Dwarna : a blockchain solution for dynamic consent in biobanking

Dynamic consent aims to empower research partners and facilitate active participation in the research process. Used within the context of biobanking, it gives individuals access to information and control to determine how and where their biospecimens and data should be used. We present Dwarna—a web portal for ‘dynamic consent’ that acts as a hub connecting the different stakeholders of the Malta Biobank: biobank managers, researchers, research partners, and the general public. The portal stores research partners’ consent in a blockchain to create an immutable audit trail of research partners’ consent changes. Dwarna’s structure also presents a solution to the European Union’s General Data Protection Regulation’s right to erasure—a right that is seemingly incompatible with the blockchain model. Dwarna’s transparent structure increases trustworthiness in the biobanking process by giving research partners more control over which research studies they participate in, by facilitating the withdrawal of consent and by making it possible to request that the biospecimen and associated data are destroyed.peer-reviewe

Are the physicochemical properties of antibacterial compounds really different from other drugs?

Background: It is now widely recognized that there is an urgent need for new antibacterial drugs, with novel mechanisms of action, to combat the rise of multi-drug resistant bacteria. However, few new compounds are reaching the market. Antibacterial drug discovery projects often succeed in identifying potent molecules in biochemical assays but have been beset by difficulties in obtaining antibacterial activity. A commonly held view, based on analysis of marketed antibacterial compounds, is that antibacterial drugs possess very different physicochemical properties to other drugs, and that this profile is required for antibacterial activity. Results: We have re-examined this issue by performing a cheminformatics analysis of the literature data available in the ChEMBL database. The physicochemical properties of compounds with a recorded activity in an antibacterial assay were calculated and compared to two other datasets extracted from ChEMBL, marketed antibacterials and drugs marketed for other therapeutic indications. The chemical class of the compounds and Gram-negative/Grampositive profile were also investigated. This analysis shows that compounds with antibacterial activity have physicochemical property profiles very similar to other drug classes. Conclusions: The observation that many current antibacterial drugs lie in regions of physicochemical property space far from conventional small molecule therapeutics is correct. However, the inference that a compound must lie in one of these “outlier” regions in order to possess antibacterial activity is not supported by our analysis

Role of protein structure in drug discovery

Many pharmaceuticals currently available were discovered either during the screening of natural of synthetic product libraries or by serendipitous observation. Such a \random" approach entails testing numerous compounds and developing countless high-throughput screening assays. On the other hand, a "rational" approach involves the structure-based route to drug discovery, where the structure of a target protein is determined. Hypothetical ligands may be predicted by molecular modelling, while movement of a molecule may be predicted by Molecular Dynamics Simulations prior to synthetic chemical synthesis of a particular molecule. Here, we will be discussing protein structure-based approaches to drug discovery.peer-reviewe

A novel population of activated cytotoxic T cells infiltrate pituitary neuroendocrine tumour subytpes

Non-functional pituitary adenomas (NFPA) are non-hormone secreting pituitary tumours while growth hormone-secreting pituitary adenomas (GHPA) are active pituitary tumours causing acromegaly. Since immunotherapy is becoming the preferred therapeutic strategy in cancers, understanding the diversity of immune cells infiltrating the tumour microenvironment is warranted. However, little is known about the immune landscape of pituitary tumours. We validated an acoustic-assisted hydrodynamic focusing cytometer based method (Attune, Thermofisher) to identify rare immune cell populations in NFPA (n=6) and GHPA (n=3) obtained from patients undergoing transphenoidal surgery. We unravelled key cellular populations of myeloid (macrophages and monocytes) and lymphocytic (CD4 and CD8 T cells) origin using a multi-colour panel of antibodies against cell surface (CD45, CD163, CD64, CD11b, CD3, CD56, CD19, CD4 and CD8) and intracellular (CD68, T-bet, GATA-3 and FOXP3) antigens and assessed the degree of T-cell activation using the CD44 marker. We also checked for the expression of immune checkpoint and exhaustion markers PD1 and TIM-3 respectively. In all samples, lymphocytic infiltrates were detected. In all except 1 NFPA and in all GHPA the CD8:CD4 ratio was greater than 1 ranging from 1.88 - 5.74 in NFPA and 1.35 - 5.21 in GHPA with no statistical difference between NFPA and GHPA. This method also revealed novel populations of activated, cytotoxic T cells in all pituitary adenomas analysed. We are currently characterising the function of these cells in such tumours and how their presence correlates with the patients’ clinical data and tumour characteristics.peer-reviewe

Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening

We present Ligity, a hybrid ligand-structurebased, non-superpositional method for virtual screening of large databases of small molecules. Ligity uses the relative spatial distribution of pharmacophoric interaction points (PIPs) derived from the conformations of small molecules. These are compared with the PIPs derived from key interaction features found in protein−ligand complexes and are used to prioritize likely binders. We investigated the effect of generating PIPs using the single lowest energy conformer versus an ensemble of conformers for each screened ligand, using different bin sizes for the distance between two features, utilizing triangular sets of pharmacophoric features (3-PIPs) versus chiral tetrahedral sets (4-PIPs), fusing data for targets with multiple protein−ligand complex structures, and applying different similarity measures. Ligity was benchmarked using the Directory of Useful Decoys-Enhanced (DUD-E). Optimal results were obtained using the tetrahedral PIPs derived from an ensemble of bound ligand conformers and a bin size of 1.5 Å, which are used as the default settings for Ligity. The high-throughput screening mode of Ligity, using only the lowest-energy conformer of each ligand, was used for benchmarking against the whole of the DUD-E, and a more resource-intensive, “information-rich” mode of Ligity, using a conformational ensemble of each ligand, were used for a representative subset of 10 targets. Against the full DUD-E database, mean area under the receiver operating characteristic curve (AUC) values ranged from 0.44 to 0.99, while for the representative subset they ranged from 0.61 to 0.86. Data fusion further improved Ligity’s performance, with mean AUC values ranging from 0.64 to 0.95. Ligity is very efficient compared to a protein−ligand docking method such as AutoDock Vina: if the time taken for the precalculation of Ligity descriptors is included in the comparison, then Ligity is about 20 times faster than docking. A direct comparison of the virtual screening steps shows Ligity to be over 5000 times faster. Ligity highly ranks the lowest-energy conformers of DUD-E actives, in a statistically significant manner, behavior that is not observed for DUD-E decoys. Thus, our results suggest that active compounds tend to bind in relatively low-energy conformations compared to decoys. This may be because actives - and thus their lowest-energy conformations - have been optimized for conformational complementarity with their cognate binding sites

Engineering adaptive user interfaces using monitoring-oriented programming

User interfaces which adapt based on usage patterns, for example based on frequency of use of certain features, have been proposed as a means of limiting the complexity of the user interface without specialising it unnecessarily to particular user profiles. However, from a software engineering perspective, adaptive user interfaces pose a challenge in code structuring, and separation of the different layers of user interface and application state and logic can introduce interdependencies which make software development and maintenance more challenging. In this paper we explore the use of monitoring-oriented programming to add adaptive features to user interfaces, an approach which has been touted as a means of separating certain layers of logic from the main system. We evaluate the approach both using standard software engineering measures and also through a user acceptance experiment - by having a number of developers use the proposed approach to add adaptation logic to an existing application.peer-reviewe

Plasmodium subtilisin-like protease 1 (SUB1): insights into the active-site structure, specificity and function of a pan-malaria drug target.

Release of the malaria merozoite from its host erythrocyte (egress) and invasion of a fresh cell are crucial steps in the life cycle of the malaria pathogen. Subtilisin-like protease 1 (SUB1) is a parasite serine protease implicated in both processes. In the most dangerous human malarial species, Plasmodium falciparum, SUB1 has previously been shown to have several parasite-derived substrates, proteolytic cleavage of which is important both for egress and maturation of the merozoite surface to enable invasion. Here we have used molecular modelling, existing knowledge of SUB1 substrates, and recombinant expression and characterisation of additional Plasmodium SUB1 orthologues, to examine the active site architecture and substrate specificity of P. falciparum SUB1 and its orthologues from the two other major human malaria pathogens Plasmodium vivax and Plasmodium knowlesi, as well as from the rodent malaria species, Plasmodium berghei. Our results reveal a number of unusual features of the SUB1 substrate binding cleft, including a requirement to interact with both prime and non-prime side residues of the substrate recognition motif. Cleavage of conserved parasite substrates is mediated by SUB1 in all parasite species examined, and the importance of this is supported by evidence for species-specific co-evolution of protease and substrates. Two peptidyl alpha-ketoamides based on an authentic PfSUB1 substrate inhibit all SUB1 orthologues examined, with inhibitory potency enhanced by the presence of a carboxyl moiety designed to introduce prime side interactions with the protease. Our findings demonstrate that it should be possible to develop 'pan-reactive' drug-like compounds that inhibit SUB1 in all three major human malaria pathogens, enabling production of broad-spectrum antimalarial drugs targeting SUB1

Runtime verification using Valour

In this paper we give an overview of Valour, a runtime verification tool which has been developed in the context of a project to act as a backend verification tool for financial transaction software. A Valour script is written by the user and is then compiled into a verification system. Although, developed as part of a project, the tool has been designed as a stand-alone general-purpose verification engine with a particular emphasis on event consumption. The strong points of Valour when compared to other runtime verification tools is its focus on scalability and robustness.peer-reviewe

Novel molecular classifiers of basal-type subset in breast cancer patients

Introduction: The basal breast cancer subtype persists as a heterogeneous group that shows worse prognosis due to lack of targeted therapy. Understanding the deregulated cellular mechanisms uncovers new therapeutic targets which require biomarkers to select eligible patients. Analysis of datasets (cBioP01tal) show that 59.6% ofvbasal cancer exhibit deregulation of the PP2A cellular feedback mechanism. Our study aims to define biomarkers for PP2A deregulation in the basal subtype.peer-reviewe

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method