SEARCH · Search bioRxiv

Results for “Bioengineering”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14Linked to original sources

bioRxiv2015

Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies.

Engineered RNAs have become integral components of the synthetic biology and bioengineering toolbox for controlling gene expression. We recently expanded this toolbox by creating small transcription activating RNAs (STARs) that act by disrupting the formation of a target transcriptional terminator hairpin placed upstream of a gene. While STARs are a promising addition to the repertoire of RNA regulators, much work remains to be done to optimize the fold activation of these systems. Here we apply rational RNA engineering strategies to improve the fold activation of two STAR regulators. We demonstrate that a combination of promoter strength tuning and multiple RNA stabilization strategies can improve fold activation from 5.4-fold to 13.4-fold for a STAR regulator derived from the pbuE riboswitch terminator. We then validate the generality of our approach and show that these same strategies improve fold activation from 2.1-fold to 14.6-fold for an unrelated STAR regulator. We also establish that the optimizations preserve the orthogonality of these STARs between themselves and a set of antisense RNA transcriptional repressors, enabling these optimized STARs to be used in more sophisticated circuits. These optimization strategies open the door for creating a generation of additional STARs to use in a broad array of biotechnologies.

Synthetic Biology↗

bioRxiv2016

Network structural features affect stability of Calvin Bassham Benson (CBB) pathway in plants

The stability of the Calvin Bassham Benson (CBB) cycle remains an area of active computational research. Our understanding of biology and the prospect for bioengineered plants with higher productivity may both be impacted by a greater understanding of this area. Here we use the ensemble modelling robustness analysis (EMRA) framework to show that the action of the phosphate/G3P antiporter is much more significant for maintenance of stability than a recently proposed G6P shunt. Additionally, we interpret recent results suggesting that overexpression of RuBiSCO does not improve growth rate of plants but overexpression of SBPase does. Our simulations reproduce this result, but only in models which do not include the G6P shunt. Taken together, these results may suggest a situational role for the G6P shunt, possibly in dynamic situations under starvation or other stress conditions.

Systems Biology↗

bioRxiv2015

Agent-based simulation of large tumors in 3-D microenvironments

Multicellular simulations of tumor growth in complex 3-D tissues, where data come from high content in vitro and bioengineered experiments, have gained significant attention by the cancer modeling community in recent years. Agent-based models are often selected for these problems because they can directly model and track cells states and their interactions with the microenvironment. We describe PhysiCell, a specific agent-based model that includes cell motion, cell cycling, and cell volume changes. The model has been performance tested on systems of 105 cells on desktop computers, and is expected to scale to 106 or more cells on single super-computer compute nodes. We plan an open source release of the software in early 2016 at PhysiCell.MathCancer.org

Cancer Biology↗

bioRxiv2016

Blind tests of RNA nearest neighbor energy prediction

The predictive modeling and design of biologically active RNA molecules requires understanding the energetic balance amongst their basic components. Rapid developments in computer simulation promise increasingly accurate recovery of RNAs nearest neighbor (NN) free energy parameters, but these methods have not been tested in predictive trials or on non-standard nucleotides. Here, we present the first such tests through a RECCES-Rosetta (Reweighting of Energy-function Collection with Conformational Ensemble Sampling in Rosetta) framework that rigorously models conformational entropy, predicts previously unmeasured NN parameters, and estimates these values systematic uncertainties. RECCES-Rosetta recovers the ten NN parameters for Watson-Crick stacked base pairs and thirty-two single-nucleotide dangling-end parameters with unprecedented accuracies - root-mean-square deviations (RMSD) of 0.28 kcal/mol and 0.41 kcal/mol, respectively. For set-aside test sets, RECCES-Rosetta gives an RMSD of 0.32 kcal/mol on eight stacked pairs involving G-U wobble pairs and an RMSD of 0.99 kcal/mol on seven stacked pairs involving non-standard isocytidine-isoguanosine pairs. To more rigorously assess RECCES-Rosetta, we carried out four blind predictions for stacked pairs involving 2,6-diaminopurine-U pairs, which achieved 0.64 kcal/mol RMSD accuracy when tested by subsequent experiments. Overall, these results establish that computational methods can now blindly predict energetics of basic RNA motifs, including chemically modified variants, with consistently better than 1 kcal/mol accuracy. Systematic tests indicate that resolving the remaining discrepancies will require energy function improvements beyond simply reweighting component terms, and we propose further blind trials to test such efforts.\n\nSignificanceUnderstanding RNA machines and how their behavior can be modulated by chemical modification is increasingly recognized as an important biological and bioengineering problem, with continuing discoveries of riboswitches, mRNA regulons, CRISPR-guided editing complexes, and RNA enzymes. Computational strategies to understanding RNA energetics are being proposed, but have not yet faced rigorous tests. We describe a modeling strategy called RECCES-Rosetta that models the full ensemble of motions of RNA in single-stranded form and in helices, including non-standard nucleotides such as 2,6-diaminopurine, a variant of adenosine. When compared to experiments, including blind tests, the energetic accuracies of RECCES-Rosetta calculations are at levels close to experimental error, suggesting that computation can now be used to predict and design basic RNA energetics.

