Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 9.235
Filtrar
1.
Water Sci Technol ; 82(6): 1205-1216, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-33055410

RESUMO

In the present study, 24 green microalgae strains were isolated from selected aquatic sites of India. These were microscopically identified as Chlamydomonas sp., Scenedesmus sp., Chlorella sp., Dictyosphaerium sp. and Dunaliella sp. Nannochloropsis sp. (MCC 25), was used as a reference strain. Results showed that Dictyosphaerium sp. (MCC 10 and MCC 12) showed relatively higher nutritive content. The total soluble proteins in the reference strain was 21.4%, whereas it showed carbohydrate content of 17.2% and the lipids were 3.4% on a dry weight basis. Best performing strains were identified by biochemical characterization. Five genera were selected for molecular identification since they were the most representative based upon their area of isolation and their optimum content of total soluble proteins, carbohydrates and lipids. 18S rRNA sequencing authenticated their identification as Scenedesmus sp., Dictyosphaerium sp. and Chlorella sp. The sequences of these have been submitted in NCBI database with accession numbers as KT808247-KT808251. The correlation matrix showed positive correlation between carbohydrates and lipids, while negative correlation was seen between proteins and carbohydrates and between proteins and lipids. This study emphasizes the need for complete compositional analysis of the biomass for the possible applicability in the area of value addition.


Assuntos
Chlorella , Microalgas , Chlorella/genética , Genes de RNAr , Índia , Microalgas/genética , RNA Ribossômico 18S/genética , Análise de Sequência
2.
Adv Exp Med Biol ; 1255: 1-6, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32949386

RESUMO

Clinical single-cell biomedicine has become a new emerging discipline, which integrates single-cell RNA and DNA sequencing, proteomics, and functions with clinical phenomes, therapeutic responses, and prognosis. It is of great value to discover disease-, phenome-, and therapy-specific diagnostic biomarkers and therapeutic targets on the basis of the principle of clinical single-cell biomedicine. This book reviews the roles of single-cell sequencing and methylation in diseases and explores disease-specific alterations of single-cell sequencing and methylation, especially focusing on potential applications of methodologies on human single-cell sequencing and methylation, on potential correlations between those changes with pulmonary diseases, and on potential roles of signaling pathways that cause heterogeneous cellular responses during treatment. This book also emphasizes the importance of methodologies in clinical practice and application, the potential of perspectives, challenges and solutions, and the significance of single-cell preparation standardization. Alterations of DNA and RNA methylation, demethylation in lung diseases, and a deep knowledge about the regulation and function of target gene methylation for diagnosing and treating diseases at the early stage are also provided. Importantly, this book aims to apply the measurement of single-cell sequencing and methylation for clinical diagnosis and treatment and to understand clinical values of those parameters and to headline and foresee the potential values of the application of single-cell sequencing in non-cancer diseases.


Assuntos
Metilação de DNA , Doença/genética , Análise de Sequência , Análise de Célula Única , DNA/genética , DNA/metabolismo , Humanos , Proteômica , RNA/genética , RNA/metabolismo
3.
Adv Exp Med Biol ; 1255: 29-50, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32949388

RESUMO

T cells recognize peptides bound to major histocompatibility complex (MHC) class I and class II molecules at the cell surface. This recognition is accomplished by the expression of T cell receptors (TCR) which are required to be diverse and adaptable in order to accommodate the various and vast number of antigens presented on the MHCs. Thus, determining TCR repertoires of effector T cells is necessary to understand the immunological process in responding to cancer progression, infection, and autoimmune development. Furthermore, understanding the TCR repertoires will provide a solid framework to predict and test the antigen which is more critical in autoimmunity. However, it has been a technical challenge to sequence the TCRs and provide a conceptual context in correlation to the vast number of TCR repertoires in the immunological system. The exploding field of single-cell sequencing has changed how the repertoires are being investigated and analyzed. In this review, we focus on the biology of TCRs, TCR signaling and its implication in autoimmunity. We discuss important methods in bulk sequencing of many cells. Lastly, we explore the most pertinent platforms in single-cell sequencing and its application in autoimmunity.


