Best practices for the manual curation of intrinsically disordered proteins in DisProt

The DisProt database is a resource containing manually curated data on experimentally validated intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) from the literature. Developed in 2005, its primary goal was to collect structural and functional information into proteins that lack a fixed three-dimensional structure. Today, DisProt has evolved into a major repository that not only collects experimental data but also contributes to our understanding of the IDPs/IDRs roles in various biological processes, such as autophagy or the life cycle mechanisms in viruses or their involvement in diseases (such as cancer and neurodevelopmental disorders). DisProt offers detailed information on the structural states of IDPs/IDRs, including state transitions, interactions and their functions, all provided as curated annotations. One of the central activities of DisProt is the meticulous curation of experimental data from the literature. For this reason, to ensure that every expert and volunteer curator possesses the requisite knowledge for data evaluation, collection and integration, training courses and curation materials are available. However, biocuration guidelines concur on the importance of developing robust guidelines that not only provide critical information about data consistency but also ensure data acquisition.This guideline aims to provide both biocurators and external users with best practices for manually curating IDPs and IDRs in DisProt. It describes every step of the literature curation process and provides use cases of IDP curation within DisProt. Database URL: https://disprot.org/.

DisProt in 2024: improving function annotation of intrinsically disordered proteins

DisProt (URL: https://disprot.org) is the gold standard database for intrinsically disordered proteins and regions, providing valuable information about their functions. The latest version of DisProt brings significant advancements, including a broader representation of functions and an enhanced curation process. These improvements aim to increase both the quality of annotations and their coverage at the sequence level. Higher coverage has been achieved by adopting additional evidence codes. Quality of annotations has been improved by systematically applying Minimum Information About Disorder Experiments (MIADE) principles and reporting all the details of the experimental setup that could potentially influence the structural state of a protein. The DisProt database now includes new thematic datasets and has expanded the adoption of Gene Ontology terms, resulting in an extensive functional repertoire which is automatically propagated to UniProtKB. Finally, we show that DisProt's curated annotations strongly correlate with disorder predictions inferred from AlphaFold2 pLDDT (predicted Local Distance Difference Test) confidence scores. This comparison highlights the utility of DisProt in explaining apparent uncertainty of certain well-defined predicted structures, which often correspond to folding-upon-binding fragments. Overall, DisProt serves as a comprehensive resource, combining experimental evidence of disorder information to enhance our understanding of intrinsically disordered proteins and their functional implications.

Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions

An unambiguous description of an experiment, and the subsequent biological observation, is vital for accurate data interpretation. Minimum information guidelines define the fundamental complement of data that can support an unambiguous conclusion based on experimental observations. We present the Minimum Information About Disorder Experiments (MIADE) guidelines to define the parameters required for the wider scientific community to understand the findings of an experiment studying the structural properties of intrinsically disordered regions (IDRs). MIADE guidelines provide recommendations for data producers to describe the results of their experiments at source, for curators to annotate experimental data to community resources and for database developers maintaining community resources to disseminate the data. The MIADE guidelines will improve the interpretability of experimental results for data consumers, facilitate direct data submission, simplify data curation, improve data exchange among repositories and standardize the dissemination of the key metadata on an IDR experiment by IDR data sources.

The Gene Ontology knowledgebase in 2023

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics.

SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion

The SARS‐CoV‐2 pandemic is maintained by the emergence of successive variants, highlighting the flexibility of the protein sequences of the virus. We show that experimentally determined intrinsically disordered regions (IDRs) are abundant in the SARS‐CoV‐2 viral proteins, making up to 28% of disorder content for the S1 subunit of spike and up to 51% for the nucleoprotein, with the vast majority of mutations occurring in the 13 major variants mapped to these IDRs. Strikingly, antigenic sites are enriched in IDRs, in the receptor‐binding domain (RBD) and in the N‐terminal domain (NTD), suggesting a key role of structural flexibility in the antigenicity of the SARS‐CoV‐2 protein surface. Mutations occurring in the S1 subunit and nucleoprotein (N) IDRs are critical for immune evasion and antibody escape, suggesting potential additional implications for vaccines and monoclonal therapeutic strategies. Overall, this suggests the presence of variable regions on S1 and N protein surfaces, which confer sequence and antigenic flexibility to the virus without altering its protein functions.

Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt

DisProt is the major repository of manually curated data for intrinsically disordered proteins collected from the literature. Although lacking a stable three-dimensional structure under physiological conditions, intrinsically disordered proteins carry out a plethora of biological functions, some of them directly arising from their flexible nature. A growing number of scientific studies have been published during the last few decades to shed light on their unstructured state, their binding modes, and their functions. DisProt makes use of a team of expert biocurators to provide up-to-date annotations of intrinsically disordered proteins from the literature, making them available to the scientific community. Here we present a comprehensive description on how to use DisProt in different contexts and provide a detailed explanation of how to explore and interpret manually curated annotations of intrinsically disordered proteins. We describe how to search DisProt annotations, both using the web interface and the API for programmatic access. Finally, we explain how to visualize and interpret a DisProt entry, the SARS-CoV-2 Nucleoprotein, characterized by the presence of unstructured N-terminal and C-terminal regions and a flexible linker. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Performing a search in DisProt Support Protocol 1: Downloading options Support Protocol 2: Programmatic access with DisProt REST API Basic Protocol 2: Exploring the DisProt Ontology page Basic Protocol 3: Visualizing and interpreting DisProt entries-the SARS-CoV-2 Nucleoprotein use case.

Conference report: Biocuration 2021 Virtual Conference

The International Society for Biocuration (ISB) aims to promote the field of biocuration and provide a community forum for information exchange and networking. Over the past 14 years, the ISB has hosted annual international conferences, entirely dedicated to the field of biocuration, that rotate between regions across the world. These meetings bring together biocurators from various roles, including database curators, bioinformaticians, ontology developers and students. Due to the ongoing global pandemic, the 14th Annual ISB Biocuration Conference (ISB2021) was held virtually in the form of four sessions and one workshop over the course of the year. Each of the four virtual sessions included panel discussions covering (i) The Future of Biocuration, (ii) Career paths and projections in Biocuration, (iii) Addressing Implicit or Unconscious Bias: Equity, Diversity and Inclusion and (iv) Strategic planning. Here we report on highlights from the virtual conference and share some of the ideas and future goals of the ISB.

Database URL:https://www.biocuration.org/14th-annual-biocuration-conference-virtual/

Databases for intrinsically disordered proteins

Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. Only a small fraction of IDRs have been functionally characterized, with heterogeneous experimental evidence that is largely buried in the literature. Predictions of IDRs are still difficult to estimate and are poorly characterized. Here, an overview of the publicly available knowledge about IDRs is reported, including manually curated resources, deposition databases and prediction repositories. The types, scopes and availability of the various resources are analyzed, and their complementarity and overlap are highlighted. The volume of information included and the relevance to the field of structural biology are compared.

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation

The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.

ECO: the Evidence and Conclusion Ontology, an update for 2022

The Evidence and Conclusion Ontology (ECO) is a community resource that provides an ontology of terms used to capture the type of evidence that supports biomedical annotations and assertions. Consistent capture of evidence information with ECO allows tracking of annotation provenance, establishment of quality control measures, and evidence-based data mining. ECO is in use by dozens of data repositories and resources with both specific and general areas of focus. ECO is continually being expanded and enhanced in response to user requests as well as our aim to adhere to community best-practices for ontology development. The ECO support team engages in multiple collaborations with other ontologies and annotating groups. Here we report on recent updates to the ECO ontology itself as well as associated resources that are available through this project. ECO project products are freely available for download from the project website (https://evidenceontology.org/) and GitHub (https://github.com/evidenceontology/evidenceontology). ECO is released into the public domain under a CC0 1.0 Universal license.

Exploring Curated Conformational Ensembles of Intrinsically Disordered Proteins in the Protein Ensemble Database

The Protein Ensemble Database (PED; https://proteinensemble.org/) is the major repository of conformational ensembles of intrinsically disordered proteins (IDPs). Conformational ensembles of IDPs are primarily provided by their authors or occasionally collected from literature, and are subsequently deposited in PED along with the corresponding structured, manually curated metadata. The modeling of conformational ensembles usually relies on experimental data from small-angle X-ray scattering (SAXS), fluorescence resonance energy transfer (FRET), NMR spectroscopy, and molecular dynamics (MD) simulations, or a combination of these techniques. The growing number of scientific studies based on these data, along with the astounding and swift progress in the field of protein intrinsic disorder, has required a significant update and upgrade of PED, first published in 2014. To this end, the database was entirely renewed in 2020 and now has a dedicated team of biocurators providing manually curated descriptions of the methods and conditions applied to generate the conformational ensembles and for checking consistency of the data. Here, we present a detailed description on how to explore PED with its protein pages and experimental pages, and how to interpret entries of conformational ensembles. We describe how to efficiently search conformational ensembles deposited in PED by means of its web interface and API. We demonstrate how to make sense of the PED protein page and its associated experimental entry pages with reference to the yeast Sic1 use case. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Performing a search in PED Support Protocol 1: Programmatic access with the PED API Basic Protocol 2: Interpreting the protein page and the experimental entry page-the Sic1 use case Support Protocol 2: Downloading options Support Protocol 3: Understanding the validation report-the Sic1 use case Basic Protocol 3: Submitting new conformational ensembles to PED Basic Protocol 4: Providing feedback in PED.

