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1.
Braz. j. biol ; 84: e255235, 2024. tab, graf
Artículo en Inglés | LILACS, VETINDEX | ID: biblio-1355897

RESUMEN

Abstract In soybean breeding program, continuous selection pressure on traits response to yield created a genetic bottleneck for improvements of soybean through hybridization breeding technique. Therefore an initiative was taken to developed high yielding soybean variety applying mutation breeding techniques at Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Bangladesh. Locally available popular cultivar BARI Soybean-5 was used as a parent material and subjected to five different doses of Gamma ray using Co60. In respect to seed yield and yield attributing characters, twelve true breed mutants were selected from M4 generation. High values of heritability and genetic advance with high genotypic coefficient of variance (GCV) for plant height, branch number and pod number were considered as favorable attributes for soybean improvement that ensure expected yield. The mutant SBM-18 obtained from 250Gy provided stable yield performance at diversified environments. It provided maximum seed yield of 3056 kg ha-1 with highest number of pods plant-1 (56). The National Seed Board of Bangladesh (NSB) eventually approved SBM-18 and registered it as a new soybean variety named 'Binasoybean-5' for large-scale planting because of its superior stability in various agro-ecological zones and consistent yield performance.


Resumo No programa de melhoramento da soja, a pressão pela seleção contínua para a resposta das características de rendimento criou um gargalo genético para melhorias da soja por meio da técnica de melhoramento por hibridação. Portanto, foi desenvolvida uma variedade de soja de alto rendimento, aplicando técnicas de reprodução por mutação, na Divisão de Melhoramento de Plantas, no Instituto de Agricultura Nuclear de Bangladesh (BINA), em Bangladesh. A cultivar popular BARI Soybean-5, disponível localmente, foi usada como material original e submetida a cinco doses diferentes de raios gama usando Co60. Em relação ao rendimento de sementes e às características de atribuição de rendimento, 12 mutantes genuínos foram selecionados a partir da geração M4. Altos valores de herdabilidade e avanço genético com alto coeficiente de variância genotípico (GCV) para altura da planta, número de ramos e número de vagens foram considerados atributos favoráveis ​​ao melhoramento da soja, garantindo, assim, a produtividade esperada. O mutante SBM-18, obtido a partir de 250Gy, proporcionou desempenho de rendimento estável em ambientes diversificados e produtividade máxima de sementes de 3.056 kg ha-1 com o maior número de vagens planta-1 (56). O Conselho Nacional de Sementes de Bangladesh (NSB) finalmente aprovou o SBM-18 e o registrou como uma nova variedade de soja, chamada 'Binasoybean-5', para plantio em larga escala por causa de sua estabilidade superior em várias zonas agroecológicas e desempenho de rendimento consistente.


Asunto(s)
Soja/crecimiento & desarrollo , Soja/genética , Fenotipo , Bangladesh , Fitomejoramiento , Genotipo , Mutación
2.
Braz. j. biol ; 84: e256933, 2024. tab, ilus
Artículo en Inglés | LILACS, VETINDEX | ID: biblio-1364505

RESUMEN

Anticarsia gemmatalis Hünber, 1818 is one of the main defoliating species in the soybean crop. Bacillus thuringiensis Berliner, 1915, is a bacterium used in the biological control of this pest species. Resistant populations and their sublethal effects caused by the use of the bacteria have already been reported; however, there are no studies on phenotypic plasticity in adulthood exposed to Bt-based bioinsecticide sub-doses. This study aimed to evaluate the morphometry of A. gemmatalis adults under laboratory conditions submitted to the Bt-based bioinsecticide Dipel® over the three generations. The body segments mensuread were width, length, and area of the anterior and posterior wings, the weight of the integument, chest, abdomen, wings, and the whole adult of males and females. Among the treatments, LC5 in the first generation and LC10 in the second generation were those with lower thresholds in relation to the weight of the chest and abdomen, considering the proportions of the body smaller than the females. The female's weight adulthood was reduced by 10% about males, and, only in the first generation. Males have larger body size and more pronounced phenotypic plasticity than females. Here, we demonstrate the first study assessing the phenotypic plasticity of A. gemmatalis adults.


