Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 267.408
Filtrar
1.
Planta ; 255(2): 33, 2022 Jan 07.
Artículo en Inglés | MEDLINE | ID: mdl-34997357

RESUMEN

MAIN CONCLUSION: A putative powdery mildew effector can elicit defense responses including reactive oxygen species and callose accumulations in model plants Nicotiana benthamiana and Arabidopsis thaliana and host plant Hevea brasiliensis. Powdery mildew fungi cause severe diseases in many agricultural plants, such as the mildew fungus Erysiphe quercicola infecting the rubber tree (Hevea brasiliensis), causing latex yield losses. However, effectors of E. quercicola were rarely functionally characterized. In this study, we identified a highly specific candidate-secreted effector protein, EqCSEP04187, from E. quercicola. This putative effector is expressed at the late stage but not the early stage during infection. The constitutive expression of EqCSEP04187 in model plants Nicotiana benthamiana and Arabidopsis thaliana elicited defense responses, as did transient expression of EqCSEP04187 in protoplasts of H. brasiliensis. Introducing EqCSEP04187 into another H. brasiliensis-associated fungal pathogen, Colletotrichum gloeosporioides, inhibited H. brasiliensis infection, and infection by E. quercicola was decreased in the A. thaliana eds1 mutant expressing EqCSEP04187. Further analysis suggests that these reductions in infection were the consequences of EqCSEP04187 eliciting defense responses. Our study suggests that this putative effector has elicitor activity that can improve plant resistance.


Asunto(s)
Ascomicetos , Hevea , Enfermedades de las Plantas , Inmunidad de la Planta , Goma , Árboles
2.
Arch Microbiol ; 204(2): 125, 2022 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-34997854

RESUMEN

A study based on a polyphasic taxonomic approach was carried out to identify and classify a novel marine alphaproteobacterium, designated as KMU-140T, isolated from coastal seawater collected at Jeju Island, Republic of Korea. Cells of strain KMU-140T were spherical, Gram-stain-negative, reddish-orange colored, strictly aerobic, catalase- and oxidase-positive, non-motile, and chemoorganoheterotrophic. The novel isolate was able to grow at NaCl concentrations of 0-5%, pH 6.0-9.5, and 10-45 °C. A phylogenetic analysis based on the 16S rRNA gene sequence showed that strain KMU-140T belongs to the family Erythrobacteraceae and was most closely related to Erythrobacter longus OCh101T (98.7%). Strain KMU-140T contained ubiquinone-10 (Q-10) as the only respiratory quinone and C18:1 ω7c, iso-C18:0, and C16:0 as the main (> 10%) cellular fatty acids. Strain KMU-140T produced carotenoid compounds that rendered the cell biomass a reddish-orange color. The assembled draft genome size of strain KMU-140T was 3.04 Mbp with G + C content of 60.6 mol%. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values of KMU-140T and the species of the genus Erythrobacter were found to be 76.6-78.4%, 14.0-18.7%, and 69.6-77.8%, respectively. Phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, and two unidentified lipids were identified as major polar lipids. On the basis of the polyphasic taxonomic features presented, the strain is considered to represent a novel species of the genus Erythrobacter for which the name Erythrobacter rubeus sp. nov. is proposed. The type strain of E. rubeus sp. nov. is KMU-140T (= KCCM 90479T = NBRC 115159T).


Asunto(s)
Sphingomonadaceae , Técnicas de Tipificación Bacteriana , Carotenoides , ADN Bacteriano/genética , Ácidos Grasos/análisis , Filogenia , ARN Ribosómico 16S/genética , Agua de Mar , Análisis de Secuencia de ADN , Sphingomonadaceae/genética
3.
Arch Microbiol ; 204(2): 127, 2022 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-34997867