APICURON: a database to credit and acknowledge the work of biocurators

APICURON is an open and freely accessible resource that tracks and credits the work of biocurators across multiple participating knowledgebases. Biocuration is essential to extract knowledge from research data and make it available in a structured and standardized way to the scientific community. However, processing biological data-mainly from literature-requires a huge effort that is difficult to attribute and quantify. APICURON collects biocuration events from third-party resources and aggregates this information, spotlighting biocurator contributions. APICURON promotes biocurator engagement implementing gamification concepts like badges, medals and leaderboards and at the same time provides a monitoring service for registered resources and for biocurators themselves. APICURON adopts a data model that is flexible enough to represent and track the majority of biocuration activities. Biocurators are identified through their Open Researcher and Contributor ID. The definition of curation events, scoring systems and rules for assigning badges and medals are resource-specific and easily customizable. Registered resources can transfer curation activities on the fly through a secure and robust Application Programming Interface (API). Here, we show how simple and effective it is to connect a resource to APICURON, describing the DisProt database of intrinsically disordered proteins as a use case. We believe APICURON will provide biological knowledgebases with a service to recognize and credit the effort of their biocurators, monitor their activity and promote curator engagement. Database URL: https://apicuron.org.

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins

The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.

MobiDB: intrinsically disordered proteins in 2021

The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in MobiDB version 4, regarding the database format, with novel types of annotations and an improved update process. The new website includes a re-designed user interface, a more effective search engine and advanced API for programmatic access. The new database schema gives more flexibility for the users, as well as simplifying the maintenance and updates. In addition, the new entry page provides more visualisation tools including customizable feature viewer and graphs of the residue contact maps. MobiDB v4 annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined. The integrated information is presented in a simplified interface, which enables faster searches and allows large customized datasets to be downloaded in TSV, Fasta or JSON formats. An alternative advanced interface allows users to drill deeper into features of interest. A new statistics page provides information at database and proteome levels. The new MobiDB version presents state-of-the-art knowledge on disordered proteins and improves data accessibility for both computational and experimental users.

Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt

DisProt is the major repository of manually curated data for intrinsically disordered proteins collected from the literature. Although lacking a stable tertiary structure under physiological conditions, intrinsically disordered proteins carry out a plethora of biological functions, some of them directly arising from their flexible nature. A growing number of scientific studies have been published during the last few decades in an effort to shed light on their unstructured state, their binding modes, and their functions. DisProt makes use of a team of expert biocurators to provide up-to-date annotations of intrinsically disordered proteins from the literature, making them available to the scientific community. Here we present a comprehensive description on how to use DisProt in different contexts and provide a detailed explanation of how to explore and interpret manually curated annotations of intrinsically disordered proteins. We describe how to search DisProt annotations, using both the web interface and the API for programmatic access. Finally, we explain how to visualize and interpret a DisProt entry, p53, a widely studied protein characterized by the presence of unstructured N-terminal and C-terminal regions. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Performing a search in DisProt Support Protocol 1: Downloading options Support Protocol 2: Programmatic access with DisProt REST API Basic Protocol 2: Visualizing and interpreting DisProt entries: the p53 use case Basic Protocol 3: Providing feedback and submitting new intrinsic disorder-related data.

Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank

Intrinsically disordered protein regions are commonly defined from missing electron density in X-ray structures. Experimental evidence for long disorder regions (LDRs) of at least 30 residues was so far limited to manually curated proteins. Here, we describe a comprehensive and large-scale analysis of experimental LDRs for 3133 unique proteins, demonstrating an increasing coverage of intrinsic disorder in the Protein Data Bank (PDB) in the last decade. The results suggest that long missing residue regions are a good quality source to annotate intrinsically disordered regions and perform functional analysis in large data sets. The consensus approach used to define LDRs allows to evaluate context dependent disorder and provide a common definition at the protein level.

