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1.
Plant Mol Biol ; 92(1-2): 193-207, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-27325119

RESUMO

Phytocystatins are well-known inhibitors of C1A cysteine proteinases. However, previous research has revealed legumain (C13) protease inhibition via a carboxy-extended phytocystatin. Among the 12 phytocystatins genes in rice, OcXII is the only gene possessing this carboxy-terminal extension. The specific legumain inhibition activity was confirmed, in our work, using a recombinant OcXII harboring only the carboxy-terminal domain and this part did not exhibit any effect on papain-like activities. Meanwhile, rice plants silenced at the whole OcXII gene presented higher legumain and papain-like proteolytic activities, resulting in a faster initial seedling growth. However, when germinated under stressful alkaline conditions, OcXII-silenced plants exhibited impaired root formation and delayed shoot growth. Interestingly, the activity of OcXII promoter gene was detected in the rice seed scutellum region, and decreases with seedling growth. Seeds from these plants also exhibited slower growth at germination under ABA or alkaline conditions, while maintaining very high levels of OcXII transcriptional activation. This likely reinforces the proteolytic control necessary for seed germination and growth. In addition, increased legumain activity was detected in OcXII RNAi plants subjected to a fungal elicitor. Overall, the results of this study highlight the association of OcXII with not only plant development processes, but also with stress response pathways. The results of this study reinforce the bifunctional ability of carboxy-extended phytocystatins in regulating legumain proteases via its carboxy-extended domain and papain-like proteases by its amino-terminal domain.


Assuntos
Cistatinas/metabolismo , Cisteína Endopeptidases/metabolismo , Oryza/enzimologia , Papaína/metabolismo , Peptídeo Hidrolases/metabolismo , Proteínas de Plantas/metabolismo , Cistatinas/farmacologia , Oryza/metabolismo , Papaína/antagonistas & inibidores , Proteínas de Plantas/antagonistas & inibidores
2.
Genet Mol Biol ; 39(4): 524-538, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27706370

RESUMO

Since the first diacylglycerol acyltransferase (DGAT) gene was characterized in plants, a number of studies have focused on understanding the role of DGAT activity in plant triacylglycerol (TAG) biosynthesis. DGAT enzyme is essential in controlling TAGs synthesis and is encoded by different genes. DGAT1 and DGAT2 are the two major types of DGATs and have been well characterized in many plants. On the other hand, the DGAT3 and WS/DGAT have received less attention. In this study, we present the first general view of the presence of putative DGAT3 and WS/DGAT in several plant species and report on the diversity and evolution of these genes and its relationships with the two main DGAT genes (DGAT1 and DGAT2). According to our analyses DGAT1, DGAT2, DGAT3 and WS/DGAT are very divergent genes and may have distinct origin in plants. They also present divergent expression patterns in different organs and tissues. The maintenance of several types of genes encoding DGAT enzymes in plants demonstrates the importance of DGAT activity for TAG biosynthesis. Evolutionary history studies of DGATs coupled with their expression patterns help us to decipher their functional role in plants, helping to drive future biotechnological studies.

3.
Plant Cell Rep ; 34(7): 1139-49, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25721200

RESUMO

KEY MESSAGE: MicroRNAs have higher expression stability than protein-coding genes in B. napus seeds and are therefore good reference genes for miRNA and mRNA RT-qPCR analysis. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) has become the "gold standard" to gain insight into function of genes. However, the accuracy of the technique depends on appropriate reference genes for quantification analysis in different experimental conditions. Accumulation of microRNAs (miRNAs) has also been studied by RT-qPCR, but there are no reference genes currently validated for normalization of Brassica napus miRNA expression data. In this study, we selected 43 B. napus miRNAs and 18 previously validated mRNA reference genes. The expression stability of the candidate reference genes was evaluated in different tissue samples (stages of seed development, flowers, and leaves) using geNorm, NormFinder, and RefFinder analysis. The best-ranked reference genes for expression studies during seed development (miR167-1_2, miR11-1, miR159-1 and miR168-1) were used to asses the expression of miR03-1. Since candidate miRNAs showed higher expression stability than protein-coding genes in most of the tested conditions, the expression profile of DGAT1 gene was compared when normalized by the four most stable miRNAs reference genes and by the four most stable mRNA reference genes. The expected expression pattern of DGAT1 during seed development was achieved with the use of miRNA as reference genes. In conclusion, the most stable miRNA reference genes can be employed in the normalization of RT-qPCR quantification of miRNAs and protein-coding genes. This work is the first to perform a comprehensive survey of the stability of miRNA reference genes in B. napus and provides guidelines to obtain more accurate RT-qPCR results in B. napus seeds studies.