RESUMEN

Two aerobic, Gram-stain variable, catalase-positive and oxidase-negative rods named strain UniB2T and UniB3T, were isolated from digestive syrup containing fungal diastase (10 mg/ml), pepsin (2 mg/ml) and sugar base containing polyethylene glycol. Based on 16S rRNA gene sequence analysis, strain UniB2T has the highest sequence similarity with Paenibacillus humicus NBRC 102415T (98.3%) and strain UniB3T showed the highest sequence similarity with Niallia circulans DSM 11T (98.9%). The DNA G + C content of UniB2T was 63.7 mol %. The dDDH and ANI values between the strain UniB2T and its phylogenetically close relative were < 38.3% and < 89.5%, respectively. The major fatty acids of the strain UniB2T were C16:0 (13.9%), C15:0 anteiso (39.7%), C17:0 anteiso (15.5%). The DNA G + C content of UniB3T was 35.6 mol %. The dDDH and ANI values between the strain UniB3T and its close relatives were < 29.1% and 84.6%, respectively. The major fatty acids of strain UniB3T were C16:0 (13.5%), C15:0 anteiso (40.1%) and C17:0 anteiso (16.0%). Major polar lipids for both strains were Diphosphatidylglycerol and phosphatidylethanolamine. Both strains showed unique carbon utilization and assimilation pattern that differentiated them from their phylogenetically related neighbours. These phenotypic, genotypic and chemotaxonomic characters indicated the strains UniB2T and UniB3T represent two novel species for which the names Paenibacillus albicereus sp. nov. (Type strain UniB2T = MCC 3997T = KCTC 43095T = JCM34513T) and Niallia alba sp. nov. (Type strain UniB3T = MCC 3998T = KCTC 43235T = JCM 34492T) are proposed.


Asunto(s)
Paenibacillus , Técnicas de Tipificación Bacteriana , ADN Bacteriano/genética , Ácidos Grasos/análisis , Paenibacillus/genética , Filogenia , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Vitamina K 2
4.
Rev Alerg Mex ; 69 Suppl 1: s38-s45, 2022.
Artículo en Español | MEDLINE | ID: mdl-34998309

RESUMEN

Pollen-food syndrome (PFS) is characterized by allergic sensitization to proteins of pollens of grasses, weeds, and trees, which produce a type I hypersensitivity reaction that is associated with the intake of plant-derived foods that are usually in raw form. The most frequently-associated protein families are: profilins, PR-10, and ns LTP; however, others such as thaumatins, isoflavones, reductases, and B1,2 glucanases have been documented. The prototype syndrome is birch-fruit-vegetables, and of these, the most common is birch-apple due to the fact that more than 70 % of patients who are sensitized to birch present symptoms associated with the intake of plant-derived foods. The symptoms are restricted to the oral cavity; however, some patients may present systemic symptoms, including anaphylaxis, so it is important to identify the type of protein that is involved since the type of reaction that the patient may present depends on that. In spite of everything, it is considered an entity that may be under diagnosed due to its complex diagnosis and treatment, since the procedure, in most cases, is an elimination diet, because treatment with immunotherapy is not yet available. The purpose of this review is to describe the pathophysiology, as well as the most common pollen-food syndromes.


Asunto(s)
Hipersensibilidad a los Alimentos , Alérgenos , Reacciones Cruzadas , Hipersensibilidad a los Alimentos/diagnóstico , Frutas , Humanos , Proteínas de Plantas , Polen , Pruebas Cutáneas
5.
J Plant Res ; 135(1): 69-79, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34973093

RESUMEN

Assessing long-term changes in the biomass of old-growth forests with consideration of climate effects is essential for understanding forest ecosystem functions under a changing climate. Long-term biomass changes are the result of accumulated short-term changes, which can be affected by endogenous processes such as gap filling in small-scale canopy openings. Here, we used 26 years (1993-2019) of repeated tree census data in an old-growth, cool-temperate, mixed deciduous forest that contains three topographic units (riparian, denuded slope, and terrace) in northern Japan to document decadal changes in aboveground biomass (AGB) and their processes in relation to endogenous processes and climatic factors. AGB increased steadily over the 26 years in all topographic units, but different tree species contributed to the increase among the topographic units. AGB gain within each topographic unit exceeded AGB loss via tree mortality in most of the measurement periods despite substantial temporal variation in AGB loss. At the local scale, variations in AGB gain were partially explained by compensating growth of trees around canopy gaps. Climate affected the local-scale AGB gain: the gain was larger in the measurement periods with higher mean air temperature during the current summer but smaller in those with higher mean air temperature during the previous autumn, synchronously in all topographic units. The influences of decadal summer and autumn warming on AGB growth appeared to be counteracting, suggesting that the observed steady AGB increase in KRRF is not fully explained by the warming. Future studies should consider global and regional environmental factors such as elevated CO2 concentrations and nitrogen deposition, and include cool-temperate forests with a broader temperature range to improve our understanding on biomass accumulation in this type of forests under climate change.


