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1.
BMC Med Genomics ; 14(1): 144, 2021 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-34074255

RESUMO

BACKGROUND: Transmission within families and multiple spike protein mutations have been associated with the rapid transmission of SARS-CoV-2. We aimed to: (1) describe full genome characterization of SARS-CoV-2 and correlate the sequences with epidemiological data within family clusters, and (2) conduct phylogenetic analysis of all samples from Yogyakarta and Central Java, Indonesia and other countries. METHODS: The study involved 17 patients with COVID-19, including two family clusters. We determined the full-genome sequences of SARS-CoV-2 using the Illumina MiSeq next-generation sequencer. Phylogenetic analysis was performed using a dataset of 142 full-genomes of SARS-CoV-2 from different regions. RESULTS: Ninety-four SNPs were detected throughout the open reading frame (ORF) of SARS-CoV-2 samples with 58% (54/94) of the nucleic acid changes resulting in amino acid mutations. About 94% (16/17) of the virus samples showed D614G on spike protein and 56% of these (9/16) showed other various amino acid mutations on this protein, including L5F, V83L, V213A, W258R, Q677H, and N811I. The virus samples from family cluster-1 (n = 3) belong to the same clade GH, in which two were collected from deceased patients, and the other from the survived patient. All samples from this family cluster revealed a combination of spike protein mutations of D614G and V213A. Virus samples from family cluster-2 (n = 3) also belonged to the clade GH and showed other spike protein mutations of L5F alongside the D614G mutation. CONCLUSIONS: Our study is the first comprehensive report associating the full-genome sequences of SARS-CoV-2 with the epidemiological data within family clusters. Phylogenetic analysis revealed that the three viruses from family cluster-1 formed a monophyletic group, whereas viruses from family cluster-2 formed a polyphyletic group indicating there is the possibility of different sources of infection. This study highlights how the same spike protein mutations among members of the same family might show different disease outcomes.


Assuntos
COVID-19/epidemiologia , RNA Viral/genética , SARS-CoV-2/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19/patologia , COVID-19/virologia , Criança , Família , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Indonésia/epidemiologia , Masculino , Pessoa de Meia-Idade , Mutação , Filogenia , RNA Viral/química , SARS-CoV-2/classificação , SARS-CoV-2/isolamento & purificação , Índice de Gravidade de Doença , Glicoproteína da Espícula de Coronavírus/genética , Glicoproteína da Espícula de Coronavírus/metabolismo , Sequenciamento Completo do Genoma
2.
Sci Total Environ ; 783: 147094, 2021 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-34088141

RESUMO

The understanding of sub-surface soil microbial diversity is limited at both saline and hypersaline ecosystems, even though salinity is found to affect the microbial community in aqueous and terrestrial environment. In this study, a phylo-taxonomy analysis as well as the functional characteristics of microbial community of flat salt basin of White Rann of Kachchh (WR), Gujarat, India was performed along the natural salinity gradient. The high throughput sequencing approach has revealed the numerical abundance of bacteria relative to the archaea. Salinity, TOC, EC and sulphate concentration might be the primary driver of the community distribution along the transect at WR. The much anticipated effect of salinity gradient on the microbial composition surprisingly turned out to be more speculative, with little variance in the community composition along the spatial distance of WR. The metabolic pathways involved in energy metabolism (like carbon, nitrogen, sulphur) along with environmental adaptive genes (like osmotic and oxidative stress response, heat and cold shock genes clusters) were abundantly annotated from shot-gun metagenomic study. The carbonic anhydrase harbouring bacteria Bacillus sp. DM4CA1 was isolated from WR, having a catalytic ability for converting the gaseous carbon dioxide in presence of calcium carbonate into calcite at 25 % higher rate as compared to non-harbouring strains. The enzyme has a role in multiple alternative pathways in microbial metabolism. With the array of results obtained, the study could become the new reference for understanding the diversity structure and functional characteristics of the microbial community of terrestrial saline environment.