Biophysics↗

bioRxiv2016

A Re-examination of the Role of AUXIN RESPONSE FACTOR 8 in Developmental Abnormalities Caused by the P1/HC-Pro Viral Suppressor of RNA Silencing

Plant viral suppressors of RNA silencing induce developmental defects similar to those caused by mutations in genes involved in the microRNA (miRNA) pathway. These abnormalities were originally thought to reflect a pleiotropic impact of silencing suppressors on miRNA control of plant development. However, subsequent work with the P1/HC-Pro potyviral suppressor of silencing showed that global impairment of the miRNA pathway was not responsible for the phenotypical anomalies. More recently, developmental defects caused by a P1/HC-Pro transgene under control of the 35S promoter were attributed to moderate upregulation of AUXIN RESPONSE FACTOR 8 (ARF8), a target of miR167. The key piece of evidence in that work was that the developmental defects in the 35S-pro:P1/HC-Pro transgenic Arabidopsis were greatly alleviated in the F1 progeny of a cross with plants carrying the arf8-6 mutation. Arf8-6 is a SALK line T-DNA insertion mutant, a class of mutations prone to inducing transcriptional silencing of transgenes expressed from the 35S promoter. Here we report a re-investigation of the role of ARF8 in P1/HC-Pro-mediated developmental defects. We characterized the progeny of a cross between our 35S-pro:P1/HC-Pro transgenic Arabidopsis line and the same arf8-6 T-DNA insertion mutant used in the earlier study. The T-DNA mutation had little effect in the F1 generation, but almost all arf8-6/P1/HC-Pro progeny had lost the P1/HC-Pro phenotype in the F2 generation. However, this loss of phenotype was not correlated with the number of functional copies of the ARF8 gene. Instead, it reflected transcriptional silencing of the 35S-pro:P1/HC-Pro transgene, as evidenced by a pronounced decrease in P1/HC-Pro mRNA2accompanied by the appearance of 35S promoter siRNAs. Furthermore, arf8-8, an independent loss-of-function point mutation, had no detectable effects on P1/HC-Pro phenotype in either the F1 or F2 generations. Together these data argue against the reported role of increased ARF8 expression in mediating developmental defects in P1/HC-Pro transgenic plants.\n\nAuthor SummaryRNA silencing is an important antiviral defense in plants that uses small RNA molecules to target the invading RNA. Plant viruses, however, have countered with proteins that suppress RNA silencing, and one of the best-studied plant viral suppressors of silencing is P1/HC-Pro. When the genetic model plant Arabidopsis thaliana is bioengineered to express P1/HC-Pro, the resulting plants display distinct developmental abnormalities. These abnormalities are thought to arise because P1/HC-Pro also interferes with the arm of RNA silencing that uses small RNAs called microRNAs (miRNAs) to regulate expression of the plant's own genes. Earlier work, however, showed that interference with all miRNAs in general could not be responsible for these developmental defects. More recently, it was reported that enhanced expression of a single miRNA-controlled gene, AUXIN RESPONSE FACTOR 8 (ARF8), underlies the developmental defects caused by P1/HC-Pro. However, using the same ARF8 mutation as that report, as well as a second, independent ARF8 loss-of function mutation, we now show that mis-regulation of ARF8 is not responsible for those defects. One or a few key miRNA-controlled factors might, in fact, underlie the developmental defects caused by P1/HC-Pro; however, our results show that ARF8 is not one of the key factors.

