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1.
Adv Exp Med Biol ; 1232: 393-399, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31893436

RESUMO

Although the existence of the primo vasculature system has been shown in many species, including mice, rats, rabbits and humans, the biological role of this system, including expression of genes and proteins, has not yet been investigated. Especially the transcriptional action by mRNA, which is required for biological action, needs to be studied in primo vasculature biology. Differentially expressed genes in both isolated primo vessels and lymphatic vessels of rabbits were analyzed by RNA sequencing experiments. Primer efficiency and RNA purity of the primo vessels under lipopolysaccharides were confirmed prior to performing real-time qRT-PCR analysis following RNA extraction. We demonstrated that FLT4 was enriched in primo vessels and that several genes, including HSPH1 and EPHB2, were highly expressed in primo vessels compared with lymphatic vessels. Our data show that almost all genes, except HSPA4, were increased or sustained in isolated primo vessels compared with lymphatic vessels (FLT4 2.58 fold, HSPH1 1.83 fold, EPHB2 1.52 fold; whereas HSPA4 decreased 0.50 fold), suggesting primo vessels as a central regulator in diverse physiology. This implies that FLT4, HSPH1, and EPHB2 in high amounts may be involved in the functional activity of primo vessels. Our experimental data show that several genes are highly enriched in primo vessels in the lymphatic vessels of the rabbit.


Assuntos
Regulação da Expressão Gênica , Vasos Linfáticos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Animais , Proteínas de Choque Térmico HSP110/genética , Vasos Linfáticos/metabolismo , RNA Mensageiro/genética , Coelhos , Receptor EphB2/genética , Análise de Sequência de RNA , Receptor 3 de Fatores de Crescimento do Endotélio Vascular/genética
2.
Chemosphere ; 238: 124563, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31454744

RESUMO

Nanoplastic pollution is widespread and persistent across global water systems and can cause a negative effect on aquatic organisms, especially the zooplankter which is the keystone of the food chain. The present study uses RNA sequencing to assess the global change in gene expression caused by 21 days of exposure to 75 nm polystyrene (PS) nanoplastics on Daphnia pulex, a model organism for ecotoxicity. With the threshold value at P value < 0.05 and fold change >2, 244 differentially expressed genes were obtained. Combined with real-time PCR validation of several selected genes, our results indicated that a distinct expression profile of key genes, including downregulated trehalose transporter, trehalose 6-phosphate synthase/phosphatase, chitinase and cathepsin-L as well as upregulated doublesex 1 and doublesex and mab-3 related transcription factor-like protein, contributed to the toxic effects of chronic nanoplastic exposure on Daphnia, such as slowed growth, subdued reproductive ability and reproductive pattern shifting. Our study also showed that chronic exposure to nanoplastic changed the sex ratio of D. pulex neonates. By integrating the gene expression pattern in an important model organism, this study gained insight into the molecular mechanisms of the toxic effect of chronic PS nanoplastic exposure on D. pulex, which may also extend to other nanoplastics or aquatic animals.


Assuntos
Daphnia/efeitos dos fármacos , Poliestirenos/toxicidade , Reprodução/efeitos dos fármacos , Razão de Masculinidade , Poluentes Químicos da Água/toxicidade , Animais , Organismos Aquáticos/efeitos dos fármacos , Daphnia/genética , Cadeia Alimentar , Expressão Gênica/efeitos dos fármacos , Humanos , Recém-Nascido , Análise de Sequência de RNA
3.
BMC Bioinformatics ; 20(Suppl 24): 596, 2019 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-31861975

RESUMO

BACKGROUND: Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have developed several new pipelines and software packages to identify RNA editing sites with a focus on downstream statistical analysis and functional interpretation. RESULTS: Here, we developed a user-friendly public webserver named MIRIA that integrates statistics and visualization techniques to facilitate the comprehensive analysis of RNA editing sites data identified by the pipelines and software packages. MIRIA is unique in that provides several analytical functions, including RNA editing type statistics, genomic feature annotations, editing level statistics, genome-wide distribution of RNA editing sites, tissue-specific analysis and conservation analysis. We collected high-throughput RNA sequencing (RNA-seq) data from eight tissues across seven species as the experimental data for MIRIA and constructed an example result page. CONCLUSION: MIRIA provides both visualization and analysis of mammal RNA editing data for experimental biologists who are interested in revealing the functions of RNA editing sites. MIRIA is freely available at https://mammal.deepomics.org.


