ESTree db: a Tool for Peach Functional Genomics

BACKGROUND: The ESTree db represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database. RESULTS: The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories. CONCLUSION: The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig

The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections

<p>Abstract</p> <p>Background</p> <p>The NCBI dbEST currently contains more than eight million human Expressed Sequenced Tags (ESTs). This wide collection represents an important source of information for gene expression studies, provided it can be inspected according to biologically relevant criteria. EST data can be browsed using different dedicated web resources, which allow to investigate library specific gene expression levels and to make comparisons among libraries, highlighting significant differences in gene expression. Nonetheless, no tool is available to examine distributions of quantitative EST collections in Gene Ontology (GO) categories, nor to retrieve information concerning library-dependent EST involvement in metabolic pathways. In this work we present the Human EST Ontology Explorer (HEOE) <url>http://www.itb.cnr.it/ptp/human_est_explorer</url>, a web facility for comparison of expression levels among libraries from several healthy and diseased tissues.</p> <p>Results</p> <p>The HEOE provides library-dependent statistics on the distribution of sequences in the GO Direct Acyclic Graph (DAG) that can be browsed at each GO hierarchical level. The tool is based on large-scale BLAST annotation of EST sequences. Due to the huge number of input sequences, this BLAST analysis was performed with the aid of grid computing technology, which is particularly suitable to address data parallel task. Relying on the achieved annotation, library-specific distributions of ESTs in the GO Graph were inferred. A pathway-based search interface was also implemented, for a quick evaluation of the representation of libraries in metabolic pathways. EST processing steps were integrated in a semi-automatic procedure that relies on Perl scripts and stores results in a MySQL database. A PHP-based web interface offers the possibility to simultaneously visualize, retrieve and compare data from the different libraries. Statistically significant differences in GO categories among user selected libraries can also be computed.</p> <p>Conclusion</p> <p>The HEOE provides an alternative and complementary way to inspect EST expression levels with respect to approaches currently offered by other resources. Furthermore, BLAST computation on the whole human EST dataset was a suitable test of grid scalability in the context of large-scale bioinformatics analysis. The HEOE currently comprises sequence analysis from 70 non-normalized libraries, representing a comprehensive overview on healthy and unhealthy tissues. As the analysis procedure can be easily applied to other libraries, the number of represented tissues is intended to increase.</p