Assessing predictors for new post translational modification sites: A case study on hydroxylation

Post-translational modification (PTM) sites have become popular for predictor development. However, with the exception of phosphorylation and a handful of other examples, PTMs suffer from a limited number of available training examples and sparsity in protein sequences. Here, proline hydroxylation is taken as an example to compare different methods and evaluate their performance on new experimentally determined sites. As a guide for effective experimental design, predictors require both high specificity and sensitivity. However, the self-reported performance may often not be indicative of prediction quality and detection of new sites is not guaranteed. We have benchmarked seven published hydroxylation site predictors on two newly constructed independent datasets. The self-reported performance is found to widely overestimate the real accuracy measured on independent datasets. No predictor performs better than random on new examples, indicating the refined models do not sufficiently generalize to detect new sites. The number of false positives is high and precision low, in particular for non-collagen proteins whose motifs are not conserved. As hydroxylation site predictors do not generalize for new data, caution is advised when using PTM predictors in the absence of independent evaluations, in particular for highly specific sites involved in signalling.

Machine learning methods are extensively used by biologists to design and interpret experiments. Predictors which take the only sequence as input are of particular interest due to the large amount of available sequence data and high self-reported performance. In this work, we evaluated post-translational modification (PTM) predictors for hydroxylation sites and found that they perform no better than random, in strong contrast to performances reported in their original publications. PTMs are chemical amino acid alterations providing the cell with conditional mechanisms to fine tune protein function, regulating complex biological processes such as signalling and cell cycle. Hydroxylation sites are a good PTM test case due to the availability of a range of predictors and an abundance of newly experimentally detected modification sites. Poor performances in our results highlight the overlooked problem of predicting PTMs when best practices are not followed and training data are likely incomplete. Experimentalists should be careful when using PTM predictors blindly and more independent assessments are needed to establish their usefulness in practice.

DisProt: intrinsic protein disorder annotation in 2020

The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the ‘dark’ proteome.

Insights into the molecular features of the von Hippel-Lindau-like protein

We present an in silico characterization of the von Hippel-Lindau-like protein (VLP), the only known human paralog of the von Hippel-Lindau tumor suppressor protein (pVHL). Phylogenetic investigation showed VLP to be mostly conserved in upper mammals and specifically expressed in brain and testis. Structural analysis and molecular dynamics simulations show VLP to be very similar to pVHL three-dimensional organization and binding dynamics. In particular, conservation of elements at the protein interfaces suggests VLP to be a functional pVHL homolog potentially possessing multiple functions beyond HIF-1α-dependent binding activity. Our findings show that VLP may share at least seven interactors with pVHL, suggesting novel functional roles for this understudied human protein. These may occur at precise hypoxia levels where functional overlap with pVHL may permit a finer modulation of pVHL functions.

Microparticle-embedded fibroin/alginate beads for prolonged local release of simvastatin hydroxyacid to mesenchymal stem cells

In the present work, we propose silk fibroin/alginate (SF/Alg) beads embedding simvastatin-loaded biodegradable microparticles as a versatile platform capable of tuning SVA release and in so doing osteogenic effects. In a first part of the study, microparticles of poly(lactic-co-glycolic) acid incorporating simvastatin either as lactone (SVL) or as hydroxyacid form (SVA) were prepared by spray-drying. While SVA-loaded microparticles released the drug in three days, long-term release of SVA could be obtained from SVL-loaded microparticles. In this latter case, SVL was promptly transformed to the osteogenic active SVA during release. When tested on mesenchymal stem cells, a time- and dose-dependent effect of SVL-loaded microparticles on cell proliferation and alkaline phosphatase (ALP) activity was found. Thereafter, SVL-loaded microparticles were embedded in SF/Alg beads to limit the initial simvastatin burst and to achieve easier implantation as well. Microparticle-embedded beads showed no cytotoxicity while ALP activity increased. If correctly exploited, the developed system may be suitable as osteogenic polymer scaffolds releasing correct amount of the drug locally for long time-frames.