Assuntos
Archaea , Bactérias , Archaea/genética , Bactérias/genética , Índia , Filogenia , RNA Ribossômico 16S , Salinidade , Microbiologia do Solo
3.
BMC Genomics ; 22(1): 415, 2021 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-34090335

RESUMO

BACKGROUND: Basic helix-loop-helix (bHLH) is a superfamily of transcription factors that is widely found in plants and animals, and is the second largest transcription factor family in eukaryotes after MYB. They have been shown to be important regulatory components in tissue development and many different biological processes. However, no systemic analysis of the bHLH transcription factor family has yet been reported in Sorghum bicolor. RESULTS: We conducted the first genome-wide analysis of the bHLH transcription factor family of Sorghum bicolor and identified 174 SbbHLH genes. Phylogenetic analysis of SbbHLH proteins and 158 Arabidopsis thaliana bHLH proteins was performed to determine their homology. In addition, conserved motifs, gene structure, chromosomal spread, and gene duplication of SbbHLH genes were studied in depth. To further infer the phylogenetic mechanisms in the SbbHLH family, we constructed six comparative syntenic maps of S. bicolor associated with six representative species. Finally, we analyzed the gene-expression response and tissue-development characteristics of 12 typical SbbHLH genes in plants subjected to six different abiotic stresses. Gene expression during flower and fruit development was also examined. CONCLUSIONS: This study is of great significance for functional identification and confirmation of the S. bicolor bHLH superfamily and for our understanding of the bHLH superfamily in higher plants.


Assuntos
Sorghum , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Genoma de Planta , Filogenia , Sorghum/genética , Estresse Fisiológico/genética
4.
Artigo em Inglês | MEDLINE | ID: mdl-34097596

RESUMO

A polyphasic approach was applied to investigate the diversity of microbiota that evolved during cold storage beef ripening. Isolate V4/DAB/S4/2aT with a unique BOX-rep-PCR fingerprint profile revealed more than 99 % nucleotide identities upon pairwise comparisons of 16S rDNA sequences from the type strains Pseudomonas versuta DSM 101070T, Pseudomonas saxonica DSM 108989T, Pseudomonas deceptionensis DSM 26521T and Pseudomonas weihenstephanensis DSM 29166T, placing it within the Pseudomonas fragi / lundensis branch of the genus Pseudomonas. Additional rpoB based comparison revealed P. versuta DSM 101070T as the nearest relative, with 98.5 % nucleotide identity. Calculation of ANIb values of the V4/DAB/S4/2aT draft genome identified P. versuta DSM 101070T with 90.1 %, P. deceptionensis DSM 26521T with 85.1 %, P. fragi DSM 3456T with 84.4 %, Pseudomonas psychrophila DSM 17535T and Pseudomonas bubulae DSM 107389T with 84.2 % similarities each. Pairwise genome-to-genome distance calculations [digital DNA-DNA hybridization (dDDH)] resulted in values of 47.1, 35.1, 34.8, 34.2 and 34.1 %, respectively. A second isolate was detected years later in ground beef and showed ANIb values of 99.3 % and dDDH of 96.1 % relatedness to V4/DAB/S4/2aT. The DNA G+C content was 58.6 mol% for both isolates. The predominant cellular fatty acids of V4/DAB/S4/2aT were C16 : 0, C18 : 1ω7c, C17 : 0 cyclo and a summed feature containing C16 : 1ω7c and/or C15 : 0 iso 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, the major respiratory quinone was Q9, with a small portion of Q8. The combined data on genotypic and phenotypic features support the proposal of a novel species, for which the name Pseudomonas paraversuta sp. nov. is proposed. The type strain is V4/DAB/S4/2aT (=DSM 111361T=LMG 31844T) and a second isolate is UBT376 (=DSM 111360=LMG 31845).


Assuntos
Microbiologia de Alimentos , Filogenia , Pseudomonas/classificação , Carne Vermelha/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , Bovinos , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Alemanha , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pseudomonas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
5.
Artigo em Inglês | MEDLINE | ID: mdl-34097598

