Biology subjects

Watson, J.

Publications and source records attributed to Watson, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Thermodynamic properties and stability of HMGB1 complexes with linear polyelectrolytes elucidated by nano differential scanning fluorimetry

The High Mobility Group Box 1 (HMGB1) protein performs multiple essential functions in the body, ranging from DNA regulation to the activation and mediation of immune responses. However, HMGB1 has been also implicated in several pathological conditions, such as rheumatoid arthritis, sepsis, autoimmune diseases, tumors, and Alzheimer's disease. As a result, HMGB1 is of increasing interest as a therapeutic target. Binding to heparin has been reported to inhibit HMGB1's pathological activity during sepsis in clinical settings. In this work, we compare the interactions of HMGB1 with heparin and its' synthetic analog linear polyglycerol sulfate (lPGS) from the viewpoint of stability and changes to association behavior. This analysis focuses on thermal stability, secondary-structure changes, and particle-size evolution using nano-differential scanning fluorimetry (nanoDSF), circular dichroism spectroscopy (CD), and dynamic light scattering (DLS).

biochemistry↗

bioRxiv2026

Microbiome Integrity Protects Against Glial-Mediated Tau and Amyloid Pathology Through Circadian and Autophagy Homeostasis

Alzheimers disease (AD) is characterized not only by tau and amyloid-{beta} aggregation but also by systemic disruptions in circadian rhythms, metabolism, and gut-brain communication that exacerbate neuroinflammation and neurodegeneration. While glial cells play central roles in inflammatory signaling and proteostasis, the contribution of the gut microbiome to glia-driven AD pathology remains poorly understood. Here, we used Drosophila models with glial-specific expressions of human tau and amyloid-associated transgenes to investigate how microbiome integrity influences disease progression. AD models exhibited significant shifts in gut microbial composition, particularly in Lactobacillus and Acetobacter species, suggesting an adaptive microbial response to pathological stress. Strikingly, microbiome depletion (axenic condition) markedly worsened behavioral and physiological outcomes, including disrupted sleep-circadian rhythms, impaired memory, and reduced locomotor function. These deficits were accompanied by amplified neuroinflammatory signaling (Upd-Dome-Hop-Stat92e axis), increased apoptotic gene expression, lipid dysregulation, and altered synaptic markers. Moreover, microbiome loss induced energy stress marked by elevated phospho-AMPK (p-AMPK), yet failed to restore proteostasis, as evidenced by accumulation of ubiquitinated proteins and the autophagy adaptor Ref2p, indicating impaired autophagic flux. This dysfunction correlated with increased tau, phospho-tau, and A{beta}42 accumulation. Together, our findings demonstrate that microbiome depletion exacerbates glial-mediated inflammation, disrupts circadian and metabolic homeostasis, impairs, and accelerates cognitive and motor decline. This work highlights a previously underappreciated role of the gut microbiome in restraining glial dysfunction and mitigating AD-like pathology, positioning microbial homeostasis as a critical modulator of neurodegenerative disease progression.

neuroscience↗

bioRxiv2025

Genome-wide analysis exploring mechanisms used by Shigella sonnei to survive long-term nutrient starvation