Transient leukocytosis in Emergency Room: an overlooked issue

Leukocytosis is regarded as a reliable marker of a serious disorder requiring hospitalization. However, leukocytosis often disappears once the patient is admitted to a medical ward; differential diagnosis of leukocytosis is often overlooked in the busy Emergency Room (ER) routine. We retrospectively evaluated the clinical records of 565 consecutive patients admitted to the Department of Internal Medicine (DIM) after examination in ER. Mean leukocyte count was 11.4×109/L in ER and 10.1×109/L in DIM (P<0.001). Leukocytosis was found in 53.1% of patients in ER, but in 33% of these it was no longer evident on the following day, unrelated to baseline white blood cells (WBC) count, age, sex, diagnosis, C-reactive protein level and early antibiotic treatment. A reduction in WBC count larger than 40% from baseline occurred in 13.6% of all subjects, and in 31.7% of those with transient leukocytosis. Leukocytosis in ER is frequent, but it is often transient and not associated with an infectious cause. Other causes, including psychological stress caused by the ER access itself, should be considered in the differential diagnosis.

Lung US features of severe interstitial pneumonia: case report and review of the literature

BACKGROUND

Chlamydia pneumonia is reported to account for a relatively large number of cases of CAP. In elderly patients in particular, the clinical presentation can be a severe form of diffuse interstitial pneumonia. The chest X-ray presentation is aspecific. Lung US can show a typical pattern of diffuse interstitial lung syndrome; in some cases, like the present one, the association of multiple B lines with a coarse and thickened pleural line points to a more likely diagnosis of interstitial pneumonia.

CASE REPORT

We present the case of an 87-year-old woman with severe interstitial chlamydial pneumonia, for whom lung US was very useful for directing diagnosis and for follow-up during therapy.

CONCLUSIONS

The use of lung US in the diagnosis of interstitial syndrome is likely to improve the care of patients in whom the diagnosis is a consideration; it offers better characterization than a chest X-ray and is free from CT radiation. Furthermore, the concept of using lung US for monitoring a patient is one of the major innovations that has emerged from recent studies.

DisProt 7.0: a major update of the database of disordered proteins

The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance (primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins.

Pure red cell aplasia caused by parvovirus B19 in a heart transplant recipient

A case of parvovirus B19-induced pure red cell aplasia occurring in a heart transplant recipient is reported. The diagnosis of this rare but clinically important complication can be suspected on the basis of the pathognomonic morphological features of the bone marrow.

Computational analysis of prolyl hydroxylase domain-containing protein 2 (PHD2) mutations promoting polycythemia insurgence in humans

Idiopathic erythrocytosis is a rare disease characterized by an increase in red blood cell mass due to mutations in proteins of the oxygen-sensing pathway, such as prolyl hydroxylase 2 (PHD2). Here, we present a bioinformatics investigation of the pathological effect of twelve PHD2 mutations related to polycythemia insurgence. We show that few mutations impair the PHD2 catalytic site, while most localize to non-enzymatic regions. We also found that most mutations do not overlap the substrate recognition site, suggesting a novel PHD2 binding interface. After a structural analysis of both binding partners, we suggest that this novel interface is responsible for PHD2 interaction with the LIMD1 tumor suppressor.

Efficacy and safety of thalidomide for the treatment of severe recurrent epistaxis in hereditary haemorrhagic telangiectasia: results of a non-randomised, single-centre, phase 2 study

BACKGROUND

Hereditary haemorrhagic telangiectasia is a genetic disease that leads to multiregional angiodysplasia. Severe recurrent epistaxis is the most common presentation, frequently leading to severe anaemia. Several therapeutic approaches have been investigated, but they are mostly palliative and have had variable results. We aimed to assess the efficacy of thalidomide for the reduction of epistaxis in patients with hereditary haemorrhagic telangiectasia that is refractory to standard therapy.

METHODS

We recruited patients aged 17 years or older with hereditary haemorrhagic telangiectasia who had severe recurrent epistaxis refractory to minimally invasive surgical procedures into an open-label, phase 2, non-randomised, single-centre study at IRCCS Policlinico San Matteo Foundation (Pavia, Italy). We gave patients thalidomide at a starting dose of 50 mg/day orally. If they had no response, we increased the thalidomide dose by 50 mg/day increments every 4 weeks, until a response was seen, up to a maximum dose of 200 mg/day. After patients had achieved a response, they continued treatment for 8-16 additional weeks. The primary endpoint was the efficacy of thalidomide measured as the percentage of patients who had reductions of at least one grade in the frequency, intensity, or duration of epistaxis. We followed up patients each month to assess epistaxis severity score and transfusion need, and any adverse events were reported. We included all patients who received any study drug and who participated in at least one post-baseline assessment in the primary efficacy population. The safety population consisted of all patients who received any dose of study treatment. This trial is registered with ClinicalTrials.gov, number NCT01485224.