RESUMO

In Iran, polyphasic studies of unicellular cyanobacteria are still scarce, with more emphasis being placed on filamentous cyanobacteria in paddy fields and fresh water regions. In an effort to increase the knowledge of the diversity of unicellular cyanobacteria from paddy fields in Iran, we have isolated and characterized a new unicellular cyanobacterium strain. The strain was studied using a polyphasic approach based on morphological, ecological and phylogenetic analyses of the 16S-23S ITS rRNA gene region. Complementarily, we have searched for the presence of cyanotoxin genes and analysed the pigment content of the strain. Results showed that the strain was morphologically indistinguishable from the genus Chroococcus, but phylogenetic analyses based on the Bayesian inference and maximum-likelihood methods placed the strain in a separated monophyletic and highly supported (0.99/98, posterior probability/maximum-likelihood) genus-level cluster, distant from Chroococcus sensu stricto and with Chalicogloea cavernicola as sister taxa. The calculated p-distance for the 16S rRNA gene also reinforced the presence of a new genus, by showing 92 % similarity to C. cavernicola. The D1-D1', Box-B and V3 ITS secondary structures showed the uniqueness of this strain, as it shared no similar pattern with closest genera within the Chroococcales. For all these reasons, and in accordance with the International Code of Nomenclature for Algae, Fungi and Plants, we here proposed the description of a new genus with the name Alborzia gen. nov. along with the description of a new species, Alborzia kermanshahica sp. nov. (holotype: CCC1399-a; reference strains CCC1399-b; MCC 4116).


Assuntos
Cianobactérias/classificação , Água Doce/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , Teorema de Bayes , Cianobactérias/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Irã (Geográfico) , Oryza , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
6.
Mol Biol (Mosk) ; 55(3): 362-391, 2021.
Artigo em Russo | MEDLINE | ID: mdl-34097673

RESUMO

WOX (WUSCHEL-RELATED HOMEOBOX) is a family of homeodomain-containing transcription factors in plants. WOX proteins maintain the activity of different types of meristems and regulate the formation of plant organs, controlling cell proliferation and differentiation. Study of the WOX family is important for the development of plant transformation and genome editing techniques. Here we review the functions of the WOX transcription factors as well as their targets, partners, and regulators. The WOX family can be divided into three phylogenetically distinct clades; so-called ancient, intermediate, and WUS clade; each clade is covered in a separate section. The WOX genes of Arabidopsis thaliana are described most comprehensively, with their orthologs in other plant species also considered. Summary tables with the described targets, regulators and partners of WOX family members are provided.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Regulação da Expressão Gênica de Plantas , Proteínas de Homeodomínio/genética , Meristema/metabolismo , Filogenia , Proteínas de Plantas/genética
7.
Mol Biol (Mosk) ; 55(3): 431-440, 2021.
Artigo em Russo | MEDLINE | ID: mdl-34097678

RESUMO

This paper reports the analysis of the nucleotide sequences of the 5'-untranslated region (5'-UTR) of tick-borne encephalitis virus (TBEV) genomic RNA isolated from 39 individual taiga ticks collected in several regions of Northern Eurasia. The sequences of 5'-UTRs of the Siberian and Far East TBEV genotypes were 89% and 95% identical to the prototype strains (Zausaev and 205), respectively. The detected nucleotide substitutions were typical for these two TBEV genotypes, which made possible unambiguous identification. Both conservative and variable motifs were detected in the 5'-UTR RNA. The B2, C1, and C2 elements of the Y-shaped 5'-UTR structure and the presumable viral RNA-dependent RNA-polymerase binding site were the most variable. The A2, CS A, CS В elements as well as the start codon were conservative. Interestingly, five substitutions in the 5'-UTR C1 variable element of the TBEVs isolated in different geographical regions were strictly conservative, while 11 different substitutions were detected in this element among the laboratory TBEV variants. A little less that a third of all nucleotide substitutions were mapped outside the main elements of the Y-shaped structure. In general, nucleotide substitutions were localized to stem structures, not being found in the hairpin regions of the TBEV 5'-UTR. The results indicated significant variability of the genomic RNA 5'-UTR in the TBEV laboratory strains and field isolates obtained from different geographical regions. It has been suggested that genetic variability of 5'-UTR is characteristic of the TBEV genome 5'-UTR organization and may serve as a structural basis for virus efficient replication in various avian, mammalian, and ixodic tick cells.


Assuntos
Vírus da Encefalite Transmitidos por Carrapatos , Encefalite Transmitida por Carrapatos , Ixodes , Animais , Sequência de Bases , Vírus da Encefalite Transmitidos por Carrapatos/genética , Encefalite Transmitida por Carrapatos/genética , Genoma Viral/genética , Filogenia , RNA Viral/genética
8.
Genes (Basel) ; 12(6)2021 05 27.
Artigo em Inglês | MEDLINE | ID: mdl-34072181

