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1.
Dis Aquat Organ ; 145: 119-137, 2021 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-34196282

RESUMEN

Myxobolus cerebralis is the causative agent of whirling disease in salmonid fishes. In 2016, this invasive parasite was detected in Alberta, Canada, for the first time, initiating a comprehensive 3 yr monitoring program to assess where the parasite had spread within the province. As part of this program, a qPCR-based test was developed to facilitate detection of the environmental stages of M. cerebralis and from the oligochaete host, Tubifex tubifex. During this program, ~1500 environmental samples were collected and tested over 3 yr. Fish were collected from the same watersheds over 2 yr and tested as part of the official provincial monitoring effort. Substrate testing identified sites positive for M. cerebralis in 3 of 6 watersheds that had been confirmed positive by fish-based testing and 3 novel detections where the parasite had not been detected previously. Testing of individually isolated Tubifex from each sample site was used to further confirm the presence of M. cerebralis. DNA barcoding of the cytochrome oxidase I (cox1) gene of 567 oligochaete specimens collected from 6 different watersheds yielded 158 unique sequences belonging to 21 genera and 37 putative species. Phylogenetic analyses of sequences assigned to the genus Tubifex predicted 5 species of Tubifex arising from this assessment. Based on our results, we propose that environmental and worm samples can be a valuable complement to the gold-standard fish testing and will be especially useful for monitoring in areas where fish collection is challenging or prohibitive because of site accessibility or vulnerability of the fish populations.


Asunto(s)
Enfermedades de los Peces , Myxobolus , Oligoquetos , Alberta , Animales , Monitoreo del Ambiente , Enfermedades de los Peces/epidemiología , Myxobolus/genética , Filogenia
2.
BMC Genomics ; 22(1): 504, 2021 Jul 04.
Artículo en Inglés | MEDLINE | ID: mdl-34218810

RESUMEN

BACKGROUND: Lignin is one of the main components of the cell wall and is directly associated with plant development and defence mechanisms in plants, especially in response to Fusarium graminearum (Fg) infection. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is the main regulator determining the efficiency of lignin synthesis and composition. Although it has been characterized in many plants, to date, the importance of the CCoAOMT family in wheat is not well understood. RESULTS: Here, a total of 21 wheat CCoAOMT genes (TaCCoAOMT) were identified through an in silico genome search method and they were classified into four groups based on phylogenetic analysis, with the members of the same group sharing similar gene structures and conserved motif compositions. Furthermore, the expression patterns and co-expression network in which TaCCoAOMT is involved were comprehensively investigated using 48 RNA-seq samples from Fg infected and mock samples of 4 wheat genotypes. Combined with qRT-PCR validation of 11 Fg-responsive TaCCoAOMT genes, potential candidates involved in the FHB response and their regulation modules were preliminarily suggested. Additionally, we investigated the genetic diversity and main haplotypes of these CCoAOMT genes in bread wheat and its relative populations based on resequencing data. CONCLUSIONS: This study identified and characterized the CCoAOMT family in wheat, which not only provided potential targets for further functional analysis, but also contributed to uncovering the mechanism of lignin biosynthesis and its role in FHB tolerance in wheat and beyond.


Asunto(s)
Fusarium , Acilcoenzima A , Metiltransferasas/genética , Filogenia , Enfermedades de las Plantas , Triticum
3.
Mymensingh Med J ; 30(3): 863-873, 2021 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-34226482

RESUMEN

Norovirus, often called winter vomiting bug, is the most common cause of outbreaks of acute gastroenteritis in all age groups all over the world. It was discovered in 1972; belong to the genus Norovirus in the family Caliciviridae. Based on genomic organization and phylogenetic analysis, the family Caliciviridae is divided into four genera- Norovirus, Sapovirus, Vesivirus and Lagovirus. The aim of this review article was to find out the present status of prevalence and evolution of norovirus strains in developed and developing countries. In this article various literature on norovirus from different countries was reviewed. The detection of norovirus in the lower middle income countries (LMIC) was reported 15% in cases and 8% in controls during 1997 to 2018. On the other hand, detection rate of norovirus in low income countries (LIC) was 11% in cases and 9% in controls during the same period. Overall detection rate of norovirus was 14% in LIMC and 8% in LIC during 1997 to 2018. Noroviruses are divided genetically into seven different type of Geno groups namely GI, GII, GIII, GIV, GV, GVI and GVII which are further classified into different genetic clusters or genotypes. For example, Geno group II, the most prevalent human Geno group, presently contains 19 genotypes. Among the genogroups I, II and IV infect humans, on the other hand genogroup III infects bovine species and genogroup V was isolated from mice. Several new noroviruses were reported and the number of genogroups increased to 10 (GI-GX) and the number of genotypes expanded to 49: 9 GI, 27 GII, 3 GIII, 2 GIV, 2 GV, 2GVI, 1 GVII, 1 GVIII, 1 GIX, 1 GX. Noroviruses are spread directly from individual to individual as well as indirectly via contaminated food and water. They are highly contagious, and around twenty virus particles can cause an infection. This virus usually exhibits winter seasonality. The global norovirus prevalence in under-5 years, ≥5 years and mixed age was similar (16% - 19%). Norovirus infection is characterized by diarrhea, vomiting, fever, headache and stomach pain. It may be complicated with dehydration and electrolyte imbalance. Gastroenteritis develops 12 to 48 hours after exposure and recovery typically occurs within 1 to 3 days. There is no specific treatment of norovirus gastroenteritis. Prevention includes proper hand washing and cleaning or disinfection of contaminated surfaces. Various genotypes of norovirus may be circulating around the world and can emerge either nationally or globally. In this overview, general characteristics of norovirus, current status of genomic diversity and classification, recent status of norovirus gastroenteritis outbreaks in the developed and developing countries is outlined for comprehensive understanding of the present status of prevalence and evolution of norovirus strains to develop strategies for prevention and control of norovirus infection in human.


Asunto(s)
Gastroenteritis , Norovirus , Animales , Bovinos , Brotes de Enfermedades , Heces , Gastroenteritis/epidemiología , Genómica , Genotipo , Humanos , Ratones , Norovirus/genética , Filogenia
4.
Int J Mol Sci ; 22(12)2021 Jun 11.
Artículo en Inglés | MEDLINE | ID: mdl-34208100

RESUMEN

Stress granules (SGs) are dynamic RNA-protein complexes localized in the cytoplasm that rapidly form under stress conditions and disperse when normal conditions are restored. The formation of SGs depends on the Ras-GAP SH3 domain-binding protein (G3BP). Formations, interactions and functions of plant and human SGs are strikingly similar, suggesting a conserved mechanism. However, functional analyses of plant G3BPs are missing. Thus, members of the Arabidopsis thaliana G3BP (AtG3BP) protein family were investigated in a complementation assay in a human G3BP knock-out cell line. It was shown that two out of seven AtG3BPs were able to complement the function of their human homolog. GFP-AtG3BP fusion proteins co-localized with human SG marker proteins Caprin-1 and eIF4G1 and restored SG formation in G3BP double KO cells. Interaction between AtG3BP-1 and -7 and known human G3BP interaction partners such as Caprin-1 and USP10 was also demonstrated by co-immunoprecipitation. In addition, an RG/RGG domain exchange from Arabidopsis G3BP into the human G3BP background showed the ability for complementation. In summary, our results support a conserved mechanism of SG function over the kingdoms, which will help to further elucidate the biological function of the Arabidopsis G3BP protein family.


Asunto(s)
Arabidopsis/metabolismo , Gránulos Citoplasmáticos/metabolismo , Estrés Fisiológico , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Línea Celular Tumoral , Proteínas Fluorescentes Verdes/metabolismo , Humanos , Fenotipo , Filogenia , Unión Proteica , Dominios Proteicos
5.
BMC Plant Biol ; 21(1): 309, 2021 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-34210268

RESUMEN

BACKGROUND: Phytohormone abscisic acid (ABA) is involved in the regulation of a wide range of biological processes. In Arabidopsis, it has been well-known that SnRK2s are the central components of the ABA signaling pathway that control the balance between plant growth and stress response, but the functions of ZmSnRK2 in maize are rarely reported. Therefore, the study of ZmSnRK2 is of great importance to understand the ABA signaling pathways in maize. RESULTS: In this study, 14 ZmSnRK2 genes were identified in the latest version of maize genome database. Phylogenetic analysis revealed that ZmSnRK2s are divided into three subclasses based on their diversity of C-terminal domains. The exon-intron structures, phylogenetic, synteny and collinearity analysis indicated that SnRK2s, especially the subclass III of SnRK2, are evolutionally conserved in maize, rice and Arabidopsis. Subcellular localization showed that ZmSnRK2 proteins are localized in the nucleus and cytoplasm. The RNA-Seq datasets and qRT-PCR analysis showed that ZmSnRK2 genes exhibit spatial and temporal expression patterns during the growth and development of different maize tissues, and the transcript levels of some ZmSnRK2 genes in kernel are significantly induced by ABA and sucrose treatment. In addition, we found that ZmSnRK2.10, which belongs to subclass III, is highly expressed in kernel and activated by ABA. Overexpression of ZmSnRK2.10 partially rescued the ABA-insensitive phenotype of snrk2.2/2.3 double and snrk2.2/2.3/2.6 triple mutants and led to delaying plant flowering in Arabidopsis. CONCLUSION: The SnRK2 gene family exhibits a high evolutionary conservation and has expanded with whole-genome duplication events in plants. The ZmSnRK2s expanded in maize with whole-genome and segmental duplication, not tandem duplication. The expression pattern analysis of ZmSnRK2s in maize offers important information to study their functions. Study of the functions of ZmSnRK.10 in Arabidopsis suggests that the ABA-dependent members of SnRK2s are evolutionarily conserved in plants. Our study elucidated the structure and evolution of SnRK2 genes in plants and provided a basis for the functional study of ZmSnRK2s protein in maize.


Asunto(s)
Ácido Abscísico/metabolismo , Genes de Plantas , Transducción de Señal , Zea mays/genética , Zea mays/metabolismo , Arabidopsis/genética , Secuencia de Bases , Núcleo Celular/metabolismo , Cromosomas de las Plantas/genética , Evolución Molecular , Duplicación de Gen , Regulación de la Expresión Génica de las Plantas , Mutación/genética , Fenotipo , Filogenia , Transducción de Señal/genética , Fracciones Subcelulares/metabolismo , Sintenía/genética
6.
BMC Plant Biol ; 21(1): 313, 2021 Jul 02.
Artículo en Inglés | MEDLINE | ID: mdl-34215178

RESUMEN

BACKGROUND: Harnessing heterosis is one of the major approaches to increase rice yield and has made a great contribution to food security. The identification and selection of outstanding parental genotypes especially among male sterile lines is a key step for exploiting heterosis. Two-line hybrid system is based on the discovery and application of photoperiod- and thermo-sensitive genic sensitive male sterile (PTGMS) materials. The development of wide-range of male sterile lines from a common gene pool leads to a narrower genetic diversity, which is vulnerable to biotic and abiotic stress. Hence, it is valuable to ascertain the genetic background of PTGMS lines and to understand their relationships in order to select and design a future breeding strategy. RESULTS: A collection of 118 male sterile rice lines and 13 conventional breeding lines from the major rice growing regions of China was evaluated and screened against the photosensitive (pms3) and temperature sensitive male sterility (tms5) genes. The total gene pool was divided into four major populations as P1 possessing the pms3, P2 possessing tms5, P3 possessing both pms3 and tms5 genes, and P4 containing conventional breeding lines without any male sterility allele. The high genetic purity was revealed by homozygous alleles in all populations. The population admixture, principle components and the phylogenetic analysis revealed the close relations of P2 and P3 with P4. The population differentiation analysis showed that P1 has the highest differentiation coefficient. The lines from P1 were observed as the ancestors of other three populations in a phylogenetic tree, while the lines in P2 and P3 showed a close genetic relation with conventional lines. A core collection of top 10% lines with maximum within and among populations genetic diversity was constructed for future research and breeding efforts. CONCLUSION: The low genetic diversity and close genetic relationship among PTGMS lines in P2, P3 and P4 populations suggest a selection sweep and they might result from a backcrossing with common ancestors including the pure lines of P1. The core collection from PTGMS panel updated with new diverse germplasm will serve best for further two-line hybrid breeding.


Asunto(s)
Oryza/genética , Fotoperiodo , Infertilidad Vegetal/genética , Semillas/genética , Temperatura , Núcleo Celular/genética , Núcleo Celular/efectos de la radiación , Análisis por Conglomerados , Ontología de Genes , Estudios de Asociación Genética , Marcadores Genéticos , Luz , Nucleótidos/genética , Oryza/efectos de la radiación , Filogenia , Infertilidad Vegetal/efectos de la radiación , Polimorfismo de Nucleótido Simple/genética , Análisis de Componente Principal , Reproducibilidad de los Resultados , Semillas/efectos de la radiación
7.
BMC Plant Biol ; 21(1): 319, 2021 Jul 03.
Artículo en Inglés | MEDLINE | ID: mdl-34217205

RESUMEN

BACKGROUND: PTI1 (Pto-interacting 1) protein kinase belongs to the receptor-like cytoplasmic kinase (RLCK) group of receptor-like protein kinases (RLK), but lack extracellular and transmembrane domains. PTI1 was first identified in tomato (Solanum lycopersicum) and named SlPTI1, which has been reported to interact with bacterial effector Pto, a serine/threonine protein kinase involved in plant resistance to bacterial disease. Briefly, the host PTI1 specifically recognizes and interacts with the bacterial effector AvrPto, which triggers hypersensitive cell death to inhibit the pathogen growth in the local infection site. Previous studies have demonstrated that PTI1 is associated with oxidative stress and hypersensitivity. RESULTS: We identified 12 putative PTI1 genes from the genome of foxtail millet (Setaria italica) in this study. Gene replication analysis indicated that both segmental replication events played an important role in the expansion of PTI1 gene family in foxtail millet. The PTI1 family members of model plants, i.e. S. italica, Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), maize (Zea mays), S. lycopersicum, and soybean (Glycine max), were classified into six major categories according to the phylogenetic analysis, among which the PTI1 family members in foxtail millet showed higher degree of homology with those of rice and maize. The analysis of a complete set of SiPTI1 genes/proteins including classification, chromosomal location, orthologous relationships and duplication. The tissue expression characteristics revealed that SiPTI1 genes are mainly expressed in stems and leaves. Experimental qRT-PCR results demonstrated that 12 SiPTI1 genes were induced by multiple stresses. Subcellular localization visualized that all of foxtail millet SiPTI1s were localized to the plasma membrane. Additionally, heterologous expression of SiPTI1-5 in yeast and E. coli enhanced their tolerance to salt stress. CONCLUSIONS: Our results contribute to a more comprehensive understanding of the roles of PTI1 protein kinases and will be useful in prioritizing particular PTI1 for future functional validation studies in foxtail millet.


Asunto(s)
Genoma de Planta , Familia de Multigenes , Proteínas de Plantas/genética , Salinidad , Setaria (Planta)/genética , Setaria (Planta)/fisiología , Cromosomas de las Plantas/genética , Escherichia coli/metabolismo , Duplicación de Gen/genética , Regulación de la Expresión Génica de las Plantas , Genes de Plantas , Anotación de Secuencia Molecular , Motivos de Nucleótidos/genética , Filogenia , Proteínas de Plantas/metabolismo , Saccharomyces cerevisiae/metabolismo , Estrés Fisiológico/genética , Sintenía/genética
8.
BMC Plant Biol ; 21(1): 322, 2021 Jul 05.
Artículo en Inglés | MEDLINE | ID: mdl-34225654

RESUMEN

BACKGROUND: Flexibility of plant metabolism is supported by redox regulation of enzymes via posttranslational modification of cysteine residues, especially in plastids. Here, the redox states of cysteine residues are partly coupled to the thioredoxin system and partly to the glutathione pool for reduction. Moreover, several plastid enzymes involved in reactive oxygen species (ROS) scavenging and damage repair draw electrons from glutathione. In addition, cysteine residues can be post-translationally modified by forming a mixed disulfide with glutathione (S-glutathionylation), which protects thiol groups from further oxidation and can influence protein activity. However, the evolution of the plastid glutathione-dependent redox network in land plants and the conservation of cysteine residues undergoing S-glutathionylation is largely unclear. RESULTS: We analysed the genomes of nine representative model species from streptophyte algae to angiosperms and found that the antioxidant enzymes and redox proteins belonging to the plastid glutathione-dependent redox network are largely conserved, except for lambda- and the closely related iota-glutathione S-transferases. Focussing on glutathione-dependent redox modifications, we screened the literature for target thiols of S-glutathionylation, and found that 151 plastid proteins have been identified as glutathionylation targets, while the exact cysteine residue is only known for 17% (26 proteins), with one or multiple sites per protein, resulting in 37 known S-glutathionylation sites for plastids. However, 38% (14) of the known sites were completely conserved in model species from green algae to flowering plants, with 22% (8) on non-catalytic cysteines. Variable conservation of the remaining sites indicates independent gains and losses of cysteines at the same position during land plant evolution. CONCLUSIONS: We conclude that the glutathione-dependent redox network in plastids is highly conserved in streptophytes with some variability in scavenging and damage repair enzymes. Our analysis of cysteine conservation suggests that S-glutathionylation in plastids plays an important and yet under-investigated role in redox regulation and stress response.


Asunto(s)
Glutatión/metabolismo , Plastidios/metabolismo , Embryophyta/metabolismo , Evolución Molecular , Oxidación-Reducción , Filogenia , Streptophyta/metabolismo
9.
BMC Res Notes ; 14(1): 266, 2021 Jul 10.
Artículo en Inglés | MEDLINE | ID: mdl-34246294

RESUMEN

OBJECTIVE: To find mutations that may have recently occurred in Plum pox virus (PPV), we collected six PPV-infected plum/peach trees from the western part of Japan and one from the eastern part. After sequencing the full-length PPV genomic RNAs, we compared the amino acid sequences with representative isolates of each PPV strain. RESULTS: All new isolates were found to belong to the PPV-D strain: the six isolates collected from western Japan were identified as the West-Japan strain while the one collected from eastern Japan as the East-Japan strain. Amino acid sequence analysis of these seven isolates suggested that the 1407th and 1529th amino acid residues are characteristic of the West-Japan and the East-Japan strains, respectively. Comparing them with the corresponding amino acid residues of the 47 non-Japanese PPV-D isolates revealed that these amino acid residues are undoubtedly unique. A further examination of the relevant amino acid residues of the other 210 PPV-D isolates collected in Japan generated a new hypothesis regarding the invasion route from overseas and the subsequent diffusion route within Japan: a PPV-D strain might have invaded the western part of Japan from overseas and spread throughout Japan.


Asunto(s)
Virus Eruptivo de la Ciruela , Genoma Viral/genética , Japón , Filogenia , Enfermedades de las Plantas , Virus Eruptivo de la Ciruela/genética , Análisis de Secuencia de ADN
10.
BMC Genomics ; 22(1): 530, 2021 Jul 12.
Artículo en Inglés | MEDLINE | ID: mdl-34247587

RESUMEN

BACKGROUND: Acinetobacter baumannii is a common nosocomial pathogen that poses a huge threat to global health. Owing to the severity of A. baumannii infections, it became necessary to investigate the epidemiological characteristics of A. baumannii in Chinese hospitals and find the reasons for the high antibiotic resistance rate and mortality. This study aimed to investigate the epidemiologic and genetic characteristics of A. baumannii isolated from patients with hospital acquired pneumonia (HAP), bloodstream infection (BSI) and urinary tract infection (UTI) in China and uncover potential mechanisms for multi-drug resistance and virulence characteristics of A. baumannii isolates. RESULTS: All isolates were classified into two primary clades in core gene-based phylogenetic relationship. Clonal complex 208 (CC208) mainly consisted of ST195 (32 %) and ST208 (24.6 %). CC208 and non-CC208 isolates had carbapenem resistance rates of 96.2 and 9.1 %, respectively. Core genes were enriched in 'Amino acid transport and metabolism', 'Translation', 'Energy production and conversion', 'Transcription', 'Inorganic ion transport and metabolism' and 'Cell wall/membrane/envelope synthesis'. Most isolates possessed virulence factors related to polysaccharide biosynthesis, capsular polysaccharide synthesis and motility. Eleven isolates belong to ST369 or ST191 (oxford scheme) all had the virulence factor cap8E and it had a higher positive rate in UTI (35.3 %) than in BSI (18.9 %) and HAP (12.9 %). ABGRI1 antibiotic resistance islands were responsible for streptomycin, tetracycline and sulfonate resistance. The blaOXA-23 gene was the most probable cause for carbapenem resistance, although the blaOXA-66 gene with nonsynonymous SNPs (F82L, I129L) was not. CONCLUSIONS: A. baumannii is a genomically variable pathogen that has the potential to cause a range of infectious diseases. There is high proportion of carbapenem resistance in isolates from all three infection sites (HAP, BSI and UTI), which can be attributed to the blaOXA-23 gene. CC208 is the predominant clone in blaOXA-23-carrying A. baumannii that should be monitored. Virulence factors involving bacteria motility and polysaccharide biosynthesis which are widespread in clinical A. baumannii strains deserve our attention.


Asunto(s)
Infecciones por Acinetobacter , Acinetobacter baumannii , Enfermedades Transmisibles , Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/genética , Antibacterianos/farmacología , Proteínas Bacterianas/genética , Carbapenémicos/farmacología , China/epidemiología , Farmacorresistencia Bacteriana Múltiple , Genómica , Humanos , Pruebas de Sensibilidad Microbiana , Filogenia , beta-Lactamasas/genética
11.
Int J Mol Sci ; 22(11)2021 Jun 04.
Artículo en Inglés | MEDLINE | ID: mdl-34199768

RESUMEN

Single mutations can confer resistance to antibiotics. Identifying such mutations can help to develop and improve drugs. Here, we systematically screen for candidate quinolone resistance-conferring mutations. We sequenced highly diverse wastewater E. coli and performed a genome-wide association study (GWAS) to determine associations between over 200,000 mutations and quinolone resistance phenotypes. We uncovered 13 statistically significant mutations including 1 located at the active site of the biofilm dispersal gene bdcA and 6 silent mutations in the aminoacyl-tRNA synthetase valS. The study also recovered the known mutations in the topoisomerases gyrase (gyrA) and topoisomerase IV (parC). In summary, we demonstrate that GWAS effectively and comprehensively identifies resistance mutations without a priori knowledge of targets and mode of action. The results suggest that mutations in the bdcA and valS genes, which are involved in biofilm dispersal and translation, may lead to novel resistance mechanisms.


Asunto(s)
Farmacorresistencia Bacteriana/genética , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Mutación/genética , Quinolonas/farmacología , Aguas Residuales/microbiología , Antibacterianos/farmacología , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Sitios Genéticos , Estudio de Asociación del Genoma Completo , Desequilibrio de Ligamiento/genética , Modelos Moleculares , Fenotipo , Filogenia
12.
Viruses ; 13(6)2021 06 04.
Artículo en Inglés | MEDLINE | ID: mdl-34199933

RESUMEN

Bovine coronavirus (BCoV) is the causative agent of winter dysentery (WD). In adult dairy cattle, WD is characterized by hemorrhagic diarrhea and a reduction in milk production. Therefore, WD leads to significant economic losses in dairy farms. In this study, we aimed to isolate and characterize local BCoV strains. BCoV positive samples, collected during 2017-2021, were used to amplify and sequence the S1 domain of S glycoprotein and the full hemagglutinin esterase gene. Based on our molecular analysis, local strains belong to different genetic variants circulating in dairy farms in Israel. Phylogenetic analysis revealed that all local strains clustered together and in proximity to other BCoV circulating in the area. Additionally, we found that local strains are genetically distant from the reference enteric strain Mebus. To our knowledge, this is the first report providing molecular data on BCoV circulating in Israel.


Asunto(s)
Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/veterinaria , Coronavirus Bovino/genética , Disentería/veterinaria , Filogenia , Animales , Antígenos Virales/genética , Bovinos , Enfermedades de los Bovinos/epidemiología , Enfermedades de los Bovinos/virología , Coronavirus Bovino/clasificación , Coronavirus Bovino/aislamiento & purificación , Industria Lechera , Disentería/virología , Heces/virología , Femenino , Variación Genética , Israel/epidemiología , Análisis de Secuencia de ADN
13.
Viruses ; 13(6)2021 06 07.
Artículo en Inglés | MEDLINE | ID: mdl-34200386

RESUMEN

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, is a readily transmissible and potentially deadly pathogen which is currently re-defining human susceptibility to pandemic viruses in the modern world. The recent emergence of several genetically distinct descendants known as variants of concern (VOCs) is further challenging public health disease management, due to increased rates of virus transmission and potential constraints on vaccine effectiveness. We report the isolation of SARS-CoV-2 VOCs imported into Australia belonging to the B.1.351 lineage, first described in the Republic of South Africa (RSA), and the B.1.1.7 lineage originally reported in the United Kingdom, and directly compare the replication kinetics of these two VOCs in Vero E6 cells. In this analysis, we also investigated a B.1.1.7 VOC (QLD1516/2021) carrying a 7-nucleotide deletion in the open reading frame 7a (ORF7a) gene, likely truncating and rendering the ORF7a protein of this virus defective. We demonstrate that the replication of the B.1.351 VOC (QLD1520/2020) in Vero E6 cells can be detected earlier than the B.1.1.7 VOCs (QLD1516/2021 and QLD1517/2021), before peaking at 48 h post infection (p.i.), with significantly higher levels of virus progeny. Whilst replication of the ORF7a defective isolate QLD1516/2021 was delayed longer than the other viruses, slightly more viral progeny was produced by the mutant compared to the unmutated isolate QLD1517/2021 at 72 h p.i. Collectively, these findings contribute to our understanding of SARS-CoV-2 replication and evolutionary dynamics, which have important implications in the development of future vaccination, antiviral therapies, and epidemiological control strategies for COVID-19.


Asunto(s)
Sistemas de Lectura Abierta/genética , SARS-CoV-2/genética , SARS-CoV-2/fisiología , Proteínas Virales/genética , Replicación Viral , Adulto , Animales , Australia , COVID-19/prevención & control , COVID-19/transmisión , COVID-19/virología , Chlorocebus aethiops , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Cinética , Persona de Mediana Edad , Mutación , Nasofaringe/virología , Filogenia , SARS-CoV-2/clasificación , Sudáfrica , Reino Unido , Células Vero
14.
Viruses ; 13(6)2021 06 10.
Artículo en Inglés | MEDLINE | ID: mdl-34200621

RESUMEN

Field epidemiology and viral sequencing provide a comprehensive characterization of transmission chains and allow a better identification of superspreading events. However, very few examples have been presented to date during the COVID-19 pandemic. We studied the first COVID-19 cluster detected in Portugal (59 individuals involved amongst extended family and work environments), following the return of four related individuals from work trips to Italy. The first patient to introduce the virus would be misidentified following the traditional field inquiry alone, as shown by the viral sequencing in isolates from 23 individuals. The results also pointed out family, and not work environment, as the primary mode of transmission.


Asunto(s)
COVID-19/epidemiología , COVID-19/transmisión , Secuenciación de Nucleótidos de Alto Rendimiento , SARS-CoV-2/genética , COVID-19/prevención & control , Estudios de Casos y Controles , Familia , Genoma Viral , Humanos , Italia/epidemiología , Filogenia , Portugal/epidemiología , ARN Viral/genética , SARS-CoV-2/clasificación , SARS-CoV-2/aislamiento & purificación , Enfermedad Relacionada con los Viajes , Secuenciación Completa del Genoma
15.
Biomolecules ; 11(6)2021 06 18.
Artículo en Inglés | MEDLINE | ID: mdl-34207362

RESUMEN

The ongoing outbreak of coronavirus disease COVID-19 is significantly implicated by global heterogeneity in the genome organization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The causative agents of global heterogeneity in the whole genome of SARS-CoV-2 are not well characterized due to the lack of comparative study of a large enough sample size from around the globe to reduce the standard deviation to the acceptable margin of error. To better understand the SARS-CoV-2 genome architecture, we have performed a comprehensive analysis of codon usage bias of sixty (60) strains to get a snapshot of its global heterogeneity. Our study shows a relatively low codon usage bias in the SARS-CoV-2 viral genome globally, with nearly all the over-preferred codons' A.U. ended. We concluded that the SARS-CoV-2 genome is primarily shaped by mutation pressure; however, marginal selection pressure cannot be overlooked. Within the A/U rich virus genomes of SARS-CoV-2, the standard deviation in G.C. (42.91% ± 5.84%) and the GC3 value (30.14% ± 6.93%) points towards global heterogeneity of the virus. Several SARS-CoV-2 viral strains were originated from different viral lineages at the exact geographic location also supports this fact. Taking all together, these findings suggest that the general root ancestry of the global genomes are different with different genome's level adaptation to host. This research may provide new insights into the codon patterns, host adaptation, and global heterogeneity of SARS-CoV-2.


Asunto(s)
COVID-19/virología , Uso de Codones , Genoma Viral , SARS-CoV-2/genética , Evolución Molecular , Humanos , Mutación , Filogenia
16.
Viruses ; 13(6)2021 06 09.
Artículo en Inglés | MEDLINE | ID: mdl-34207490

RESUMEN

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in an extraordinary global public health crisis. In early 2020, Cyprus, among other European countries, was affected by the SARS-CoV-2 epidemic and adopted lockdown measures in March 2020 to limit the initial outbreak on the island. In this study, we performed a comprehensive retrospective molecular epidemiological analysis (genetic, phylogenetic, phylodynamic and phylogeographic analyses) of SARS-CoV-2 isolates in Cyprus from April 2020 to January 2021, covering the first ten months of the SARS-CoV-2 infection epidemic on the island. The primary aim of this study was to assess the transmissibility of SARS-CoV-2 lineages in Cyprus. Whole SARS-CoV-2 genomic sequences were generated from 596 clinical samples (nasopharyngeal swabs) obtained from community-based diagnostic testing centers and hospitalized patients. The phylogenetic analyses revealed a total of 34 different lineages in Cyprus, with B.1.258, B.1.1.29, B.1.177, B.1.2, B.1 and B.1.1.7 (designated a Variant of Concern 202012/01, VOC) being the most prevalent lineages on the island during the study period. Phylodynamic analysis showed a highly dynamic epidemic of SARS-CoV-2 infection, with three consecutive surges characterized by specific lineages (B.1.1.29 from April to June 2020; B.1.258 from September 2020 to January 2021; and B.1.1.7 from December 2020 to January 2021). Genetic analysis of whole SARS-CoV-2 genomic sequences of the aforementioned lineages revealed the presence of mutations within the S protein (L18F, ΔH69/V70, S898F, ΔY144, S162G, A222V, N439K, N501Y, A570D, D614G, P681H, S982A and D1118H) that confer higher transmissibility and/or antibody escape (immune evasion) upon the virus. Phylogeographic analysis indicated that the majority of imports and exports were to and from the United Kingdom (UK), although many other regions/countries were identified (southeastern Asia, southern Europe, eastern Europe, Germany, Italy, Brazil, Chile, the USA, Denmark, the Czech Republic, Slovenia, Finland, Switzerland and Pakistan). Taken together, these findings demonstrate that the SARS-CoV-2 infection epidemic in Cyprus is being maintained by a continuous influx of lineages from many countries, resulting in the establishment of an ever-evolving and polyphyletic virus on the island.


Asunto(s)
COVID-19/epidemiología , Genoma Viral , Filogenia , SARS-CoV-2/genética , COVID-19/transmisión , Control de Enfermedades Transmisibles , Chipre/epidemiología , Evolución Molecular , Humanos , Mutación , Nasofaringe/virología , Filogeografía , ARN Viral/genética , Estudios Retrospectivos , SARS-CoV-2/clasificación , SARS-CoV-2/aislamiento & purificación
17.
Bioengineered ; 12(1): 2836-2850, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-34227905

RESUMEN

Angiotensin I-converting enzyme 2 (ACE2), type II transmembrane serine protease 2 and 4 (TMPRSS2 and TMPRSS4) are important receptors for SARS-CoV-2 infection. In this study, the full-length tree shrewACE2 gene was cloned and sequenced, and its biological information was analyzed. The expression levels of ACE2, TMPRSS2 and TMPRSS4 in various tissues or organs of the tree shrew were detected. The results showed that the full-length ACE2 gene in tree shrews was 2,786 bp, and its CDS was 2,418 bp, encoding 805 amino acids. Phylogenetic analysis based on the CDS of ACE2 revealed that tree shrews were more similar to rabbits (85.93%) and humans (85.47%) but far from mice (82.81%) and rats (82.58%). In silico analysis according to the binding site of SARS-CoV-2 with the ACE2 receptor of different species predicted that tree shrews had potential SARS-CoV-2 infection possibility, which was similar to that of rabbits, cats and dogs but significantly higher than that of mice and rats. In addition, various tissues or organs of tree shrews expressed ACE2, TMPRSS2 and TMPRSS4. Among them, the kidney most highly expressed ACE2, followed by the lung and liver. The esophagus, lung, liver, intestine and kidney had relatively high expression levels of TMPRSS2 and TMPRSS4. In general, we reported for the first time the expression of ACE2, TMPRSS2 and TMPRSS4 in various tissues or organs in tree shrews. Our results revealed that tree shrews could be used as a potential animal model to study the mechanism underlying SARS-CoV-2 infection.


Asunto(s)
Enzima Convertidora de Angiotensina 2/genética , COVID-19/etiología , Proteínas de la Membrana/genética , SARS-CoV-2 , Serina Endopeptidasas/genética , Tupaiidae/genética , Tupaiidae/metabolismo , Secuencia de Aminoácidos , Enzima Convertidora de Angiotensina 2/química , Enzima Convertidora de Angiotensina 2/metabolismo , Animales , Bioingeniería , COVID-19/enzimología , COVID-19/genética , Biología Computacional , Modelos Animales de Enfermedad , Femenino , Humanos , Masculino , Proteínas de la Membrana/química , Proteínas de la Membrana/metabolismo , Modelos Moleculares , Filogenia , Estructura Terciaria de Proteína , Homología de Secuencia de Aminoácido , Serina Endopeptidasas/química , Serina Endopeptidasas/metabolismo , Homología Estructural de Proteína , Distribución Tisular , Tupaiidae/virología
18.
BMC Plant Biol ; 21(1): 305, 2021 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-34193036

RESUMEN

BACKGROUND: Natural variations derived from both evolutionary selection and genetic recombination, presume to have important functions to respond to various abiotic stresses, which could be used to improve drought tolerance via genomic selection. RESULTS: In the present study, the NAC-encoding gene of ZmNAC080308 was cloned and sequenced in 199 inbred lines in maize. Phylogenetic analysis showed that ZmNAC080308 is closely clusteredinto the same group with other well-known NAC genes responding to improve drought tolerance. In total, 86 SNPs and 47 InDels were identified in the generic region of ZmNAC080308, 19 of these variations were associated with GY (grain yield) in different environments. Nine variations in the 5'-UTR region of ZmNAC080308 are closely linked, they might regulate the gene expression and respond to improve GY under drought condition via Sp1-mediated transactivation. Two haplotypes (Hap1 and Hap2) identified in the, 5'-UTR region using the nine variations, and Hap2 containing insertion variants, exhibited 15.47 % higher GY under drought stress condition. Further, a functional marker was developed to predict the drought stress tolerance in a US maize inbred line panel. Lines carrying Hap2 exhibited > 10 % higher GY than those carrying Hap1 under drought stress condition. In Arabidopsis, overexpression ZmNAC080308 enhanced drought tolerance. CONCLUSIONS: ZmNAC080308 is an important gene responding to drought tolerance, a functional marker is developed for improving maize drought tolerance by selecting this gene.


Asunto(s)
Sequías , Variación Genética , Proteínas de Plantas/genética , Semillas/crecimiento & desarrollo , Estrés Fisiológico/genética , Zea mays/genética , Zea mays/fisiología , Regiones no Traducidas 5'/genética , Secuencia de Aminoácidos , Arabidopsis/genética , Núcleo Celular/metabolismo , Regulación de la Expresión Génica de las Plantas , Marcadores Genéticos , Genotipo , Desequilibrio de Ligamiento/genética , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Plantas Modificadas Genéticamente , Polimorfismo de Nucleótido Simple/genética , Plantones/metabolismo , Fracciones Subcelulares/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
19.
Int J Mol Sci ; 22(12)2021 Jun 14.
Artículo en Inglés | MEDLINE | ID: mdl-34198531

RESUMEN

Sesquiterpenes are important defense and signal molecules for plants to adapt to the environment, cope with stress, and communicate with the outside world, and their evolutionary history is closely related to physiological functions. In this study, the information of plant sesquiterpene synthases (STSs) with identified functions were collected and sorted to form a dataset containing about 500 members. The phylogeny of spermatophyte functional STSs was constructed based on the structural comparative analysis to reveal the sequence-structure-function relationships. We propose the evolutionary history of plant sesquiterpene skeletons, from chain structure to small rings, followed by large rings for the first time and put forward a more detailed function-driven hypothesis. Then, the evolutionary origins and history of spermatophyte STSs are also discussed. In addition, three newly identified STSs CaSTS2, CaSTS3, and CaSTS4 were analyzed in this functional evolutionary system, and their germacrene D products were consistent with the functional prediction. This demonstrates an application of the structure-based phylogeny in predicting STS function. This work will help us to understand evolutionary patterns and dynamics of plant sesquiterpenes and STSs and screen or design STSs with specific product profiles as functional elements for synthetic biology application.


Asunto(s)
Transferasas Alquil y Aril/genética , Evolución Molecular , Plantas/enzimología , Sesquiterpenos/metabolismo , Transferasas Alquil y Aril/química , Secuencia de Aminoácidos , Filogenia , Sesquiterpenos/química
20.
BMC Genomics ; 22(1): 506, 2021 Jul 05.
Artículo en Inglés | MEDLINE | ID: mdl-34225643

RESUMEN

BACKGROUND: Teleosts display a spectacular diversity of craniofacial adaptations that often mediates ecological specializations. A considerable amount of research has revealed molecular players underlying skeletal craniofacial morphologies, but less is known about soft craniofacial phenotypes. Here we focus on an example of lip hypertrophy in the benthivorous Lake Tangnayika cichlid, Gnathochromis permaxillaris, considered to be a morphological adaptation to extract invertebrates out of the uppermost layer of mud bottom. We investigate the molecular and regulatory basis of lip hypertrophy in G. permaxillaris using a comparative transcriptomic approach. RESULTS: We identified a gene regulatory network involved in tissue overgrowth and cellular hypertrophy, potentially associated with the formation of a locally restricted hypertrophic lip in a teleost fish species. Of particular interest were the increased expression level of apoda and fhl2, as well as reduced expression of cyp1a, gimap8, lama5 and rasal3, in the hypertrophic lip region which have been implicated in lip formation in other vertebrates. Among the predicted upstream transcription factors, we found reduced expression of foxp1 in the hypertrophic lip region, which is known to act as repressor of cell growth and proliferation, and its function has been associated with hypertrophy of upper lip in human. CONCLUSION: Our results provide a genetic foundation for future studies of molecular players shaping soft and exaggerated, but locally restricted, craniofacial morphological changes in fish and perhaps across vertebrates. In the future, we advocate integrating gene regulatory networks of various craniofacial phenotypes to understand how they collectively govern trophic and behavioural adaptations.


Asunto(s)
Cíclidos , Labio/crecimiento & desarrollo , Transcriptoma , Animales , Cíclidos/genética , Factores de Transcripción Forkhead , Hipertrofia , Proteínas con Homeodominio LIM , Proteínas Musculares , Filogenia , Proteínas Represoras , Factores de Transcripción/genética , Vacio
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