FINDINGS

Between Dec 1, 2011, and May 12, 2014, we enrolled 31 patients. Median follow-up was 15·9 months (IQR 10·1-22·3). Three (10%, 95% CI 2-26) patients had a complete response, with bleeding stopped, 28 (90%, 95% CI 74-98) patients had partial responses. Overall, all 31 (100%, 89-100) patients responded to therapy with a significant decrease in all epistaxis parameters (p<0·0001 for frequency, intensity, and duration). A response was achieved by 25 (81%) patients at 50 mg/day of thalidomide, five (16%) patients at 100 mg/day, and one (3%) patient at 150 mg/day. Patients had only non-serious, grade 1 adverse effects, the most common of which were constipation (21 patients), drowsiness (six patients), and peripheral oedema (eight patients). One patient died a month after the end of treatment, but this was not deemed to be related to treatment.

INTERPRETATION

Low-dose thalidomide seems to be safe and effective for the reduction of epistaxis in patients with hereditary haemorrhagic telangiectasia. Our findings should be validated by further studies with larger patient populations, longer follow-up, and that also assess the benefit for quality of life.

FUNDING

Telethon Foundation.

Insights into the proline hydroxylase (PHD) family, molecular evolution and its impact on human health

PHDs (proline hydroxylases) are a small protein family found in all organisms, considered the central regulator of the molecular hypoxia response due to PHDs being completely inactivated under low oxygen concentration. At physiological oxygen concentration, PHDs drive the degradation of the HIF-1α (hypoxia-inducible factor 1-α), which is responsible for upregulating the expression of genes involved in the cellular response to hypoxia. Hypoxia is a common feature of most tumors, in particular during metastasis development. Indeed, cancer reacts by activating pathways promoting new blood vessel formation and activating strategies aimed to improve survival. In this scenario, the PHD family regulates the activation of HIF-1α and cell-cycle regulation. Several PHD mutations were found in cancer patients, underlining their importance for human health. Here, we propose a Bayesian model able to predict the pathological effect of human PHD mutations and their correlation with cancer outcome. The model was developed through an integrative in silico approach, where data collected from the literature has been coupled with sequence evolution and structural analysis. The model was used to assess 135 human PHD variants. Finally, bioinformatics characterization was used to demonstrate how few amino acid changes are able to explain the functional specialization of PHD family members and their physiological role in human health.

Alginate-hyaluronan composite hydrogels accelerate wound healing process

In this paper we propose polysaccharide hydrogels combining alginate (ALG) and hyaluronan (HA) as biofunctional platform for dermal wound repair. Hydrogels produced by internal gelation were homogeneous and easy to handle. Rheological evaluation of gelation kinetics of ALG/HA mixtures at different ratios allowed understanding the HA effect on ALG cross-linking process. Disk-shaped hydrogels, at different ALG/HA ratio, were characterized for morphology, homogeneity and mechanical properties. Results suggest that, although the presence of HA does significantly slow down gelation kinetics, the concentration of cross-links reached at the end of gelation is scarcely affected. The in vitro activity of ALG/HA dressings was tested on adipose derived multipotent adult stem cells (Ad-MSC) and an immortalized keratinocyte cell line (HaCaT). Hydrogels did not interfere with cell viability in both cells lines, but significantly promoted gap closure in a scratch assay at early (1 day) and late (5 days) stages as compared to hydrogels made of ALG alone (p<0.01 and 0.001 for Ad-MSC and HaCaT, respectively). In vivo wound healing studies, conducted on a rat model of excised wound indicated that after 5 days ALG/HA hydrogels significantly promoted wound closure as compared to ALG ones (p<0.001). Overall results demonstrate that the integration of HA in a physically cross-linked ALG hydrogel can be a versatile strategy to promote wound healing that can be easily translated in a clinical setting.

A case of feverish neutropenia

Key Clinical Message

A case of feverish benign neutropenia occurring in a diabetic patient receiving pregabalin for peripheral neuropathy is reported. Although pregabalin-induced neutropenia is very rare, it is important to keep in mind that this drug like other anticonvulsants used for neuropathic pain, can cause severe neutropenia.