RESUMO

The genomic diversity of SARS-CoV-2 has been a focus during the ongoing COVID-19 pandemic. Here, we analyzed the distribution and character of emerging mutations in a data set comprising more than 95,000 virus genomes covering eight major SARS-CoV-2 lineages in the GISAID database, including genotypes arising during COVID-19 therapy. Globally, the C>U transitions and G>U transversions were the most represented mutations, accounting for the majority of single-nucleotide variations. Mutational spectra were not influenced by the time the virus had been circulating in its host or medical treatment. At the amino acid level, we observed about a 2-fold excess of substitutions in favor of hydrophobic amino acids over the reverse. However, most mutations constituting variants of interests of the S-protein (spike) lead to hydrophilic amino acids, counteracting the global trend. The C>U and G>U substitutions altered codons towards increased amino acid hydrophobicity values in more than 80% of cases. The bias is explained by the existing differences in the codon composition for amino acids bearing contrasting biochemical properties. Mutation asymmetries apparently influence the biochemical features of SARS CoV-2 proteins, which may impact protein-protein interactions, fusion of viral and cellular membranes, and virion assembly.


Assuntos
COVID-19/virologia , Genoma Viral , Interações Hidrofóbicas e Hidrofílicas , Mutação , SARS-CoV-2/genética , Proteínas Virais/química , Proteínas Virais/genética , Desaminases APOBEC , Alelos , Substituição de Aminoácidos , Aminoácidos/química , Aminoácidos/genética , Evolução Molecular , Variação Genética , Genótipo , Interações Hospedeiro-Patógeno , Humanos , Filogenia , Polimorfismo de Nucleotídeo Único , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética
9.
J Pak Med Assoc ; 71(5): 1467-1471, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-34091636

RESUMO

In December 2016 physicians in Karachi, Pakistan,witnessed an increase in patients presenting with febrile illness and severe polyarthralgia. Subsequently, chikungunya virus (CHIKV)) was isolated from three patients. This virus was sequenced and compared with other isolates of CHIKV obtained in India and Pakistan during recent outbreaks. Phylogenetic analysis indicated that the Karachi isolates were most similar to the East Central South African CHIKV lineage and showed sequence homology to isolates obtained in other parts of Pakistan and India. More importantly, two of the CHIKV isolates had a nucleotide substitution in the E1 gene corresponding to an amino acid change at chain F portion of the E1 protein.


Assuntos
Febre de Chikungunya , Febre de Chikungunya/epidemiologia , Surtos de Doenças , Humanos , Índia/epidemiologia , Paquistão/epidemiologia , Filogenia
10.
Int J Mol Sci ; 22(10)2021 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-34069068

RESUMO

MADS-box genes are involved in various developmental processes including vegetative development, flower architecture, flowering, pollen formation, seed and fruit development. However, the function of most MADS-box genes and their regulation mechanism are still unclear in woody plants compared with model plants. In this study, a MADS-box gene (CiMADS43) was identified in citrus. Phylogenetic and sequence analysis showed that CiMADS43 is a GOA-like Bsister MADS-box gene. It was localized in the nucleus and as a transcriptional activator. Overexpression of CiMADS43 promoted early flowering and leaves curling in transgenic Arabidopsis. Besides, overexpression or knockout of CiMADS43 also showed leaf curl phenotype in citrus similar to that of CiMADS43 overexpressed in Arabidopsis. Protein-protein interaction found that a SEPALLATA (SEP)-like protein (CiAGL9) interacted with CiMADS43 protein. Interestingly, CiAGL9 also can bind to the CiMADS43 promoter and promote its transcription. Expression analysis also showed that these two genes were closely related to seasonal flowering and the development of the leaf in citrus. Our findings revealed the multifunctional roles of CiMADS43 in the vegetative and reproductive development of citrus. These results will facilitate our understanding of the evolution and molecular mechanisms of MADS-box genes in citrus.