Plant Biology↗

bioRxiv2016

How do Research Faculty in the Biosciences Evaluate Paper Authorship Criteria?

Authorship of peer-reviewed journal articles and abstracts has become the primary currency and reward unit in academia. Such a reward is crucial for students and postdocs who are often under-compensated and thus highly value authorship as an incentive. While numerous scientific and publishing organizations have written guidelines for determining author qualifications and author order, there remains much ambiguity when it comes to how these criteria are weighed by research faculty. Here, we sought to provide some initial insight on how faculty view the relative importance of 11 criteria for scientific authorship. We distributed an online survey to 564 biomedical engineering, biology, and bioengineering faculty members at 10 research institutions across the United States. The response rate was approximately 18%, resulting in a final sample of 102 respondents. Results revealed a consensus on some criteria, such as time spent conducting experiments, but there was a lack of agreement regarding the role of funding procurement. This study provides quantitative assessments of how faculty members in the biosciences evaluate authorship criteria. We discuss the implications of these findings for researchers, especially new graduate students, to help navigate the discrepancy between official policies for authorship and the contributions that faculty truly value.

Preprint↗

bioRxiv2016

PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems

Many multicellular systems problems can only be understood by studying how cells move, grow, divide, interact, and die. Tissue-scale dynamics emerge from systems of many interacting cells as they respond to and influence their microenvironment. The ideal \"virtual laboratory\" for such multicellular systems simulates both the biochemical microenvironment (the \"stage\") and many mechanically and biochemically interacting cells (the \"players\" upon the stage).\n\nPhysiCell--physics-based multicellular simulator--is an open source agent-based simulator that provides both the stage and the players for studying many interacting cells in dynamic tissue microenvironments. It builds upon a multi-substrate biotransport solver to link cell phenotype to multiple diffusing substrates and signaling factors. It includes biologically-driven sub-models for cell cycling, apoptosis, necrosis, solid and fluid volume changes, mechanics, and motility \"out of the box.\" The C++ code has minimal dependencies, making it simple to maintain and deploy across platforms. PhysiCell has been parallelized with OpenMP, and its performance scales linearly with the number of cells. Simulations up to 105-106 cells are feasible on quad-core desktop workstations; larger simulations are attainable on single HPC compute nodes.\n\nWe demonstrate PhysiCell by simulating the impact of necrotic core biomechanics, 3-D geometry, and stochasticity on the dynamics of hanging drop tumor spheroids and ductal carcinoma in situ (DCIS) of the breast. We demonstrate stochastic motility, chemical and contact-based interaction of multiple cell types, and the extensibility of PhysiCell with examples in synthetic multicellular systems (a \"cellular cargo delivery\" system, with application to anti-cancer treatments), cancer heterogeneity, and cancer immunology. PhysiCell is a powerful multicellular systems simulator that will be continually improved with new capabilities and performance improvements. It also represents a significant independent code base for replicating results from other simulation platforms. The PhysiCell source code, examples, documentation, and support are available under the BSD license at http://PhysiCell.MathCancer.org and http://PhysiCell.sf.net.\n\nAuthor SummaryThis paper introduces PhysiCell: an open source, agent-based modeling framework for 3-D multicellular simulations. It includes a standard library of sub-models for cell fluid and solid volume changes, cycle progression, apoptosis, necrosis, mechanics, and motility. PhysiCell is directly coupled to a biotransport solver to simulate many diffusing substrates and cell-secreted signals. Each cell can dynamically update its phenotype based on its microenvironmental conditions. Users can customize or replace the included sub-models.\n\nPhysiCell runs on a variety of platforms (Linux, OSX, and Windows) with few software dependencies. Its computational cost scales linearly in the number of cells. It is feasible to simulate 500,000 cells on quad-core desktop workstations, and millions of cells on single HPC compute nodes. We demonstrate PhysiCell by simulating the impact of necrotic core biomechanics, 3-D geometry, and stochasticity on hanging drop tumor spheroids (HDS) and ductal carcinoma in situ (DCIS) of the breast. We demonstrate contact- and chemokine-based interactions among multiple cell types with examples in synthetic multicellular bioengineering, cancer heterogeneity, and cancer immunology.\n\nWe developed PhysiCell to help the scientific community tackle multicellular systems biology problems involving many interacting cells in multi-substrate microenvironments. PhysiCell is also an independent, cross-platform codebase for replicating results from other simulators.