Assuntos
Receptores de Antígenos de Linfócitos T/genética , Análise de Sequência , Análise de Célula Única , Animais , Autoimunidade/imunologia , Antígenos de Histocompatibilidade Classe I/imunologia , Humanos , Receptores de Antígenos de Linfócitos T/imunologia , Linfócitos T/imunologia , Linfócitos T/metabolismo
4.
Adv Exp Med Biol ; 1255: 109-121, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32949394

RESUMO

Cancer is one of the leading causes of death worldwide and well known for its complexity. Cancer cells within the same tumor or from different tumors are highly heterogeneous. Furthermore, stromal and immune cells within tumor microenvironment interact with cancer cells to play important roles in how tumors progress and respond to different treatments. Recent advances in single cell technologies, especially massively parallel single cell sequencing, have made it possible to analyze cancer cells and cells in its tumor microenvironment in parallel with unprecedented high resolution. In this chapter, we will review recent developments in single cell sequencing technologies and their applications in cancer research. We will also explain how insights generated from single cell sequencing can be used to develop novel diagnostic and therapeutic approaches to conquer cancer.


Assuntos
Neoplasias/diagnóstico , Neoplasias/terapia , Análise de Sequência , Análise de Célula Única , Humanos , Neoplasias/genética , Microambiente Tumoral
5.
Adv Exp Med Biol ; 1255: 153-164, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32949398

RESUMO

Single-cell sequencing (SCS) is a powerful new tool that applies Next Generation Sequencing at the cellular level. SCS has revolutionized our understanding of tumor heterogeneity and the tumor microenvironment, immune infiltration, cancer stem cells (CSCs), circulating tumor cells (CTCs), and clonal evolution. The following chapter highlights the current literature on SCS in genitourinary (GU) malignancies and discusses future applications of SCS technology. The renal cell carcinoma (RCC) section highlights the use of SCS in characterizing the initial cells driving tumorigenesis, the intercellular mutational landscape of RCC, intratumoral heterogeneity (ITH) between primary and metastatic lesions, and genes driving RCC cancer stem cells (CSCs). The bladder cancer section will also illustrate molecular drivers of bladder cancer stem cells (BCSCs), SCS use in reconstructing tumor developmental history and underlying subclones, and understanding the effect of cisplatin on intratumoral heterogeneity in vitro and potential mechanisms behind platinum resistance. The final section featuring prostate cancer will discuss how SCS can be used to identify the cellular origins of benign prostatic hyperplasia and prostate cancer, the plasticity and heterogeneity of prostate cancer cells with regard to androgen dependence, and the use of SCS in CTCs to understand chemotherapy resistance and gene expression changes after androgen deprivation therapy (ADT). The studies listed in this chapter illustrate many translational applications of SCS in GU malignancies, including diagnostic, prognostic, and treatment-related approaches. The ability of SCS to resolve intratumor heterogeneity and better define the genomic landscape of tumors and CTCs will be fundamental in the new era of precision-based care.


Assuntos
Neoplasias Renais/genética , Neoplasias da Próstata/genética , Análise de Sequência , Análise de Célula Única , Androgênios , Humanos , Neoplasias Renais/patologia , Masculino , Neoplasias da Próstata/patologia
6.
Adv Exp Med Biol ; 1255: 175-193, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32949400

RESUMO

Personalized medicine has been driven by improvements in genomic sequencing and analysis. For several diseases, in particular cancers, it has for nearly a decade been standard clinical practice to analyze the genome and expression of the genes of patients. The results are reflected directly in the treatment plan for the patient, in targeted medical inventions. This specialized mode of diagnostics has been restricted to account for averaged trends in the tumor. The approach sharply contrasts our knowledge on heterogeneity within tumors. Several studies further describe how treatment against one tumor subclone in some cases merely serves to provide space and support for uncontrolled growth of more aggressive subclones. In this chapter, we describe current possibilities for implementation of single cell sequencing of malignomas in clinic, as well as discuss hands-on practical advice for single cell routine diagnostics that allows for full delineation of tumor clonality.


Assuntos
Neoplasias/diagnóstico , Neoplasias/genética , Medicina de Precisão , Análise de Sequência , Análise de Célula Única , Humanos , Neoplasias/patologia
7.
Adv Exp Med Biol ; 1255: 203-220, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32949402

RESUMO

Human genital infections are one of the most concerning issues worldwide and can be categorized into sexually transmitted, urinary tract and vaginal infections. These infections, if left untreated, can disseminate to the other parts of the body and cause more complicated illnesses such as pelvic inflammatory disease, urethritis, and anogenital cancers. The effective treatment against these infections is further complicated by the emergence of antimicrobial resistance in the genital infection causing pathogens. Furthermore, the development and applications of single-cell sequencing technologies have open new possibilities to study the drug resistant clones, cell to cell variations, the discovery of acquired drug resistance mutations, transcriptional diversity of a pathogen across different infection stages, to identify rare cell types and investigate different cellular states of genital infection causing pathogens, and to develop novel therapeutical strategies. In this chapter, I will provide a complete review of the applications of single-cell sequencing in human genital infections before discussing their limitations and challenges.