Assuntos
Mamíferos , Edição de RNA , Análise de Sequência de RNA , Transcriptoma , Animais , Genoma , Genômica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Mamíferos/genética , RNA/genética , Análise de Sequência de RNA/métodos
5.
BMC Bioinformatics ; 20(1): 497, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31615418

RESUMO

BACKGROUND: It is widely believed that tertiary nucleotide-nucleotide interactions are essential in determining RNA structure and function. Currently, direct coupling analysis (DCA) infers nucleotide contacts in a sequence from its homologous sequence alignment across different species. DCA and similar approaches that use sequence information alone typically yield a low accuracy, especially when the available homologous sequences are limited. Therefore, new methods for RNA structural contact inference are desirable because even a single correctly predicted tertiary contact can potentially make the difference between a correct and incorrectly predicted structure. Here we present a new method DIRECT (Direct Information REweighted by Contact Templates) that incorporates a Restricted Boltzmann Machine (RBM) to augment the information on sequence co-variations with structural features in contact inference. RESULTS: Benchmark tests demonstrate that DIRECT achieves better overall performance than DCA approaches. Compared to mfDCA and plmDCA, DIRECT produces a substantial increase of 41 and 18%, respectively, in accuracy on average for contact prediction. DIRECT improves predictions for long-range contacts and captures more tertiary structural features. CONCLUSIONS: We developed a hybrid approach that incorporates a Restricted Boltzmann Machine (RBM) to augment the information on sequence co-variations with structural templates in contact inference. Our results demonstrate that DIRECT is able to improve the RNA contact prediction.


Assuntos
Algoritmos , Modelos Moleculares , Conformação de Ácido Nucleico , Análise de Sequência de RNA/métodos , Software
6.
Cancer Discov ; 9(10): 1343-1345, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31575563

RESUMO

In this issue of Cancer Discovery, Halbritter and colleagues utilize single-cell RNA sequencing to dissect the cellular hierarchy in Langerhans cell histiocytosis. They identified a remarkably consistent composition of 14 cellular subsets across all patients with a range of clinical spectrums consistent with a shared developmental hierarchy driven by key transcriptional regulators.See related article by Halbritter et al., p. 1406.


Assuntos
Epigenômica , Histiocitose de Células de Langerhans , Humanos , Análise de Sequência de RNA
7.
DNA Cell Biol ; 38(11): 1223-1232, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31566423

RESUMO

To date, the clinical course of idiopathic membranous nephropathy (iMN) remains unclear and lacks direct and effective diagnostic methods. To better understand the host gene expression changes involved in the iMN process and identify the potential signatures for clinical diagnosis, we performed a whole genome-wide transcriptome profile of peripheral blood cells (PBC) from patients with iMN and healthy controls (HCs). A total of 188 differentially expressed genes (DEGs) were detected in patients with iMN versus HCs. Gene ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that these DEGs were mainly correlated with protein targeting, ion homeostasis GO terms, and ribosome and phagosome pathways. The top 10 differentially expressed protein-coding genes with >2-fold changes and high expression levels were validated using quantitative real-time PCR, and showed high consistency with the high-throughput sequencing results. HLA-C, S100A8, and FTH1 genes were selected for further validation and showed the most significant difference between the iMN and HC group, indicating that they could be used as potential clinical diagnostic biomarkers. Our results provide novel potential diagnostic signatures for iMN and have important implications for better understanding the pathogenesis of iMN.