Prenatal diagnosis of congenital rubella infection and ultrasonography: a preliminary study

AIM

The aim of this study was to analyze the role of ultrasonography in the prenatal diagnosis of women with confirmed rubella infection in pregnancy.

METHODS

We performed a retrospective, population-based study on 175 women referred to our Centre of Infectious Disease in Pregnancy of AOU Federico II for rubella infection, in the period between January 1999 and December 2009. In confirmed cases of infection we performed periodic ultrasonographic assessment of fetal anatomy looking for prenatal findings of rubeovirus infection. Neonatal outcomes were collected.

RESULTS

Among 175 women, 48 (27.4%) were confirmed cases, in 83 (47.4%) cases rubella infection remain suspected. The remaining 44 (25.1%) women were excluded to having rubella infection in pregnancy. No defined probable cases were found. Among children born to mother with confirmed rubella infection, 9 (18.7%) resulted infected by rubella virus. In particular 6 newborns (66% of the affected) were asymptomatic, two babies showed incomplete congenital rubella syndrome (CRS), due to the presence of deafness in the absence of other congenital abnormalities without showing any USG findings. Only one baby showed a complete CRS: USG prenatal rubella infection findings were IUGR, polydramnios, cardiomegaly, defects of atrial septum, hepatosplenomegaly, ascites, echogenic bowel, placentomegaly. USG specificity and sensitivity was 100% and 11% respectively.

CONCLUSION

USG has an important role in the detection rubella intrauterine infection in case of severe abnormalities. The obstetricians should understand the limitations of ultrasound in detection of deafness and minor abnormalities.

Modeling and simulation of ultrasound fields generated by 2D phased array transducers for medical applications

Modern ultrasound imaging instrumentation for clinical applications allows real-time volumetric scanning of the patients' body. 4D imaging has been made possible thanks to the development of new echographic probes which consist in 2D phased arrays of piezoelectric transducers. In these new devices it is the system electronics which properly drives the matrix elements and focuses the beam in order to obtain a sequence of volumetric images. This paper introduces an ultrasound field simulator based on the Spatial Impulse Response method which is being properly developed to analyze the characteristics of the ultrasound field generated by a 2D phased array of transducers. Thanks to its high configurability by the user, it will represent a very useful tool for electronics designers in developing 4D ultrasound imaging systems components.

Mitochondrial DNA sequence variations in some Italian wild boar populations

In order to investigate the relationships between Italian wild boar and major pig breeds, we studied the genetic variability of four wild boar populations in Italy (Arezzo, Pisa, Parma, Bergamo) using a 533-bp fragment of the mitochondrial control region. Sixty-nine wild boar samples were analysed, allowing the identification of 10 distinct haplotypes, which involve a total of 15 single nucleotide polymorphisms. Phylogenetic and network analyses were performed also considering several sequences of wild and domesticated forms available in the databases. The Bayesian phylogenetic tree and the Median-Joining network analyses show three main groups: the Italian (IT), European (EU) and Asian (AS) clades. The IT clade corresponds to the Maremma endemic wild boar population and also includes Sardinian individuals, while the EU and AS groups include wild boars as well as domestic pig breeds. Only two individuals from Pisa cluster in the IT group, whereas two haplotypes from Bergamo cluster in the AS group and all other samples cluster in the EU clade. These findings suggest that in Italy wild boar populations have a mixed origin, both EU and AS, and that an interbreeding between wild and domesticated strains has probably occurred. Eight of the 10 wild boars coming from the Migliarino-San Rossore-Massaciuccoli Regional Park (Pisa) belong to H2 and H3 haplotypes, and cluster into the EU clade, suggesting that this regional park is not anymore exclusive of the endemic Maremma wild boar.

Fetal borderline cerebral ventriculomegaly: clinical significance and management

AIM

The aim of this study was to evaluate the clinical significance and the management of fetal borderline lateral cerebral ventriculomegaly.

METHODS

Fetuses with a sonographic diagnosis of lateral cerebral ventriculomegaly isolated or associated to other fetal malformations were followed monthly and a review of the English-language literature was made.

RESULTS

Of 86 fetuses analyzed, 30 suffered from hydrocephaly (monolateral, bilateral), 56 showed also several other malformations . Chromosomal aberrations is possible also in case of isolated hydrocephaly. Neurological sequelae, mostly a mild to moderate delay in cognitive and/or motor development, is present in 10% of the cases.

CONCLUSIONS

In most cases, isolated borderline lateral cerebral ventriculomegaly has no consequence. However, the risk of cerebral maldevelopment, delayed neurological development and, possibly, chromosomal aberrations is increased. The optimum management of these cases remains uncertain.