Shigella is a major cause of severe diarrhoea with S. flexneri and S. sonnei accounting for over 90% of infections. As economies grow, S. sonnei replaces S. flexneri as the dominant cause of shigellosis, however the basis of this epidemiological shift remains unclear. Here we investigated whether S. sonnei is better equipped to survive nutrient starvation, a crucial condition for persistence both outside the host and within the colonic lumen. S. sonnei exhibited greater survival under long-term nutrient starvation (LTNS) than S. flexneri, rapidly activating survival mechanisms. We interrogated the genome of S. sonnei using Transposon Directed Insertion-site Sequencing (TraDIS) revealing that metabolic pathways (ATP, nucleotide, and amino acid synthesis), and envelope homeostasis complexes (e.g., Tol-Pal, Bam) are conditionally essential for LTNS. TraDIS findings were validated by non-competitive and competitive survival of wild-type and deletion mutant strains. We compared the homology of conditionally essential genes between S. sonnei and S. flexneri to identify putative genetic markers of differential interspecies LTNS survival. Analysis of ldcA (a peptidoglycan carboxypeptidase) and rseA (the anti-sigma factor regulator) indicated a major role in sustaining survival in LTNS in S. sonnei; however, allele-swap with S. flexneri alleles restored wild-type survival in S. sonnei suggesting that monogenic changes may not explain the divergent survival of these two species. Together, these data define the molecular adaptations of starvation resistance in S. sonnei and provide insights into its epidemiological dominance in high-income countries. Author summaryUnderstanding why S. sonnei has a higher prevalence over S. flexneri as a country undergoes economic growth is one of the most important challenges in Shigella research. The investigation of their biological and genetic differences is key to tackle the impact of the disease. We discovered that S. sonnei resists nutrient deprivation better than S. flexneri, suggesting a better adaptation to an extracellular lifestyle and a greater preservation of metabolic capabilities. Using a genome-wide transposon sequencing approach we uncovered the key pathways behind the survival of S. sonnei facing nutrient starvation, which include ATP, nucleotide, and amino acid synthesis as well as maintenance of cell envelope integrity. Comparative analysis between S. sonnei and S. flexneri did not identify a single gene responsible for the differing survival and we suggest that the differing survival may stem from the coordination of multigenic differences. Our data provides a genome-wide basis for understanding how S. sonnei adapted to nutrient-deprived settings, which may be advantageous in the gut lumen and also in hostile environments, potentially contributing to its dominance in high-income countries.

microbiology↗

bioRxiv2025

De-novo design of a random protein walker

Molecular machines hold great potential. Design of static monomeric and oligomeric protein structures has advanced tremendously, but few dynamic protein systems have been designed. Here we present the design and characterization of a random protein walker that diffuses along a designed protein track. For the track, we designed micro-meter long fibres and developed a method to rigidly decorate them with arbitrary proteins. The walkers consist of homo-oligomers that reversibly bind the track using heterodimeric feet; we tested multiple heterodimer interfaces for reversibility and designed six walkers with different numbers of feet. Cryo-EM experiments confirmed the structure of the track and walkers. We performed detailed single molecule tracking and kinetics characterisation and found that the walkers with more feet diffuse along the track faster. The system represents a tuneable starting point for future powered protein molecular robots.

synthetic biology↗

bioRxiv2025

Regulation of lipid dysmetabolism and neuroinflammation linked with Alzheimer's disease through modulation of Dgat2

Alzheimers disease (AD), an age-associated neurodegenerative disorder, is characterized by progressive cognitive decline, amyloid-{beta} (A{beta}) deposition, lipid dysregulation, and neuroinflammation. Although mutations in the amyloid precursor protein (APP) and accumulation of A{beta}42 are established drivers of pathology, the mechanisms connecting amyloid toxicity with lipid metabolism and inflammatory responses remain poorly understood. Here, we employed complementary Drosophila and mouse models to dissect these relationships. Expression of AppNLG and A{beta}42 in Drosophila resulted in locomotor deficits, disrupted sleep-circadian rhythms, memory impairments, lipid accumulation, synaptic loss, and neuroinflammatory signatures. Comparable lipid metabolic disturbances and inflammatory alterations were detected in the AppNLG-F knock-in mouse model, underscoring their conserved relevance to AD pathogenesis. We further identified diacylglycerol O-acyltransferase 2 (Dgat2), a key enzyme catalyzing the final step of triglyceride synthesis, as a critical modulator of AD-related phenotypes. Dgat2 expression was altered in both animal models and human AD tissues. Notably, panneuronal knockdown of Dgat2 in Drosophila attenuated lipid accumulation, restored synaptic integrity, and ameliorated locomotor and cognitive deficits, while also reducing neuroinflammation. Dgat2 suppression additionally improved sleep and circadian behavior, highlighting its pleiotropic protective effects. Together, these findings demonstrate a mechanistic link between amyloid pathology, lipid dysregulation, and neuroinflammatory processes. Targeting Dgat2 may therefore represent a novel therapeutic strategy to counteract AD-associated metabolic and neuronal dysfunction. The conservation of lipid homeostasis mechanisms across species underscores the translational potential of this approach for delaying or mitigating AD progression.