Assuntos
Análise de Sequência , Doenças Sexualmente Transmissíveis/genética , Análise de Célula Única , Infecções Urinárias/genética , Vagina/microbiologia , Feminino , Humanos , Masculino
8.
Nat Commun ; 11(1): 4682, 2020 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-32943628

RESUMO

The ongoing Corona Virus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has emphasized the urgent need for antiviral therapeutics. The viral RNA-dependent-RNA-polymerase (RdRp) is a promising target with polymerase inhibitors successfully used for the treatment of several viral diseases. We demonstrate here that Favipiravir predominantly exerts an antiviral effect through lethal mutagenesis. The SARS-CoV RdRp complex is at least 10-fold more active than any other viral RdRp known. It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. The coronavirus RdRp complex represents an Achilles heel for SARS-CoV, supporting nucleoside analogues as promising candidates for the treatment of COVID-19.


Assuntos
Amidas/farmacologia , Antivirais/farmacologia , Betacoronavirus/efeitos dos fármacos , Betacoronavirus/genética , Infecções por Coronavirus/tratamento farmacológico , Pneumonia Viral/tratamento farmacológico , Pirazinas/farmacologia , Amidas/farmacocinética , Animais , Antivirais/farmacocinética , Chlorocebus aethiops , Infecções por Coronavirus/virologia , Modelos Moleculares , Mutagênese/efeitos dos fármacos , Pandemias , Pneumonia Viral/virologia , Pirazinas/farmacocinética , RNA Replicase/química , RNA Replicase/metabolismo , RNA Viral/genética , RNA Viral/metabolismo , Análise de Sequência , Células Vero , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/metabolismo , Replicação Viral/efeitos dos fármacos
9.
ACS Infect Dis ; 6(9): 2319-2336, 2020 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-32786280

RESUMO

In December 2019, a novel beta (ß) coronavirus eventually named SARS-CoV-2 emerged in Wuhan, Hubei province, China, causing an outbreak of severe and even fatal pneumonia in humans. The virus has spread very rapidly to many countries across the world, resulting in the World Health Organization (WHO) to declare a pandemic on March 11, 2020. Clinically, the diagnosis of this unprecedented illness, called coronavirus disease-2019 (COVID-19), becomes difficult because it shares many symptoms with other respiratory pathogens, including influenza and parainfluenza viruses. Therefore, laboratory diagnosis is crucial for the clinical management of patients and the implementation of disease control strategies to contain SARS-CoV-2 at clinical and population level. Here, we summarize the main clinical and imaging findings of COVID-19 patients and discuss the advances, features, advantages, and limitations of different laboratory methods used for SARS-CoV-2 diagnosis.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Infecções por Coronavirus/virologia , Humanos , Microscopia Eletrônica , Pandemias , Pneumonia Viral/virologia , Reação em Cadeia da Polimerase/métodos , Análise de Sequência , Testes Sorológicos/métodos , Manejo de Espécimes/métodos
10.
Plant Mol Biol ; 104(3): 283-296, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32740897

RESUMO

KEY MESSAGE: Differences in FAE1 enzyme affinity for the acyl-CoA substrates, as well as the balance between the different pathways involved in their incorporation to triacylglycerol might be determinant of the different composition of the seed oil in Brassicaceae. Brassicaceae present a great heterogeneity of seed oil and fatty acid composition, accumulating Very Long Chain Fatty Acids with industrial applications. However, the molecular determinants of these differences remain elusive. We have studied the ß-ketoacyl-CoA synthase from the high erucic feedstock Thlaspi arvense (Pennycress). Functional characterization of the Pennycress FAE1 enzyme was performed in two Arabidopsis backgrounds; Col-0, with less than 2.5% of erucic acid in its seed oil and the fae1-1 mutant, deficient in FAE1 activity, that did not accumulate erucic acid. Seed-specific expression of the Pennycress FAE1 gene in Col-0 resulted in a 3 to fourfold increase of erucic acid content in the seed oil. This increase was concomitant with a decrease of eicosenoic acid levels without changes in oleic ones. Interestingly, only small changes in eicosenoic and erucic acid levels occurred when the Pennycress FAE1 gene was expressed in the fae1-1 mutant, with high levels of oleic acid available for elongation, suggesting that the Pennycress FAE1 enzyme showed higher affinity for eicosenoic acid substrates, than for oleic ones in Arabidopsis. Erucic acid was incorporated to triacylglycerol in the transgenic lines without significant changes in their levels in the diacylglycerol fraction, suggesting that erucic acid was preferentially incorporated to triacylglycerol via DGAT1. Expression analysis of FAE1, AtDGAT1, AtLPCAT1 and AtPDAT1 genes in the transgenic lines further supported this conclusion. Differences in FAE1 affinity for the oleic and eicosenoic substrates among Brassicaceae, as well as their incorporation to triacylglycerol might explain the differences in composition of their seed oil.


