Methods for the refinement of genome-scale metabolic networks

More accurate metabolic networks of pathogens and parasites are required to support the identification of important enzymes or transporters that could be potential targets for new drugs. The overall aim of this thesis is to contribute towards a new level of quality for metabolic network reconstruction, through the application of several different approaches. After building a draft metabolic network using an automated method, a large amount of manual curation effort is still necessary before an accurate model can be reached. PathwayBooster, a standalone software package, which I developed in Python, supports the first steps of model curation, providing easy access to enzymatic function information and a visual pathway display to enable the rapid identification of inaccuracies in the model. A major current problem in model refinement is the identification of genes encoding enzymes which are believed to be present but cannot be found using standard methods. Current searches for enzymes are mainly based on strong sequence similarity to proteins of known function, although in some cases it may be appropriate to consider more distant relatives as candidates for filling these pathway holes. With this objective in mind, a protocol was devised to search a proteome for superfamily relatives of a given enzymatic function, returning candidate enzymes to perform this function. Another, related approach tackles the problem of misannotation errors in public gene databases and their influence on metabolic models through the propagation of erroneous annotations. I show that the topological properties of metabolic networks contains useful information about annotation quality and can therefore play a role in methods for gene function assignment. An evolutionary perspective into functional changes within homologous domains opens up the possibility of integrating information from multiple genomes to support the reconstruction of metabolic models. I have therefore developed a methodology to predict functional change within a gene superfamily phylogeny

Effectors and regulators of cellular immune response in autoimmune liver disease

Medicina e Oncologia MolecularMolecular and Oncology Medicin

PathwayBooster:a tool to support the curation of metabolic pathways

BACKGROUND: Despite several recent advances in the automated generation of draft metabolic reconstructions, the manual curation of these networks to produce high quality genome-scale metabolic models remains a labour-intensive and challenging task. RESULTS: We present PathwayBooster, an open-source software tool to support the manual comparison and curation of metabolic models. It combines gene annotations from GenBank files and other sources with information retrieved from the metabolic databases BRENDA and KEGG to produce a set of pathway diagrams and reports summarising the evidence for the presence of a reaction in a given organism’s metabolic network. By comparing multiple sources of evidence within a common framework, PathwayBooster assists the curator in the identification of likely false positive (misannotated enzyme) and false negative (pathway hole) reactions. Reaction evidence may be taken from alternative annotations of the same genome and/or a set of closely related organisms. CONCLUSIONS: By integrating and visualising evidence from multiple sources, PathwayBooster reduces the manual effort required in the curation of a metabolic model. The software is available online at http://www.theosysbio.bio.ic.ac.uk/resources/pathwaybooster/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-014-0447-2) contains supplementary material, which is available to authorized users

Exploración de grafos para el análisis de datos

Se propone una técnica de análisis de datos a través de la exploración de redes que se forman con entidades existentes en la base de datos de estudio. El principal aporte del método es la exploración de la red a través de ambientes definidos por los demás atributos de la base de datos. Este método ha sido utilizado con éxito en el análisis de datos biológicos relacionados con el Mal de Río Cuarto virus. Se presenta además a Yatel, la herramienta en desarrollo que da soporte al análisis propuesto.Eje: Bases de Datos y Minería de DatosRed de Universidades con Carreras en Informática (RedUNCI

Exploración de grafos para el análisis de datos

Se propone una técnica de análisis de datos a través de la exploración de redes que se forman con entidades existentes en la base de datos de estudio. El principal aporte del método es la exploración de la red a través de ambientes definidos por los demás atributos de la base de datos. Este método ha sido utilizado con éxito en el análisis de datos biológicos relacionados con el Mal de Río Cuarto virus. Se presenta además a Yatel, la herramienta en desarrollo que da soporte al análisis propuesto.Eje: Bases de Datos y Minería de DatosRed de Universidades con Carreras en Informática (RedUNCI

Clube Português do Pâncreas Recommendations for Chronic Pancreatitis: Medical, Endoscopic, and Surgical Treatment (Part II)

Chronic pancreatitis (CP) is a complex disease that should be treated by experienced teams of gastroenterologists, radiologists, surgeons, and nutritionists in a multidisciplinary environment. Medical treatment includes lifestyle modification, nutrition, exocrine and endocrine pancreatic insufficiency correction, and pain management. Up to 60% of patients will ultimately require some type of endoscopic or surgical intervention for treatment. However, regardless of the modality, they are often ineffective unless smoking and alcohol cessation is achieved. Surgery retains a major role in the treatment of CP patients with intractable chronic pain or suspected pancreatic mass. For other complications like biliary or gastroduodenal obstruction, pseudocyst drainage can be performed endoscopically. The recommendations for CP were developed by Clube Português do Pâncreas (CPP), based on literature review to answer predefined topics, subsequently discussed and approved by all members of CPP. Recommendations are separated in two parts: "chronic pancreatitis etiology, natural history, and diagnosis," and "chronic pancreatitis medical, endoscopic, and surgical treatment." This abstract pertains to part II.info:eu-repo/semantics/publishedVersio