Assuntos
Citrus/crescimento & desenvolvimento , Flores/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Proteínas de Domínio MADS/metabolismo , Folhas de Planta/crescimento & desenvolvimento , Proteínas de Plantas/metabolismo , Domínios e Motivos de Interação entre Proteínas , Sequência de Aminoácidos , Citrus/genética , Citrus/metabolismo , Flores/genética , Flores/metabolismo , Proteínas de Domínio MADS/genética , Fenótipo , Filogenia , Folhas de Planta/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/genética , Homologia de Sequência
11.
Viruses ; 13(6)2021 05 31.
Artigo em Inglês | MEDLINE | ID: mdl-34072981

RESUMO

Infectious bronchitis virus (IBV) was first identified in the 1930s and it imposes a major economic burden on the poultry industry. In particular, GI-19 lineage has spread globally and has evolved constantly since it was first detected in China. In this study, we analyzed S1 gene sequences from 60 IBVs isolated in South Korea. Two IBV lineages, GI-15 and GI-19, were identified in South Korea. Phylogenetic analysis suggested that there were six distinct subgroups (KM91-like, K40/09-like, and QX-like I to IV) of the South Korean GI-19 IBVs. Among them, QX-type III and IV subgroups, which are phylogenetically different from those reported in South Korea in the past, accounted for more than half of the total. Moreover, the phylogeographic analysis of the QX-like subgroups indicated at least four distinct introductions of GI-19 IBVs into South Korea during 2001-2020. The efficacy of commercialized vaccines against the recently introduced QX-like subgroups should be verified, and continuous international surveillance efforts and quarantine procedures should be enhanced to prevent the incursion of viruses.


Assuntos
Infecções por Coronavirus/veterinária , Vírus da Bronquite Infecciosa/genética , Doenças das Aves Domésticas/virologia , Animais , Galinhas , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Genômica , Genótipo , Vírus da Bronquite Infecciosa/classificação , Vírus da Bronquite Infecciosa/isolamento & purificação , Filogenia , Doenças das Aves Domésticas/epidemiologia , República da Coreia/epidemiologia , Análise de Sequência de RNA , Homologia de Sequência , Glicoproteína da Espícula de Coronavírus/genética
13.
BMC Med Inform Decis Mak ; 21(1): 177, 2021 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-34082739

RESUMO

BACKGROUND: The ability to prioritize people living with HIV (PLWH) by risk of future transmissions could aid public health officials in optimizing epidemiological intervention. While methods exist to perform such prioritization based on molecular data, their effectiveness and accuracy are poorly understood, and it is unclear how one can directly compare the accuracy of different methods. We introduce SEPIA (Simulation-based Evaluation of PrIoritization Algorithms), a novel simulation-based framework for determining the effectiveness of prioritization algorithms. SEPIA expands upon prior related work by defining novel metrics of effectiveness with which to compare prioritization techniques, as well as by creating a simulation-based tool with which to perform such effectiveness comparisons. Under several metrics of effectiveness that we propose, we compare two existing prioritization approaches: one phylogenetic (ProACT) and one distance-based (growth of HIV-TRACE transmission clusters). RESULTS: Using all proposed metrics, ProACT consistently slightly outperformed the transmission cluster growth approach. However, both methods consistently performed just marginally better than random, suggesting that there is significant room for improvement in prioritization tools. CONCLUSION: We hope that, by providing ways to quantify the effectiveness of prioritization methods in simulation, SEPIA will aid researchers in developing novel risk prioritization tools for PLWH.


Assuntos
Infecções por HIV , Sepia , Algoritmos , Animais , Simulação por Computador , Humanos , Filogenia
14.
Artigo em Inglês | MEDLINE | ID: mdl-34085922

RESUMO

Two Gram-stain-negative and non-flagellated bacteria, YSTF-M3T and YSTF-M6T, were isolated from a tidal flat from Yellow Sea, Republic of Korea, and subjected to a polyphasic taxonomic study. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strains YSTF-M3T and YSTF-M6T belong to the genera Kordia and Olleya of the family Flavobacteriaceae, respectively. The 16S rRNA gene sequence similarities between strain YSTF-M3T and the type strains of Kordia species and between strain YSTF-M6T and the type strains of Olleya species were 94.1-98.4 and 97.3-98.3 %, respectively. The ANI and dDDH values between genomic sequences of strain YSTF-M3T and the type strains of five Kordia species and between those of strain YSTF-M6T and the type strains of three Olleya species were in ranges of 77.0-83.2 and 20.7-27.1 % and 79.4-81.5 and 22.3-23.9 %, respectively. The DNA G+C contents of strain YSTF-M3T and YSTF-M6T from genomic sequences were 34.1 and 31.1 %, respectively. Both strains contained MK-6 as predominant menaquinone and phosphatidylethanolamine as only major phospholipid identified. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strains YSTF-M3T and YSTF-M6T are separated from recognized species of the genera Kordia and Olleya, respectively. On the basis of the data presented, strains YSTF-M3T (=KACC 21639T=NBRC 114499T) and YSTF-M6T (=KACC 21640T=NBRC 114500T) are considered to represent novel species of the genera Kordia and Olleya, respectively, for which the names Kordia aestuariivivens sp. nov. and Olleya sediminilitoris sp. nov. are proposed.


Assuntos
Flavobacteriaceae/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
15.
Nat Commun ; 12(1): 3214, 2021 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-34088904

RESUMO

Most archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.


Assuntos
Proteínas Arqueais/metabolismo , Divisão Celular/fisiologia , Methanobrevibacter/metabolismo , Proteínas Arqueais/química , Proteínas Arqueais/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Ciclo Celular , Divisão Celular/genética , Sequência Conservada , Cristalografia por Raios X , Evolução Molecular , Methanobrevibacter/genética , Methanobrevibacter/ultraestrutura , Microscopia Eletrônica de Transmissão , Modelos Moleculares , Filogenia , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Estrutura Quaternária de Proteína , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/ultraestrutura
16.
BMC Genomics ; 22(1): 419, 2021 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-34090344

RESUMO

BACKGROUND: Recent advances in single cell sequencing technologies allow for greater resolution in assessing tumor clonality using chromosome copy number variations (CNVs). While single cell DNA sequencing technologies are ideal to identify tumor sub-clones, they remain expensive and in contrast to single cell RNA-seq (scRNA-seq) methods are more limited in the data they generate. However, CNV data can be inferred from scRNA-seq and bulk RNA-seq, for which several tools have been developed, including inferCNV, CaSpER, and HoneyBADGER. Inferences regarding tumor clonality from CNV data (and other sources) are frequently visualized using phylogenetic plots, which previously required time-consuming and error-prone, manual analysis. RESULTS: Here, we present Uphyloplot2, a python script that generates phylogenetic plots directly from inferred RNA-seq data, or any Newick formatted dendrogram file. The tool is publicly available at https://github.com/harbourlab/UPhyloplot2/ . CONCLUSIONS: Uphyloplot2 is an easy-to-use tool to generate phylogenetic plots to depict tumor clonality from scRNA-seq data and other sources.


Assuntos
Variações do Número de Cópias de DNA , Análise de Célula Única , Perfilação da Expressão Gênica , Filogenia , RNA-Seq , Análise de Sequência de RNA , Software
17.
BMC Genomics ; 22(1): 421, 2021 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-34098869

RESUMO

BACKGROUND: Microsatellite repeats are ubiquitous in organism genomes and play an important role in the chromatin organization, regulation of gene activity, recombination and DNA replication. Although microsatellite distribution patterns have been studied in most phylogenetic lineages, they are unclear in fish species. RESULTS: Here, we present the first systematic examination of microsatellite distribution in coding and non-coding regions of 14 fish genomes. Our study showed that the number and type of microsatellites displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation and DNA replication slippage theories alone were insufficient to explain the distribution patterns. Our results showed that microsatellites are dominant in non-coding regions. The total number of microsatellites ranged from 78,378 to 1,012,084, and the relative density varied from 4925.76 bp/Mb to 25,401.97 bp/Mb. Overall, (A + T)-rich repeats were dominant. The dependence of repeat abundance on the length of the repeated unit (1-6 nt) showed a great similarity decrease, whereas more tri-nucleotide repeats were found in exonic regions than tetra-nucleotide repeats of most species. Moreover, the incidence of different repeated types appeared species- and genomic-specific. These results highlight potential mechanisms for maintaining microsatellite distribution, such as selective forces and mismatch repair systems. CONCLUSIONS: Our data could be beneficial for the studies of genome evolution and microsatellite DNA evolutionary dynamics, and facilitate the exploration of microsatellites structural, function, composition mode and molecular markers development in these species.