Assuntos
3-Oxoacil-(Proteína de Transporte de Acila) Sintase/metabolismo , Biocombustíveis , Vias Biossintéticas , Brassicaceae/metabolismo , Thlaspi/enzimologia , Thlaspi/metabolismo , Triglicerídeos/biossíntese , 1-Acilglicerofosfocolina O-Aciltransferase/metabolismo , 3-Oxoacil-(Proteína de Transporte de Acila) Sintase/genética , Aciltransferases/metabolismo , Sequência de Aminoácidos , Proteínas de Arabidopsis/metabolismo , Vias Biossintéticas/genética , Diacilglicerol O-Aciltransferase/metabolismo , Ácidos Erúcicos/metabolismo , Elongases de Ácidos Graxos/genética , Elongases de Ácidos Graxos/metabolismo , Ácidos Graxos/metabolismo , Regulação da Expressão Gênica de Plantas , Fenótipo , Óleos Vegetais/metabolismo , Plantas Geneticamente Modificadas , Sementes/genética , Análise de Sequência , Thlaspi/genética , Transcriptoma
11.
Plant Mol Biol ; 104(3): 263-281, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32740898

RESUMO

KEY MESSAGE: Plant-specific Dof transcription factors VDOF1 and VDOF2 are novel regulators of vascular cell differentiation through the course of a lifetime in Arabidopsis, with shifting their transcriptional target genes. Vascular system is one of critical tissues for vascular plants to transport low-molecular compounds, such as water, minerals, and the photosynthetic product, sucrose. Here, we report the involvement of two Dof transcription factors, named VASCULAR-RELATED DOF1 (VDOF1)/VDOF4.6 and VDOF2/VDOF1.8, in vascular cell differentiation and lignin biosynthesis in Arabidopsis. VDOF genes were expressed in vascular tissues, but the detailed expression sites were partly different between VDOF1 and VDOF2. Vein patterning and lignin analysis of VDOF overexpressors and double mutant vdof1 vdof2 suggested that VDOF1 and VDOF2 would function as negative regulators of vein formation in seedlings, and lignin deposition in inflorescence stems. Interestingly, effects of VDOF overexpression in lignin deposition were different by developmental stages of inflorescence stems, and total lignin contents were increased and decreased in VDOF1 and VDOF2 overexpressors, respectively. RNA-seq analysis of inducible VDOF overexpressors demonstrated that the genes for cell wall biosynthesis, including lignin biosynthetic genes, and the transcription factor genes related to stress response and brassinosteroid signaling were commonly affected by VDOF1 and VDOF2 overexpression. Taken together, we concluded that VDOF1 and VDOF2 are novel regulators of vascular cell differentiation through the course of a lifetime, with shifting their transcriptional target genes: in seedlings, the VDOF genes negatively regulate vein formation, while at reproductive stages, the VDOF proteins target lignin biosynthesis.


Assuntos
Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Arabidopsis/metabolismo , Diferenciação Celular/fisiologia , Lignina/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Proteínas de Ligação a DNA , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Ontologia Genética , Inflorescência , Mutação , Caules de Planta/citologia , Caules de Planta/metabolismo , Plantas Geneticamente Modificadas/genética , Sementes , Análise de Sequência
12.
BMC Bioinformatics ; 21(1): 343, 2020 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-32758139

RESUMO

BACKGROUND: Nanopore sequencing enables portable, real-time sequencing applications, including point-of-care diagnostics and in-the-field genotyping. Achieving these outcomes requires efficient bioinformatic algorithms for the analysis of raw nanopore signal data. However, comparing raw nanopore signals to a biological reference sequence is a computationally complex task. The dynamic programming algorithm called Adaptive Banded Event Alignment (ABEA) is a crucial step in polishing sequencing data and identifying non-standard nucleotides, such as measuring DNA methylation. Here, we parallelise and optimise an implementation of the ABEA algorithm (termed f5c) to efficiently run on heterogeneous CPU-GPU architectures. RESULTS: By optimising memory, computations and load balancing between CPU and GPU, we demonstrate how f5c can perform ∼3-5 × faster than an optimised version of the original CPU-only implementation of ABEA in the Nanopolish software package. We also show that f5c enables DNA methylation detection on-the-fly using an embedded System on Chip (SoC) equipped with GPUs. CONCLUSIONS: Our work not only demonstrates that complex genomics analyses can be performed on lightweight computing systems, but also benefits High-Performance Computing (HPC). The associated source code for f5c along with GPU optimised ABEA is available at https://github.com/hasindu2008/f5c .