Asunto(s)
Ecosistema , Bosques , Biomasa , Japón , Árboles
6.
Microb Pathog ; 162: 105375, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34974119

RESUMEN

Enterobacter hormaechei is a zoonotic bacteria that may cause respiratory diseases in animals and neonatal sepsis in humans. Bacteriophages are increasingly considered as potential biocontrol agents to control pathogens in the food industry. In this study, five E. hormaechei virulent phages, named as Ehp-YZU08, Ehp-YZU10, Ehp-YZU9-1, Ehp-YZU9-2 and Ehp-YZU9-3, were isolated from sewage in China and analyzed for their biological and whole-genome characteristics, and a comparative genomic analysis was performed to study the functional genes and phylogenetic evolution of phages. The results showed that four of the phage strains belong to the Podoviridae family and one belongs to the Myoviridae family. The burst sizes were 70-283 PFU/cell after a latent period of 5-40 min. Phages were able to survive in a pH range of 5-10 and resist temperatures up to 60 °C for 60 min. The sequencing results showed that the full length of the genomes of the five phages ranged from 39,502 to 173,418 bp. Each phage contained multiple genes related to phage replication, and genes related to bacterial virulence or drug resistance were not found. The five phages belonged to three different groups by a construction of a phylogenetic tree, and the significant genetic evolutionary distance from each E. hormaechei phage was observed. The inhibition assay showed that all five phages could completely inhibit the growth of E. hormaechei at 37 °C within 8 h, suggesting that the phages in this study have great potential for the development of biocontrol agents against E. hormaechei in the food industry.


Asunto(s)
Bacteriófagos , Animales , Bacteriófagos/genética , Enterobacter , Genoma Viral , Genómica , Humanos , Filogenia
7.
BMC Genomics ; 23(1): 46, 2022 Jan 11.
Artículo en Inglés | MEDLINE | ID: mdl-35016609

RESUMEN

BACKGROUND: Drug resistant Mycobacterium tuberculosis is complicating the effective treatment and control of tuberculosis disease (TB). With the adoption of whole genome sequencing as a diagnostic tool, machine learning approaches are being employed to predict M. tuberculosis resistance and identify underlying genetic mutations. However, machine learning approaches can overfit and fail to identify causal mutations if they are applied out of the box and not adapted to the disease-specific context. We introduce a machine learning approach that is customized to the TB setting, which extracts a library of genomic variants re-occurring across individual studies to improve genotypic profiling. RESULTS: We developed a customized decision tree approach, called Treesist-TB, that performs TB drug resistance prediction by extracting and evaluating genomic variants across multiple studies. The application of Treesist-TB to rifampicin (RIF), isoniazid (INH) and ethambutol (EMB) drugs, for which resistance mutations are known, demonstrated a level of predictive accuracy similar to the widely used TB-Profiler tool (Treesist-TB vs. TB-Profiler tool: RIF 97.5% vs. 97.6%; INH 96.8% vs. 96.5%; EMB 96.8% vs. 95.8%). Application of Treesist-TB to less understood second-line drugs of interest, ethionamide (ETH), cycloserine (CYS) and para-aminosalisylic acid (PAS), led to the identification of new variants (52, 6 and 11, respectively), with a high number absent from the TB-Profiler library (45, 4, and 6, respectively). Thereby, Treesist-TB had improved predictive sensitivity (Treesist-TB vs. TB-Profiler tool: PAS 64.3% vs. 38.8%; CYS 45.3% vs. 30.7%; ETH 72.1% vs. 71.1%). CONCLUSION: Our work reinforces the utility of machine learning for drug resistance prediction, while highlighting the need to customize approaches to the disease-specific context. Through applying a modified decision learning approach (Treesist-TB) across a range of anti-TB drugs, we identified plausible resistance-encoding genomic variants with high predictive ability, whilst potentially overcoming the overfitting challenges that can affect standard machine learning applications.