USE OF SYSTEMIC FUNGICIDES COMBINED WITH MULTISITE TO CONTROL OF ASIAN RUST AND SOYBEAN YIELD

Asian soybean rust is an aggressive disease and chemical control must be handled assertively to minimize productivity damage. The objective was to evaluate systemic fungicides and multisite mancozeb, combined or not, and the effects on disease control and soybean yield, cv. 'BMX Lança'. The work was conducted in the field in the 2016/17 and 2017/18 crops, in a randomized complete block design, with four replications. The following treatments were evaluated: T+P) trifloxystrobin + prothioconazole; A+B) azoxystrobin + benzovindiflupyr; T+P+MB) trifloxystrobin + prothioconazole + mancozeb; A+B+MB) azoxystrobin + benzovindiflupyr + mancozeb; MB) mancozeb; and Control (without fungicide application). After the occurrence of the first symptoms of the disease, the severity (%) was evaluated in five trifolia per plot, every seven days, making it possible to calculate the area under the disease progress curve (AUDPC). The yield components and productivity (kg ha-1) were also evaluated. In both crops, the combination of systemic fungicides and mancozeb reduced the severity (%) and progress of Asian rust, reaching a control above 81%. Treatment with trifloxystrobin + prothioconazole + mancozeb (T+P+MB) obtained the highest percentages of control (94.5% - 2016/17, and 93.7% - 2017/18) of Asian rust, and provided, in the 2016/17 crop, productivity at 15 sc ha-1, in relation to the fungicide applied alone (T+P). The combination of systemic fungicides and mancozeb, as proposed in this work, reduces the severity and progress of Asian rust and ensures the maintenance of the productive potential of the soybean.A ferrugem asiática da soja é uma doença agressiva e o controle químico deve ser manejado assertivamente, para minimizar danos sobre a produtividade. Objetivou-se avaliar fungicidas sistêmicos e o multissítio mancozeb, combinados ou não, e os efeitos sobre o controle da doença e a produtividade da soja, cv. ‘BMX Lança’. O trabalho foi conduzido à campo nas safras 2016/17 e 2017/18, em delineamento de blocos ao acaso, com quatro repetições. Foram avaliados os tratamentos: T+P) trifloxistrobina + protioconazol; A+B) azoxistrobina + benzovindiflupyr; T+P+MB) trifloxistrobina + protioconazol + mancozeb; A+B+MB) azoxistrobina + benzovindiflupyr + mancozebe; MB) mancozeb; e Testemunha (sem aplicação de fungicidas). Após o surgimento dos primeiros sintomas da doença, a severidade (%) foi avaliada em cinco trifólios por parcela, a cada sete dias, possibilitando o cálculo da área abaixo da curva de progresso da doença (AACPD). Avaliou-se também os componentes de rendimento e a produtividade (kg ha-1). Em ambas as safras, a combinação entre fungicidas sistêmicos e o mancozeb reduziu a severidade (%) e o progresso de ferrugem asiática, atingindo um controle acima de 81%. O tratamento com trifloxistrobina + protioconazol + mancozeb (T+P+MB) obteve os maiores percentuais de controle (94,5% - 2016/17; e 93,7% - 2017/18) da ferrugem asiática, e proporcionou, na safra 2016/17, produtividade superior em 15 sc ha-1, em relação ao fungicida aplicado isoladamente (T+P). A combinação entre fungicidas sistêmicos e mancozeb, conforme proposto nesse trabalho, reduz a severidade e o progresso da ferrugem asiática e assegura a manutenção do potencial produtivo da soja

New Insights on the Emerging Genomic Landscape of CXCR4 in Cancer: A Lesson from WHIM

Deciphering the molecular alterations leading to disease initiation and progression is currently crucial to identify the most relevant targets for precision therapy in cancer patients. Cancers express a complex chemokine network influencing leucocyte infiltration and angiogenesis. Moreover, malignant cells also express a selective repertoire of chemokine receptors that sustain their growth and spread. At present, different cancer types have been shown to overexpress C-X-C chemokine receptor type 4 (CXCR4) and to respond to its ligand C-X-C motif chemokine 12 (CXCL12). The CXCL12/CXCR4 axis influences cancer biology, promoting survival, proliferation, and angiogenesis, and plays a pivotal role in directing migration of cancer cells to sites of metastases, making it a prognostic marker and a therapeutic target. More recently, mutations in the C-terminus of CXCR4 have been identified in the genomic landscape of patients affected by Waldenstrom's macroglobulinemia, a rare B cell neoplasm. These mutations closely resemble those occurring in Warts, Hypogammaglobulinemia, Immunodeficiency, and Myelokathexis (WHIM) syndrome, an immunodeficiency associated with CXCR4 aberrant expression and activity and with chemotherapy resistance in clinical trials. In this review, we summarize the current knowledge on the relevance of CXCR4 mutations in cancer biology, focusing on its importance as predictors of clinical presentation and response to therapy

Proteasome system dysregulation and treatment resistance mechanisms in major depressive disorder

Several studies have demonstrated that allelic variants related to inflammation and the immune system may increase the risk for major depressive disorder (MDD) and reduce patient responsiveness to antidepressant treatment. Proteasomes are fundamental complexes that contribute to the regulation of T-cell function. Only one study has shown a putative role of proteasomal PSMA7, PSMD9 and PSMD13 genes in the susceptibility to an antidepressant response, and sparse data are available regarding the potential alterations in proteasome expression in psychiatric disorders such as MDD. The aim of this study was to clarify the role of these genes in the mechanisms underlying the response/resistance to MDD treatment. We performed a case-control association study on 621 MDD patients, of whom 390 were classified as treatment-resistant depression (TRD), and we collected peripheral blood cells and fibroblasts for mRNA expression analyses. The analyses showed that subjects carrying the homozygous GG genotype of PSMD13 rs3817629 had a twofold greater risk of developing TRD and exhibited a lower PSMD13 mRNA level in fibroblasts than subjects carrying the A allele. In addition, we found a positive association between PSMD9 rs1043307 and the presence of anxiety disorders in comorbidity with MDD, although this result was not significant following correction for multiple comparisons. In conclusion, by confirming the involvement of PSMD13 in the MDD treatment response, our data corroborate the hypothesis that the dysregulation of the complex responsible for the degradation of intracellular proteins and potentially controlling autoimmunity- and immune tolerance–related processes may be involved in several phenotypes, including the TRD

Ontology-based, Tissue MicroArray oriented, image centered tissue bank

<p>Abstract</p> <p>Background</p> <p>Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many images which need to be properly managed, if possible with an infrastructure able to support tissue sharing between institutes. Moreover, the available frameworks oriented to Tissue MicroArray provide good storage for clinical patient, sample treatment and block construction information, but their utility is limited by the lack of data integration with biomolecular information.</p> <p>Results</p> <p>In this work we propose a Tissue MicroArray web oriented system to support researchers in managing bio-samples and, through the use of ontologies, enables tissue sharing aimed at the design of Tissue MicroArray experiments and results evaluation. Indeed, our system provides ontological description both for pre-analysis tissue images and for post-process analysis image results, which is crucial for information exchange. Moreover, working on well-defined terms it is then possible to query web resources for literature articles to integrate both pathology and bioinformatics data.</p> <p>Conclusions</p> <p>Using this system, users associate an ontology-based description to each image uploaded into the database and also integrate results with the ontological description of biosequences identified in every tissue. Moreover, it is possible to integrate the ontological description provided by the user with a full compliant gene ontology definition, enabling statistical studies about correlation between the analyzed pathology and the most commonly related biological processes.</p

Human iPSC modelling of a familial form of atrial fibrillation reveals a gain of function of I-f and I-CaL in patient-derived cardiomyocytes

Aims: Atrial fibrillation (AF) is the most common type of cardiac arrhythmias, whose incidence is likely to increase with the aging of the population. It is considered a progressive condition, frequently observed as a complication of other cardiovascular disorders. However, recent genetic studies revealed the presence of several mutations and variants linked to AF, findings that define AF as a multifactorial disease. Due to the complex genetics and paucity of models, molecular mechanisms underlying the initiation of AF are still poorly understood. Here we investigate the pathophysiological mechanisms of a familial form of AF, with particular attention to the identification of putative triggering cellular mechanisms, using patient's derived cardiomyocytes (CMs) differentiated from induced pluripotent stem cells (iPSCs). Methods and results: Here we report the clinical case of three siblings with untreatable persistent AF whose whole-exome sequence analysis revealed several mutated genes. To understand the pathophysiology of this multifactorial form of AF we generated three iPSC clones from two of these patients and differentiated these cells towards the cardiac lineage. Electrophysiological characterization of patient-derived CMs (AF-CMs) revealed that they have higher beating rates compared to control (CTRL)-CMs. The analysis showed an increased contribution of the If and ICaL currents. No differences were observed in the repolarizing current IKr and in the sarcoplasmic reticulum calcium handling. Paced AF-CMs presented significantly prolonged action potentials and, under stressful conditions, generated both delayed after-depolarizations of bigger amplitude and more ectopic beats than CTRL cells. Conclusions: Our results demonstrate that the common genetic background of the patients induces functional alterations of If and ICaL currents leading to a cardiac substrate more prone to develop arrhythmias under demanding conditions. To our knowledge this is the first report that, using patient-derived CMs differentiated from iPSC, suggests a plausible cellular mechanism underlying this complex familial form of AF