Assuntos
Gráficos por Computador , Nanoporos , Processamento de Sinais Assistido por Computador , Algoritmos , Biologia Computacional , Bases de Dados como Assunto , Genoma Humano , Humanos , Análise de Sequência
13.
PLoS One ; 15(8): e0237368, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32780777

RESUMO

Soil archives are an important resource in agronomic and ecosystem sciences. If microbial communities could be reconstructed from archived soil DNA, as prehistoric plant communities are reconstructed via pollen data, soil archive resources would assume even greater value for reconstructing land-use history, forensic science, and biosphere modelling. Yet, the effects of long-term soil archival on the preservation of microbial DNA is still largely unknown. To address this, we assessed the capacity of high-throughput sequencing (Illumina MiSeq) of ITS (internal transcribed spacer) and prokaryotic 16S rRNA genes for reconstructing soil microbial communities across a 20 years time-series. We studied air-dried soil archives and fresh soil samples taken from Populus bioenergy and deciduous forest research plots at the Kellogg Biological Station. Habitat and archival time explained significant amounts of variation in soil microbial α- and ß-diversity both in fungal and prokaryotic communities. We found that microbial richness, diversity, and abundance generally decreased with storage time, but varied between habitat and taxonomic groups. The high relative abundance of ectomycorrhizal species including Hebeloma and Cortinarius detected in older soil archives raises questions regarding traits such as long-term persistence and viability of ectomycorrhizal propagules in soils, with relevance to forest health and ecosystem succession. Talaromyces, Paecilomyces and Epicoccum spp. were detected in fresh and across 20-year-old archived soils and were also cultured from these soils demonstrating their long-term spore viability. In summary, we found that microbial DNA in air-dried soils archived over the past 20 years degraded with time, in a manner that differed between soil types and phylogenetic groups of microbes.


Assuntos
Fungos/genética , Células Procarióticas/metabolismo , Biodiversidade , Ecossistema , Fungos/classificação , Análise de Sequência , Microbiologia do Solo
14.
Infect Dis Poverty ; 9(1): 88, 2020 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-32741372

RESUMO

BACKGROUND: An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. This study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine development. METHODS: The genome sequence and protein sequences of SARS-CoV-2 were retrieved from the National Center for Biotechnology Information (NCBI) database. ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DiscoTope 2.0 program. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forecasted epitopes were characterized for immunogen potential evaluation. RESULTS: A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides (Spike315-324, Spike333-338, Spike648-663, Spike1064-1079) exhibited high antigenicity score and good surface accessibility. Ten residues within spike protein (Gly496, Glu498, Pro499, Thr500, Leu1141, Gln1142, Pro1143, Glu1144, Leu1145, Asp1146) are forecasted as components of discontinuous B-cell epitopes. The bioinformatics analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind MHC class I and MHC class II molecules respectively. The peptides (Nucleocapsid66-75, Nucleocapsid104-112) were predicted to bind a wide spectrum of both HLA-1 and HLA-2 molecules. CONCLUSIONS: B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.


Assuntos
Betacoronavirus/genética , Betacoronavirus/imunologia , Biologia Computacional/métodos , Infecções por Coronavirus/prevenção & controle , Epitopos de Linfócito B/imunologia , Epitopos de Linfócito T/imunologia , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Vacinas Virais/imunologia , Sequência de Aminoácidos , Infecções por Coronavirus/imunologia , Infecções por Coronavirus/virologia , Desenho de Fármacos , Epitopos de Linfócito B/química , Epitopos de Linfócito T/química , Humanos , Imunogenicidade da Vacina/imunologia , Modelos Moleculares , Pneumonia Viral/imunologia , Pneumonia Viral/virologia , Alinhamento de Sequência , Análise de Sequência , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética , Glicoproteína da Espícula de Coronavírus/imunologia , Proteínas do Envelope Viral/imunologia
15.
Euro Surveill ; 25(26)2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32643599

RESUMO

Following SARS-CoV-2 emergence in China, a specific surveillance was implemented in France. Phylogenetic analysis of sequences retrieved through this surveillance suggests that detected initial introductions, involving non-clade G viruses, did not seed local transmission. Nevertheless, identification of clade G variants subsequently circulating in the country, with the earliest from a patient who neither travelled to risk areas nor had contact with travellers, suggests that SARS-CoV-2 might have been present before the first recorded local cases.