Assuntos
Biomarcadores/sangue , Células Sanguíneas/metabolismo , Glomerulonefrite Membranosa , Transcriptoma , Biomarcadores/análise , Estudos de Casos e Controles , Perfilação da Expressão Gênica , Glomerulonefrite Membranosa/sangue , Glomerulonefrite Membranosa/diagnóstico , Glomerulonefrite Membranosa/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , RNA/análise , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de RNA
8.
J Agric Food Chem ; 67(45): 12408-12418, 2019 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-31644287

RESUMO

Vegetables are an ideal source of human Se intake; it is important to understand selenium (Se) speciation in plants due to the distinct biological functions of selenocompounds. In this hydroponic study, the accumulation and assimilation of selenite and selenate in pak choi (Brassica rapa), a vastly consumed vegetable, were investigated at 1-168 h with HPLC speciation and RNA-sequencing. The results showed that the Se content in shoots and Se translocation factors with selenate addition were at least 10.81 and 11.62 times, respectively, higher than those with selenite addition. Selenite and selenate up-regulated the expression of SULT1;1 and PHT1;2 in roots by over 240% and 400%, respectively. Selenite addition always led to higher proportions of seleno-amino acids, while SeO42- was dominant under selenate addition (>49% of all Se species in shoots). However, in roots, SeO42- proportions declined substantially by 51% with a significant increase of selenomethionine proportions (63%) from 1 to 168 h. Moreover, with enhanced transcript of methionine gamma-lyase (60% of up-regulation compared to the control) plus high levels of methylselenium in shoots (approximately 70% of all Se species), almost 40% of Se was lost during the exposure under the selenite treatment. This work provides evidence that pak choi can rapidly transform selenite to methylselenium, and it is promising to use the plant for Se biofortification.


Assuntos
Brassica rapa/genética , Brassica rapa/metabolismo , Ácido Selênico/metabolismo , Ácido Selenioso/metabolismo , Selênio/metabolismo , Biotransformação , Brassica rapa/química , Brassica rapa/crescimento & desenvolvimento , Cromatografia Líquida de Alta Pressão , Hidroponia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raízes de Plantas/química , Raízes de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , Raízes de Plantas/metabolismo , Ácido Selênico/análise , Ácido Selenioso/análise , Selênio/análise , Análise de Sequência de RNA
9.
BMC Bioinformatics ; 20(1): 520, 2019 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-31653208

RESUMO

BACKGROUND: Due the computational complexity of sequence alignment algorithms, various accelerated solutions have been proposed to speedup this analysis. NVBIO is the only available GPU library that accelerates sequence alignment of high-throughput NGS data, but has limited performance. In this article we present GASAL2, a GPU library for aligning DNA and RNA sequences that outperforms existing CPU and GPU libraries. RESULTS: The GASAL2 library provides specialized, accelerated kernels for local, global and all types of semi-global alignment. Pairwise sequence alignment can be performed with and without traceback. GASAL2 outperforms the fastest CPU-optimized SIMD implementations such as SeqAn and Parasail, as well as NVIDIA's own GPU-based library known as NVBIO. GASAL2 is unique in performing sequence packing on GPU, which is up to 750x faster than NVBIO. Overall on Geforce GTX 1080 Ti GPU, GASAL2 is up to 21x faster than Parasail on a dual socket hyper-threaded Intel Xeon system with 28 cores and up to 13x faster than NVBIO with a query length of up to 300 bases and 100 bases, respectively. GASAL2 alignment functions are asynchronous/non-blocking and allow full overlap of CPU and GPU execution. The paper shows how to use GASAL2 to accelerate BWA-MEM, speeding up the local alignment by 20x, which gives an overall application speedup of 1.3x vs. CPU with up to 12 threads. CONCLUSIONS: The library provides high performance APIs for local, global and semi-global alignment that can be easily integrated into various bioinformatics tools.


