Biology subjects

Ward, D.

Publications and source records attributed to Ward, D..

25 records · Page 2Linked to original sources

bioRxiv2020

Structure-function analyses of dual-BON domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation

The Gram-negative outer membrane envelops the bacterium and functions as a permeability barrier against antibiotics, detergents and environmental stresses. Some virulence factors serve to maintain the integrity of the outer membrane, including DolP (formerly YraP) a protein of unresolved structure and function. Here we reveal DolP is a lipoprotein functionally conserved among Gram-negative bacteria and that loss of DolP increases membrane fluidity. We present the NMR solution structure for DolP, which is composed of two BON domains that form an interconnected opposing pair. The C-terminal BON domain binds to anionic phospholipids through an extensive membrane:protein interface providing evidence of subcellular localization of these phospholipids within the outer membrane. This interaction is essential for DolP function and is required for sub-cellular localization of the protein to the cell division site. The structure of DolP provides a new target for developing therapies that disrupt the integrity of the bacterial cell envelope.

biochemistry↗

bioRxiv2020

Content-Based Similarity Search in Large-Scale DNA Data Storage Systems

Synthetic DNA has the potential to store the worlds continuously growing amount of data in an extremely dense and durable medium. Current proposals for DNA-based digital storage systems include the ability to retrieve individual files by their unique identifier, but not by their content. Here, we demonstrate content-based retrieval from a DNA database by learning a mapping from images to DNA sequences such that an encoded query image will retrieve visually similar images from the database via DNA hybridization. We encoded and synthesized a database of 1.6 million images and queried it with a variety of images, showing that each query retrieves a sample of the database containing visually similar images are retrieved at a rate much greater than chance. We compare our results with several algorithms for similarity search in electronic systems, and demonstrate that our molecular approach is competitive with state-of-the-art electronics. One Sentence SummaryLearned encodings enable content-based image similarity search from a database of 1.6 million images encoded in synthetic DNA.

bioengineering↗

bioRxiv2020

An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets

BackgroundThe COVID-19 pandemic, caused by the SARS-CoV-2 virus, has a major global health and socio-economic burden. It has instigated the mobilisation of resources into the development of control tools, such as diagnostics and vaccines. The poor performance of some diagnostic serological tools has emphasised the need for up to date immune-informatic analyses to inform the selection of viable targets for further study. This requires the integration and analysis of genetic and immunological data for SARS-CoV-2 and its homology with other human coronavirus species to understand cross-reactivity. MethodsWe have developed an online "immuno-analytics" resource to facilitate SARS-CoV-2 research, combining an extensive B/T-cell epitope mapping and prediction meta-analysis, and human CoV sequence homology mapping and protein database annotation, with an updated variant database and geospatial tracking for >7,800 non-synonymous mutation positions derived from >150,000 whole genome sequences. To demonstrate its utility, we present an integrated analysis of SARS-CoV-2 spike and nucleocapsid proteins, both being vaccine and serological diagnostic targets, including an analysis of changes in relevant mutation frequencies over time. ResultsOur analysis reveals that the nucleocapsid protein in its native form appears to be a sub-optimal target for use in serological diagnostic platforms. The most frequent mutations were the spike protein D614G and nsp12 L314P, which were common (>86%) across all the geographical regions. Some mutations in the spike protein (e.g. A222V and L18F) have increased in frequency in Europe during the latter half of 2020, detected using our automated algorithms. The tool also suggests that orf3a proteins may be a suitable alternative target for diagnostic serologic assays in a post-vaccine surveillance setting. ConclusionsThe immuno-analytics tool can be accessed online (http://genomics.lshtm.ac.uk/immuno) and will serve as a useful resource for biological discovery and surveillance in the fight against SARS-CoV-2. Further, the tool may be adapted to inform on biological targets in future outbreaks, including potential emerging human coronaviruses that spill over from animal hosts.

bioinformatics↗

bioRxiv2020

Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world

BackgroundSARS-CoV-2 most likely evolved from a bat beta-coronavirus and started infecting humans in December 2019. Since then it has rapidly infected people around the world, with more than 4.5 million confirmed cases by the middle of May 2020. Early genome sequencing of the virus has enabled the development of molecular diagnostics and the commencement of therapy and vaccine development. The analysis of the early sequences showed relatively few evolutionary selection pressures. However, with the rapid worldwide expansion into diverse human populations, significant genetic variations are becoming increasingly likely. The current limitations on social movement between countries also offers the opportunity for these viral variants to become distinct strains with potential implications for diagnostics, therapies and vaccines. MethodsWe used the current sequencing archives (NCBI and GISAID) to investigate 15,487 whole genomes, looking for evidence of strain diversification and selective pressure. ResultsWe used 6,294 SNPs to build a phylogenetic tree of SARS-CoV-2 diversity and noted strong evidence for the existence of two major clades and six sub-clades, unevenly distributed across the world. We also noted that convergent evolution has potentially occurred across several locations in the genome, showing selection pressures, including on the spike glycoprotein where we noted a potentially critical mutation that could affect its binding to the ACE2 receptor. We also report on mutations that could prevent current molecular diagnostics from detecting some of the sub-clades. ConclusionThe worldwide whole genome sequencing effort is revealing the challenge of developing SARS-CoV-2 containment tools suitable for everyone and the need for data to be continually evaluated to ensure accuracy in outbreak estimations.