physiology↗

bioRxiv2025

A typology of Australian terrestrial bird communities

AimIncreasing interest in holistic measurement of the response of fauna communities to interventions requires suitable community condition metrics. However, the development of such metrics is hindered by the absence of broad-scale typologies at suitable spatial and ecological resolutions. We aimed to derive a preliminary typology of terrestrial bird communities for Australia, based on bird co-occurrence data, and describe and map the likely distribution of each community type across the continent. LocationMainland Australia, continental islands Time period1973-2022 Major taxa studiedAves MethodsWe used fine-scale co-occurrence data from standard 2-ha surveys in BirdLife Australias citizen-science database. After filtering to reduce bias, we used hierarchical clustering followed by iterative consultation with experts to identify reliably distinct and recognisable terrestrial bird communities across Australia. We used Maxent to model the likely distributions of each community, and developed community descriptions based on each communitys composition and distribution. ResultsThe resultant typology included 29 reliably distinct and recognisable bird communities with major clusters corresponding with seven broad geographical regions. The distributions of bird communities did not correspond tightly to the boundaries of major vegetation groups, with most communities occurring across multiple vegetation types. Main ConclusionsOur preliminary typology of bird communities provides a standard classification at a continental scale. It newly defines distinct bird communities as entities for which condition benchmarks can be established to allow assessment of their conservation status and monitoring of change over time. Refinement will enable cryptic communities in areas with sparse data to be identified. The method could be translated to other regions where adequate coverage of data in the form of standardised surveys of fauna are available. Vast biodiversity datasets delivered through citizen science programs provide the opportunity to develop such typologies for fauna communities, as a precursor to developing targeted and informative community condition metrics.

ecology↗

bioRxiv2023

Proteomics of Patient-derived Breast Tumours Identifies a Pro-migratory Osteomodulin-Cyclin Dependent Kinase 1 Axis which Drives Bone Metastasis

Metastasis to different organs remains the main cause of mortality in breast cancer. Molecular predictors of metastasis are limited as well as therapeutic options. Here, we conducted quantitative proteomics and phosphoproteomics analysis of patient-derived tumours, identifying osteomodulin (OMD) as a dysregulated protein and associated with bone metastases. Cancer-associated fibroblasts secrete OMD which increases breast cancer migration in vitro and promotes the formation of bone metastases in vivo. Downstream of OMD, phosphoproteomics identified the activation of cyclin-dependent kinase 1 (CDK1). The OMD-CDK1 signalling axis drives a pro-migratory and pro-survival phenotype in vitro and bone metastasis in vivo. Our findings highlight the importance of OMD and CDK1 in breast cancer bone metastasis and proposes an alternative therapeutic avenue for the treatment and the prevention of organ-specific metastases.

cancer biology↗

bioRxiv2023

The impacts of contemporary logging after 250 years of deforestation and degradation on forest-dependent threatened species