systems biology↗

bioRxiv2017

Synthetic OCP Heterodimers are Photoactive and Recapitulate the Fusion of Two Primitive Carotenoproteins in the Evolution of Cyanobacterial Photoprotection

The Orange Carotenoid Protein (OCP) governs photoprotection in the majority of cyanobacteria. It is structurally and functionally modular, comprised of a C-terminal regulatory domain (CTD), an N-terminal effector domain (NTD) and a ketocarotenoid; the chromophore spans the two domains in the ground state and translocates fully into the NTD upon illumination. Using both the canonical OCP1 and the presumably more primitive OCP2 from Fremyella diplosiphon, we show that an NTD-CTD heterodimer forms when the domains are expressed as separate polypeptides. The carotenoid is required for the heterodimeric association, assembling an orange complex which is stable in the dark. Both OCP1 and OCP2 heterodimers are photoactive, undergoing light-driven heterodimer dissociation, but differ in their ability to reassociate in darkness, setting the stage for bioengineering photoprotection in cyanobacteria as well as for developing new photoswitches for biotechnology. Additionally, we reveal that homodimeric CTD can bind carotenoid in the absence of NTD, and name this truncated variant the C-terminal domain-like Carotenoid Protein (CCP). This finding supports the hypothesis that the OCP evolved from an ancient fusion event between genes for two different carotenoid-binding proteins ancestral to the NTD and CTD. We suggest that the CCP and its homologs constitute a new family of carotenoproteins within the NTF2-like superfamily found across all kingdoms of life.

plant biology↗

bioRxiv2017

Finding analytic stationary solutions to the chemical master equation by gluing state spaces at one or two states recursively

Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture its dynamics. The chemical master equation (CME) is a commonly used stochastic model that describes how the probability distribution of a chemically reacting system varies with time. Knowing analytic solutions to the CME can have benefits, such as expediting simulations of multiscale biochemical reaction networks and aiding the design of distributional responses. However, analytic solutions are rarely known. A recent method of computing analytic stationary solutions relies on gluing simple state spaces together recursively at one or two states. We explore the capabilities of this method and introduce algorithms to derive analytic stationary solutions to the CME. We first formally characterise state spaces that can be constructed by performing single-state gluing of paths, cycles or both sequentially. We then study stochastic biochemical reaction networks that consist of reversible, elementary reactions with two-dimensional state spaces. We also discuss extending the method to infinite state spaces and designing stationary distributions that satisfy user-specified constraints. Finally, we illustrate the aforementioned ideas using examples that include two interconnected transcriptional components and chemical reactions with two-dimensional state spaces.\n\nSubject AreasSystems biology, synthetic biology, biomathematics, bioengineering

systems biology↗

bioRxiv2017

High-Throughput Laboratory Evolution Of Escherichia coli Under Multiple Stress Environments

Bacterial cells have a remarkable capacity to adapt and to evolve to environmental changes. Although many mutations contributing to adaptive evolution have been identified, the relationship between the mutations and the phenotypic changes responsible for fitness gain has yet to be fully elucidated. For a better understanding of phenotype-genotype relationship in evolutionary dynamics, we performed high-throughput laboratory evolution of Escherichia coli under various stress conditions using an automated culture system. One measure of phenotype, transcriptome analysis, revealed that the expression changes which occurred during the evolution were generally similar among the strains evolved in the same stress environment. We also found several genes and gene functions for which mutations were commonly fixed in the strains resistant to the same stress, and whose effects on resistance were verified experimentally. We demonstrated that the integration of transcriptome and genome data enables us to extract the mechanisms for stress resistance.\n\nAuthor summaryUnderstanding the relationship between phenotypic and genetic changes is a fundamental goal in evolutionary biology, which can provide insights into the past and future evolutionary trajectories. Evolution of microorganisms in a laboratory has been the primary approach to clarify the mappings of phenotypic and genotypic changes. Here, we performed high-throughput laboratory evolution with bacteria using an automated culture system, to quantify phenotypic and genotypic changes occurred under various stress conditions. We identified various stress-specific gene expression changes and mutations, and contributions of them to fitness gain were validated. These results demonstrated that the integration of phenotypic and genotypic changes makes it possible to extract the mechanisms for stress resistance evolution, which will contribute to bioengineering applications.