Assuntos
Brassica napus/embriologia , Brassica napus/genética , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Sementes/embriologia , Sementes/genética , Perfilação da Expressão Gênica , MicroRNAs/genética , MicroRNAs/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Reação em Cadeia da Polimerase em Tempo Real/normas , Padrões de Referência , Reprodutibilidade dos Testes , Software
4.
Mol Genet Genomics ; 289(6): 1321-30, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-25098420

RESUMO

Phytocystatins encompass a family of plant competitive cysteine proteinase inhibitors. They are encoded by part of a conserved monophyletic group of genes that are found in all eukaryotes. The primary targets of phytocystatins are papain-like cysteine proteinases. However, a group of larger phytocystatins is also able to inhibit proteinases such as legumains. Phytocystatins have been implicated in several physiological processes and act within an intricate proteolytic regulatory network. The present work characterizes the gene family of rice phytocystatins, which contains twelve genes with different features. Phylogenetic analyses cluster rice phytocystatins into three main groups. Group 1 is composed of OcI, OcIII and OcXII and is nearly ubiquitous and highly expressed in plants under normal and stressed conditions including salt, wounding, ABA or a fungal elicitor such as chitosan. Rice phytocystatins can contribute to plant senescence and may exhibit an inverse correlation between their gene expression and the activities of their target proteinases. This work contributes to clarifying the roles of individual phytocystatin genes in plant processes such as germination and response to environmental stresses.


Assuntos
Cistatinas/metabolismo , Família Multigênica , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Cistatinas/química , Cistatinas/genética , Expressão Gênica , Oryza/genética , Oryza/crescimento & desenvolvimento , Proteínas de Plantas/química , Proteínas de Plantas/genética
5.
Bioinformatics ; 29(20): 2521-3, 2013 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-23946501

RESUMO

SUMMARY: MicroRNAs (miRNAs) have been extensively studied owing to their important regulatory roles in genic expression. An increasingly number of reports are performing extensive data mining in small RNA sequencing libraries to detect miRNAs isoforms and also 5' and 3' post-transcriptional nucleotide additions, as well as edited miRNAs sequences. A ready to use pipeline, isomiRID, was developed to standardize and automatize the search for miRNAs isoforms in high-throughput small RNA sequencing libraries. AVAILABILITY: isomiRID is a command line Python script available at http://www.ufrgs.br/RNAi/isomiRID/.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , MicroRNAs/análise , Análise de Sequência de RNA/métodos , Software , Sequência de Bases , Humanos , Internet , MicroRNAs/genética , Isoformas de Proteínas/análise , Isoformas de Proteínas/genética
6.
Viruses ; 14(4)2022 03 27.
Artigo em Inglês | MEDLINE | ID: mdl-35458424

RESUMO

The western mesoregion of the state of Santa Catarina (SC), Southern Brazil, was heavily affected as a whole by the COVID-19 pandemic in early 2021. This study aimed to evaluate the dynamics of the SARS-CoV-2 virus spreading patterns in the SC state from March 2020 to April 2021 using genomic surveillance. During this period, there were 23 distinct variants, including Beta and Gamma, among which the Gamma and related lineages were predominant in the second pandemic wave within SC. A regionalization of P.1-like-II in the Western SC region was observed, concomitant to the increase in cases, mortality, and the case fatality rate (CFR) index. This is the first evidence of the regionalization of the SARS-CoV-2 transmission in SC and it highlights the importance of tracking the variants, dispersion, and impact of SARS-CoV-2 on the public health systems.