Assuntos
Biblioteca Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Alinhamento de Sequência , Software , Algoritmos , Biologia Computacional , DNA/genética , RNA/genética , Análise de Sequência de DNA , Análise de Sequência de RNA
10.
Nature ; 574(7779): 553-558, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31645721

RESUMO

Age-associated chronic inflammation (inflammageing) is a central hallmark of ageing1, but its influence on specific cells remains largely unknown. Fibroblasts are present in most tissues and contribute to wound healing2,3. They are also the most widely used cell type for reprogramming to induced pluripotent stem (iPS) cells, a process that has implications for regenerative medicine and rejuvenation strategies4. Here we show that fibroblast cultures from old mice secrete inflammatory cytokines and exhibit increased variability in the efficiency of iPS cell reprogramming between mice. Variability between individuals is emerging as a feature of old age5-8, but the underlying mechanisms remain unknown. To identify drivers of this variability, we performed multi-omics profiling of fibroblast cultures from young and old mice that have different reprogramming efficiencies. This approach revealed that fibroblast cultures from old mice contain 'activated fibroblasts' that secrete inflammatory cytokines, and that the proportion of activated fibroblasts in a culture correlates with the reprogramming efficiency of that culture. Experiments in which conditioned medium was swapped between cultures showed that extrinsic factors secreted by activated fibroblasts underlie part of the variability between mice in reprogramming efficiency, and we have identified inflammatory cytokines, including TNF, as key contributors. Notably, old mice also exhibited variability in wound healing rate in vivo. Single-cell RNA-sequencing analysis identified distinct subpopulations of fibroblasts with different cytokine expression and signalling in the wounds of old mice with slow versus fast healing rates. Hence, a shift in fibroblast composition, and the ratio of inflammatory cytokines that they secrete, may drive the variability between mice in reprogramming in vitro and influence wound healing rate in vivo. This variability may reflect distinct stochastic ageing trajectories between individuals, and could help in developing personalized strategies to improve iPS cell generation and wound healing in elderly individuals.


Assuntos
Envelhecimento/metabolismo , Reprogramação Celular , Senescência Celular/fisiologia , Fibroblastos/metabolismo , Cicatrização , Animais , Linhagem Celular , Reprogramação Celular/efeitos dos fármacos , Meios de Cultivo Condicionados/farmacologia , Citocinas/metabolismo , Fibroblastos/citologia , Fibroblastos/efeitos dos fármacos , Humanos , Células-Tronco Pluripotentes Induzidas/citologia , Células-Tronco Pluripotentes Induzidas/efeitos dos fármacos , Células-Tronco Pluripotentes Induzidas/metabolismo , Mediadores da Inflamação/metabolismo , Judeus/genética , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Análise de Sequência de RNA , Transdução de Sinais/efeitos dos fármacos , Análise de Célula Única , Processos Estocásticos , Fatores de Tempo , Cicatrização/efeitos dos fármacos
11.
Cell Physiol Biochem ; 53(5): 760-773, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31647206

RESUMO

BACKGROUND/AIMS: Perturbations in the expression of microRNAs (miRNAs) and their maturing machinery components such as Dicer have been previously described for basal cell carcinoma (BCC). However, the mutational status of Dicer in BCC is unclear. Further, the sclerodermiform subtype of BCC (sBCC) has not been previously investigated regarding its methylation profile or its smallRNA expression profile via RNA sequencing. We conducted this study to investigate the mutational status of Dicer in BCC. METHODS: Dicer sequencing was performed on the Illumina MiSeq System in a total of 16 BCC samples (8 nodular BCCs, 8 sBCCs) and mapped against the human reference genome (i.e., hg19). Dicer sequencing was performed in all 16 BCC samples. We performed whole genome methylation profiling with Infinium MethylationEPIC BeadChips as well as mRNA and smallRNA sequencing in 5 sBCCs with the Illumina NextSeq500 next-generation sequencing system. RESULTS: Compared to the wildtype Dicer sequence, we found 5 to 7 variants per sBCC sample including insertion, deletion, and multiple nucleotide variants. Global methylation profiles were highly similar between groups. mRNA sequencing revealed S100A9, KRT14, KRT10, S100A8, S100A7, COX1, KRT1, COX3, and smallRNA sequencing analysis miR-21, miR-99a, miR26-a-2, let-7f, let-7g, let-7i, miR-100, and miR-205 were the most strongly expressed in sBCCs. CONCLUSION: We identified a variety of Dicer mutations that could play a role in aberrant miRNA expression in BCC. The noted RNA sequences should be further evaluated in functional studies to explore their potential pathogenetic role in sBCC.