evolutionary biology↗

bioRxiv2017

Silver fluoride as a treatment for the disease dental caries

The current paradigm of treatment for dental caries (tooth decay) in primary teeth is dangerous, fails to reach many children, and suffers high recurrence. Acceptance of the paradigm arises from a misperception that untreated caries in primary teeth is a threat to life. We show a linear relationship between age and deaths in the United States from 1999 through 2015 caused by dental caries, pulpal / periapical abscess, or facial cellulitis. The intercept of 6 years coincides with emergence of the first permanent tooth: it appears that caries in primary teeth is not a threat to life. Thus, treatment goals should be to avoid pain, which is not possible with operative dentistry, as it causes pain. Medical management of caries is a distinct treatment philosophy which employs topical minimally invasive therapies that treat the disease, and is not merely prevention. Silver diamine fluoride (SDF) is a central agent to enable effective non-invasive treatment. The announcement of FDA Breakthrough Therapy designation suggests that SDF will become the first FDA approved drug for treating the disease dental caries. Since our last review, 4 clinical trials have been completed, which inform an update to the application protocol and frequency regimen. Suggestions from these studies are to skip the rinsing step due to demonstration of safety and concern of diminished effectiveness by dilution, and to start patients with an intensive regimen of multiple applications over the first few weeks. Breakthroughs in elucidating the impact of SDF on tooth structure and the plaque microbiome inform potential opportunities for bioengineering and understanding caries arrest, respectively. Dentists have been surprised by preference of this treatment over traditional invasive approaches. Renewed interest in this old material has delivered progress to optimize the judicious use of SDF, and enable a revolution in caries management - particularly for primary teeth.\n\nONE SENTENCE SUMMARYAnesthesia is inappropriate for first-line treatment of early childhood caries now that safe topical treatments such as silver diamine fluoride are available.

pharmacology and toxicology↗

bioRxiv2017

A Synthetic Microbial Operational Amplifier

Synthetic biology has created oscillators, latches, logic gates, logarithmically linear circuits, and load drivers that have electronic analogs in living cells. The ubiquitous operational amplifier, which allows circuits to operate robustly and precisely has not been built with bio-molecular parts. As in electronics, a biological operational-amplifier could greatly improve the predictability of circuits despite noise and variability, a problem that all cellular circuits face. Here, we show how to create a synthetic 3-stage inducer-input operational amplifier with a differential transcription-factor stage, a CRISPR-based push-pull stage, and an enzymatic output stage with just 5 proteins including dCas9. Our Bio-OpAmp expands the toolkit of fundamental circuits available to bioengineers or biologists, and may shed insight into biological systems that require robust and precise molecular homeostasis and regulation.\n\nOne Sentence SummaryA synthetic bio-molecular operational amplifier that can enable robust, precise, and programmable homeostasis and regulation in living cells with just 5 protein parts is described.

synthetic biology↗

bioRxiv2017

Mechanism of genome interrogation: How CRISPR RNA-guided Cas9 proteins locate specific targets on DNA

The ability to precisely edit and modify genome opens endless opportunities to investigate fundamental properties of living systems as well as to advance various medical techniques and bioengineering applications. This possibility is now close to reality due to a recent discovery of the adaptive bacterial immune system, which is based on clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins (Cas) that utilize RNA to find and cut the double-stranded DNA molecules at specific locations. Here we develop a quantitative theoretical approach to analyze the mechanism of target search on DNA by CRISPR RNA-guided Cas9 proteins, which is followed by a selective cleavage of nucleic acids. It is based on a discrete-state stochastic model that takes into account the most relevant physical-chemical processes in the system. Using a method of first-passage processes, a full dynamic description of the target search is presented. It is found that the location of specific sites on DNA by CRISPR Cas9 proteins is governed by binding first to protospacer adjacent motif (PAM) sequences on DNA, which is followed by reversible transitions into DNA interrogation states. In addition, the search dynamics is strongly influenced by the off-target cutting. Our theoretical calculations allows us to explain the experimental observations and to give experimentally testable predictions. Thus, the presented theoretical model clarifies some molecular aspects of the genome interrogation by CRISPR RNA-guided Cas9 proteins.\n\nInsert Received for publication Date and in final form Date.

biophysics↗

bioRxiv2017

Native and engineered clifednamide biosynthesis in multiple Streptomyces spp.