Assuntos
Infecções por Coronavirus/genética , Coronavirus/genética , Surtos de Doenças/prevenção & controle , Vigilância de Evento Sentinela , Betacoronavirus , Coronavirus/classificação , Coronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , França/epidemiologia , Genoma Viral/genética , Humanos , Pandemias/prevenção & controle , Filogenia , Pneumonia Viral/diagnóstico , Pneumonia Viral/epidemiologia , Pneumonia Viral/transmissão , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Análise de Sequência , Proteínas Virais/genética
16.
PLoS Negl Trop Dis ; 14(6): e0008419, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32603325

RESUMO

Enterocytozoon bieneusi is a human pathogen with a broad range of animal hosts. Initially, E. bieneusi was considered an emerging opportunistic pathogen in immunocompromised, mainly HIV-infected patients, but it has been increasingly reported in apparently healthy individuals globally. As in other African countries, the molecular epidemiology of E. bieneusi in Mozambique remains completely unknown. Therefore, we undertook a study to investigate the occurrence and genetic diversity of E. bieneusi infections in children with gastrointestinal symptoms as well as in asymptomatic children in Mozambique. Individual stool specimens were collected from 1,247 children aged between 0 and 14 years-old living in urban and rural settings in Zambézia (n = 1,097) and Maputo (n = 150) provinces between 2016 and 2019. Samples were analysed for E. bieneusi by nested-PCR targeting the internal transcribed spacer (ITS) region of the rRNA gene. All positive amplicons were confirmed and genotyped. Penalised logistic regression (Firth) was used to evaluate risk associations. The overall prevalence of E. bieneusi in this children population was 0.7% (9/1,247). A 10-fold higher prevalence was found in Maputo (4.0%; 6/150) than in Zambézia (0.3%; 3/1,097). All E. bieneusi-positive samples were from children older than 1-year of age, and most (8/9) from asymptomatic children. Nucleotide sequence analysis of the ITS region revealed the presence of four genotypes, three previously reported (Peru11, n = 1; Type IV, n = 2, and S2, n = 2) and a novel genotype (named HhMzEb1, n = 4). Novel genotype HhMzEb1 was identified in both asymptomatic (75%, 3/4) and symptomatic (25%, 1/4) children from a rural area in Maputo province in southern Mozambique. Genotypes HhMzEb1, Peru11, S2, and Type IV belonged to the Group 1 that includes genotypes with low host specificity and the potential for zoonotic and cross-species transmission. Being infected by enteric protozoan parasites and no handwashing were identified as risk associations for E. bieneusi infection. This study reports the first investigation of E. bieneusi genotypes in Mozambique with the identification of three previously reported genotypes in humans as well as a novel genotype (HhMzEb1). Findings highlight the need to conduct additional research to elucidate the epidemiology of E. bieneusi in the country, especially in rural areas where poor hygiene conditions still prevail. Special attention should be paid to the identification of suitable animal and environmental reservoirs of this parasite and to the characterization of transmission pathways.


Assuntos
Enterocytozoon/genética , Enterocytozoon/isolamento & purificação , Genótipo , Microsporidiose/microbiologia , Epidemiologia Molecular , Adolescente , África/epidemiologia , Animais , Criança , Pré-Escolar , Estudos Transversais , DNA Fúngico/análise , Enterocytozoon/classificação , Feminino , Variação Genética , Especificidade de Hospedeiro , Humanos , Lactente , Recém-Nascido , Masculino , Microsporidiose/epidemiologia , Moçambique/epidemiologia , Filogenia , Reação em Cadeia da Polimerase , Prevalência , Estudos Prospectivos , População Rural , Análise de Sequência , População Urbana , Zoonoses/epidemiologia , Zoonoses/microbiologia
17.
MMWR Morb Mortal Wkly Rep ; 69(28): 918-922, 2020 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-32678072