Assuntos
RNA Helicases DEAD-box/genética , Metilação de DNA , MicroRNAs/química , RNA Mensageiro/química , Ribonuclease III/genética , Idoso , Idoso de 80 Anos ou mais , Carcinoma Basocelular , Linhagem Celular Tumoral , Feminino , Genoma Humano , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , MicroRNAs/metabolismo , RNA Mensageiro/metabolismo , Análise de Sequência de RNA
12.
Genome Biol ; 20(1): 194, 2019 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-31500660

RESUMO

BACKGROUND: Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible. The exponential growth in the number of cells and samples has prompted the adaptation and development of supervised classification methods for automatic cell identification. RESULTS: Here, we benchmarked 22 classification methods that automatically assign cell identities including single-cell-specific and general-purpose classifiers. The performance of the methods is evaluated using 27 publicly available single-cell RNA sequencing datasets of different sizes, technologies, species, and levels of complexity. We use 2 experimental setups to evaluate the performance of each method for within dataset predictions (intra-dataset) and across datasets (inter-dataset) based on accuracy, percentage of unclassified cells, and computation time. We further evaluate the methods' sensitivity to the input features, number of cells per population, and their performance across different annotation levels and datasets. We find that most classifiers perform well on a variety of datasets with decreased accuracy for complex datasets with overlapping classes or deep annotations. The general-purpose support vector machine classifier has overall the best performance across the different experiments. CONCLUSIONS: We present a comprehensive evaluation of automatic cell identification methods for single-cell RNA sequencing data. All the code used for the evaluation is available on GitHub ( https://github.com/tabdelaal/scRNAseq_Benchmark ). Additionally, we provide a Snakemake workflow to facilitate the benchmarking and to support the extension of new methods and new datasets.


Assuntos
Perfilação da Expressão Gênica/métodos , Análise de Sequência de RNA/métodos , Análise de Célula Única/métodos , Máquina de Vetores de Suporte
13.
Genome Biol ; 20(1): 193, 2019 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-31500668

RESUMO

Technical variation in feature measurements, such as gene expression and locus accessibility, is a key challenge of large-scale single-cell genomic datasets. We show that this technical variation in both scRNA-seq and scATAC-seq datasets can be mitigated by analyzing feature detection patterns alone and ignoring feature quantification measurements. This result holds when datasets have low detection noise relative to quantification noise. We demonstrate state-of-the-art performance of detection pattern models using our new framework, scBFA, for both cell type identification and trajectory inference. Performance gains can also be realized in one line of R code in existing pipelines.


Assuntos
Genômica/métodos , Análise de Célula Única/métodos , Perfilação da Expressão Gênica , Modelos Genéticos , Análise de Sequência de RNA , Software
14.
Nucleic Acids Res ; 47(18): 9480-9494, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31504786

RESUMO

Small endonucleolytic ribozymes promote the self-cleavage of their own phosphodiester backbone at a specific linkage. The structures of and the reactions catalysed by members of individual families have been studied in great detail in the past decades. In recent years, bioinformatics studies have uncovered a considerable number of new examples of known catalytic RNA motifs. Importantly, entirely novel ribozyme classes were also discovered, for most of which both structural and biochemical information became rapidly available. However, for the majority of the new ribozymes, which are found in the genomes of a variety of species, a biological function remains elusive. Here, we concentrate on the different approaches to find catalytic RNA motifs in sequence databases. We summarize the emerging principles of RNA catalysis as observed for small endonucleolytic ribozymes. Finally, we address the biological functions of those ribozymes, where relevant information is available and common themes on their cellular activities are emerging. We conclude by speculating on the possibility that the identification and characterization of proteins that we hypothesize to be endogenously associated with catalytic RNA might help in answering the ever-present question of the biological function of the growing number of genomically encoded, small endonucleolytic ribozymes.


Assuntos
Biologia Computacional/métodos , Motivos de Nucleotídeos/genética , RNA Catalítico/genética , Análise de Sequência de RNA/métodos , Catálise , Modelos Moleculares , Conformação de Ácido Nucleico , RNA Catalítico/química , RNA Catalítico/isolamento & purificação
15.
Braz J Med Biol Res ; 52(10): e8380, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31531524

RESUMO

The present study aimed to identify microRNAs (miRNAs) that are involved in neuropathic pain and predict their corresponding roles in the pathogenesis and development process of neuropathic pain. The rat model of neuropathic pain caused by spared nerve injury (SNI) was established in Sprague-Dawley male rats, followed by small RNA sequencing of the L3-L6 dorsal root ganglion. Real-time PCR was performed to validate the differently expressed miRNAs. Functional verification was performed by intrathecally injecting the animals with miRNA agomir. A total of 72 differentially expressed miRNAs were identified in the SNI rats, including 33 upregulated and 39 downregulated miRNAs. The results of qPCR further verified the expression levels of rno-miR-6215 (P=0.015), rno-miR-1224 (P=0.030), rno-miR-1249 (P=0.038), and rno-miR-488-3p (P=0.048), which were all significantly downregulated in the SNI rats compared to the control ones. The majority of differentially expressed miRNAs were associated with phosphorylation, intracellular signal transduction, and cell death. Target prediction, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses suggested that these differentially expressed miRNAs targeted genes that are related to axon guidance, focal adhesion, and Ras and Wnt signaling pathways. Moreover, miR-1224 agomir significantly alleviated SNI-induced neuropathic pain. The current findings provide new insights into the role of miRNAs in the pathogenesis of neuropathic pain.


Assuntos
MicroRNAs/genética , Neuralgia/genética , Análise de Sequência de RNA , Animais , Sequência de Bases , Modelos Animais de Doenças , Masculino , MicroRNAs/metabolismo , Neuralgia/metabolismo , Ratos , Ratos Sprague-Dawley , Reação em Cadeia da Polimerase em Tempo Real , Transdução de Sinais
16.
DNA Cell Biol ; 38(11): 1207-1222, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31483163

RESUMO

Multiple studies have shown that cancer-specific alternative splicing (AS) alterations are associated with clinical outcome. In this study, we aimed to profile prognostic AS signatures for pancreatic ductal adenocarcinoma (PDAC). We integrated the percent-spliced-in (PSI) data of AS in 140 PDAC patients based on the Cancer Genome Atlas (TCGA) dataset. We identified overall survival (OS)-associated AS events using univariate Cox regression analysis. Then, prognostic AS signatures were constructed for OS and chemoresistance prediction using the least absolute shrinkage and selection operator (LASSO) method. We also analyzed splicing factors (SFs) regulatory networks by Pearson's correlation. We detected 677 OS-related AS events in 485 genes by profiling 10,354 AS events obtained from 140 PDAC patients. Gene functional enrichment analysis demonstrated the pathways enriched by survival-associated AS. The AS signatures constructed with significant survival-associated AS events revealed high performance in predicting PDAC survival and gemcitabine chemoresistance. The area under the receiver operator characteristic curve was 0.937 in training cohort and 0.748 in validation cohort at 2000 days of OS. Furthermore, we identified prognostic SFs (e.g., ESRP1 and HNRNPC) to build the AS regulatory network. We constructed AS signatures for OS and gemcitabine chemoresistance in PDAC patients, which may provide clues for further experiment-based mechanism study.