genomics↗

bioRxiv2018

Cross-talk between Hippo and Wnt signalling pathways in intestinal crypts: insightsfrom an agent-based model

Intestinal crypts are responsible for the total cell renewal of the lining of the intestines, occurring every 4-7 days in humans. This rapid turnover is governed by the complex interplay between signalling pathways and the cell cycle within individual cells in the crypts. The role of Wnt signalling in governing cell proliferation and differentiation in the intestinal crypt has been extensively studied, with increased signalling found towards the lower regions of the crypt. Recent studies have shown that the Wnt signalling gradient found within the crypt may arise as a result of division-based spreading from a Wnt reservoir at the crypt base. The discovery of the Hippo pathways involvement in maintaining crypt homeostasis is more recent; a mechanistic understanding of Hippo pathway dynamics, and its possible cross-talk with the Wnt pathway, remains lacking. To explore how the interplay between these pathways may control crypt homeostasis and dysplasia we developed and analysed a mathematical model coupling an ordinary differential equation description of Wnt and Hippo signalling with a cell-based description of cell movement, proliferation and contact inhibition. Furthermore, we compared an imposed Wnt gradient with a division-based Wnt gradient model. Our results suggest that Hippo signalling affects the Wnt pathway by reducing the presence of free cytoplasmic {beta}-catenin, causing cell cycle arrest. This process slows the rate of crypt turnover, previously attributed only to mutations in Wnt pathway components commonly observed in colorectal cancers. We also show that a division-based spreading of Wnt can form a Wnt gradient, resulting in proliferative dynamics comparable to imposed-gradient models. This suggests that imposed-gradient models are a reasonable approximation of experimentally observed Wnt gradients, however they provide little insight into the source of Wnt. Finally, a simulated APC double mutant, with misregulated Wnt and Hippo signalling activity, is predicted to be capable of completing a more rapid monoclonal conversion of the crypt than a Wnt-only mutant.\n\nAuthor summaryColorectal cancer is the fourth leading cause of cancer death worldwide. It is generally established that colorectal cancer occurs upon disruption of the dynamics of crypts, tubular indentations lining the walls of the gastrointestinal tract that are responsible for renewal of the intestinal epithelium. Thus, understanding the mechanisms that regulate intestinal crypt dynamics is instrumental to understand how colorectal cancer can emerge. We used mathematical modelling to explore how crypt dynamics emerge from the interactions across several biological scales, including mutations that cause an abnormal cell response to changes at the cell or tissue level, cell proliferation and motility within the crypt. Our model describes, in each cell within the crypt, levels and dynamics of genes involved in two signalling pathways - the canonical Wnt and Hippo pathways - relevant for cell proliferation and adhesion. In simulations, we predict how the crosstalk between these pathways affects crypt dynamics in both healthy and dysplastic cases. Furthermore, our simulations match recent biological evidence of a novel mechanism, based on cell division, causing heterogeneous and graded localisation of different cell types (dividing or not) within the crypt. Our results suggest the possibility of combined disease treatment, targeting both the Wnt and Hippo pathways.

systems biology↗

bioRxiv2018

The C-terminal tail of the bacterial translocation ATPase SecA modulates its activity

In bacteria, the translocation of a subset of proteins across the cytoplasmic membrane by the Sec machinery requires SecA. Although SecA can recognise nascent polypeptides, the mechanism of cotranslational substrate protein recognition is not known. Here, we investigated the role of the C-terminal tail (CTT) of SecA, which consists of a flexible linker (FLD) and a small metal-binding domain (MBD), in its interaction with nascent polypeptides. Phylogenetic analysis and ribosome binding experiments indicated that the MBD interacts with 70S ribosomes. Disruption of the entire CTT or the MBD alone had opposing effects on ribosome binding, substrate-protein binding, ATPase activity and in vivo function. Autophotocrosslinking, mass spectrometry, x-ray crystallography and small-angle x-ray scattering experiments provided insight into the CTT-mediated conformational changes in SecA. Finally, photocrosslinking experiments indicated that binding of SecA to substrate protein affected its interaction with the ribosome. Taken together, our results suggest a mechanism for substrate protein recognition.\n\nImpact StatementSecA is an evolutionarily conserved ATPase that is required for the translocation of a subset of proteins across the cytoplasmic membrane in bacteria. We investigated how SecA recognises its substrate proteins at the ribosome as they are still being synthesised (i.e. cotranslationally).

biochemistry↗

bioRxiv2018

Historic collections as a tool for assessing the global pollinator crisis

There is increasing concern about the decline of pollinators worldwide. However, despite reports that pollinator declines are widespread, data are scarce and often geographically and taxonomically biased. These biases limit robust inference about any potential pollinator crisis. Non-structured and opportunistic historical specimen collection data provide the only source of historical information which can serve as a baseline for identifying pollinator declines. Specimens historically collected and preserved in museums not only provide information on where and when species were collected, but also contain other ecological information such as species interactions and morphological traits. Here, we provide a synthesis of how researchers have used historical data to identify long-term changes in biodiversity, species abundances, morphology and pollination services. Despite recent advances, we show that information on the status and trends of most pollinators is absent, but we highlight opportunities and limitations to progress the assessment of pollinator declines globally. Finally, we demonstrate different approaches to analysing museum collection data using two contrasting case studies from distinct geographical regions (New Zealand and Spain) for which long-term pollinator declines have never been assessed. There is immense potential for museum specimens to play a central role in assessing the extent of the global pollination crisis.

ecology↗