Polycyclic tetramate macrolactam (PTM) natural products are produced by actinomycetes and other bacteria. PTMs are often bioactive, and the simplicity of their biosynthetic clusters make them attractive for bioengineering. Clifednamide-type PTMs from Streptomyces sp. JV178 contain a distinctive ketone group, suggesting the existence of a novel PTM oxidizing enzyme. Here, we report the new cytochrome P450 enzyme (CftA) is required for clifednamide production. Genome mining was used to identify several new clifednamide producers, some having improved clifednamide yields. Using a parallel synthetic biology approach, CftA isozymes were used to engineer the ikarugamycin pathway of Streptomyces sp. NRRL F-2890 to yield clifednamides. Further, we observed that strong CftA expression leads to the production of a new PTM, clifednamide C. We demonstrate the utility of both genome mining and synthetic biology to rapidly increase clifednamide production and identify a PTM tailoring enzyme for rational molecule design.

synthetic biology↗

bioRxiv2020

GAPDH controls extracellular vesicle biogenesis and enhances therapeutic potential of EVs in silencing the Huntingtin gene in mice via siRNA delivery

Extracellular vesicles (EVs) are biological nanoparticles with important roles in intercellular communication and pathophysiology. Their capacity to transfer biomolecules between cells has sparked efforts to bioengineer EVs as drug delivery vehicles. However, a better understanding of EV biogenesis mechanisms and function is required to unleash their considerable therapeutic potential. Here we demonstrate a novel role for GAPDH, a glycolytic enzyme, in EV assembly and secretion, and we exploit these findings to develop a GAPDH-based methodology to load therapeutic siRNAs onto EVs for targeted drug delivery to the brain. In a series of experiments, we observe high levels of GAPDH binding to the outer surface of EVs via a phosphatidylserine binding motif, designated as G58, and discover that the tetrameric nature of GAPDH promotes extensive EV aggregation. Studies in a Drosophila EV biogenesis model demonstrate that GAPDH is absolutely required for normal generation of intraluminal vesicles in endosomal compartments and promotes vesicle clustering both inside and outside the cell. Fusing a GAPDH-derived G58 peptide to dsRNA-binding motifs permits highly efficient loading of RNA-based drugs such as siRNA onto the surface of EVs. Such vesicles efficiently deliver siRNA to target cells in vitro and into the brain of a Huntingtons disease mouse model after systemic injection, resulting in silencing of the huntingtin gene in multiple anatomical regions of the brain and modulation of phenotypic features of disease. Taken together, our study demonstrates a novel role for GAPDH in EV biogenesis, and that the presence of free GAPDH binding sites on EVs can be effectively exploited to substantially enhance the therapeutic potential of EV-mediated drug delivery to the brain.

neuroscience↗

bioRxiv2020

Structured clustering of the glycosphingolipid GM1 is required for membrane curvature induced by cholera toxin

AB5 bacterial toxins and polyomaviruses induce membrane curvature as a mechanism to facilitate their entry into host cells. How membrane bending is accomplished is not yet fully understood but has been linked to the simultaneous binding of the pentameric B-subunit to multiple copies of their glycosphingolipid receptors. Here, we probe the toxin membrane binding and internalization mechanisms by using a combination of super-resolution and polarized localization microscopy. We show that cholera toxin subunit B (CTxB) can induce membrane curvature only when bound to multiple copies of its glycosphingolipid receptor, GM1, and the ceramide structure of GM1 is likely not a determinant of this activity as assessed in model membranes. A mutant CTxB capable of binding only a single GM1 fails to generate curvature either in model membranes or in cells and clustering the mutant CTxB-single-GM1 complexes by antibody cross-linking does not rescue the membrane curvature phenotype. We conclude that both the multiplicity and specific geometry of GM1 binding sites are necessary for the induction of membrane curvature. We expect this to be a general rule of membrane behavior for all AB5 toxins and polyomaviruses that bind glycosphingolipids to invade host cells. SIGNIFICANCE STATEMENTMembrane binding toxins demonstrate both a public health challenge and a bioengineering opportunity due to their efficient internalization into cells. These toxins multivalently bind to naturally occurring lipid receptors at the plasma membrane and initiate endocytosis. This manuscript reports the importance of structured lipid-receptor clustering for the induction of membrane bending. We also observed that the magnitude of membrane curvature was correlated to the stoichiometry of toxin-bound receptors. By identifying how these bacterial proteins initiate membrane curvature, these findings provide mechanistic insights into the early steps of pathogenic endocytosis.