Assuntos
Processamento Alternativo/genética , Biomarcadores Tumorais/genética , Carcinoma Ductal Pancreático , Neoplasias Pancreáticas , Transcriptoma , Carcinoma Ductal Pancreático/diagnóstico , Carcinoma Ductal Pancreático/genética , Carcinoma Ductal Pancreático/mortalidade , Estudos de Coortes , Feminino , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Redes Reguladoras de Genes , Humanos , Masculino , Neoplasias Pancreáticas/diagnóstico , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/mortalidade , Prognóstico , Análise de Sequência de RNA , Análise de Sobrevida
17.
Arch Virol ; 164(11): 2829-2836, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31486908

RESUMO

The complete sequence of the medium (M) and small (S) RNA genome segments were determined for twelve isolates of impatiens necrotic spot virus from eight plant species. The M- and S-RNAs of these isolates shared 97-99% and 93-98% nucleotide sequence identity, respectively, with the corresponding full-length sequences available in public databases. Phylogenetic analysis based on the M- or S-RNA sequences showed incongruence in the phylogenetic position of some isolates, suggesting intraspecies segment reassortment. The lack of phylogenetic discordance in individual and concatenated sequences of individual genes encoded by M- or S-RNAs suggests that segment reassortment rather than recombination is driving evolution of these INSV isolates.


Assuntos
RNA Viral/genética , Vírus Reordenados/genética , Tospovirus/genética , Sequência de Bases , Genoma Viral/genética , Plantas/virologia , Análise de Sequência de RNA , Tospovirus/isolamento & purificação
18.
Nat Methods ; 16(9): 803, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31471610
19.
Nat Methods ; 16(9): 875-878, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31471617

RESUMO

Single-cell RNA sequencing (scRNA-seq) data are noisy and sparse. Here, we show that transfer learning across datasets remarkably improves data quality. By coupling a deep autoencoder with a Bayesian model, SAVER-X extracts transferable gene-gene relationships across data from different labs, varying conditions and divergent species, to denoise new target datasets.


Assuntos
Neoplasias da Mama/metabolismo , Biologia Computacional/métodos , Leucócitos Mononucleares/metabolismo , Análise de Sequência de RNA/normas , Análise de Célula Única/métodos , Linfócitos T/metabolismo , Transcriptoma , Animais , Teorema de Bayes , Feminino , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Humanos , Camundongos , Análise de Sequência de RNA/métodos
20.
Exp Parasitol ; 206: 107754, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31473211

RESUMO

Dermatophagoides farinae is an important source of indoor allergens that shows strong tolerance to external temperatures. However, the regularity and mechanism of tolerance are still unclear. Based on our previous RNA-seq and annotation of D. farinae under temperature stress, it is planned to identify differentially expressed genes (DEGs) involved in the temperature stress response by quantitative real-time PCR (qRT-PCR). However, the lack of reference genes directly limited the detection and confirmation of DEGs. Accordingly, in this study, we have selected six candidates as reference genes in D. farinae: 60S RP L11, 60S RP L21, α tubulin, GAPDH, Der f Mal f 6, and calreticulin, and evaluated their expression stabilities as affected by heat and cold stresses, using geNorm, NormFinder, BestKeeper, comparative ΔCt and RefFinder methods. Then the expression level of 15 DEGs were detected and verified. geNorm analysis showed that α tubulin and calreticulin were the most stable reference genes under heat stress and cold stress of D. farinae. Similar evaluation results were obtained by NormFinder and BestKeeper, in which 60S RP L21 and α tubulin were the most stable reference genes. By comparative ΔCt method and a comprehensive evaluation of RefFinder, α tubulin was identified as the most ideal reference gene of D. farinae under heat and cold stresses. Furthermore, qRT-PCR detection results of 15 DEGs were almost identical to the RNA-seq results, indicating that α tubulin is stable as a reference gene. This study provided technical support for DEGs expression studies in D. farinae using qRT-PCR.


Assuntos
Calreticulina/genética , Dermatophagoides farinae/genética , Temperatura Ambiente , Tubulina (Proteína)/genética , Animais , Antígenos de Dermatophagoides/genética , Primers do DNA/química , Dermatophagoides farinae/fisiologia , Feminino , Amplificação de Genes , Perfilação da Expressão Gênica , Gliceraldeído-3-Fosfato Desidrogenase (Fosforiladora)/genética , Anotação de Sequência Molecular , RNA/química , RNA/genética , RNA/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real , Proteínas Ribossômicas/genética , Análise de Sequência de RNA , Transcriptoma/genética , Temperatura de Transição , Sequenciamento Completo do Exoma
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