Assuntos
COVID-19 , SARS-CoV-2 , Brasil/epidemiologia , COVID-19/epidemiologia , Humanos , Mutação , Pandemias , Filogenia , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/genética
7.
Front Microbiol ; 12: 638231, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33717032

RESUMO

High-throughput sequencing of 16S rRNA amplicon has been extensively employed to perform microbiome characterization worldwide. As a culture-independent methodology, it has allowed high-level profiling of sample bacterial composition directly from samples. However, most studies are limited to information regarding relative bacterial abundances (sample proportions), ignoring scenarios in which sample microbe biomass can vary widely. Here, we use an equivolumetric protocol for 16S rRNA amplicon library preparation capable of generating Illumina sequencing data responsive to input DNA, recovering proportionality between observed read counts and absolute bacterial abundances within each sample. Under specified conditions, we show that the estimation of colony-forming units (CFU), the most common unit of bacterial abundance in classical microbiology, is challenged mostly by resolution and taxon-to-taxon variation. We propose Bayesian cumulative probability models to address such issues. Our results indicate that predictive errors vary consistently below one order of magnitude for total microbial load and abundance of observed bacteria. We also demonstrate our approach has the potential to generalize to previously unseen bacteria, but predictive performance is hampered by specific taxa of uncommon profile. Finally, it remains clear that high-throughput sequencing data are not inherently restricted to sample proportions only, and such technologies bear the potential to meet the working scales of traditional microbiology.

8.
PLoS One ; 16(2): e0246544, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33539474

RESUMO

To minimize sample dilution effect on SARS-CoV-2 pool testing, we assessed analytical and diagnostic performance of a new methodology, namely swab pooling. In this method, swabs are pooled at the time of collection, as opposed to pooling of equal volumes from individually collected samples. Paired analysis of pooled and individual samples from 613 patients revealed 94 positive individuals. Having individual testing as reference, no false-positives or false-negatives were observed for swab pooling. In additional 18,922 patients screened with swab pooling (1,344 pools), mean Cq differences between individual and pool samples ranged from 0.1 (Cr.I. -0.98 to 1.17) to 2.09 (Cr.I. 1.24 to 2.94). Overall, 19,535 asymptomatic patients were screened using 4,400 RT-qPCR assays. This corresponds to an increase of 4.4 times in laboratory capacity and a reduction of 77% in required tests. Therefore, swab pooling represents a major alternative for reliable and large-scale screening of SARS-CoV-2 in low prevalence populations.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , SARS-CoV-2/genética , Manejo de Espécimes/métodos , COVID-19/virologia , Humanos , Programas de Rastreamento/métodos , Nasofaringe/virologia , RNA Viral/análise , RNA Viral/genética , Estudos Retrospectivos , SARS-CoV-2/isolamento & purificação
9.
Sci Total Environ ; 778: 146198, 2021 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-33714813

RESUMO

Human sewage from Florianopolis (Santa Catarina, Brazil) was analyzed for severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) from October 2019 until March 2020. Twenty five ml of sewage samples were clarified and viruses concentrated using a glycine buffer method coupled with polyethylene glycol precipitation, and viral RNA extracted using a commercial kit. SARS-CoV-2 RNA was detected by RT-qPCR using oligonucleotides targeting N1, S and two RdRp regions. The results of all positive samples were further confirmed by a different RT-qPCR system in an independent laboratory. S and RdRp amplicons were sequenced to confirm identity with SARS-CoV-2. Genome sequencing was performed using two strategies; a sequence-independent single-primer amplification (SISPA) approach, and by direct metagenomics using Illumina's NGS. SARS-CoV-2 RNA was detected on 27th November 2019 (5.49 ± 0.02 log10 SARS-CoV-2 genome copies (GC) L-1), detection being confirmed by an independent laboratory and genome sequencing analysis. The samples in the subsequent three events were positive by all RT-qPCR assays; these positive results were also confirmed by an independent laboratory. The average load was 5.83 ± 0.12 log10 SARS-CoV-2 GC L-1, ranging from 5.49 ± 0.02 log10 GC L-1 (27th November 2019) to 6.68 ± 0.02 log10 GC L-1 (4th March 2020). Our findings demonstrate that SARS-CoV-2 was likely circulating undetected in the community in Brazil since November 2019, earlier than the first reported case in the Americas (21st January 2020).


Assuntos
COVID-19 , RNA Viral , Brasil , Humanos , SARS-CoV-2 , Esgotos
10.
Front Microbiol ; 12: 711471, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34484149

RESUMO

Hospital-built environment colonization by healthcare-associated infections-related bacteria (HAIrB) and the interaction with their occupants have been studied to support more effective tools for HAI control. To investigate HAIrB dynamics and antimicrobial resistance (AMR) profile we carried out a 6-month surveillance program in a developing country public hospital, targeting patients, hospital environment, and healthcare workers, using culture-dependent and culture-independent 16S rRNA gene sequencing methods. The bacterial abundance in both approaches shows that the HAIrB group has important representativeness, with the taxa Enterobacteriaceae, Pseudomonas, Staphylococcus, E. coli, and A. baumannii widely dispersed and abundant over the time at the five different hospital units included in the survey. We observed a high abundance of HAIrB in the patient rectum, hands, and nasal sites. In the healthcare workers, the HAIrB distribution was similar for the hands, protective clothing, and mobile phones. In the hospital environment, the healthcare workers resting areas, bathrooms, and bed equipment presented a wide distribution of HAIrB and AMR, being classified as contamination hotspots. AMR is highest in patients, followed by the environment and healthcare workers. The most frequently detected beta-lactamases genes were, bla SHV-like, bla OXA- 23 -like, bla OXA- 51 -like, bla KPC-like, bla CTX-M- 1, bla CTX-M- 8, and bla CTX-M- 9 groups. Our results demonstrate that there is a wide spread of antimicrobial resistance due to HAIrB in the hospital environment, circulating among patients and healthcare workers. The contamination hotspots identified proved to be constant over time. In the fight for patient safety, these findings can reorient practices and help to set up new guidelines for HAI control.

11.
Diagnostics (Basel) ; 10(3)2020 Mar 17.
Artigo em Inglês | MEDLINE | ID: mdl-32192080

RESUMO

This work aimed to identify and compare the bacterial patterns present in endometriotic lesions, eutopic endometrium and vaginal fluid from endometriosis patients with those found in the vaginal fluid and eutopic endometrium of control patients. Vaginal fluid, eutopic endometrium and endometriotic lesions were collected. DNA was extracted and the samples were analyzed to identify microbiome by high-throughput DNA sequencing of the 16S rRNA marker gene. Amplicon sequencing from vaginal fluid, eutopic endometrium and endometriotic lesion resulted in similar profiles of microorganisms, composed most abundantly by the genus Lactobacillus, Gardnerella, Streptococcus and Prevotella. No significant differences were found in the diversity analysis of microbiome profiles between control and endometriotic patients; however deep endometriotic lesions seems to present different bacterial composition, less predominant of Lactobacillus and with more abundant Alishewanella, Enterococcus and Pseudomonas.

12.
PLoS One ; 15(6): e0234127, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32492060

RESUMO

Several studies have shown the ubiquitous presence of bacteria in hospital surfaces, staff, and patients. Frequently, these bacteria are related to HAI (healthcare-associated infections) and carry antimicrobial resistance (AMR). These HAI-related bacteria contribute to a major public health issue by increasing patient morbidity and mortality during or after hospital stay. Bacterial high-throughput amplicon gene sequencing along with identification of AMR genes, as well as whole genome sequencing (WGS), are biotechnological tools that allow multiple-sample screening for a diversity of bacteria. In this paper, we used these methods to perform a one-year cross sectional profiling of bacteria and AMR genes in adult and neonatal intensive care units (ICU and NICU) in a Brazilian public, tertiary hospital. Our results showed high abundances of HAI-related bacteria such as S. epidermidis, S. aureus, K. pneumoniae, A. baumannii complex, E. coli, E. faecalis, and P. aeruginosa in patients and hospital surfaces. Most abundant AMR genes detected throughout ICU and NICU were mecA, blaCTX-M-1 group, blaSHV-like, and blaKPC-like. We found that NICU environment and patients were more widely contaminated with pathogenic bacteria than ICU. Patient samples, despite the higher bacterial load, have lower bacterial diversity than environmental samples in both units. Finally, we also identified contamination hotspots in the hospital environment showing constant frequencies of bacterial and AMR contamination throughout the year. Whole genome sequencing (WGS), 16S rRNA oligotypes, and AMR identification allowed a high-resolution characterization of the hospital microbiome profile.


Assuntos
Bactérias/genética , Farmacorresistência Bacteriana/genética , Adulto , Antibacterianos/farmacologia , Anti-Infecciosos/farmacologia , Bactérias/efeitos dos fármacos , Bactérias/isolamento & purificação , Carga Bacteriana , Brasil , Infecção Hospitalar/microbiologia , Infecção Hospitalar/patologia , Estudos Transversais , Farmacorresistência Bacteriana/efeitos dos fármacos , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Escherichia coli/isolamento & purificação , Humanos , Recém-Nascido , Unidades de Terapia Intensiva , Unidades de Terapia Intensiva Neonatal , RNA Ribossômico 16S/química , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/metabolismo , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/genética , Staphylococcus aureus/isolamento & purificação , Centros de Atenção Terciária , Sequenciamento Completo do Genoma
13.
J Biotechnol ; 238: 42-51, 2016 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-27671698

RESUMO

Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) that are involved in transcriptional and posttranscriptional gene expression regulation. The development of deep sequencing of ribosomal RNA (rRNA)-depleted RNA libraries, associated with improved computational tools, has provided the identification of several new circRNAs in all sorts of organisms, from protists, plants and fungi to animals. Recently, it was discovered that endogenous circRNAs can work as microRNA (miRNA) sponges. This means that the circRNAs bind to miRNAs and consequently repress their function, providing a new model of action for this class of ncRNA, as well as indicating another mechanism that regulates miRNA activity. As miRNAs control a large set of biological processes, circRNA sponge activity will also affect these pathways. Several studies have associated miRNA sponges with human diseases, including osteoarthritis, diabetes, neurodegenerative pathologies and several types of cancer. Additionally, high stability, abundance and tissue-specific expression patterns make circRNA sponges very attractive for clinical research. Herein, we review the biogenesis, properties and function of endogenous circRNA sponges, with a special focus on those related to human cancer. A list of web tools available for the study of circRNAs is also given. Additionally, we discuss the possibility of using circRNAs as molecular markers for the diagnosis of diseases.


Assuntos
Biomarcadores , MicroRNAs , RNA , Animais , Regulação da Expressão Gênica/genética , Regulação da Expressão Gênica/fisiologia , Humanos , Camundongos , MicroRNAs/genética , MicroRNAs/fisiologia , Neoplasias/genética , RNA/genética , RNA/fisiologia , RNA Circular
14.
Plant Sci ; 215-216: 100-9, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24388520

RESUMO

Legumains are Asn specific cysteine proteases physiologically related to the biosynthesis of vacuolar components, degradation of storage proteins and programmed cell death. The present work identifies and characterizes the genic family of legumains in rice (Oryza sativa), which comprises five different loci. Rice legumains (OsaLegs) were ubiquitously detected in all plant tissues analyzed. However, phylogenetic analyses and gene expression studies demonstrated greater association of OsaLeg2 and OsaLeg3 to seed-related legumains, whereas OsaLeg1, 4 and 5 would act as vegetative-related proteases. Additionally, OsaLeg1 mRNA is strongly induced in senescent leaves. All rice legumain genes respond in different ways to environmental conditions such as wounding, salt and abscisic acid treatments. Mainly, wounding is capable of inducing all the four expressed genes OsaLeg1, 2, 3 and 4. Alternative splicing isoforms, with potential to generate pre-activated OsaLeg1 and OsaLeg2 nonvacuolar enzymes under different environmental situations were also observed.


Assuntos
Cisteína Endopeptidases/genética , Genes de Plantas , Família Multigênica , Oryza/genética , Proteínas de Plantas/genética , Estruturas Vegetais/metabolismo , Estresse Fisiológico/genética , Ácido Abscísico/farmacologia , Senescência Celular/genética , Cisteína Endopeptidases/metabolismo , Meio Ambiente , Expressão Gênica , Regulação da Expressão Gênica de Plantas , Oryza/metabolismo , Filogenia , Proteínas de Plantas/metabolismo , Isoformas de Proteínas , RNA Mensageiro/metabolismo , Tolerância ao Sal/genética
15.
Plant Sci ; 229: 181-192, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-25443845