Exploración de grafos para el análisis de datos

Se propone una técnica de análisis de datos a través de la exploración de redes que se forman con entidades existentes en la base de datos de estudio. El principal aporte del método es la exploración de la red a través de ambientes definidos por los demás atributos de la base de datos. Este método ha sido utilizado con éxito en el análisis de datos biológicos relacionados con el Mal de Río Cuarto virus. Se presenta además a Yatel, la herramienta en desarrollo que da soporte al análisis propuesto.Eje: Bases de Datos y Minería de DatosRed de Universidades con Carreras en Informática (RedUNCI

Aberrant hepatic trafficking of gut-derived T cells is not specific to primary sclerosing cholangitis

Background and Aims The “gut homing” hypothesis suggests the pathogenesis of primary sclerosing cholangitis (PSC) is driven by aberrant hepatic expression of gut adhesion molecules and subsequent recruitment of gut‐derived T cells to the liver. However, inconsistencies lie within this theory including an absence of investigations and comparisons with other chronic liver diseases (CLD). Here, we examine “the gut homing theory” in patients with PSC with associated inflammatory bowel disease (PSC‐IBD) and across multiple inflammatory liver diseases. Approach and Results Expression of MAdCAM‐1, CCL25, and E‐Cadherin were assessed histologically and using RT‐PCR on explanted liver tissue from patients with CLD undergoing OLT and in normal liver. Liver mononuclear cells were isolated from explanted tissue samples and the expression of gut homing integrins and cytokines on hepatic infiltrating gut‐derived T cells was assessed using flow cytometry. Hepatic expression of MAdCAM‐1, CCL25 and E‐Cadherin was up‐regulated in all CLDs compared with normal liver. There were no differences between disease groups. Frequencies of α4β7, αEβ7, CCR9, and GPR15 expressing hepatic T cells was increased in PSC‐IBD, but also in CLD controls, compared with normal liver. β7 expressing hepatic T cells displayed an increased inflammatory phenotype compared with β7 negative cells, although this inflammatory cytokine profile was present in both the inflamed and normal liver. Conclusions These findings refute the widely accepted “gut homing” hypothesis as the primary driver of PSC and indicate that aberrant hepatic recruitment of gut‐derived T cells is not unique to PSC, but is a panetiological feature of CLD

Clube Português do Pâncreas Recommendations for Chronic Pancreatitis: Etiology, Natural History, and Diagnosis (Part I)

Chronic pancreatitis (CP) is a heterogeneous disease, with different causes and often a long delay between onset and full classic presentation. Clinical presentation depends on the stage of the disease. In earlier stages, recurrent episodes of acute pancreatitis are the major signs dominating clinical presentation. As the inflammatory process goes on, less acute episodes occur, and pain adopts different aspects or may even disappear. After 10–15 years from onset, functional insufficiency occurs. Then, a classic presentation with pain and pancreatic exocrine and endocrine insufficiency appears. Diagnosis remains challenging in the early stages of the disease, as its initial presentation is usually ill-defined and overlaps with other digestive disorders. Computed tomography and magnetic resonance cholangiopancreatography should be the first choice in patients with suspected CP. If the results are normal or equivocal but still there is a high suspicion of CP, the next option should be endoscopic ultrasound. Endoscopic retrograde cholangiopancreatography is mainly a therapeutic technique, and for the diagnostic purpose should only be used when all other imaging modalities and pancreatic function tests have been exhausted. Indirect tests are used to quantify the degree of insufficiency in already-established late CP. Recommendations on CP were developed by Clube Português do Pâncreas (CPP), based on literature review to answer predefined topics, subsequently discussed and approved by all members of CPP. Recommendations are separated in two parts: “chronic pancreatitis etiology, natural history, and diagnosis,” and “chronic pancreatitis medical, endoscopic, and surgical treatment.” This abstract pertains to part I

Nomenclature, diagnosis and management of drug-induced autoimmune-like hepatitis (DI-ALH): An expert opinion meeting report

Drug-induced liver injury (DILI) can mimic almost all other liver disorders. A phenotype increasingly ascribed to drugs is autoimmune-like hepatitis (ALH). This article summarises the major topics discussed at a joint International Conference held between the Drug-Induced Liver Injury consortium and the International Autoimmune Hepatitis Group. DI-ALH is a liver injury with laboratory and/or histological features that may be indistinguishable from those of autoimmune hepatitis (AIH). Previous studies have revealed that patients with DI-ALH and those with idiopathic AIH have very similar clinical, biochemical, immunological and histological features. Differentiating DI-ALH from AIH is important as patients with DI-ALH rarely require long-term immunosuppression and the condition often resolves spontaneously after withdrawal of the implicated drug, whereas patients with AIH mostly require long-term immunosuppression. Therefore, revision of the diagnosis on long-term follow-up may be necessary in some cases. More than 40 different drugs including nitrofurantoin, methyldopa, hydralazine, minocycline, infliximab, herbal and dietary supplements (such as Khat and Tinospora cordifolia) have been implicated in DI-ALH. Understanding of DI-ALH is limited by the lack of specific markers of the disease that could allow for a precise diagnosis, while there is similarly no single feature which is diagnostic of AIH. We propose a management algorithm for patients with liver injury and an autoimmune phenotype. There is an urgent need to prospectively evaluate patients with DI-ALH systematically to enable definitive characterisation of this condition