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1.
Blood ; 135(8): 534-541, 2020 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-31877211

RESUMO

In chronic myeloid leukemia (CML) patients, tyrosine kinase inhibitors (TKIs) may select for drug-resistant BCR-ABL1 kinase domain (KD) mutants. Although Sanger sequencing (SS) is considered the gold standard for BCR-ABL1 KD mutation screening, next-generation sequencing (NGS) has recently been assessed in retrospective studies. We conducted a prospective, multicenter study (NEXT-in-CML) to assess the frequency and clinical relevance of low-level mutations and the feasibility, cost, and turnaround times of NGS-based BCR-ABL1 mutation screening in a routine setting. A series of 236 consecutive CML patients with failure (n = 124) or warning (n = 112) response to TKI therapy were analyzed in parallel by SS and NGS in 1 of 4 reference laboratories. Fifty-one patients (22 failure, 29 warning) who were negative for mutations by SS had low-level mutations detectable by NGS. Moreover, 29 (27 failure, 2 warning) of 60 patients who were positive for mutations by SS showed additional low-level mutations. Thus, mutations undetectable by SS were identified in 80 out of 236 patients (34%), of whom 42 (18% of the total) had low-level mutations somehow relevant for clinical decision making. Prospective monitoring of mutation kinetics demonstrated that TKI-resistant low-level mutations are invariably selected if the patients are not switched to another TKI or if they are switched to a inappropriate TKI or TKI dose. The NEXT-in-CML study provides for the first time robust demonstration of the clinical relevance of low-level mutations, supporting the incorporation of NGS-based BCR-ABL1 KD mutation screening results in the clinical decision algorithms.


Assuntos
Proteínas de Fusão bcr-abl/genética , Leucemia Mielogênica Crônica BCR-ABL Positiva/tratamento farmacológico , Leucemia Mielogênica Crônica BCR-ABL Positiva/genética , Inibidores de Proteínas Quinases/uso terapêutico , Adulto , Idoso , Idoso de 80 Anos ou mais , Resistencia a Medicamentos Antineoplásicos , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Pessoa de Meia-Idade , Mutação , Taxa de Mutação , Estudos Prospectivos
2.
Int Arch Allergy Immunol ; 183(2): 186-200, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34673641

RESUMO

BACKGROUND: Specific drugs and/or immunotherapies are widely used to treat allergies, but drug-induced adverse effects recently led to explore new additional strategies. We studied whether a probiotic preparation (iPROB®; Anallergo SpA, Florence, Italy) is effective in allergic patients and the mechanisms underlying clinical outcomes. METHODS: Eligible patients (n = 28), all suffering from allergic rhinitis with/without bronchial asthma, were consecutively recruited at the Allergology Medical Unit (Novara, Italy) and treated with this probiotic. From each patient, we collected blood and stool samples at the baseline, after 60 days of probiotic supplementation, and after 60 days from probiotic discontinuation. In each blood sample, the percentage of hematopoietic stem cells, eosinophils, and basophils was measured by FACS. To analyze stool microbiota composition, genomic DNA was extracted, bacterial 16S DNA libraries sequenced by Illumina platform (Miseq), and raw sequences processed. Generated data were statistically analyzed. RESULTS: Probiotic-treated patients showed a significant decrease in Average Rhinitis Total Symptom Score (d = -10.5714), and Visual Analog Scale (d = -2.00) clinical indices, as well as important improvements in quality of life. In whole blood, a significant reduction in the percentage of activated eosinophils and basophils was determined, and this effect persisted after specific cell stimulation. Consistently, the serum levels of IL-4 and IL-5 decreased after probiotic treatment, suggesting a reduction in the Th2 cytokine profile. In addition, microbiome genomic analysis (n = 6) showed an increase in microbiome biodiversity, which positively correlates with clinical and cellular data. CONCLUSION: Present study suggests that iPROB® preparation has clinical/biological properties to be a valid add-on supplementation in allergic patients with asthma and rhinitis.


Assuntos
Asma/diagnóstico , Asma/etiologia , Asma/terapia , Rinite/diagnóstico , Rinite/etiologia , Rinite/terapia , Adulto , Biomarcadores , Citocinas/metabolismo , Gerenciamento Clínico , Suscetibilidade a Doenças , Feminino , Humanos , Imunidade , Imunofenotipagem , Contagem de Leucócitos , Masculino , Metagenômica/métodos , Microbiota , Pessoa de Meia-Idade , Projetos Piloto , Probióticos/uso terapêutico , Prognóstico , Resultado do Tratamento , Adulto Jovem
3.
Br J Haematol ; 193(2): 271-279, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33403687

RESUMO

BCR-ABL1 kinase domain mutation testing in tyrosine kinase inhibitor (TKI)-resistant Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukaemia (ALL) patients is routinely performed by Sanger sequencing (SS). Recently, next-generation sequencing (NGS)-based approaches have been developed that afford greater sensitivity and straightforward discrimination between compound and polyclonal mutations. We performed a study to compare the results of SS and NGS in a consecutive cohort of 171 Ph+ ALL patients. At diagnosis, 0/44 and 3/44 patients were positive for mutations by SS and NGS respectively. Out of 47 patients with haematologic resistance, 45 had mutations according to both methods, but in 25 patients NGS revealed additional mutations undetectable by SS. Out of 80 patients in complete haematologic response but with BCR-ABL1 ≥0·1%, 28 (35%) and 52 (65%) were positive by SS and NGS respectively. Moreover, in 12 patients positive by SS, NGS detected additional mutations. NGS resolved clonal complexity in 34 patients with multiple mutations at the same or different codons and identified 35 compound mutations. Our study demonstrates that, in Ph+ ALL on TKI therapy, NGS enables more accurate assessment of mutation status both in patients who fail therapy and in patients with minimal residual disease above 0·1%.


Assuntos
Resistencia a Medicamentos Antineoplásicos/genética , Proteínas de Fusão bcr-abl/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Neoplasia Residual/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética , Adulto , Idoso , Tomada de Decisão Clínica , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Mutação/genética , Neoplasia Residual/epidemiologia , Cromossomo Filadélfia/efeitos dos fármacos , Leucemia-Linfoma Linfoblástico de Células Precursoras/diagnóstico , Leucemia-Linfoma Linfoblástico de Células Precursoras/tratamento farmacológico , Inibidores de Proteínas Quinases/uso terapêutico
4.
FASEB J ; 33(12): 13572-13589, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31570000

RESUMO

Transposable elements (TEs) compose about half of the mammalian genome and, as embedded sequences, up to 40% of long noncoding RNA (lncRNA) transcripts. Embedded TEs may represent functional domains within lncRNAs, providing a structured RNA platform for protein interaction. Here we show the interactome profile of the mouse inverted short interspersed nuclear element (SINE) of subfamily B2 (invSINEB2) alone and embedded in antisense (AS) ubiquitin C-terminal hydrolase L1 (Uchl1), an lncRNA that is AS to Uchl1 gene. AS Uchl1 is the representative member of a functional class of AS lncRNAs, named SINEUPs, in which the invSINEB2 acts as effector domain (ED)-enhancing translation of sense protein-coding mRNAs. By using RNA-interacting domainome technology, we identify the IL enhancer-binding factor 3 (ILF3) as a protein partner of AS Uchl1 RNA. We determine that this interaction is mediated by the RNA-binding motif 2 of ILF3 and the invSINEB2. Furthermore, we show that ILF3 is able to bind a free right Arthrobacter luteus (Alu) monomer sequence, the embedded TE acting as ED in human SINEUPs. Bioinformatic analysis of Encyclopedia of DNA Elements-enhanced cross-linking immunoprecipitation data reveals that ILF3 binds transcribed human SINE sequences at transcriptome-wide levels. We then demonstrate that the embedded TEs modulate AS Uchl1 RNA nuclear localization to an extent moderately influenced by ILF3. This work unveils the existence of a specific interaction between embedded TEs and an RNA-binding protein, strengthening the model of TEs as functional modules in lncRNAs.-Fasolo, F., Patrucco, L., Volpe, M., Bon, C., Peano, C., Mignone, F., Carninci, P., Persichetti, F., Santoro, C., Zucchelli, S., Sblattero, D., Sanges, R., Cotella, D., Gustincich, S. The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs.


Assuntos
Elementos de DNA Transponíveis , Proteínas do Fator Nuclear 90/metabolismo , RNA Antissenso/genética , RNA Longo não Codificante/metabolismo , RNA Mensageiro/metabolismo , Ubiquitina Tiolesterase/metabolismo , Animais , Biologia Computacional , Ensaios de Triagem em Larga Escala , Humanos , Camundongos , Proteínas do Fator Nuclear 90/genética , Biossíntese de Proteínas , Domínios e Motivos de Interação entre Proteínas , RNA Longo não Codificante/genética , RNA Mensageiro/genética , Ubiquitina Tiolesterase/genética
5.
BMC Bioinformatics ; 19(Suppl 7): 184, 2018 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-30066630

RESUMO

BACKGROUND: De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. Given the high number of sequences obtained from NGS approaches, a critical step in any analysis workflow is the assembly of reads to reconstruct transcripts thus reducing the complexity of the analysis. Despite many available tools show a good sensitivity, there is a high percentage of false positives due to the high number of assemblies considered and it is likely that the high frequency of false positive is underestimated by currently used benchmarks. The reconstruction of not existing transcripts may false the biological interpretation of results as - for example - may overestimate the identification of "novel" transcripts. Moreover, benchmarks performed are usually based on RNA-seq data from annotated genomes and assembled transcripts are compared to annotations and genomes to identify putative good and wrong reconstructions, but these tests alone may lead to accept a particular type of false positive as true, as better described below. RESULTS: Here we present a novel methodology of de novo assembly, implemented in a software named STAble (Short-reads Transcriptome Assembler). The novel concept of this assembler is that the whole reads are used to determine possible alignments instead of using smaller k-mers, with the aim of reducing the number of chimeras produced. Furthermore, we applied a new set of benchmarks based on simulated data to better define the performance of assembly method and carefully identifying true reconstructions. STAble was also used to build a prototype workflow to analyse metatranscriptomics data in connection to a steady state metabolic modelling algorithm. This algorithm was used to produce high quality metabolic interpretations of small gene expression sets obtained from already published RNA-seq data that we assembled with STAble. CONCLUSIONS: The presented results, albeit preliminary, clearly suggest that with this approach is possible to identify informative reactions not directly revealed by raw transcriptomic data.


Assuntos
Redes e Vias Metabólicas/genética , Modelos Genéticos , Análise de Sequência de RNA/métodos , Software , Transcriptoma/genética , Fluxo de Trabalho , Algoritmos , Animais , Humanos , Metano/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Ruminantes
6.
RNA Biol ; 12(12): 1289-300, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26512911

RESUMO

We describe here a platform for high-throughput protein expression and interaction analysis aimed at identifying the RNA-interacting domainome. This approach combines the selection of a phage library displaying "filtered" open reading frames with next-generation DNA sequencing. The method was validated using an RNA bait corresponding to the AU-rich element of α-prothymosin, an RNA motif that promotes mRNA stability and translation through its interaction with the RNA-binding protein ELAVL1. With this strategy, we not only confirmed known RNA-binding proteins that specifically interact with the target RNA (such as ELAVL1/HuR and RBM38) but also identified proteins not previously known to be ARE-binding (R3HDM2 and RALY). We propose this technology as a novel approach for studying the RNA-binding proteome.


Assuntos
Elementos Ricos em Adenilato e Uridilato/genética , Fases de Leitura Aberta/genética , Domínios e Motivos de Interação entre Proteínas/genética , Precursores de Proteínas/genética , Proteínas de Ligação a RNA/metabolismo , Timosina/análogos & derivados , Células HEK293 , Humanos , Ligação Proteica , Precursores de Proteínas/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Reprodutibilidade dos Testes , Timosina/genética , Timosina/metabolismo
7.
RNA ; 18(3): 368-84, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22237150

RESUMO

The sequence elements that mediate post-transcriptional gene regulation often reside in the 5' and 3' untranslated regions (UTRs) of mRNAs. Using six different families of dicotyledonous plants, we developed a comparative transcriptomics pipeline for the identification and annotation of deeply conserved regulatory sequences in the 5' and 3' UTRs. Our approach was robust to confounding effects of poor UTR alignability and rampant paralogy in plants. In the 3' UTR, motifs resembling PUMILIO-binding sites form a prominent group of conserved motifs. Additionally, Expansins, one of the few plant mRNA families known to be localized to specific subcellular sites, possess a core conserved RCCCGC motif. In the 5' UTR, one major subset of motifs consists of purine-rich repeats. A distinct and substantial fraction possesses upstream AUG start codons. Half of the AUG containing motifs reveal hidden protein-coding potential in the 5' UTR, while the other half point to a peptide-independent function related to translation. Among the former, we added four novel peptides to the small catalog of conserved-peptide uORFs. Among the latter, our case studies document patterns of uORF evolution that include gain and loss of uORFs, switches in uORF reading frame, and switches in uORF length and position. In summary, nearly three hundred post-transcriptional elements show evidence of purifying selection across the eudicot branch of flowering plants, indicating a regulatory function spanning at least 70 million years. Some of these sequences have experimental precedent, but many are novel and encourage further exploration.


Assuntos
Regiões 3' não Traduzidas , Regiões 5' não Traduzidas , Sequência Conservada , Plantas/genética , Processamento Pós-Transcricional do RNA/genética , RNA de Plantas/química , Sequência de Aminoácidos , Sequência de Bases , Evolução Molecular , Regulação da Expressão Gênica de Plantas , Dados de Sequência Molecular , Motivos de Nucleotídeos , Fases de Leitura Aberta , RNA Mensageiro/genética , RNA de Plantas/metabolismo , Sequências Reguladoras de Ácido Nucleico , Alinhamento de Sequência
8.
BMC Bioinformatics ; 14 Suppl 7: S10, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23815181

RESUMO

BACKGROUND: Next-Generation Sequencing (NGS) technology has exceptionally increased the ability to sequence DNA in a massively parallel and cost-effective manner. Nevertheless, NGS data analysis requires bioinformatics skills and computational resources well beyond the possibilities of many "wet biology" laboratories. Moreover, most of projects only require few sequencing cycles and standard tools or workflows to carry out suitable analyses for the identification and annotation of genes, transcripts and splice variants found in the biological samples under investigation. These projects can take benefits from the availability of easy to use systems to automatically analyse sequences and to mine data without the preventive need of strong bioinformatics background and hardware infrastructure. RESULTS: To address this issue we developed an automatic system targeted to the analysis of NGS data obtained from large-scale transcriptome studies. This system, we named NGS-Trex (NGS Transcriptome profile explorer) is available through a simple web interface http://www.ngs-trex.org and allows the user to upload raw sequences and easily obtain an accurate characterization of the transcriptome profile after the setting of few parameters required to tune the analysis procedure. The system is also able to assess differential expression at both gene and transcript level (i.e. splicing isoforms) by comparing the expression profile of different samples.By using simple query forms the user can obtain list of genes, transcripts, splice sites ranked and filtered according to several criteria. Data can be viewed as tables, text files or through a simple genome browser which helps the visual inspection of the data. CONCLUSIONS: NGS-Trex is a simple tool for RNA-Seq data analysis mainly targeted to "wet biology" researchers with limited bioinformatics skills. It offers simple data mining tools to explore transcriptome profiles of samples investigated taking advantage of NGS technologies.


Assuntos
Mineração de Dados , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de RNA , Software , Transcriptoma , Biologia Computacional/métodos
9.
Clin Immunol ; 148(1): 99-109, 2013 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-23685219

RESUMO

The aim of this study was to dissect the autoantibody response in celiac disease (CD) that remains largely unknown, with the goal of identifying the disease-specific autoantigenic protein pattern or the so called epitome. Sera from CD patients were used to select immunoreactive antigens from a cDNA phage-display library. Candidate genes were identified, the corresponding proteins produced and their immunoreactivity validated with sera from CD patients and controls. Thirteen CD-specific antigens were identified and further validated by protein microarray. The specificity for 6 of these antigens was confirmed by ELISA. Furthermore we showed that this antibody response was not abolished on a gluten free diet and was not shared with other autoimmune diseases. These antigens appear to be CD specific and independent of gluten induction. The utility of this panel extends beyond its diagnostic value and it may drive the attention to new targets for unbiased screens in autoimmunity research.


Assuntos
Autoanticorpos/imunologia , Autoantígenos/imunologia , Doença Celíaca/imunologia , Adolescente , Adulto , Autoanticorpos/sangue , Autoantígenos/genética , Doença Celíaca/sangue , Doença Celíaca/diagnóstico , Doença Celíaca/genética , Técnicas de Visualização da Superfície Celular , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Análise de Sequência com Séries de Oligonucleotídeos , Análise Serial de Proteínas , Curva ROC , Adulto Jovem
10.
Nucleic Acids Res ; 39(Database issue): D80-5, 2011 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-21051348

RESUMO

Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www.caspur.it/ASPicDB/.


Assuntos
Processamento Alternativo , Bases de Dados Genéticas , Proteínas/química , Proteínas/genética , Éxons , Variação Genética , Humanos , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , RNA Mensageiro/química , Análise de Sequência de Proteína , Interface Usuário-Computador
11.
Nucleic Acids Res ; 38(Database issue): D75-80, 2010 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-19880380

RESUMO

The 5' and 3' untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and message stability. UTRdb is a curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. Experimentally validated functional motifs are annotated and also collated as the UTRsite database where more specific information on the functional motifs and cross-links to interacting regulatory protein are provided. In the current update, the UTR entries have been organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. All internet resources implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http://utrdb.ba.itb.cnr.it/.


Assuntos
Regiões 3' não Traduzidas , Regiões 5' não Traduzidas , Biologia Computacional/métodos , Bases de Dados Genéticas , Bases de Dados de Ácidos Nucleicos , Algoritmos , Animais , Biologia Computacional/tendências , Bases de Dados de Proteínas , Genoma de Planta , Humanos , Armazenamento e Recuperação da Informação/métodos , Internet , Isoformas de Proteínas , Software , Interface Usuário-Computador
12.
Nucleic Acids Res ; 38(9): e110, 2010 May.
Artigo em Inglês | MEDLINE | ID: mdl-20144949

RESUMO

We have developed a high-throughput protein expression and interaction analysis platform that combines cDNA phage display library selection and massive gene sequencing using the 454 platform. A phage display library of open reading frame (ORF) fragments was created from mRNA derived from different tissues. This was used to study the interaction network of the enzyme transglutaminase 2 (TG2), a multifunctional enzyme involved in the regulation of cell growth, differentiation and apoptosis, associated with many different pathologies. After two rounds of panning with TG2 we assayed the frequency of ORFs within the selected phage population using 454 sequencing. Ranking and analysis of more than 120,000 sequences allowed us to identify several potential interactors, which were subsequently confirmed in functional assays. Within the identified clones, three had been previously described as interacting proteins (fibronectin, SMOC1 and GSTO2), while all the others were new. When compared with standard systems, such as microtiter enzyme-linked immunosorbant assay, the method described here is dramatically faster and yields far more information about the interaction under study, allowing better characterization of complex systems. For example, in the case of fibronectin, it was possible to identify the specific domains involved in the interaction.


Assuntos
Mapeamento de Interação de Proteínas/métodos , Análise de Sequência de DNA/métodos , DNA Complementar/química , Proteínas de Ligação ao GTP/metabolismo , Humanos , Fases de Leitura Aberta , Biblioteca de Peptídeos , Proteína 2 Glutamina gama-Glutamiltransferase , Domínios e Motivos de Interação entre Proteínas , Transglutaminases/metabolismo
13.
Microorganisms ; 10(12)2022 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-36557723

RESUMO

The role of the microbiota in health and disease has long been recognized and, so far, the cutaneous microbiota in humans has been widely investigated. The research regarded mainly the microbiota variations between body districts and disease skin states (i.e., atopic dermatitis, psoriasis, acne). In fact, relatively little information is available about the composition of the healthy skin microbiota. The cosmetic industry is especially interested in developing products that maintain and/or improve a healthy skin microbiota. Therefore, in the present work, the authors chose to investigate in detail the structure and composition of the basal bacterial community of the face. Ninety-six cheek samples (48 women and 48 men) were collected in the same season and the same location in central northern Italy. Bacterial DNA was extracted, the 16S rDNA gene was amplified by PCR, the obtained amplicons were subjected to next generation sequencing. The principal members of the community were identified at the genus level, and statistical analyses showed significant variations between the two sexes. This study identified abundant members of the facial skin microbiota that were rarely reported before in the literature and demonstrated the differences between male and female microbiota in terms of both community structure and composition.

14.
PLoS One ; 17(8): e0273036, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36001607

RESUMO

The key role played by host-microbiota interactions on human health, disease onset and progression, and on host response to treatments has increasingly emerged in the latest decades. Indeed, dysbiosis has been associated to several human diseases such as obesity, diabetes, cancer and also neurodegenerative disease, such as Parkinson, Huntington and Alzheimer's disease (AD), although whether causative, consequence or merely an epiphenomenon is still under investigation. In the present study, we performed a metabologenomic analysis of stool samples from a mouse model of AD, the 3xTgAD. We found a significant change in the microbiota of AD mice compared to WT, with a longitudinal divergence of the F/B ratio, a parameter suggesting a gut dysbiosis. Moreover, AD mice showed a significant decrease of some amino acids, while data integration revealed a dysregulated production of desaminotyrosine (DAT) and dihydro-3-coumaric acid. Collectively, our data show a dysregulated gut microbiota associated to the onset and progression of AD, also indicating that a dysbiosis can occur prior to significant clinical signs, evidenced by early SCFA alterations, compatible with gut inflammation.


Assuntos
Doença de Alzheimer , Microbioma Gastrointestinal , Doenças Neurodegenerativas , Animais , Modelos Animais de Doenças , Disbiose , Microbioma Gastrointestinal/fisiologia , Humanos , Camundongos
15.
BMC Genomics ; 12 Suppl 1: S5, 2011 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-21810207

RESUMO

BACKGROUND: In order to carry out experimental gene annotation, DNA encoding open reading frames (ORFs) derived from real genes (termed "genic") in the correct frame is required. When genes are correctly assigned, isolation of genic DNA for functional annotation can be carried out by PCR. However, not all genes are correctly assigned, and even when correctly assigned, gene products are often incorrectly folded when expressed in heterologous hosts. This is a problem that can sometimes be overcome by the expression of protein fragments encoding domains, rather than full-length proteins. One possible method to isolate DNA encoding such domains would to "filter" complex DNA (cDNA libraries, genomic and metagenomic DNA) for gene fragments that confer a selectable phenotype relying on correct folding, with all such domains present in a complex DNA sample, termed the "domainome". RESULTS: In this paper we discuss the preparation of diverse genic ORF libraries from randomly fragmented genomic DNA using ß-lactamase to filter out the open reading frames. By cloning DNA fragments between leader sequences and the mature ß-lactamase gene, colonies can be selected for resistance to ampicillin, conferred by correct folding of the lactamase gene. Our experiments demonstrate that the majority of surviving colonies contain genic open reading frames, suggesting that ß-lactamase is acting as a selectable folding reporter. Furthermore, different leaders (Sec, TAT and SRP), normally translocating different protein classes, filter different genic fragment subsets, indicating that their use increases the fraction of the "domainone" that is accessible. CONCLUSIONS: The availability of ORF libraries, obtained with the filtering method described here, combined with screening methods such as phage display and protein-protein interaction studies, or with protein structure determination projects, can lead to the identification and structural determination of functional genic ORFs. ORF libraries represent, moreover, a useful tool to proceed towards high-throughput functional annotation of newly sequenced genomes.


Assuntos
Clostridium thermocellum/genética , Genômica/métodos , Fases de Leitura Aberta , DNA Bacteriano , Biblioteca Gênica , Anotação de Sequência Molecular , Análise de Sequência de DNA , beta-Lactamases/genética , beta-Lactamases/metabolismo
16.
Front Microbiol ; 12: 676610, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34349738

RESUMO

Arbuscular mycorrhizal fungi (AMF) are beneficial soil microorganisms that can establish symbiotic associations with Vitis vinifera roots, resulting in positive effects on grapevine performance, both in terms of water use efficiency, nutrient uptake, and replant success. Grapevine is an important perennial crop cultivated worldwide, especially in Mediterranean countries. In Italy, Piedmont is one of the regions with the longest winemaking tradition. In the present study, we characterized the AMF communities of the soil associated or not with the roots of V. vinifera cv. Pinot Noir cultivated in a vineyard subjected to conventional management using 454 Roche sequencing technology. Samplings were performed at two plant phenological stages (flowering and early fruit development). The AMF community was dominated by members of the family Glomeraceae, with a prevalence of the genus Glomus and the species Rhizophagus intraradices and Rhizophagus irregularis. On the contrary, the genus Archaeospora was the only one belonging to the family Archaeosporaceae. Since different AMF communities occur in the two considered soils, independently from the plant phenological stage, a probable role of V. vinifera in determining the AMF populations associated to its roots has been highlighted.

17.
Microorganisms ; 9(7)2021 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-34201731

RESUMO

Algeria is the largest country in Africa characterized by semi-arid and arid sites, located in the North, and hypersaline zones in the center and South of the country. Several autochthonous plants are well known as medicinal plants, having in common tolerance to aridity, drought and salinity. In their natural environment, they live with a great amount of microbial species that altogether are indicated as plant microbiota, while the plants are now viewed as a "holobiont". In this work, the microbiota of the soil associated to the roots of fourteen economically relevant autochthonous plants from Algeria have been characterized by an innovative metagenomic approach with a dual purpose: (i) to deepen the knowledge of the arid and semi-arid environment and (ii) to characterize the composition of bacterial communities associated with indigenous plants with a strong economic/commercial interest, in order to make possible the improvement of their cultivation. The results presented in this work highlighted specific signatures which are mainly determined by climatic zone and soil properties more than by the plant species.

18.
J Pers Med ; 11(8)2021 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-34442460

RESUMO

BACKGROUND: The aim of this study is to identify miRNAs able to predict the outcomes in breast cancer patients after neoadjuvant chemotherapy (NAC). PATIENTS AND METHODS: We retrospectively analyzed 24 patients receiving NAC and not reaching pathologic complete response (pCR). miRNAs were analyzed using an Illumina Next-Generation-Sequencing (NGS) system. RESULTS: Event-free survival (EFS) and overall survival (OS) were significantly higher in patients with up-regulation of let-7a-5p (EFS p = 0.006; OS p = 0.0001), mirR-100-5p (EFS s p = 0.01; OS p = 0.03), miR-101-3p (EFS p = 0.05; OS p = 0.01), and miR-199a-3p (EFS p = 0.02; OS p = 0.01) in post-NAC samples, independently from breast cancer subtypes. At multivariate analysis, only let-7a-5p was significantly associated with EFS (p = 0.009) and OS (p = 0.0008). CONCLUSION: Up-regulation of the above miRNAs could represent biomarkers in breast cancer.

19.
Mol Cancer ; 9: 230, 2010 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-20813049

RESUMO

BACKGROUND: Many evidences report that alternative splicing, the mechanism which produces mRNAs and proteins with different structures and functions from the same gene, is altered in cancer cells. Thus, the identification and characterization of cancer-specific splice variants may give large impulse to the discovery of novel diagnostic and prognostic tumour biomarkers, as well as of new targets for more selective and effective therapies. RESULTS: We present here a genome-wide analysis of the alternative splicing pattern of human genes through a computational analysis of normal and cancer-specific ESTs from seventeen anatomical groups, using data available in AspicDB, a database resource for the analysis of alternative splicing in human. By using a statistical methodology, normal and cancer-specific genes, splice sites and cassette exons were predicted in silico. The condition association of some of the novel normal/tumoral cassette exons was experimentally verified by RT-qPCR assays in the same anatomical system where they were predicted. Remarkably, the presence in vivo of the predicted alternative transcripts, specific for the nervous system, was confirmed in patients affected by glioblastoma. CONCLUSION: This study presents a novel computational methodology for the identification of tumor-associated transcript variants to be used as cancer molecular biomarkers, provides its experimental validation, and reports specific biomarkers for glioblastoma.


Assuntos
Biologia Computacional/métodos , Etiquetas de Sequências Expressas , Genoma Humano/genética , Neoplasias/genética , Processamento Alternativo/genética , Estudo de Associação Genômica Ampla , Humanos
20.
Sci Rep ; 10(1): 6453, 2020 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-32296119

RESUMO

The structure of the bacteriome associated with grapevine roots can affect plant development, health and grape quality. We previously investigated the bacterial biodiversity of the Vitis vinifera cv. Pinot Noir rhizosphere in a vineyard subjected to integrated pest management. The aim of this work is to characterize the bacteriome of V. vinifera cv. Pinot Noir in a conventionally managed vineyard using a metabarcoding approach. Comparisons between the microbial community structure in bulk soil and rhizosphere (variable space) were performed and shifts of bacteriome according to two sampling times (variable time) were characterized. Bacterial biodiversity was higher at the second than at the first sampling and did not differ according to the variable space. Actinobacteria was the dominant class, with Gaiella as the most represented genus in all the samples. Among Proteobacteria, the most represented classes were Alpha, Beta and Gamma-Proteobacteria, with higher abundance at the second than at the first sampling time. Bradyrhizobium was the most frequent genus among Alpha-Proteobacteria, while Burkholderia was the predominant Beta-Proteobacteria. Among Firmicutes, the frequency of Staphylococcus was higher than 60% in bulk soil and rhizosphere. Finally, the sampling time can be considered as one of the drivers responsible for the bacteriome variations assessed.


Assuntos
Bactérias/isolamento & purificação , Microbiota , Rizosfera , Microbiologia do Solo , Vitis/microbiologia , Produção Agrícola , Fazendas , Raízes de Plantas/microbiologia , Vitis/fisiologia
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