Anticarsia gemmatalis Hünber, 1818 é uma das principais espécies desfolhadoras da cultura da soja. Bacillus thuringiensis Berliner, 1915, é uma bactéria utilizada no controle biológico dessa espécie de praga. Populações resistentes e seus efeitos subletais causados pelo uso da bactéria já foram relatados, no entanto, não há estudos sobre a plasticidade fenotípica na idade adulta exposta a subdoses de bioinseticida à base de Bt. Este trabalho teve como objetivo avaliar a morfometria de adultos de A. gemmatalis em condições de laboratório submetidos ao bioinseticida Dipel® ao longo de três gerações. Os segmentos corporais mensuráveis eram largura, comprimento e área das asas anterior e posterior, o peso do tegumento, tórax, abdômen, asas e todo o adulto de machos e fêmeas. Dentre os tratamentos, CL5 na primeira geração e CL10 na segunda geração foram aqueles com limiares mais baixos em relação ao peso do tórax e abdômen, considerando as proporções do corpo menores que as do sexo feminino. O peso da fêmea na idade adulta foi reduzido em 10% em relação aos machos e, apenas na primeira geração. Os machos têm tamanho corporal maior e plasticidade fenotípica mais pronunciada do que as fêmeas. Este estudo demonstra o primeiro estudo avaliando a plasticidade fenotípica de adultos de A. gemmatalis.


Asunto(s)
Animales , Fenotipo , Soja , Bacillus thuringiensis , Control Biológico de Vectores
3.
Oxid Med Cell Longev ; 2022: 4564471, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35308167

RESUMEN

The polarization of microglia is recognized as a crucial factor in reducing neuroinflammation and promoting hematoma clearance after intracerebral hemorrhage (ICH). Previous studies have revealed that redox components participate in the regulation of microglial polarization. Recently, the novel Nrf2 activator omaveloxolone (Omav) has been validated to improve neurological function in patients with neurodegenerative disorders by regulating antioxidant responses. In this study, we examined the efficacy of Omav in ICH. Omav significantly promoted Nrf2 nuclear accumulation and the expression of HO-1 and NQO1 in BV2 cells. In addition, both in vitro and in vivo experiments showed that Omav treatment inhibited M1-like activation and promoted the activation of the M2-like microglial phenotype. Omav inhibited OxyHb-induced ROS generation and preserved the function of mitochondria in BV2 cells. Intraperitoneal administration of Omav improved sensorimotor function in the ICH mouse model. Importantly, these effects were blocked by pretreatment with ML385, a selective inhibitor of Nrf2. Collectively, Omav modulated microglial polarization by activating Nrf2 and inhibiting ROS generation in ICH models, suggesting that it might be a promising drug candidate for the treatment of ICH.


Asunto(s)
Lesiones Encefálicas , Microglía , Animales , Lesiones Encefálicas/tratamiento farmacológico , Hemorragia Cerebral/complicaciones , Hemorragia Cerebral/tratamiento farmacológico , Hemorragia Cerebral/metabolismo , Humanos , Ratones , Microglía/metabolismo , Factor 2 Relacionado con NF-E2/metabolismo , Fenotipo , Triterpenos
4.
Front Public Health ; 10: 922863, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36091521

RESUMEN

Background: This study aimed to explore the relationship between iron markers and metabolic obesity phenotypes and the role of age. Methods: Data were from the China Health and Nutrition Survey 2009. Metabolic obesity phenotypes included metabolically healthy with normal weight (MHNW), metabolically unhealthy with normal weight (MUNW), metabolically healthy with overweight/obesity (MHO), and metabolically unhealthy with overweight/obesity (MUO). Iron markers including ferritin, transferrin, and soluble transferrin receptor were calculated as Log and quartered. The linear regression and multinomial logistic regression were used to explore the association of iron markers with age and metabolic obesity phenotypes, respectively. Results: Ferritin was linearly related with age, with ß (95% confidence interval, CI) of 0.029 (0.027 to 0.032) and -0.005 (-0.007 to -0.002) for women and men. Transferrin was negatively associated with age in both men and women (ß < -0.011). Furthermore, compared with participants in the quartile 1 ferritin group, those in the quartile 4 had increased odds of MUNW, MHO, and MUO, with odds ratio and 95% confidence interval (OR, 95% CI) of 3.06 (2.20 to 4.25), 1.66 (1.35 to 2.05), and 5.27 (4.17 to 6.66). Transferrin showed similar relationships with MUNW, MUO, and MHO; whereas transferrin receptor showed no significance. We also found joint associations of ferritin and transferrin with MUNW, MUO, and MHO. The interactive effect of ferritin and transferrin on MUO was significant (P = 0.015). Conclusion: Increased ferritin and transferrin were associated with MUNW, MHO, and MUO. Age should be considered when investigating iron.