RESUMO

To limit introduction of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), the United States restricted travel from China on February 2, 2020, and from Europe on March 13. To determine whether local transmission of SARS-CoV-2 could be detected, the New York City (NYC) Department of Health and Mental Hygiene (DOHMH) conducted deidentified sentinel surveillance at six NYC hospital emergency departments (EDs) during March 1-20. On March 8, while testing availability for SARS-CoV-2 was still limited, DOHMH announced sustained community transmission of SARS-CoV-2 (1). At this time, twenty-six NYC residents had confirmed COVID-19, and ED visits for influenza-like illness* increased, despite decreased influenza virus circulation.† The following week, on March 15, when only seven of the 56 (13%) patients with known exposure histories had exposure outside of NYC, the level of community SARS-CoV-2 transmission status was elevated from sustained community transmission to widespread community transmission (2). Through sentinel surveillance during March 1-20, DOHMH collected 544 specimens from patients with influenza-like symptoms (ILS)§ who had negative test results for influenza and, in some instances, other respiratory pathogens.¶ All 544 specimens were tested for SARS-CoV-2 at CDC; 36 (6.6%) tested positive. Using genetic sequencing, CDC determined that the sequences of most SARS-CoV-2-positive specimens resembled those circulating in Europe, suggesting probable introductions of SARS-CoV-2 from Europe, from other U.S. locations, and local introductions from within New York. These findings demonstrate that partnering with health care facilities and developing the systems needed for rapid implementation of sentinel surveillance, coupled with capacity for genetic sequencing before an outbreak, can help inform timely containment and mitigation strategies.


Assuntos
Betacoronavirus/genética , Betacoronavirus/isolamento & purificação , Infecções Comunitárias Adquiridas/diagnóstico , Infecções Comunitárias Adquiridas/virologia , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/virologia , Pneumonia Viral/diagnóstico , Pneumonia Viral/virologia , Vigilância de Evento Sentinela , Adolescente , Adulto , Idoso , Criança , Pré-Escolar , Infecções Comunitárias Adquiridas/epidemiologia , Infecções por Coronavirus/epidemiologia , Serviço Hospitalar de Emergência , Feminino , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Cidade de Nova Iorque/epidemiologia , Pandemias , Pneumonia Viral/epidemiologia , Análise de Sequência , Doença Relacionada a Viagens , Adulto Jovem
18.
Plant Mol Biol ; 104(1-2): 113-136, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32627097

RESUMO

KEY MESSAGE: Present study revealed a complex relationship among histone H3 methylation (examined using H3K4/K27me3 marks), cytosine DNA methylation and differential gene expression during Lr28 mediated leaf rust resistance in wheat. During the present study, genome-wide histone modifications were examined in a pair of near isogenic lines (NILs) (with and without Lr28 in the background of cv. HD2329). The two histone marks used included H3K4me3 (an activation mark) and H3K27me3 (a repression mark). The results were compared with levels of expression (using RNA-seq) and DNA methylation (MeDIP) data obtained using the same pair of NILs. Some of the salient features of the present study include the following: (i) large scale differential binding sites (DBS) were available for only H3K4me3 in the susceptible cultivar, but for both H3K4me3 and H3K27me3 in its resistant NIL; (ii) DBSs for H3K27me3 mark were more abundant (> 80%) in intergenic regions, whereas DBSs for H3K4me3 were distributed in all genomic regions including exons, introns, intergenic, TTS (transcription termination sites) and promoters; (iii) fourteen (14) genes associated with DBSs showed co-localization for both the marks; (iv) only a small fraction (7% for H3K4me3 and 12% for H3K27me3) of genes associated with DBSs matched with the levels of gene expression inferred from RNA-seq data; (v) validation studies using qRT-PCR were conducted on 26 selected representative genes; results for only 11 genes could be validated. The proteins encoded by important genes involved in promoting infection included domains generally carried by R gene proteins such as Mlo like protein, protein kinases and purple acid phosphatase. Similarly, proteins encoded by genes involved in resistance included those carrying domains for lectin kinase, R gene, aspartyl protease, etc. Overall, the results suggest a very complex network of downstream genes that are expressed during compatible and incompatible interactions; some of the genes identified during the present study may be used in future validation studies involving RNAi/overexpression approaches.