[Retroperitoneal abscess due to asymptomatic duodenal perforation by foreign body. A case report]

We present a case of retroperitoneal abscess due to asymptomatic duodenal perforation by foreign body. Patient has been admitted for lumbar pain and subocclusive crisis, with a medical history negative for acute symptomatology. After both clinical and radiologic evaluation, an abscess-like mass was detected in the context of right psoas muscle. Patient underwent surgical operation and a lumbar abscess has been found containing a foreign body (toothpick). There has been a transduodenal migration of the foreign body, without clinical signs of duodenal perforation.

Prenatal diagnosis of placental chorioangioma: our experience

Placental chorioangioma is the most common benign tumor of placenta. The relationship of vascularized chorioangiomas to adverse pregnancy outcome is well recognized. We report 3 cases of placental chorioangioma. Hypervascularization of the lesions in all patients and the immune hydrops with adverse fetal outcome in 2 cases are the complications of our mini-series. Ultrasonography and Doppler ultrasonography findings were useful in establishing the prenatal diagnosis and the prognosis.

[Cryosurgery with transpleurodiaphragmatic approach in the treatment of non-resectable and recurrent hepatic metastasis from the colorectum]

Cryotherapy allows the destruction of unresectable liver malignancies. The abdominal approach is uneasy for recurrent colorectal metastases located in the upper part of the liver and close to the inferior vena cava, the hepatic veins and the diaphragm. A transpleurodiaphragmatic access was employed. From 1999 to 2003, ten patients with recurrent colorectal liver metastases underwent transdiaphragmatic cryotherapy via a right thoracotomy. Median diameter was 30 mm. One to 4 cryoprobes were used, depending on the size and location of the metastasis. There were no operative deaths, and only 3 patients developed minor complications. Computerized tomography examination of the liver performed one week, three months after cryotherapy, assessed treatment completeness in all patients. At 14 months, 9 patients were alive and 6 were disease-free. Two patients had liver recurrences outside the cryolesion. A transthoracic access may represent the safest and easiest surgical approach for liver tumor cryoablation in selected patients with non resectable recurrent metastases of the upper liver.

[Surgical resection of gastrointestinal stromal tumor after treatment with imatinib: clinical case]

The stromal tumor is the most common mesenchymal tumor of the gastrointestinal tract. Surgical resection is the first-line therapy for operable lesions, however for inoperable imatinib is an effective therapy. In this setting a patient has been operated after a remarkable response to imatinib, used as both neoadjuvant and adjuvant. This approach led to a disease-free condition without toxicity and complications.

Improvement of gliquidone hypoglycaemic effect in rats by cyclodextrin formulations

This study was carried out with the aim to optimize the pharmacological profile of gliquidone (GLI)--a poorly bioavailable hypoglycaemic agent sparingly soluble in water--through complexation with cyclodextrins. In order to increase the apparent solubility of GLI, two cyclodextrins, namely beta-cyclodextrin (betaCD) and hydroxypropyl-beta-cyclodextrin (HPbetaCD), were tested. The effect of cyclodextrin addition on the aqueous solubility of GLI was evaluated by the phase solubility method at different pH values. The amount of GLI in solution increased upon CD addition according to A type plots. The aqueous solubility of GLI was enhanced more at higher pH values and using HPbetaCD. On the basis of its performance, HPbetaCD was selected as host to prepare GLI oral formulations. GLI/HPbetaCD solid systems were prepared at 1:2 molar ratio by co-grinding, spray-drying and freeze-drying and characterized by DSC, FTIR and X-ray powder diffractometry. Powders were amorphous and showed an improved dissolution rate in comparison with GLI. GLI/HPbetaCD co-ground and freeze-dried products were the most interesting systems, since they dissolved 62 and 94% of total drug after 15 min, respectively. The hypoglycaemic effect of the most rapidly dissolving binary systems was evaluated after oral administration in fasted rats by measuring plasma glucose level in the time interval 0.5-36 h and compared to free GLI. Our findings indicate that cyclodextrin-containing formulations not only provide an onset of hypoglycaemic effect faster than GLI, but also enhance significantly the pharmacological effect due to improved biopharmaceutics. The association GLI/HPbetaCD allows a reduction of the oral dose and is expected to provide a better control over drug side effects, contributing to improve safety and efficacy of GLI.