Despite the importance of safeguarding forests and woodlands for achieving global climate and biodiversity agendas, logging continues across most forested countries. Forestry advocates often claim logging has minimal impacts, but rarely consider the cumulative threat deforestation and degradation has had, and continue to have, on species. Using New South Wales (Australia) as a case study, we quantify the extent of deforestation and degradation from 1750 - current. Using these estimates of overall loss as a baseline, we then quantify the relative extent of contemporary (2000 - 2022) logging and the condition of the remaining native forest and woodland (quantified by measuring the similarity of a current ecosystem to a historical reference state with high ecological integrity). Using these data, we measure the impacts on distinct vegetation types and on 484 terrestrial forest-dependent now-threatened species. We show that more than half (29 million ha) of pre-1750 (pre-European colonization of Australia) native forest and woodland vegetation in NSW has been lost. Of the remaining 25 million ha, 9 million ha is degraded. We found contemporary degradation from logging affected 244 forest-dependent now-threatened species that had already been affected by this historical deforestation and degradation, but the impacts varied across species and vegetation types. We found that 70 now-threatened species that were impacted by historical deforestation and degradation and continue to be impacted by logging, now have [≤]50% of their pre-1750 extent remaining that is intact (with three species now having <20%). By quantifying the historical impacts of deforestation and degradation, our research sets the impact of contemporary degradation from logging in perspective and highlights shortfalls in current environmental assessments that fail to consider appropriate baselines when reporting on overall impact. Future land management decisions need to consider not only the extent of remaining habitat based on pre-1750 extents, but also its condition. Article impact statementThe impact of logging needs to be placed in perspective by considering past losses and degradation due to human land use decisions.

ecology↗

bioRxiv2022

A report card methodology to showcase progress towards threatened species recovery

Among the conservation community, it is well known that Earths mass species extinction crisis is getting worse. Yet, an often neglected problem is the need for effectively communicating the species extinction crisis to diverse audiences in ways that catalyse immediate action. Here we generated a streamlined threatened species recovery report card methodology, which combined two input indicators including planning and funding, one output indicator capturing habitat protection, and one outcome indicator which highlights threatened species trajectories, to provide simple scores for all Australian threatened species. We show that just 41 (2.3%) of species achieved an A grade for the input indicator (i.e., recovery plans and federal funding), 240 (13.3%) achieved a C grade, and 1,521 (84.4%) achieved an F. Five hundred and twenty nine (29.3%) species achieved an A for the output indicator (i.e, habitat protection), 130 (7.2%) achieved a B, 158 (8.8%) achieved a C, 189 (10.5%) achieved a D, 212 (11.8%) achieved an E, and 584 (32.4%) achieved a F. While five (0.3%) species achieved an A for the output indicator (i.e., threat status improvement), every other species (99.7%) achieved an F. We provide a method to combine scores to test how individual jurisdictions are tracking and show that Australia is achieving an F for the input and outcome indicators, and a D for the output indicator. While the threatened species recovery report card highlighted a clear failure in many federal environmental legislation responsibilities, it provides a baseline from which different governments can track policy progress and outlines clear direction for immediate improvement including developing adequate recovery plans, funding the actions in the recovery plans, protecting habitat from further destruction, verifying recovery through monitoring and evaluation of species trajectories, and supporting transparency and collaboration on the execution on the plans through an improved data infrastructure. Without an immediate step change in how Australia communicates and faces its species crisis, we will leave a tragic legacy of extinction and fail our obligations to future generations of Australians, and the international community.

scientific communication and education↗

bioRxiv2022

A statistical censoring approach accounts for hook competition in abundance indices from longline surveys

Fishery-independent longline surveys provide valuable data to monitor fish populations. However, competition for bait on the finite number of hooks leads to biased estimates of relative abundance when using simple catch-per-unit-effort methods. Numerous bias-correcting instantaneous-catch-rate methods have been proposed, modelling the bait removal times as independent random variables. However, experiments have cast doubts on the many assumptions required for these to accurately infer relative abundance. We develop a new approach by treating some observations as right-censored, acknowledging that observed catch counts are lower bounds of what they would have been in the absence of hook competition. Through simulation experiments we confirm that our approach consistently outperforms previous methods. We demonstrate performance of all methods on longline survey data of eleven species. Accounting for hook competition leads to large differences in relative indices (often -50% to +100%), with effects of hook competition varying between species (unlike other methods). Our method can be applied using existing statistical packages and can include environmental influences, making it a general and reliable method for analyzing longline survey data.

ecology↗

bioRxiv2021

Spatially Resolved Phosphoproteomics Reveals Fibroblast Growth Factor Receptor Recycling-driven Regulation of Autophagy and Survival

Receptor Tyrosine Kinase (RTK) endocytosis-dependent signalling drives cell proliferation and motility during development and adult homeostasis, but is dysregulated in diseases, including cancer. The recruitment of RTK signalling partners during endocytosis, specifically during recycling to the plasma membrane, is still unknown. Focusing on Fibroblast Growth Factor Receptor 2b (FGFR2b) recycling, we revealed FGFR signalling partners proximal to recycling endosomes (REs) by developing a Spatially Resolved Phosphoproteomics (SRP) approach based on APEX2-driven biotinylation followed by phosphopeptide enrichment. Combining this with traditional phosphoproteomics, bioinformatics, and targeted assays, we uncovered that FGFR2b stimulated by its recycling ligand FGF10 activates mTOR-dependent signalling and ULK1 at the REs, leading to autophagy suppression and cell survival. This adds to the growing importance of RTK recycling in orchestrating cell fate and suggests a therapeutically targetable vulnerability in ligand-responsive cancer cells. Integrating SRP with other systems biology approaches provides a powerful tool to spatially resolve celllar signalling.

cell biology↗

bioRxiv2021

SubcellulaRVis: an app to visualize subcellular compartment enrichment

High-throughput omics methods result in lists of differentially regulated or expressed genes or proteins, whose function is generally studied through statistical methods such as enrichment analyses. One aspect of protein regulation is subcellular localization, which is crucial for their correct processing and function and can change in response to various cellular stimuli. Enrichment of proteins for subcellular compartments is often based on Gene Ontology Cellular Compartment annotations. Results of enrichment are typically visualized using bar-charts, however enrichment analyses can result in a long list of significant annotations which are highly specific, preventing researchers from gaining a broad understanding of the subcellular compartments their proteins of interest may be located in. Schematic visualization of known subcellular locations has become increasingly available for single proteins via the UniProt and COMPARTMENTS platforms. However, it is not currently available for a list of proteins (e.g. from the same experiment) or for visualizing the results of enrichment analyses. To generate an easy-to-interpret visualization of protein subcellular localization after enrichment we developed the SubcellulaRVis web app, which visualizes the enrichment of subcellular locations of gene lists in an easy and impactful manner. SubcellulaRVis projects the results of enrichment analysis on a graphical representation of a eukaryotic cell. Implemented as a web app and an R package, this tool is user-friendly, provides exportable results in different formats, and can be used for gene lists derived from multiple organisms. Here, we show the power of SubcellulaRVis to assign proteins to the correct subcellular compartment using gene list enriched in previously published spatial proteomics datasets. We envision SubcellulaRVis will be useful for cell biologists with limited bioinformatics expertise wanting to perform precise and quick enrichment analysis and immediate visualization of gene lists. Author SummaryCells contain intracellular compartments, such as membrane-bound organelles and the nucleus, and are surrounded by a plasma membrane. Proteins can be found in different cellular compartments; depending on the subcellular compartment they are localized to, they can be differentially regulated or perform location-specific functions. High-throughput omics experiments result in a list of proteins or genes of interest; one way in which their functional role can be understood is through their subcellular localization, as deduced through statistical enrichment for Gene Ontology Cellular Component (GOCC) annotations or similar. We have designed a bioinformatic tool, named SubcellulaRVis, that compellingly visualizes the results of protein localization after enrichment and simplifies the results for a quick interpretation. We demonstrate that SubcellulaRVis precisely describes the subcellular localization of gene lists whose locations have been previously ascertained in publications. SubcellulaRVis can be accessed via the web or as a stand-alone app. SubcellulaRVis will be useful for experimental biologists with limited bioinformatics expertise analyzing data related to cellular signalling, protein (re)localization and regulation, and location-specific functional modules within the cell.

bioinformatics↗

bioRxiv2021

Shared hotspot mutations in spontaneously arising cancers position dog as an unparalleled comparative model for precision therapeutics

Naturally occurring canine cancers have remarkable similarities to their human counterparts. In order to determine whether these similarities occur at the molecular level, we investigated hotspot mutations in a variety of spontaneously arising canine cancers and found high concordance in oncogenic drivers between cancers in both species. These findings suggest that canines may present a powerful and complementary model for preclinical investigations for targeted cancer therapeutics. Through analysis of 708 client-owned dogs from 96 breeds (plus mixed breeds) with 23 common tumor types, we discovered mutations in 50 well-established oncogenes and tumor suppressors, and compared them to those reported in human cancers. TP53 is the most commonly mutated gene, detected in 30.81% of canine tumors overall and >40% in hemangiosarcoma and osteosarcoma. Canine tumors share mutational hotspots with human tumors in oncogenes including PIK3CA, KRAS, NRAS, BRAF, KIT and EGFR. Hotspot mutations with significant (P<0.0001) association to tumor type include NRAS G61R and PIK3CA H1047R in hemangiosarcoma, ERBB2 V659E in pulmonary carcinoma, and BRAF V588E in urothelial carcinoma. This work positions canines as excellent spontaneous models of human cancers that can help to investigate a wide spectrum of targeted therapies.

cancer biology↗

bioRxiv2021

ATM phosphorylates PP2A subunit A resulting in nuclearexport and spatiotemporal regulation of the DNA damageresponse

Ataxia telangiectasia mutated (ATM) is a serine-threonine protein kinase and important regulator of the DNA damage response (DDR). One critical ATM target is the structural subunit A (PR65) of protein phosphatase 2A (PP2A), known to regulate diverse cellular processes such as mitosis and cell growth as well as dephosphorylating many proteins during the recovery from the DDR. We generated mouse embryonic fibroblasts expressing PR65-WT, -S401A (cannot be phosphorylated), and -S401D (phosphomimetic) transgenes. Significantly, S401 mutants exhibited extensive chromosomal aberrations, impaired DNA double-strand break (DSB) repair and underwent increased mitotic catastrophe after radiation. Our study demonstrates that the phosphorylation of a single, critical PR65 amino acid (S401) by ATM fundamentally controls the DDR, and balances DSB repair quality, cell survival and growth by spatiotemporal PR65 nuclear-cytoplasmic shuttling mediated by the nuclear export receptor CRM1.

cancer biology↗

bioRxiv2021

The global rarity of intact coastal regions

Management of the land-sea interface is considered essential for global conservation and sustainability objectives, as coastal regions maintain natural processes that support biodiversity and the livelihood of billions of people. However, assessments of coastal regions have focused on either strictly the terrestrial or marine realm, and as a consequence, we still have a poor understanding of the overall state of Earths coastal regions. Here, by integrating the terrestrial human footprint and marine cumulative human impact maps, we provide a global assessment of the anthropogenic pressures affecting coastal areas. Just 15.5% of coastal areas globally can be considered having low anthropogenic pressure, mostly found in Canada, Russia, and Greenland. Conversely, 47.9% of coastal regions are heavily impacted by humanity with most countries (84.1%) having >50% of their coastal regions degraded. Nearly half (43.3%) of protected areas across coastal regions are exposed to high human pressures. In order to meet global sustainability objectives, we identify those nations that must undertake greater actions to preserve and restore coastal regions so as to ensure global sustainable development objectives can be met.

ecology↗

bioRxiv2021

Reciprocal Priming between RTKs within Recycling Endosomes Orchestrates Cellular Signaling Outputs

Integration of signalling downstream of individual receptor tyrosine kinases (RTKs) is crucial to fine tune cellular homeostasis during development and in pathological conditions, including breast cancer. However, how signalling integration is regulated and whether the endocytic fate of single receptors controls such signalling integration remains poorly elucidated. Combining quantitative phosphoproteomics and targeted assays, we generated a detailed picture of recycling-dependent fibroblast growth factor (FGF) signalling in breast cancer cells, with a focus on distinct FGF receptors (FGFRs). We discovered reciprocal priming between FGFRs and epidermal growth factor (EGF) receptor (EGFR) that is coordinated at recycling endosomes. FGFR recycling ligands induce EGFR phosphorylation on threonine 693. This phosphorylation event alters both FGFR and EGFR trafficking and primes FGFR-mediated proliferation but not cell invasion. In turn, FGFR signalling primes EGF-mediated outputs via EGFR threonine 693 phosphorylation. This reciprocal priming between distinct families of RTKs from recycling endosomes exemplifies a novel signalling integration hub where recycling endosomes orchestrate cellular behaviour. Therefore, targeting reciprocal priming over individual receptors may improve personalized therapies in breast and other cancers.

cell biology↗

bioRxiv2020

Design of Biologically Active Binary Protein 2D Materials

Proteins that assemble into ordered two-dimensional arrays such as S-layers1,2 and designed analogues3-5 have intrigued bioengineers,6,7 but with the exception of a single lattice formed through non-rigid template streptavidin linkers,8 they are constituted from just one protein component. For modulating assembly dynamics and incorporating more complex functionality, materials composed of two components would have considerable advantages.9-12 Here we describe a computational method to generate de-novo binary 2D non-covalent co-assemblies by designing rigid asymmetric interfaces between two distinct protein dihedral building-blocks. The designed array components are soluble at mM concentrations, but when combined at nM concentrations, rapidly assemble into nearly-crystalline micrometer-scale p6m arrays nearly identical to the computational design model in vitro and in cells without the need of a two-dimensional support. Because the material is designed from the ground up, the components can be readily functionalized, and their symmetry reconfigured, enabling formation of ligand arrays with distinguishable surfaces to drive extensive receptor clustering, downstream protein recruitment, and signaling. Using quantitative microscopy we show that arrays assembled on living cells have component stoichiometry and likely structure similar to arrays formed in vitro, suggesting that our material can impose order onto fundamentally disordered substrates like cell membranes. We find further that in sharp contrast to previously characterized cell surface receptor binding assemblies such as antibodies and nanocages, which are rapidly endocytosed, large arrays assembled at the cell surface suppress endocytosis in a tunable manner, with potential therapeutic relevance for extending receptor engagement and immune evasion. Our work paves the way towards synthetic cell biology, where a new generation of multi-protein macroscale materials is designed to modulate cell responses and reshape synthetic and living systems. One Sentence SummaryCo-assembling binary 2D protein crystals enables robust formation of complex large scale ordered biologically active materials

synthetic biology↗

bioRxiv2020

Using Multilayer Heterogeneous Networks to Infer Functions of Phosphorylated Sites

1Mass spectrometry-based quantitative phosphoproteomics has become an essential approach in the study of cellular processes such as signaling. Commonly used methods to analyze phosphoproteomics datasets depend on generic, gene-centric annotations such as Gene Ontology terms which do not account for the function of a protein in a particular phosphorylation state. Analysis of phosphoproteomics data is hampered by a lack of phosphorylated site-specific annotations. We propose a method that combines shotgun phosphoproteomics data, protein-protein interactions, and functional annotations into a heterogeneous multilayer network. Phosphorylation sites are associated to potential functions using a random walk on heterogeneous network (RWHN) algorithm. We validated our approach against a model of the MAPK/ERK pathway and functional annotations from PhosphoSite Plus and were able to associate differentially regulated sites on the same proteins to their previously described specific functions. We further tested the algorithm on three previously published datasets and were able to reproduce their experimentally validated conclusions and to associate phosphorylation sites with known functions based on their regulatory patterns. Our approach provides a refinement of commonly used analysis methods and accurately predicts context-specific functions for sites with similar phosphorylation profiles. For table of contents onlyWe confirm that the eTOC figure contains original material drawn by the authors. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/266072v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@f11983org.highwire.dtl.DTLVardef@c21d48org.highwire.dtl.DTLVardef@1078ecorg.highwire.dtl.DTLVardef@1730d96_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