Assuntos
Basidiomycota/metabolismo , Resistência à Doença/genética , Genes de Plantas/genética , Genoma de Planta/genética , Histonas/genética , Doenças das Plantas/genética , Triticum/genética , Triticum/metabolismo , Imunoprecipitação da Cromatina , Metilação de DNA , Regulação da Expressão Gênica de Plantas , Ligação Genética , Histonas/metabolismo , Anotação de Sequência Molecular , Doenças das Plantas/microbiologia , Folhas de Planta/genética , Folhas de Planta/microbiologia , Regiões Promotoras Genéticas , Reprodutibilidade dos Testes , Alinhamento de Sequência , Análise de Sequência , Análise de Sequência de RNA , Transcrição Genética , Triticum/microbiologia
19.
Plant Mol Biol ; 104(1-2): 151-171, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32656674

RESUMO

KEY MESSAGE: Pollen abortion could be mainly attributed to abnormal meiosis in the mutant. Multiomics analysis uncovered significant epigenetic variations between the mutant and its wild type during the pollen abortion process. Male sterility caused by aborted pollen can result in seedless fruit. A seedless Ponkan mandarin mutant (bud sport) was used to compare the transcriptome, methylome, and metabolome with its progenitor to understand the mechanism of citrus pollen abortion. Cytological observations showed that the anther of the mutant could form microspore mother cells, although the microspores failed to develop fertile pollen at the anther dehiscence stage. Based on pollen phenotypic analysis, pollen abortion could be mainly attributed to abnormal meiosis in the mutant. A transcriptome analysis uncovered the molecular mechanisms underlying pollen abortion between the mutant and its wild type. A total of 5421 differentially expressed genes were identified, and some of these genes were involved in the meiosis, hormone biosynthesis and signaling, carbohydrate, and flavonoid pathways. A total of 50,845 differentially methylated regions corresponding to 15,426 differentially methylated genes in the genic region were found between the mutant and its wild type by the methylome analysis. The expression level of these genes was negatively correlated with their methylation level, especially in the promoter regions. In addition, 197 differential metabolites were identified between the mutant and its wild type based on the metabolome analysis. The transcription and metabolome analysis further indicated that the expression of genes in the flavonoid, carbohydrate, and hormone metabolic pathways was significantly modulated in the pollen of the mutant. These results indicated that demethylation may alleviate the silencing of carbohydrate genes in the mutant, resulting in excessive starch and sugar hydrolysis and thereby causing pollen abortion in the mutant.


Assuntos
Citrus/metabolismo , Epigenoma , Metaboloma , Proteínas de Plantas/metabolismo , Pólen/metabolismo , Transcriptoma , Citrus/citologia , Citrus/genética , Citrus/crescimento & desenvolvimento , Metilação de DNA , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Genótipo , Meiose , Reguladores de Crescimento de Planta/metabolismo , Infertilidade das Plantas/genética , Infertilidade das Plantas/fisiologia , Proteínas de Plantas/genética , Pólen/genética , Análise de Sequência
20.
Plant Mol Biol ; 104(1-2): 203-215, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32683610

RESUMO

KEY MESSAGE: Distinct catalytic features of the Poaceae TPS-a subfamily arose early in grass evolution and the reactions catalyzed have become more complex with time. The structural diversity of terpenes found in nature is mainly determined by terpene synthases (TPS). TPS enzymes accept ubiquitous prenyl diphosphates as substrates and convert them into the various terpene skeletons by catalyzing a carbocation-driven reaction. Based on their sequence similarity, terpene synthases from land plants can be divided into different subfamilies, TPS-a to TPS-h. In this study, we aimed to understand the evolution and functional diversification of the TPS-a subfamily in the Poaceae (the grass family), a plant family that contains important crops such as maize, wheat, rice, and sorghum. Sequence comparisons showed that aside from one clade shared with other monocot plants, the Poaceae TPS-a subfamily consists of five well-defined clades I-V, the common ancestor of which probably originated very early in the evolution of the grasses. A survey of the TPS literature and the characterization of representative TPS enzymes from clades I-III revealed clade-specific substrate and product specificities. The enzymes in both clade I and II function as sesquiterpene synthases with clade I enzymes catalyzing initial C10-C1 or C11-C1 ring closures and clade II enzymes catalyzing C6-C1 closures. The enzymes of clade III mainly act as monoterpene synthases, forming cyclic and acyclic monoterpenes. The reconstruction and characterization of clade ancestors demonstrated that the differences among clades I-III were already present in their ancestors. However, the ancestors generally catalyzed simpler reactions with less double-bond isomerization and fewer cyclization steps. Overall, our data indicate an early origin of key enzymatic features of TPS-a enzymes in the Poaceae, and the development of more complex reactions over the course of evolution.


Assuntos
Alquil e Aril Transferases/genética , Alquil e Aril Transferases/metabolismo , Poaceae/enzimologia , Poaceae/genética , Alquil e Aril Transferases/classificação , Clonagem Molecular , Escherichia coli/genética , Evolução Molecular , Genes de Plantas/genética , Liases Intramoleculares/metabolismo , Proteínas de Plantas/genética , Análise de Sequência , Terpenos/metabolismo
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA