alcoholic liver disease (ALD) is correlated with alcohol consumption, and ALD progression depends on various factors. Some lactic acid bacteria (LAB) are beneficial for mitigating ALD. However, the valuable effects of LAB-derived dairy products remain unclear. Here, we evaluated the effects of Lactococcus chungangensis CAU 1447 dry cells (CAU 1447) and cream cheese derived from CAU 1447 on ALD progression following long-term alcohol consumption in rats. Oral administration of CAU 1447 and CAU 1447 cream cheese significantly reduced alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, and triglyceride levels. We found that CAU 1447 and CAU 1447 cream cheese downregulated mRNA encoding various cytokines and antioxidative factors in the liver. Oral CAU 1447 cream cheese administration increased short-chain fatty acid, butyrate, and acetate levels in feces. Thus, administration of CAU 1447 and CAU 1447 cream cheese induced hepatoprotective effects, indicating potential applications as a supplement for ALD mitigation.


Assuntos
Lactococcus , Hepatopatias Alcoólicas/terapia , Probióticos/uso terapêutico , Animais , Fatores Biológicos/uso terapêutico , Queijo/microbiologia , Suplementos Nutricionais , Fezes/química , Fermentação , Masculino , Substâncias Protetoras/uso terapêutico , Ratos , Ratos Sprague-Dawley
20.
Bioresour Technol ; 291: 121913, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31387050

RESUMO

For improving the economic efficiency of the biorefining concept, selective decomposition and separation of biomass components is indispensable. In this respect, a sequential pretreatment process consisting of liquid hot water treatment and diluted peracetic acid (PAA) treatment was proposed for total utilization of lignocellulosic woody biomass. During the liquid hot water treatment, hemicellulose can be decomposed efficiently without significant loss of cellulose and lignin, implying the possibility for xylooligomer production by thermochemical treatment. In the PAA treatment, lignin was successfully degraded and liquefied using a 50% diluted PAA solvent, suggesting the possibility of dicarboxylic acid production. After the sequential process proposed in this study, the cellulose accessibility to the enzyme could be maximized by inducing selective deconstruction of hemicellulose and lignin.


Assuntos
Lignina , Polissacarídeos , Biomassa , Hidrólise
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