Asunto(s)
Obesidad Metabólica Benigna , Sobrepeso , China/epidemiología , Femenino , Ferritinas , Humanos , Hierro , Encuestas Nutricionales , Obesidad/epidemiología , Fenotipo , Receptores de Transferrina , Transferrina
5.
Tumour Biol ; 44(1): 171-185, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36093649

RESUMEN

BACKGROUND: Hereditary ovarian cancers (HOC) represent about 23% of ovarian cancer (OC) cases: they are most frequently related to germline mutations in the BRCA genes. OBJECTIVE: We aimed to compare CA125/HE4 serum levels and Computed Tomography (CT) features at time of ovarian cancer (OC) diagnosis in two populations: BRCA mutant and BRCA wild-type (WT) OC, and to investigate the relationship between this laboratory and radiological biomarker and BRCA mutation status. METHODS: This retrospective study included 60 newly diagnosed OC patients with FIGO stage IIIC-IV disease, tested for BRCA1/2 germline mutation status of which preoperative CT scan and serum tumor marker assay were available. RESULTS: The median level of CA125 (708 U/mL) was significantly higher (p < 0.002) in BRCA1/2 mutated patients than in WT patients (176 U/mL), whereas the median level of HE4 (492 pmol/L) was significantly higher (p < 0.002) in WT than in BRCA-mutated patients (252 pmol/L). BRCA mutation carriers showed a higher incidence of bilateral ovarian masses (p = 0.0303) characterized by solid structures (p < 0.00001), higher peritoneal tumor load, macronodular implants >2 cm (p = 0.000099), increased frequency of lymphadenopathies (p = 0.019), and metastasis (p = 0.052) compared to patients with BRCA WT. CONCLUSIONS: Tumor markers and CT patterns may help in identifying BRCA mutation status in OC directing patients towards a personalized treatment.


Asunto(s)
Antígeno Ca-125 , Neoplasias Ováricas , Biomarcadores de Tumor/genética , Carcinoma Epitelial de Ovario , Femenino , Humanos , Neoplasias Ováricas/diagnóstico por imagen , Neoplasias Ováricas/genética , Neoplasias Ováricas/patología , Fenotipo , Estudios Retrospectivos , Tomografía Computarizada por Rayos X
6.
Methods Mol Biol ; 2543: 113-128, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36087263

RESUMEN

Phosphoflow is a powerful tool that allows researchers to measure distinct signaling responses to various stimuli in multiple subpopulations of cells. Extension of this technique to mass cytometry (cytometry by time-of-flight or CyTOF) allows many more cell phenotypes and signaling nodes to be interrogated in parallel. The use of fresh whole blood is ideal for capturing the in vivo signaling state of all leukocytes, including granulocytes. In this chapter, we provide a detailed protocol for performing CyTOF phosphoflow in human whole blood, using cytokines and other stimuli. Barcoding and combining of multiple samples and other techniques to reduce batch effects and provide optimal comparability between samples/stimulations are also described.


Asunto(s)
Pruebas Inmunológicas , Transducción de Señal , Citocinas , Citometría de Flujo/métodos , Humanos , Fenotipo
8.
Trop Anim Health Prod ; 54(5): 303, 2022 Sep 15.
Artículo en Inglés | MEDLINE | ID: mdl-36107255

RESUMEN

Feed restriction (FR) occurs commonly in sheep production systems in the Brazilian semi-arid region and can cause physiological changes in the progeny. We assessed the effects of the FR pre and postnatal on the performance and carcass traits of Morada Nova lambs. Twenty-four lambs born from a group of 68 ewes were distributed in three treatments of 8 replicates as follows: ewes fed ad libitum pre and postnatal (AL-AL); postnatal restriction (POSTN-R): included lambs born from ewes fed ad libitum in the last third of pregnancy with FR postnatal; and prenatal feeding restriction (PREN-AL): comprised lambs born from ewes subjected to FR in the last third of pregnancy but ad libitum postnatal. Slaughter body weight (20.96 kg); total weight gain (11.34 kg); average daily weight (0.096 kg); fasting carcass weight (19.45); hot carcass weight (9.33 kg); and cold carcass weight (9.11 kg) were smaller (P < 0.05) in POSTN-R but similar between AL-AL and PREN-AL. Rib (0.47 kg), shoulder (0.85 kg), loin (0.50 kg), and chest-flank (0.97 kg) had lower weight in lambs under POSTN-R (P < 0.05). The treatments did not affect the tissue composition of the 12th rib. The non-carcass components and carcass traits are the variables that best discriminate animals under FR plans. The postpartum FR in native lambs has an impact on the performance and carcass weight of the progeny, unlike lambs submitted to prepartum FR, which demonstrates the adaptation to intrauterine nutritional deficiency in Morada Nova ewes to produce lambs with heavy carcasses in regions semi-arid.


Asunto(s)
Periodo Posparto , Aumento de Peso , Animales , Femenino , Cabello , Parto , Fenotipo , Embarazo , Ovinos
9.
Shanghai Kou Qiang Yi Xue ; 31(2): 201-204, 2022 Apr.
Artículo en Chino | MEDLINE | ID: mdl-36110081

RESUMEN

PURPOSE: To identify the microbial characteristics and diversity in supragingival plaque and caries tissue of patients with different dental caries phenotypes. METHODS: From January 2019 to December 2019, randomized double-blind method was used to select 10 healthy people without caries and 33 patients with caries of mild, moderate and severe degrees in dental clinic of our hospital. Supragingival plaque and caries tissues were collected, and detected by pyrosequencing through amplification of the 16S rRNA-cDNA hypervariable regions. Then the microbial species and relative abundance were compared among patients with different severity degrees. SPSS 23.0 software package was used to analyze the data. RESULTS: Compared with non-caries group, the content and abundance of microorganisms in supragingival plaque and carious tissue of caries group were significantly decreased (P<0.05). The main caries tissue of three severity degree groups were dominated by Bacteroidetes, Spirochaetes, Proteobacteria, Fusobacteria, Firmicutes and Actinobacteria, and the proportion of the predominant bacteria had significant difference among three groups(P<0.05). There were 21 species of supragingival bacteria in three groups, among which Fusobacteriales, Coriobacteriales, Neisseriales, Actinomycetales and Lactobacillales accounted for a high proportion, and the remainings were all below 1%, while the proportion of five main bacteria showed no significant difference among three groups (P>0.05). CONCLUSIONS: Caries is caused by a variety of bacteria, and is the result of microbial communities rather than a single pathogen; Moreover, the microbial abundance of plaque and caries tissue vary among patients with different dental caries phenotypes, and the microbial diversity has a decreasing trend in the progress of dental caries.


Asunto(s)
Caries Dental , Placa Dental , Bacterias/genética , ADN Complementario , Humanos , Fenotipo , ARN Ribosómico 16S/genética
10.
Biomed Res Int ; 2022: 8537959, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36119932

RESUMEN

Tendon-derived stem cells (TDSCs) play a vital role in repair of rotator cuff tear injuries by secreting paracrine proteins that regulate resident cell functions. Secreted exosomes may play a role in tendon injury repair by mediating intercellular communication; however, the detailed mechanisms by which TDSC-derived exosomes affect tenocyte development remain unknown. Here, we examined the effects of exosomes isolated from conditioned medium of TDSCs on tenocyte differentiation, migration, and transition to a fibroblastic phenotype in vitro. Successful isolation of exosomes from TDSCs was confirmed by high expression levels of CD81, CD63, CD9, and TSG101. Treatment with TDSC-derived exosomes promoted the growth and migration of cultured rat tenocytes, and increased the levels of the fibrosis markers collagen I, collagen III, scleraxis, tenascin C, and α-smooth muscle actin. Furthermore, vascular endothelial growth factor A (VEGFA) expression was higher in TDSC-derived exosomes than in TDSCs, and genetic knockdown of VEGFA suppressed the stimulatory effect of TDSC-derived exosomes on tenocyte development. Overall, these results demonstrate that VEGFA-enriched exosomes isolated from TDSCs promote differentiation and migration of cultured tenocytes and their transition to a fibroblastic phenotype. These data provide a new potential clinical treatment strategy for tendon injury.


Asunto(s)
Exosomas , Traumatismos de los Tendones , Actinas/metabolismo , Animales , Colágeno/metabolismo , Medios de Cultivo Condicionados/farmacología , Fenotipo , Ratas , Células Madre/metabolismo , Tenascina/metabolismo , Traumatismos de los Tendones/terapia , Tendones/metabolismo , Tenocitos , Factor A de Crecimiento Endotelial Vascular/metabolismo
11.
Physiol Rep ; 10(17): e15459, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-36065883

RESUMEN

Eight Constitution Medicine (ECM), a ramification of traditional Korean medicine, has categorized people into eight constitutions. The main criteria of classification are inherited differences or predominance in the functions of organs, such as the liver or lung, diagnosed through ECM-specific pulse patterns. This study investigated the association between single nucleotide polymorphism (SNP) genotypes and ECM phenotypes and explored candidate genetic makeups responsible for each constitution using a genome-wide association study (GWAS). Sixty-three healthy volunteers, who were either categorized as the Hepatonia (HEP, n = 32) or Pulmotonia (PUL, n = 31) constitution, were enrolled. HEP and PUL are two contrasting ECM types representing the dominant liver and lung phenotypes, respectively. SNPs were analyzed from the oral mucosa DNA using a commercially available microarray chip that can identify 820,000 SNPs. We conducted GWAS using logistic regression analysis and additive mode genotypes and constructed phylogenetic trees using the SNPhylo program with 8 SNPs specific for the liver phenotype and 15 SNPs for the lung phenotype. Although genome-wide significant SNPs were not found, the phylogenetic tree showed a clear difference between the two constitutions. This is the first observation suggesting genetic involvement in the ECM and can be extended to all ECM constitutions.


Asunto(s)
Estudio de Asociación del Genoma Completo , Polimorfismo de Nucleótido Simple , Genotipo , Humanos , Hígado , Pulmón , Fenotipo , Filogenia , República de Corea
12.
J Anat ; 241(4): 896-918, 2022 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-36082500

RESUMEN

Descriptive morphology of tooth roots traditionally focuses on number of canals and roots. However, how or if canal and root number are related is poorly understood. While it is often assumed that canal number is concomitant with root number and morphology, in practice canal number and morphology do not always covary with external root features. To investigate the relationship between canal and root number, fully developed, adult post-canine teeth were examined and quantified from computerized tomography scans from a global sample of 945 modern humans. We tested the hypotheses that root and canal number do not follow a 1:1 ratio, that canal to root ratios differ between teeth, and that canal to root ratios differ across major human geographical groups. Results indicate that not only is root number dependent on canal number, but that this relationship becomes more variable as canal number increases, varies between individual teeth and by major geographical group, and changes as these groups increase in geographical distance from Sub-Saharan Africa. These results show that the ratio of canal number to root number is an important indicator of variation in dental phenotypes.


Asunto(s)
Tomografía Computarizada de Haz Cónico , Raíz del Diente , Adulto , Tomografía Computarizada de Haz Cónico/métodos , Diente Canino , Cavidad Pulpar/diagnóstico por imagen , Humanos , Fenotipo , Tomografía Computarizada por Rayos X , Raíz del Diente/anatomía & histología , Raíz del Diente/diagnóstico por imagen
13.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 39(9): 979-982, 2022 Sep 10.
Artículo en Chino | MEDLINE | ID: mdl-36082569

RESUMEN

OBJECTIVE: To explore the genetic basis for a neonate featuring developmental delay. METHODS: Clinical examination and laboratory tests were carried out for the patient. Peripheral venous blood samples of the proband and his parents were extracted and subjected to target capture next generation sequencing. Candidate variant was verified by Sanger sequencing. RESULTS: The patient, a four-month-old male, has presented with developmental delay and weakness of limbs. Genetic testing revealed that he had harbored a novel c.1432C>T variant of the TNPO3 gene, which was inherited from his mother. The nonsense variant has resulted in premature termination of protein translation and was predicted to be pathogenic by bioinformatics analysis. CONCLUSION: The heterozygous c.1432C>T variant of the TNPO3 gene probably underlay the limb-girdle muscular dystrophies form 1F in this patient. Above finding has enriched the variation spectrum of the TNPO3 gene.


Asunto(s)
Distrofia Muscular de Cinturas , Pruebas Genéticas , Heterocigoto , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Lactante , Masculino , Distrofia Muscular de Cinturas/genética , Mutación , Fenotipo , beta Carioferinas/genética
14.
Oncol Rep ; 48(4)2022 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-36082807

RESUMEN

The present study aimed to investigate the clinical and biological significance of Src­associated in mitosis 68 kDa (Sam68) in oral squamous cell carcinoma (OSCC). Immunohistochemical analysis was performed on tissue samples obtained from 77 patients with OSCC. Univariate analysis revealed that the high expression of Sam68 was significantly correlated with advanced pathological T stage (P=0.01), positive lymphovascular invasion (P=0.01), and pathological cervical lymph node metastasis (P<0.01). Moreover, multivariate analysis demonstrated that the high expression of Sam68 was an independent predictive factor for cervical lymph node metastasis (odds ratio, 4.39; 95% confidence interval, 1.49­14.23; P<0.01). These results indicated that high Sam68 expression contributed to tumor progression, especially cervical lymph node metastasis, in OSCC. mRNA sequencing was also performed to assess the changes in the transcriptome between OSCC cells with Sam68 knockdown and control cells with the aim of elucidating the biological roles of Sam68. Gene Ontology enrichment analysis revealed that downregulated differentially expressed genes (DEGs) were concentrated in some biological processes related to epithelial­mesenchymal transition. Among these DEGs, it was established that vimentin was particularly downregulated in these cells. It was also confirmed that Sam68 knockdown reduced the motility of OSCC cells. Furthermore, the immunohistochemical study of vimentin identified the association between vimentin expression and Sam68 expression as well as cervical lymph node metastasis. In conclusion, the present study suggested that the high expression of Sam68 may contribute to metastasis by regulating vimentin expression and a motile mesenchymal phenotype in OSCC.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales , Proteínas de Unión al ADN , Neoplasias de la Boca , Proteínas de Unión al ARN , Carcinoma de Células Escamosas de Cabeza y Cuello , Proteínas Adaptadoras Transductoras de Señales/genética , Proteínas de Unión al ADN/genética , Humanos , Metástasis Linfática , Neoplasias de la Boca/genética , Neoplasias de la Boca/patología , Fenotipo , Proteínas de Unión al ARN/genética , Carcinoma de Células Escamosas de Cabeza y Cuello/patología , Vimentina/genética
15.
Methods Mol Biol ; 2569: 255-266, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36083452

RESUMEN

The fossil record is the best evidence of the characteristics of extinct species, but only a narrow range of traits fossilize or survive the fossilization process. Lacking fossil or other evidence about the past, ancestral states can be reconstructed. Three pieces of information are combined when reconstructing ancestral states: extant or known trait values (data); the evolutionary history, linking the species of interest (phylogeny); and the evolutionary model of trait change. These reconstructed ancestral states can be interpreted as our best guess as to the route evolution took, given the distribution of the trait across species, the relationships among them, and our model of evolution. Because the information we use to reconstruct the past is often not known without error, uncertainty about their true values should be accounted for when reconstructing ancestral states. In this chapter we describe how ancestral states can be reconstructed using a Bayesian framework implemented in the software BayesTraits to account for uncertainty in the phylogenetic tree and the model of evolution.


Asunto(s)
Fósiles , Programas Informáticos , Teorema de Bayes , Fenotipo , Filogenia
16.
Methods Mol Biol ; 2569: 305-326, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36083455

RESUMEN

The relative contribution of speciation and extinction into current diversity is certainly unknown, but mathematical frameworks that use genetic information have been developed to provide estimates of these processes. To that end, it is necessary to reconstruct molecular phylogenetic trees which summarize ancestor-descendant relationships as well as the timing of evolutionary events (i.e., rates). Nevertheless, diversification models show poor fit when assuming that single rate of speciation/extinction is constant over time and across lineages: species exhibit such a great variation in features that it is unlikely they give birth and die at the same pace. The state-dependent diversification framework (SSE) reconciles the species phenotypic variation with heterogeneous rates of diversification observed in a clade. This family of models allows testing contrasting hypotheses on mode of speciation, trait evolution, and its influence on speciation/extinction regimes. Although microbial species richness outnumbers diversity in plants and animals, diversification models are underused in microbiology. Here, we introduce microbiologists to models that estimate diversification rates and provide a detailed description of SSE models. Besides theoretical principles underlying the method, we also show how SSE analysis should be set up in R. We use pH evolution in Thaumarchaeota to explain its evolutionary dynamic in the light of SSE model. We hope this chapter spurs the study of trait evolution and evolutionary outcomes in microorganisms.


Asunto(s)
Extinción Biológica , Especiación Genética , Animales , Fenotipo , Filogenia
17.
Methods Mol Biol ; 2569: 327-342, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36083456

RESUMEN

Phylogenetic comparative methods (PCMs) combine statistics and evolutionary models to infer the dynamics of trait evolution and diversification that underlie the observed phylogeny. While PCMs have been used to study macro-evolutionary processes and evolutionary transitions of macroorganisms, their application to microbes is still limited. With the abundance of publicly available genomic and trait character data for diverse microbes nowadays, applications of PCMs on these data can provide insights into the fundamental principles that govern microbial evolution. Here, we introduce the Binary-State Speciation and Extinction (BiSSE) model, which is a relatively simple yet powerful approach for analyzing trait evolution. We begin by explaining the theoretical background and intuition behind the BiSSE model. Then, R commands for running the BiSSE model are presented. Finally, we introduce a case study that successfully applied the BiSSE model to investigate generalist and specialist microbial lifestyle evolution.


Asunto(s)
Extinción Biológica , Especiación Genética , Evolución Biológica , Estilo de Vida , Fenotipo , Filogenia
18.
J Proteomics ; 268: 104717, 2022 Sep 30.
Artículo en Inglés | MEDLINE | ID: mdl-36084919

RESUMEN

IgG N-glycans levels change with advancing age, making it a potential biomarker of aging. ß-1,4-galactosyltransferase (B4GALT) gene expression levels also increase with aging. Ultra performance liquid chromatography (UPLC) was used to examine changes inserum IgG N-glycans at six time points during the aging process. Most serum IgG N-glycans changed with aging in WT but not in CD19-cre B4GALT1 floxed mice. The relative abundance of fucosylated biantennary glycans with or without Neu5Gc structures changed with aging in heterozygous B4GALT1 floxed mice but not in homozygous B4GALT1 floxed mice. Additionally, the aging phenotype was more apparent in WT mice than in B4GALT1 floxed mice. These results demonstrate that fucosylated biantennary glycans and fucosylated biantennary glycans containing N-glycolylneuraminic acid (Neu5Gc)-linked N-acetyllactosamine (LacNAc) were highly associated with aging and were affected by the B4GALT1 floxed mouse genotype. The changing levels of fucosylated monoantennary glycans observed with aging in WT mice was reversed in B4GALT1 floxed mice and was not sex specific. In summary, B-cell-specific ablation of B4GALT1 from a glycoproteomic perspective prevented age-related changes in IgG N-glycans in mice. SIGNIFICANCE: In this study, serum IgG glycoproteomic data in wild-type (WT) and B-cell-specific ablation of ß-1,4-galactosyltransferase 1 mice (B4GALT) were analyzed. Results showed that fucosylated biantennary glycans with or without N-glycolylneuraminic acid (Neu5Gc)-linked N-acetyllactosamine (LacNAc) were highly associated with aging and were also affected by the B4GALT1 floxed mouse genotype. In terms of gender-specific information, the trend towards elevated fucosylated monoantennary glycans in WT mice was not seen in CD19-cre B4GALT1 floxed mice in either sex. B-cell-specific ablation of B4GALT1 plays an important role in age-related glycan changes; its specific functions and mechanisms are worthy of in-depth study. Our data suggest that investigating the relationship between galactosylation and aging may help advance the field of glycoproteomics and aging research.