Assuntos
Genoma , Repetições de Microssatélites , Animais , DNA Intergênico , Peixes/genética , Repetições de Microssatélites/genética , Filogenia
18.
Artigo em Inglês | MEDLINE | ID: mdl-34100698

RESUMO

A novel Gram-stain positive, facultatively anaerobic, motile, irregularly rod-shaped bacterium, designated GY 10621T, was isolated from rhizosphere soil of Spartina alterniflora in Beihai City, Guangxi Province, PR China, and characterized using a polyphasic taxonomic approach. GY 10621T was positive for catalase and oxidase. Growth occurred at 4-42 °C (optimum 30-37 °C), at pH 5.0-9.0 (optimum pH 7.0) and in the presence of 0-5% NaCl (w/v) (optimum 1-3%). The main menaquinones were MK-9 (H4) (92.2 %) and MK-10 (7.8 %). The major cellular fatty acids were anteiso-C15 : 0 and C14 : 0. The peptidoglycan was the type A4α (l-Lys-Ser-d-Glu). The polar lipids included four phosphoglycolipids, four glycolipids, an unidentified lipid and six unidentified phospholipids. The DNA G+C content of the type strain was 71.7 mol%. On the basis of the results of 16S rRNA gene analysis, the type strain of a species with a validly published name with the highest similarity to GY 10621T was Flavimobilis soli KCTC 13155T (97.16 %), followed by Sanguibacter suarezii NBRC 16159T (96.39 %). The calculated results indicated that compared with GY 10621T, the average nucleotide identity (ANI) values of three strains closely related to GY 10621T (the two aforementioned type strains and 'S. massiliensis' Marseille-P3815) were 74.18-94.97 %, and the digital DNA-DNA hybridization (dDDH) values were 20.3-60.6 %. The results of 16S rRNA-based and genome-based phylogenetic tree analysis indicated that GY 10621T should be assigned to the genus Flavimobilis. On the basis of evidence from polyphasic studies, GY 10621T should be designated as representing a novel species of the genus Flavimobilis, for which the name Flavimobilis rhizosphaerae sp. nov. is proposed. The type strain is GY 10621T (=CGMCC 1.17411T=KCTC 49515T).


Assuntos
Actinobacteria/classificação , Filogenia , Poaceae/microbiologia , Rizosfera , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
19.
Braz J Biol ; 82: e240725, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34105650

RESUMO

Molecular based identification of bat fauna in Pakistan has been relatively less explored. The current study was therefore planned to report for the first time the molecular classification of insectivorous bats (Pipistrellus coromandra) based on mitochondrion gene (COI) from Punjab, Pakistan. Specimens were collected from five different locations followed by DNA extraction with subsequent gene amplification and sequencing. All samples in the study had shown close identity matches with species (Pipistrellus coromandra) from India and (Pipistrellus tenuis) from Vietnam with percentage identity score of 96.11 and 95.58 respectively except one sequence which only revealed 86.78% identity match on Basic Local Alignment Search Tool (BLAST) and could only be assigned to genus level Pipistrellus sp. The results indicated negligible intra-population genetic distance among collected samples whereas the comparison with species from other countries had shown high intraspecific (P. coromandra) and interspecific (P. tenuis) mean genetic distances. The current study hence successfully proved the efficiency of COI gene as a molecular marker for species identification and in analyzing the patterns of genetic variation with species from other countries.


Assuntos
Quirópteros , Animais , Quirópteros/genética , Paquistão , Filogenia
20.
Braz J Biol ; 82: e235395, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34105660

RESUMO

Several records of associated fauna, including parasitoids, inquilines, predators, and successors, have been reported by insect gall inventories in Brazilian restingas. Although most guilds are well established, inquilines have frequently been misinterpreted. In this paper, the inquilinous fauna of insect galls is revised based on five criteria: food habit; coexistence with the inducer; modification of gall tissues or production of new tissues; phylogenetic relationship with the inducer; and mobility. Gall inventories dated from 1988 to 2019 were examined, totaling 16 publications, eight of them with inquiline records. This guild was reported in 53 gall morphotypes in 44 plant species and four morphospecies distributed among 36 genera of 24 host families for a total of 65 records. Most inquilines were repositioned into the cecidophage guild and others into the kleptoparasite guild, resulting in a large reduction in the frequency of inquilines (from 65 to five records), and in first reports of cecidophages and kleptoparasites, with 46 and 13 records, respectively. Cecidophage was the most diverse guild with insects of five orders (Diptera, Coleoptera, Lepidoptera, Hemiptera, and Thysanoptera) while kleptoparasites were represented only by two orders (Diptera and Hymenoptera) and inquiline solely by Hymenoptera. Other results indicate that Leptothorax sp. (Formicidae) could be a successor and not an inquiline.


Assuntos
Insetos , Tumores de Planta , Animais , Brasil , Interações Hospedeiro-Parasita , Humanos , Filogenia , Plantas
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