RESUMO

The environment is a dynamic system in which life forms adapt. Wall-Associated Kinases (WAK) are a subfamily of receptor-like kinases associated with the cell wall. These genes have been suggested as sensors of the extracellular environment and triggers of intracellular signals. They belong to the ePK superfamily with or without a conserved arginine before the catalytic subdomain VIB, which characterizes RD and non-RD WAKs. WAK is a large subfamily in rice. We performed an extensive comparison of WAK genes from A. thaliana (AtWAK), O. sativa japonica and indica subspecies (OsWAK). Phylogenetic studies and WAK domain characterization allowed for the identification of two distinct groups of WAK genes in Arabidopsis and rice. One group corresponds to a cluster containing only OsWAKs that most likely expanded after the monocot-dicot separation, which evolved into a non-RD kinase class. The other group comprises classical RD-kinases with both AtWAK and OsWAK representatives. Clusterization analysis using extracellular and kinase domains demonstrated putative functional redundancy for some genes, but also highlighted genes that could recognize similar extracellular stimuli and activate different cascades. The gene expression pattern of WAKs in response to cold suggests differences in the regulation of the OsWAK genes in the indica and japonica subspecies. Our results also confirm the hypothesis of functional diversification between A. thaliana and O. sativa WAK genes. Furthermore, we propose that plant WAKs constitute two evolutionarily related but independent subfamilies: WAK-RD and WAK-nonRD. Recognition of this structural division will further provide insights to understanding WAK functions and regulations.


Assuntos
Parede Celular/enzimologia , Parede Celular/genética , Genes de Plantas , Família Multigênica , Oryza/enzimologia , Oryza/genética , Proteínas Quinases/genética , Motivos de Aminoácidos , Sequência de Aminoácidos , Teorema de Bayes , Análise por Conglomerados , Temperatura Baixa , Perfilação da Expressão Gênica , Regulação Enzimológica da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genes Duplicados , Anotação de Sequência Molecular , Dados de Sequência Molecular , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Proteínas Quinases/química , Proteínas Quinases/metabolismo , Estrutura Terciária de Proteína , Homologia de Sequência de Aminoácidos , Estresse Fisiológico
16.
Plant Sci ; 210: 214-23, 2013 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-23849128

RESUMO

The miRNAs play important roles in regulation of gene expression at the post-transcriptional level. A small RNA and RNA-seq of libraries were constructed to identify miRNAs in Vriesea carinata, a native bromeliad species from Brazilian Atlantic Rainforest. Illumina technology was used to perform high throughput sequencing and data was analyzed using bioinformatics tools. We obtained 2,191,509 mature miRNAs sequences representing 54 conserved families in plant species. Further analysis allowed the prediction of secondary structures for 19 conserved and 16 novel miRNAs. Potential targets were predicted from pre-miRNAs by sequence homology and validated using RTqPCR approach. This study provides the first identification of miRNAs and their potential targets of a bromeliad species.


Assuntos
Bromeliaceae/genética , MicroRNAs/genética , Sequência de Bases , Brasil , Bromeliaceae/metabolismo , Sequência Conservada , Regulação da Expressão Gênica de Plantas , Biblioteca Gênica , Genes de Plantas/genética , Sequenciamento de Nucleotídeos em Larga Escala , MicroRNAs/química , MicroRNAs/metabolismo , Conformação de Ácido Nucleico , RNA de Plantas/química , RNA de Plantas/genética , RNA de Plantas/metabolismo , Alinhamento de Sequência , Análise de Sequência de RNA , Estresse Fisiológico
17.
Plant Sci ; 208: 93-101, 2013 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-23683934

RESUMO

Glutathione (GSH) peroxidases (GPXs: EC 1.11.1.9 and EC1.11.1.12) are non-heme thiol peroxidases that catalyze the reduction of H2O2 or organic hydroperoxides to water, and they have been identified in almost all kingdoms of life. The rice glutathione peroxidase (OsGPX) gene family is comprised of 5 members spread throughout a range of sub cellular compartments. The OsGPX gene family is induced in response to exogenous H2O2 and cold stress. In contrast, they are down regulated in response to drought and UV-B light treatments. Transgenic rice plants have been generated that lack mitochondrial OsGPX3. These GPX3s plants showed shorter roots and shoots compared to non-transformed (NT) plants, and higher amounts of H2O2 mitochondrial release were observed in the roots of these plants cultivated under normal conditions. This accumulation of H2O2 is positively associated with shorter root length in GPX3s plants compared to NT ones. Moreover, GPX3 promoter analysis indicated that it is mainly expressed in root tissue. These results suggest that silencing the mitochondrial OsGPX3 gene impairs normal plant development and leads to a stress-induced morphogenic response via H2O2 accumulation.


Assuntos
Glutationa Peroxidase/metabolismo , Homeostase , Peróxido de Hidrogênio/metabolismo , Mitocôndrias/enzimologia , Oryza/enzimologia , Raízes de Plantas/crescimento & desenvolvimento , Brotos de Planta/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Técnicas de Silenciamento de Genes , Inativação Gênica/efeitos dos fármacos , Homeostase/efeitos dos fármacos , Peróxido de Hidrogênio/farmacologia , Mitocôndrias/efeitos dos fármacos , Oryza/efeitos dos fármacos , Oryza/genética , Oryza/crescimento & desenvolvimento , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raízes de Plantas/efeitos dos fármacos , Raízes de Plantas/enzimologia , Brotos de Planta/efeitos dos fármacos , Brotos de Planta/enzimologia , Brotos de Planta/genética , Regiões Promotoras Genéticas/genética , Transcrição Gênica/efeitos dos fármacos
18.
Genet Mol Biol ; 35(2): 460-5, 2012 04.
Artigo em Inglês | MEDLINE | ID: mdl-22888296

RESUMO

Tip100 is an Ac-like transposable element that belongs to the hAT superfamily. First discovered in Ipomoea purpurea (common morning glory), it was classified as an autonomous element capable of movement within the genome. As Tip100 data were already available in databases, the sequences of related elements in ten additional species of Ipomoea and five commercial varieties were isolated and analyzed. Evolutionary analysis based on sequence diversity in nuclear ribosomal Internal Transcribed Spacers (ITS), was also applied to compare the evolution of these elements with that of Tip100 in the Ipomoea genus. Tip100 sequences were found in I. purpurea, I. nil, I. indica and I. alba, all of which showed high levels of similarity. The results of phylogenetic analysis of transposon sequences were congruent with the phylogenetic topology obtained for ITS sequences, thereby demonstrating that Tip100 is restricted to a particular group of species within Ipomoea. We hypothesize that Tip100 was probably acquired from a common ancestor and has been transmitted vertically within this genus.

19.
Stem Cells Dev ; 21(10): 1761-8, 2012 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-21970410

RESUMO

Mesenchymal stem cells (MSCs) have received great attention due to their remarkable regenerative, angiogenic, antiapoptotic, and immunosuppressive properties. Although conventionally isolated from the bone marrow, they are known to exist in all tissues and organs, raising the question on whether they are identical cell populations or have important differences at the molecular level. To better understand the relationship between MSCs residing in different tissues, we analyzed the expression of genes related to pluripotency (SOX2 and OCT-4) and to adipogenic (C/EBP and ADIPOR1), osteogenic (OMD and ALP), and chondrogenic (COL10A1 and TRPV4) differentiation in cultures derived from murine endodermal (lung) and mesodermal (adipose) tissue maintained in different conditions. MSCs were isolated from lungs (L-MSCs) and inguinal adipose tissue (A-MSCs) and cultured in normal conditions, in overconfluence or in inductive medium for osteogenic, adipogenic, or chondrogenic differentiation. Cultures were characterized for morphology, immunophenotype, and by quantitative real-time reverse transcription-polymerase chain reaction for expression of pluripotency genes or markers of differentiation. Bone marrow-derived MSCs were also analyzed for comparison of these parameters. L-MSCs and A-MSCs exhibited the typical morphology, immunophenotype, and proliferation and differentiation pattern of MSCs. The analysis of gene expression showed a higher potential of adipose tissue-derived MSCs toward the osteogenic pathway and of lung-derived MSCs to chondrogenic differentiation, representing an important contribution for the definition of the type of cell to be used in clinical trials of cell therapy and tissue engineering.


Assuntos
Gordura Abdominal/citologia , Diferenciação Celular , Pulmão/citologia , Células-Tronco Mesenquimais/fisiologia , Animais , Antígenos CD/metabolismo , Proliferação de Células , Forma Celular , Células Cultivadas , Endoderma/citologia , Proteínas da Matriz Extracelular/genética , Proteínas da Matriz Extracelular/metabolismo , Perfilação da Expressão Gênica , Células-Tronco Mesenquimais/metabolismo , Mesoderma/citologia , Camundongos , Camundongos Endogâmicos C57BL , Fator 3 de Transcrição de Octâmero/genética , Fator 3 de Transcrição de Octâmero/metabolismo , Fenótipo , Proteoglicanas/genética , Proteoglicanas/metabolismo , Canais de Cátion TRPV/genética , Canais de Cátion TRPV/metabolismo
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