Asunto(s)
Mycobacterium tuberculosis , Tuberculosis Resistente a Múltiples Medicamentos , Antituberculosos/farmacología , Antituberculosos/uso terapéutico , Árboles de Decisión , Resistencia a Medicamentos , Humanos , Pruebas de Sensibilidad Microbiana , Mutación , Mycobacterium tuberculosis/genética , Tuberculosis Resistente a Múltiples Medicamentos/diagnóstico , Tuberculosis Resistente a Múltiples Medicamentos/tratamiento farmacológico , Tuberculosis Resistente a Múltiples Medicamentos/genética
8.
BMC Mol Cell Biol ; 23(1): 2, 2022 Jan 07.
Artículo en Inglés | MEDLINE | ID: mdl-34991443

RESUMEN

BACKGROUND: SARS-CoV-2, the causative agent of COVID-19 pandemic is a RNA virus prone to mutations. Formation of a stable binding interface between the Receptor Binding Domain (RBD) of SARS-CoV-2 Spike (S) protein and Angiotensin-Converting Enzyme 2 (ACE2) of host is pivotal for viral entry. RBD has been shown to mutate frequently during pandemic. Although, a few mutations in RBD exhibit enhanced transmission rates leading to rise of new variants of concern, most RBD mutations show sustained ACE2 binding and virus infectivity. Yet, how all these mutations make the binding interface constantly favourable for virus remain enigmatic. This study aims to delineate molecular rearrangements in the binding interface of SARS-CoV-2 RBD mutants. RESULTS: Here, we have generated a mutational and structural landscape of SARS-CoV-2 RBD in first six months of the pandemic. We analyzed 31,403 SARS-CoV-2 genomes randomly across the globe, and identified 444 non-synonymous mutations in RBD that cause 49 distinct amino acid substitutions in contact and non-contact amino acid residues. Molecular phylogenetic analysis suggested independent emergence of RBD mutants. Structural mapping of these mutations on the SARS-CoV-2 Wuhan reference strain RBD and structural comparison with RBDs from bat-CoV, SARS-CoV, and pangolin-CoV, all bound to human or mouse ACE2, revealed several changes in the interfacial interactions in all three binding clusters. Interestingly, interactions mediated via N487 residue in cluster-I and Y449, G496, T500, G502 residues in cluster-III remained largely unchanged in all RBD mutants. Further analysis showed that these interactions are evolutionarily conserved in sarbecoviruses which use ACE2 for entry. Importantly, despite extensive changes in the interface, RBD-ACE2 stability and binding affinities were maintained in all the analyzed mutants. Taken together, these findings reveal how SARS-CoV-2 uses its RBD residues to constantly remodel the binding interface. CONCLUSION: Our study broadly signifies understanding virus-host binding interfaces and their alterations during pandemic. Our findings propose a possible interface remodelling mechanism used by SARS-CoV-2 to escape deleterious mutations. Future investigations will focus on functional validation of in-silico findings and on investigating interface remodelling mechanisms across sarbecoviruses. Thus, in long run, this study may provide novel clues to therapeutically target RBD-ACE2 interface for pan-sarbecovirus infections.


Asunto(s)
COVID-19 , SARS-CoV-2 , Animales , Interacciones Microbiota-Huesped , Humanos , Ratones , Mutación , Pandemias , Filogenia , Glicoproteína de la Espiga del Coronavirus/genética
9.
BMC Genomics ; 23(1): 32, 2022 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-34991463

RESUMEN

BACKGROUND: Rubus is the largest genus of the family Rosaceae and is valued as medicinal, edible, and ornamental plants. Here, we sequenced and assembled eight chloroplast (cp) genomes of Rubus from the Dabie Mountains in Central China. Fifty-one Rubus species were comparatively analyzed for the cp genomes including the eight newly discovered genomes and forty-three previously reported in GenBank database (NCBI). RESULTS: The eight newly obtained cp genomes had the same quadripartite structure as the other cp genomes in Rubus. The length of the eight plastomes ranged from 155,546 bp to 156,321 bp with similar GC content (37.0 to 37.3%). The results indicated 133-134 genes were annotated for the Rubus plastomes, which contained 88 or 89 protein coding genes (PCGs), 37 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). Among them, 16 (or 18) of the genes were duplicated in the IR region. Structural comparative analysis results showed that the gene content and order were relatively preserved. Nucleotide variability analysis identified nine hotspot regions for genomic divergence and multiple simple sequences repeats (SSRs), which may be used as markers for genetic diversity and phylogenetic analysis. Phylogenetic relationships were highly supported within the family Rosaceae, as evidenced by sub-clade taxa cp genome sequences. CONCLUSION: Thus, the whole plastome may be used as a super-marker in phylogenetic studies of this genus.


Asunto(s)
Genoma del Cloroplasto , Rubus , Composición de Base , Repeticiones de Microsatélite/genética , Filogenia , Rubus/genética
10.
BMC Genomics ; 23(1): 28, 2022 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-34991465

RESUMEN

BACKGROUND: Histone deacetylases (HDACs) play an important role in the regulation of gene expression, which is indispensable in plant growth, development, and responses to environmental stresses. In Arabidopsis and rice, the molecular functions of HDACs have been well-described. However, systematic analysis of the HDAC gene family and gene expression in response to biotic and abiotic stresses has not been reported for sorghum. RESULTS: We conducted a systematic analysis of the sorghum HDAC gene family and identified 19 SbHDACs mainly distributed on eight chromosomes. Phylogenetic tree analysis of SbHDACs showed that the gene family was divided into three subfamilies: RPD3/HDA1, SIR2, and HD2. Tissue-specific expression results showed that SbHDACs displayed different expression patterns in different tissues, indicating that these genes may perform different functions in growth and development. The expression pattern of SbHDACs under different stresses (high and low temperature, drought, osmotic and salt) and pathogen-associated molecular model (PAMPs) elf18, chitin, and flg22) indicated that SbHDAC genes may participate in adversity responses and biological stress defenses. Overexpression of SbHDA1, SbHDA3, SbHDT2 and SbSRT2 in Escherichia coli promoted the growth of recombinant cells under abiotic stress. Interestingly, we also showed that the sorghum acetylation level was enhanced when plants were under cold, heat, drought, osmotic and salt stresses. The findings will help us to understand the HDAC gene family in sorghum, and illuminate the molecular mechanism of the responses to abiotic and biotic stresses. CONCLUSION: We have identified and classified 19 HDAC genes in sorghum. Our data provides insights into the evolution of the HDAC gene family and further support the hypothesis that these genes are important for the plant responses to abiotic and biotic stresses.


Asunto(s)
Sorghum , Regulación de la Expresión Génica de las Plantas , Histona Desacetilasas/genética , Histona Desacetilasas/metabolismo , Patrón Molecular Asociado a Patógenos , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Sorghum/genética , Sorghum/metabolismo , Estrés Fisiológico/genética
11.
BMC Genomics ; 23(1): 27, 2022 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-34991482

RESUMEN

BACKGROUND: Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. RESULTS: The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisting of Aesculus chinensis and A. wangii and strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. CONCLUSION: This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.


Asunto(s)
Genoma del Cloroplasto , Sapindaceae , Animales , Especies en Peligro de Extinción , Genómica , Filogenia , Sapindaceae/genética
12.
Parasitol Res ; 121(1): 155-166, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34993630

RESUMEN

Rhabdias Stiles and Hassal, 1905 comprises approximately 90 species of parasitic lung nematodes of amphibians and reptiles that have a wide distribution, with 21 species occurring in the Neotropics. In the present study, we describe Rhabdias waiapi n. sp. found parasitizing the lungs of the anuran species Pristimantis chiastonotus from the Amazon Biome in the Amapá State, Northern Brazil. The new species is characterized by having an elongated body, expansions of the cuticular inflation in the anterior end that become more discrete along the body, an anterior end with a slight constriction at the level of the esophageal apex with four rounded subapical elevations of the body wall, six lips, four near the edge of the oral opening and two more distant lateral ones, and a gradually tapering elongated tail. In addition, molecular analyses and phylogenetic reconstructions were made, with sequences from the coding region of the mitochondrial cytochrome c oxidase subunit I gene. Those results strongly support the status of the new taxon, which formed a poorly supported clade with Rhabdias sp. 5 from Anolis brasiliensis from Northeast Brazil. Rhabdias waiapi n. sp. is the 19th species of the genus described in the Neotropics for amphibians, the 10th in Brazil, the second described from hosts of the family Strabomantidae from the Neotropical region, and the first amphibian nematode species described in the Amapá State.