biophysics↗

bioRxiv2020

Mechanical Heterogeneity in the Bone Microenvironment as Characterised by Atomic Force Microscopy

Bones are structurally heterogeneous organs with diverse functions that undergo mechanical stimuli across multiple length scales. Mechanical characterisation of the bone microenvironment is important for understanding how bones function in health and disease. Here we describe the mechanical architecture of cortical bone, the growth plate, metaphysis and marrow in fresh murine bones, probed using atomic force microscopy in physiological buffer. Both elastic and viscoelastic properties are found to be highly heterogeneous with moduli ranging over 3 to 5 orders of magnitude, both within and across regions. All regions include extremely soft areas, with moduli of a few Pascal and viscosities as low as tens Pa*s. Aging impacts the viscoelasticity of the bone marrow strongly but has limited effect on the other regions studied. Our approach provides the opportunity to explore the mechanical properties of complex tissues at the length scale relevant to cellular processes and how these impact on aging and disease. SIGNIFICANCEThe mechanical properties of biological materials at cellular scale are involved in guiding cell fate. However, there is a critical gap in our knowledge of such properties in complex tissues. The physiochemical environment surrounding the cells in in-vitro studies differs significantly from that found in vivo. Existing mechanical characterisation of real tissues are largely limited to properties at larger scales, structurally simple (e.g. epithelial monolayers) or non-intact (e.g. through fixation) tissues. In this paper, we address this critical gap and present the micro-mechanical properties of the relatively intact bone microenvironment. The measured Youngs moduli and viscosity provide a sound guidance in bioengineering designs. The striking heterogeneity at supracellular scale reveals the potential contribution of the mechanical properties in guiding cell behaviour.

biophysics↗

bioRxiv2020

The phylogenetic functional conservation of Drosophila Seven-In-Absentia (SINA) E3 ligase and its two human paralogs, SIAH1 and SIAH2, in Drosophila eye development

Seven-IN-Absentia (SINA) is the most downstream signaling gatekeeper identified thus far in the RAS/EGFR pathway that controls photoreceptor cell fate determination in Drosophila. Underscoring the central importance of SINA is its phylogenetic conservation in metazoans, with over 83% amino acid identities shared between Drosophila SINA and human SINA homologs (SIAHs). SIAH is a major tumor vulnerability in multidrug-resistant and incurable cancer. SIAH inhibition is an effective strategy to shut down the tumor-driving K-RAS/EGFR/HER2 pathway activation that promotes malignant tumor growth and metastatic dissemination. To further delineate the SINA function in the RAS/EGFR pathway, a genetic modifier screen was conducted, and 28 new sina mutant alleles were isolated via ethyl methanesulfonate (EMS) and X-ray mutagenesis. Among them, 26 of the new sina mutants are embryonic, larval, or pupal lethal, and stronger than the five published sina mutants (sina1, sina2, sina3, sina4, and sina5) which are early adult lethal. By sequencing the SINA-coding region of sinaES10, sinaES26, sinaES79, and sinaES473 homozygous mutant animals, we identified three invariable amino acid residues in SINAs RING-domain whose single point mutation ablates SINA function. To demonstrate the functional conservation of this medically important family of RING domain E3 ligases in Drosophila, we established a collection of transgenic lines, expressing either wild type (WT) or proteolysis-deficient (PD) SINA/SIAH inhibitors of Drosophila SINAWT/PD and human SIAH1WT/PD/2WT/PD under tissue-specific GAL4-drivers in Drosophila eye, wing, and salary gland. Our results showed that Drosophila SINA and human SIAH1/2 are functionally conserved. Our bioengineered SINAPD/SIAHPD inhibitors are effective in blocking the RAS-dependent neuronal cell fate determination in Drosophila.

developmental biology↗