Asunto(s)
N-Acetil-Lactosamina Sintasa , Polisacáridos , Envejecimiento , Animales , Inmunoglobulina G , Ratones , Ácidos Neuramínicos , Fenotipo , Polisacáridos/química
19.
Front Immunol ; 13: 945485, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36105813

RESUMEN

Microglia are phagocytosis-competent CNS cells comprising a spectrum of subtypes with beneficial and/or detrimental functions in acute and chronic neurodegenerative disorders. The heterogeneity of microglia suggests differences in phagocytic activity and phenotype plasticity between microglia subtypes. To study these issues, primary murine glial cultures were cultivated in the presence of serum, different growth factors and cytokines to obtain M0-like, M1-like, and M2-like microglia as confirmed by morphology, M1/M2 gene marker expression, and nitric oxide assay. Single-cell analysis after 3 hours of phagocytosis of E.coli particles or IgG-opsonized beads showed equal internalization by M0-like microglia, whereas M1-like microglia preferably internalized E.coli particles and M2-like microglia preferably internalized IgG beads, suggesting subtype-specific preferences for different phagocytosis substrates. Time-lapse live-cells imaging over 16 hours revealed further differences between microglia subtypes in phagocytosis preference and internalization dynamics. M0- and, more efficiently, M1-like microglia continuously internalized E.coli particles for 16 hours, whereas M2-like microglia discontinued internalization after approximately 8 hours. IgG beads were continuously internalized by M0- and M1-like microglia but strikingly less by M2-like microglia. M2-like microglia initially showed continuous internalization similar to M0-like microglia but again discontinuation of internalization after 8 hours suggesting that the time of substrate exposure differently affect microglia subtypes. After prolonged exposure to E.coli particles or IgG beads for 5 days all microglia subtypes showed increased internalization of E.coli particles compared to IgG beads, increased nitric oxide release and up-regulation of M1 gene markers, irrespectively of the phagocytosis substrate, suggesting phenotype plasticity. In summary, microglia subtypes show substrate- and time-dependent phagocytosis preferences and phenotype plasticity. The results suggest that prolonged phagocytosis substrate exposure enhances M1-like profiles and M2-M1 repolarization of microglia. Similar processes may also take place in conditions of acute and chronic brain insults when microglia encounter different types of phagocytic substrates.


Asunto(s)
Microglía , Óxido Nítrico , Animales , Inmunoglobulina G/metabolismo , Ratones , Microglía/metabolismo , Óxido Nítrico/metabolismo , Fagocitosis , Fenotipo
20.
Hum Exp Toxicol ; 41: 9603271221127429, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36112883

RESUMEN

BACKGROUND: As an aggressive human malignancy, esophageal squamous cell carcinoma (ESCC) is prevalent globally, especially in China. Verbascoside (VE) exerts anti-cancer effects in several human cancers. This work was to investigate the effects of VE on ESCC cells. METHODS: Esophageal squamous cell carcinoma cell proliferation, apoptosis, migration, and invasion were assessed by CCK-8, TUNEL, and Transwell assays. Gene and protein levels were detected by RT-qPCR and western blotting. CDC42 activity was evaluated by G-lisa assay. RESULTS: Verbascoside significantly inhibited cell proliferation, migration, and invasion and induced cell apoptosis in ESCC cells. Furthermore, it was found that VE markedly inhibited HMGB1 and RAGE expression in a dose-dependent manner. Besides, HMGB1/RAGE upregulation partially reversed the anti-cancer effects of VE on ESCC cells. VE repressed HMGB1/RAGE-induced CDC42 activation in ESCC cells. In addition, ML141-mediated CDC42 inactivation further enhanced the effect of VE on ESCC cell proliferation, apoptosis, migration, and invasion. CONCLUSIONS: Our findings indicated that VE has significant anti-tumor potential in ESCC by suppressing HMGB1/RAGE-dependent CDC42 activation.


Asunto(s)
Neoplasias Esofágicas , Carcinoma de Células Escamosas de Esófago , Proteína HMGB1 , Línea Celular Tumoral , Movimiento Celular , Neoplasias Esofágicas/tratamiento farmacológico , Neoplasias Esofágicas/metabolismo , Carcinoma de Células Escamosas de Esófago/tratamiento farmacológico , Carcinoma de Células Escamosas de Esófago/genética , Carcinoma de Células Escamosas de Esófago/metabolismo , Glucósidos , Proteína HMGB1/genética , Proteína HMGB1/metabolismo , Humanos , Invasividad Neoplásica , Fenotipo , Polifenoles , Sincalida/genética
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