Asunto(s)
Nematodos , Parásitos , Animales , Anuros , Brasil , Pulmón , Filogenia
13.
Parasitol Res ; 121(1): 395-402, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34993636

RESUMEN

Theileria orientalis is known to be a group of benign cattle parasites with a cosmopolitan distribution, and has been classified into 11 genotypes through MPSP gene phylogenetic analysis. In China, T. orientalis is the most prevalent Theileria species, with several genotypes, but few fatal cases have been reported. In June 2020, dairy cattle in Zhangjiakou, Hebei Province, showed clinical symptoms of piroplasmosis, causing many animals to die. Blood smears and PCR detection results confirmed T. orientalis infection with a 66.7% positive rate of collected blood samples. The MPSP sequences analysis revealed parasite genotypes 1 (Chitose) and 2 (Ikeda). Aiming to isolate the pathogens, experimental animal was infected with T. orientalis via inoculation of the positive blood samples. The results has shown that only T. orientalis genotype 2 (Ikeda) was obtained that has confirmed by MPSP and 18S rRNA sequences analysis, indicating that the Ikeda type was predominant and responsible for the disease. Although many T. orientalis genotypes are present in China, the possibility of T. orientalis genotypes 1 and 2 infections in confined dairy cattle should be considered to avoid additional economic losses.


Asunto(s)
Enfermedades de los Bovinos , Theileria , Theileriosis , Animales , Bovinos , Genotipo , Filogenia , ARN Ribosómico 18S , Theileria/genética
14.
BMC Genomics ; 23(1): 38, 2022 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-34998383

RESUMEN

BACKGROUND: The coronatine insensitive 1 (COI1) gene is the core member of jasmonate signaling pathway, which is closely related to plant biotic and abiotic resistance. However, there have been no reports on COI1 in sugarcane (Sacharum spp.). Hence, systematically investigating the characteristics of the COI1 multigene family in sugarcane can provide a means to study and manipulate the jasmonic acid signaling pathway. RESULTS: A total of 156 COI1 proteins were obtained from the genomes of 19 land plants, while none were obtained from five algae species. A phylogenetic tree demonstrated that these COI1 proteins were classified into four groups, while 31 proteins of SsCOI1 from Saccharum spontaneum, SbCOI1 from Sorghum bicolor, and ShCOI1 from Saccharum spp. hybrid cultivar R570 clustered into three groups. Synteny analysis and duplication patterns revealed that COI1 genes expanded through various genome replication events and could have experienced strong purifying selective pressure during evolution in S. spontaneum, S. bicolor, and R570. An investigation of cis-acting elements suggests that COI1 genes may be involved in plant growth and development and response to various stresses. Expression analysis implied that 21 SsCOI1 genes were constitutively expressed, and had positive responses to drought, cold, and Sporisorium scitamineum stresses with different expression patterns. Among them, seven SsCOI1 haplotype genes may play different roles in response to methyl jasmonate. Furthermore, the ShCOI1-4, ShCOI1-5, and ShCOI1-6 genes were cloned from Saccharum spp. hybrid cultivar ROC22. Real-time quantitative PCR (RT-qPCR) analysis demonstrated that these three ShCOI1 genes had divergent expression profiles in response to salicylic acid, abscisic acid, polyethylene glycol, cold, and S. scitamineum. CONCLUSIONS: These results suggest that COI1 genes may act in sugarcane growth, development, and response to various stresses via different regulatory mechanisms, which laying a foundation for the functional identification of the sugarcane COI1 gene.


Asunto(s)
Saccharum , Aminoácidos , Regulación de la Expresión Génica de las Plantas , Indenos , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Saccharum/genética , Saccharum/metabolismo , Estrés Fisiológico/genética
15.
Biol Res ; 55(1): 1, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-35012672

RESUMEN

BACKGROUND: Maize (Zea mays L.) is a widely cultivated cereal and has been used as an optimum heavy metal phytoremediation crop. Metallothionein (MT) proteins are small, cysteine-rich, proteins that play important roles in plant growth and development, and the regulation of stress response to heavy metals. However, the MT genes for maize have not been fully analyzed so far. METHODS: The putative ZmMT genes were identified by HMMER.The heat map of ZmMT genes spatial expression analysis was generated by using R with the log2 (FPKM + 1).The expression profiles of ZmMT genes under three kinds of heavy metal stresses were quantified by using qRT-PCR. The metallothionein proteins was aligned using MAFFT and phylogenetic analysis were constructed by ClustalX 2.1. The protein theoretical molecular weight and pI, subcellular localization, TFs binding sites, were predicted using ProtParam, PSORT, PlantTFDB, respectively. RESULTS: A total of 9 ZmMT genes were identified in the whole genome of maize. The results showed that eight of the nine ZmMT proteins contained one highly conserved metallothio_2 domain, while ZmMT4 contained a Metallothio_PEC domain. All the ZmMT proteins could be classified into three major groups and located on five chromosomes. The ZmMT promoters contain a large number of hormone regulatory elements and hormone-related transcription factor binding sites. The ZmMT genes exhibited spatiotemporal specific expression patterns in 23 tissues of maize development stages and showed the different expression patterns in response to Cu, Cd, and Pb heavy metal stresses. CONCLUSIONS: We identified the 9 ZmMT genes, and explored their conserved motif, tissue expression patterns, evolutionary relationship. The expression profiles of ZmMT genes under three kinds of heavy metal stresses (Cu, Cd, Pb) were analyzed. In summary, the expression of ZmMTs have poteintial to be regulated by hormones. The specific expression of ZmMTs in different tissues of maize and the response to different heavy metal stresses are revealed that the role of MT in plant growth and development, and stress resistance to heavy metals.


Asunto(s)
Metales Pesados , Zea mays , Regulación de la Expresión Génica de las Plantas , Metalotioneína/genética , Metalotioneína/metabolismo , Filogenia , Proteínas de Plantas/genética , Estrés Fisiológico
16.
Arch Microbiol ; 204(2): 129, 2022 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-34999970

RESUMEN

A novel endophytic strain, designated YIM B02564T, was isolated from the root of Paris polyphylla Smith var. yunnanensis obtained from Yunnan Province, southwest China. By using a polyphasic approach, cells of the strain were characterized as facultative anaerobic, Gram-positive and rod-shaped. The growth conditions of the strain were found to occur at 20-55 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, pH 7.0). Strain YIM B02564T can tolerate 2% NaCl concentration. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM B02564T belonged to the genus Neobacillus and the 16S rRNA gene sequence similarity values of strain YIM B02564T to the type strains of members of this genus ranged from 95.6 to 97.8%. The DNA G+C content of strain YIM B02564T calculated from the whole genome sequence was 41.6 mol%. Values of the ANI and the dDDH between strain YIM B02564T and its closely related Neobacillus species were below 77.9% and 21.5%. Strain YIM B02564T contained MK-7 as the major menaquinone, iso-C15:0 and anteiso-C15:0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and four unidentified lipids. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. On the basis of polyphasic analysis, strain YIM B02564T could be differentiated genotypically and phenotypically from recognized species of the genus Neobacillus. The isolate therefore represents a novel species, for which the name Neobacillus paridis is proposed. The type strain is YIM B02564T (= JCM 34668T = CGMCC 1.18655T).


Asunto(s)
Endófitos , Liliaceae , Técnicas de Tipificación Bacteriana , China , ADN Bacteriano/genética , Endófitos/genética , Ácidos Grasos/análisis , Hibridación de Ácido Nucleico , Fosfolípidos , Filogenia , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN
17.
Curr Microbiol ; 79(2): 63, 2022 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-35000019

RESUMEN

A novel acidophilic fungal strain isolated from snottites in the active sulfuric acid speleogenesis (SAS) Sheki-Heh Cave (North Caucasus, Chechen Republic) was identified and characterized. The Sheki-Heh Cave is one of three cavities of the joint SAS speleosystem; to date, it remains the only of such cave explored in Russia. Highly acidic biofilms termed snottites are found sporadically on the cave roof in sulfurous water degassing zones. Only dark-colored micromycete colonies were isolated from these microbial biofilms using direct inoculation onto Czapek agar. The dominant fungal isolate was selected for further characterization. This work aimed to identify the micromycete strain isolated from cave snottites and explore its growth characteristics. Based on the phylogenetic analysis of the rDNA ITS region (540 bp), the novel fungal strain was identified as Acidomyces acidophilum with a similarity level of 99.26%. The physiological properties of the strain were examined; the optimal pH and temperature for its growth were pH 3 and 20-28 °C, respectively. Strain IB-G85 is able to grow under NaCl concentrations up to 3%. Although IB-G85 was isolated from an oligotrophic environment and was growing under nutrient deficiency, it could utilize some sugars and proteins as well as recalcitrant substrates, such as chitin and tannin. Compared to base Czapek-Dox Agar, lactic acid and colloidal chitin as the sole carbon sources enhanced fungal growth by 100 and 59%, respectively. The occurrence of A. acidophilum and closely related fungal species within acidophilic microbial communities inhabiting sulfur-containing ecosystems is discussed in view of their contribution to snottite structure formation in SAS caves.


