International sustainable development goals for the elimination of viral hepatitis as a public health problem by 2030 highlight the pressing need to optimize strategies for prevention, diagnosis and treatment. Selected or transmitted resistance associated mutations (RAMs) and vaccine escape mutations (VEMs) in hepatitis B virus (HBV) may reduce the success of existing treatment and prevention strategies. These issues are particularly pertinent for many settings in Africa where there is high HBV prevalence and co-endemic HIV infection, but lack of robust epidemiological data and limited education, diagnostics and clinical care. The prevalence, distribution and impact of RAMs and VEMs in these populations are neglected in the current literature. We therefore set out to assimilate data for sub-Saharan Africa through a systematic literature review and analysis of published sequence data, and present these in an on-line database (https://livedataoxford.shinyapps.io/1510659619-3Xkoe2NKkKJ7Drg/). The majority of the data were from HIV/HBV coinfected cohorts. The commonest RAM was rtM204I/V, either alone or in combination with associated mutations, and identified in both reportedly treatment-naïve and treatment-experienced adults. We also identified the suite of mutations rtM204V/I + rtL180M + rtV173L, that has been associated with vaccine escape, in over 1/3 of cohorts. Although tenofovir has a high genetic barrier to resistance, it is of concern that emerging data suggest polymorphisms that may be associated with resistance, although the precise clinical impact of these is unknown. Overall, there is an urgent need for improved diagnostic screening, enhanced laboratory assessment of HBV before and during therapy, and sustained roll out of tenofovir in preference to lamivudine alone. Further data are needed in order to inform population and individual approaches to HBV diagnosis, monitoring and therapy in these highly vulnerable settings.
Increased clinical and scientific scrutiny is being applied to hepatitis B virus (HBV), with focus on the development of new therapeutic approaches, ultimately aiming for cure. Defining the optimum natural CD8+ T cell immune responses that arise in HBV, mediated by HLA class I epitope presentation, may help to inform novel immunotherapeutic strategies. Therefore, we have set out to develop a comprehensive database of these epitopes in HBV, coined ‘Hepitopes’. This undertaking has its foundations in a systematic literature review to identify the sites and sequences of all published class I epitopes in HBV. We also collected information regarding the methods used to define each epitope, and any reported associations between an immune response to this epitope and disease outcome. The results of this search have been collated into a new open-access interactive database that is available at http://www.expmedndm.ox.ac.uk/hepitopes. Over time, we will continue to refine and update this resource, as well as inviting contributions from others in the field to support its development. This unique new database is an important foundation for ongoing investigations into the nature and impact of the CD8+ T cell response to HBV.
A cell's phenotype is the set of observable characteristics resulting from the interaction of the genotype with the surrounding environment, determining cell behavior. Deciphering genotype-phenotype relationships has been crucial to understanding normal and disease biology. Analysis of molecular pathways has provided an invaluable tool to such understanding; however, typically it does not consider the physical microenvironment, which is a key determinant of phenotype.In this study, we present a novel modeling framework that enables the study of the link between genotype, signaling networks, and cell behavior in a three-dimensional microenvironment. To achieve this, we bring together Agent-Based Modeling, a powerful computational modeling technique, and gene networks. This combination allows biological hypotheses to be tested in a controlled stepwise fashion, and it lends itself naturally to model a heterogeneous population of cells acting and evolving in a dynamic microenvironment, which is needed to predict the evolution of complex multi-cellular dynamics. Importantly, this enables modeling co-occurring intrinsic perturbations, such as mutations, and extrinsic perturbations, such as nutrient availability, and their interactions.Using cancer as a model system, we illustrate how this framework delivers a unique opportunity to identify determinants of single-cell behavior, while uncovering emerging properties of multi-cellular growth.This framework is freely available at http://www.microc.org.
Journal of Materials Chemistry B www.rsc.org/MaterialsB Volume 1 | Number 35 | 21 September 2013 | Pages 4351-4522 PAPER Liam M. Grover et al. Thiol modifi cation of silicon-substituted hydroxyapatite nanocrystals facilitates fl uorescent labelling and visualisation of cellular internalisation Calcium phosphates are used widely as orthopaedic implants and in nanocrystalline form to enable the transfer of genetic material into cells. Despite widespread use, little is known about their fate after they have crossed the cell membrane. Here we present a method of surface modification of siliconsubstituted hydroxyapatite (SiHA) through a silane group, which enables the engraftment of a fluorescent dye to facilitate real-time biological tracking. Surface modification of the nanocrystal surface was undertaken using (3-mercaptopropyl)trimethoxysilane (MPTS), which presented a thiol for the further attachment of a fluorophore. Successful modification of the surface was demonstrated using zeta potential measurements and fluorescence microscopy and the number of thiol groups at the surface was quantified using Ellman's reagent. In vitro experiments using the fluorescently modified particles enabled the discrimination of the calcium phosphate particulate from other biological debris following internalisation by a population of MC3T3 (pre-osteoblast) cells and the particles were shown to maintain fluorescence for 24 hours without quenching. The successful modification of the surface ofSiHA with thiol groups offers the tantalising possibility of the intracellular growth factor delivery.
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