Asunto(s)
Cuevas , Microbiota , Biopelículas , Filogenia , ARN Ribosómico 16S/genética , Azufre
18.
Sensors (Basel) ; 22(1)2022 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-35009920

RESUMEN

The article presents an extensive analysis of the literature related to the diagnosis of the extrusion process and proposes a new, unique method. This method is based on the observation of the punch displacement signal in relation to the die, and then approximation of this signal using a polynomial. It is difficult to find in the literature even an attempt to solve the problem of diagnosing the extrusion process by means of a simple distance measurement. The dominant feature is the use of strain gauges, force sensors or even accelerometers. However, the authors managed to use the displacement signal, and it was considered a key element of the method presented in the article. The aim of the authors was to propose an effective method, simple to implement and not requiring high computing power, with the possibility of acting and making decisions in real time. At the input of the classifier, authors provided the determined polynomial coefficients and the SSE (Sum of Squared Errors) value. Based on the SSE values only, the decision tree algorithm performed anomaly detection with an accuracy of 98.36%. With regard to the duration of the experiment (single extrusion process), the decision was made after 0.44 s, which is on average 26.7% of the extrusion experiment duration. The article describes in detail the method and the results achieved.


Asunto(s)
Algoritmos , Árboles de Decisión
19.
BMC Genomics ; 23(1): 40, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-35012446

RESUMEN

BACKGROUND: RADIALIS (RAD), belongs to the MYB gene family and regulates a variety of functions including floral dorsoventral asymmetry in Antirrhinum majus and development of fruit proteins in Solanum lycopersicum. RAD genes contain an SNF2_N superfamily domain. Here, we comprehensively identified 68 RAD genes from six different species including Arabidopsis and five species of cotton. RESULTS: Phylogenetic analysis classified RAD genes into five groups. Gene structure, protein motifs and conserved amino acid residues indicated that GhRAD genes were highly conserved during the evolutionary process. Chromosomal location information showed that GhRAD genes were distributed unevenly on different chromosomes. Collinearity and selection pressure analysis indicated RAD gene family expansion in G. hirsutum and G. barbadense with purifying selection pressure. Further, various growth and stress related promotor cis-acting elements were observed. Tissue specific expression level indicated that most GhRAD genes were highly expressed in roots and flowers (GhRAD2, GhRAD3, GhRAD4 and GhRAD11). Next, GhRAD genes were regulated by phytohormonal stresses (JA, BL and IAA). Moreover, Ghi-miRN1496, Ghi-miR1440, Ghi-miR2111b, Ghi-miR2950a, Ghi-miR390a, Ghi-miR390b and Ghi-miR7495 were the miRNAs targeting most of GhRAD genes. CONCLUSIONS: Our study revealed that RAD genes are evolutionary conserved and might be involved in different developmental processes and hormonal stress response. Data presented in our study could be used as the basis for future studies of RAD genes in cotton.


Asunto(s)
Regulación de la Expresión Génica de las Plantas , Genes de Plantas , Gossypium/genética , Familia de Multigenes , Flores/fisiología , Filogenia , Reguladores del Crecimiento de las Plantas , Proteínas de Plantas/genética , Estrés Fisiológico
20.
BMC Genomics ; 23(1): 43, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-35012465

RESUMEN

BACKGROUND: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms. RESULTS: We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264-364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring. CONCLUSIONS: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.


Asunto(s)
Poaceae , Polimorfismo de Nucleótido Simple , Asia , Secuenciación de Nucleótidos de Alto Rendimiento , Filogenia , Poaceae/genética
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA
...