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Results for “Biophysics”

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 307 records · Page 17Linked to original sources

bioRxiv2017

A mathematical and computational model of the calcium dynamics in Caenorhabditis elegans ASH sensory neuron

We propose a mathematical and computational model that captures the stimulus-generated Ca2+ transients in the C. elegans ASH sensory neuron. The model is built based on biophysical events and molecular cascades known to unfold as part of neurons Ca2+ homeostasis mechanism, as well as on Ca2+ signaling events. The state of ion channels is described by their probability of being activated or inactivated, and the remaining molecular states are based on biochemically defined kinetic equations with phenomenological adjustments. We estimate the parameters of the model using experimental data of hyperosmotic stimulus-evoked Ca2+ transients detected with a FRET sensor in young and aged worms, unstressed and exposed to oxidative stress. We use a hybrid optimization method composed of a multi-objective genetic algorithm and nonlinear least-squares to estimate the model parameters. We first obtain the model parameters for young unstressed worms. Next, we use these values of the parameters as a starting point to identify the model parameters for stressed and aged worms. We show that the model, in combination with experimental data, corroborates literature results. In addition, we demonstrate that our model can be used to predict ASH response to complex combinations of stimulation pulses. The proposed model includes for the first time the ASH Ca2+ dynamics observed during both \"on\" and \"off\" responses. This mathematical and computational effort is the first to propose a dynamic model of the Ca2+ transients mechanism in C. elegans neurons, based on biochemical pathways of the cells Ca2+ homeostasis machinery.\n\nSignificance StatementC. elegans is widely used as a model system for monitoring neuronal Ca2+ transients. The ASH neuron is the subject of several such studies, primarily due to its key importance as a polymodal nociceptor. However, despite its pivotal role in C. elegans biology, and the special characteristics of its stimulus-evoked Ca2+ transients (e.g., the \"off\" response), no mathematical or computational model has been developed to include special features of ASH Ca2+ dynamics, i.e. the \"off\" response. The model includes for the first time the ASH Ca2+ dynamics observed during both \"on\" and \"off\" responses, and is the first to propose a dynamical model of the C. elegans Ca2+ transients mechanism based on biochemical pathways of the cells Ca2+ homeostasis machinery.\n\nAbbreviations

neuroscience↗

bioRxiv2017

Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory

Natural biochemical systems are ubiquitously organized both in space and time. Engineering the spatial organization of biochemistry has emerged as a key theme of synthetic biology, with numerous technologies promising improved biosynthetic pathway performance. One strategy, however, may produce disparate results for different biosynthetic pathways. We propose a spatially resolved kinetic model to explore this fundamental design choice in systems and synthetic biology. We predict that two example biosynthetic pathways have distinct optimal organization strategies that vary based on pathway-dependent and cell-extrinsic factors. Moreover, we outline this design space in general as a function of kinetic and biophysical properties, as well as culture conditions. Our results suggest that organizing biosynthesis has the potential to substantially improve performance, but that choosing the appropriate strategy is key. The flexible mathematical framework we propose can be adapted to diverse biosynthetic pathways, and lays a foundation to rationally choose organization strategies for biosynthesis.

synthetic biology↗

bioRxiv2017

Neural Interactome: Interactive Simulation of a Neuronal System

Both connectivity and biophysical processes determine the functionality of neuronal networks. We, therefore, develop a real-time framework, called Neural Interactome1, to simultaneously visualize and interact with the structure and dynamics of such networks. Neural Interactome is a cross-platform framework, which combines graph visualization with the simulation of neural dynamics, or experimentally recorded multi neural time series, to allow application of stimuli to neurons to examine network responses. In addition, Neural Interactome supports structural changes, such as disconnection of neurons from the network (ablation feature), as typically done in experiments. Neural dynamics can be explored on a single neuron level (using a zoom feature), back in time (using a review feature) and recorded (using presets feature). We implement the framework using a model of the nervous system of Caenorhabditis elegans (C. elegans) nematode, a model organism for which full connectome and neural dynamics have been resolved. We show that Neural Interactome assists in studying neural response patterns associated with locomotion and other stimuli. In particular, we demonstrate how stimulation and ablation help in identifying neurons that shape particular dynamics. We examine scenarios that were experimentally studied, such as touch response circuit, and explore new scenarios that did not undergo elaborate experimental studies. The development of the Neural Interactome was guided by generic concepts to be applicable to neuronal networks with different neural connectivity and dynamics.\n\nAuthor SummaryEmerging neuroimaging techniques and novel optical interfaces which record and control neural dynamics enable detailed computational connectivity and dynamics models for neurobiological systems. An open question stemming from these advances is how to validate, simulate and apply these models to predict network functionality. Supervised empirical exploration to identify functional stimulations is an elaborate process, and direct computational approach of sequential stimulation is also formidable since produces large amounts of data without clarity on how it can be used to steer toward meaningful functionalities. We therefore develop a platform to inspect network dynamics in real time while preserving structural connectivity properties, displaying the dynamics on a graph, with possibilities to identify functional sub circuits and review the simulated dynamics. The platform allows for real time interactions with the network such as variation of stimuli and performing connectivity changes as neural ablation. We apply the platform to Caenorhabditis elegans nematode nervous system model. We revisit experimentally known scenarios of stimulations and show how our platform helps to detect associated neural dynamic patterns within seconds through few interactions. In addition, we show how the platform could provide novel hypotheses for scenarios that were not yet explored empirically. By implementing the platform with flexibility for changes in connectivity and dynamic models, this work sets forth a generic methodology applicable to various neurobiological systems.

neuroscience↗

bioRxiv2017

Adaptive feature detection from differential processing in parallel retinal pathways

To transmit information efficiently in a changing environment, the retina adapts to visual contrast by adjusting its gain, latency and mean response. Additionally, the temporal frequency selectivity, or bandwidth changes to encode the absolute intensity when the stimulus environment is noisy, and intensity differences when noise is low. We show that the On pathway of On-Off retinal amacrine and ganglion cells is required to change temporal bandwidth but not other adaptive properties. This remarkably specific adaptive mechanism arises from differential effects of contrast on the On and Off pathways. We analyzed a biophysical model fit only to a cell's membrane potential, and verified pharmacologically that it accurately revealed the two pathways. We conclude that changes in bandwidth arise mostly from differences in synaptic threshold in the two pathways, rather than differences in synaptic release dynamics. Different efficient codes are selected by different thresholds in two independently adapting neural pathways.

neuroscience↗

bioRxiv2017

Prediction and interpretation of deleterious coding variants in terms of protein structural stability

The classification of human genetic variants into deleterious and neutral is a challenging issue, whose complexity is rooted in the large variety of biophysical mechanisms that can be responsible for disease conditions. For non-synonymous mutations in structured proteins, one of these is the protein stability change, which can lead to functionality loss. We developed a stability-driven knowledge-based classifier that uses protein structure, artificial neural networks and solvent accessibility-dependent combinations of statistical potentials to predict whether destabilizing or stabilizing mutations are disease-causing. Our predictor yields a balanced accuracy of 71% in cross validation. As expected, it has a very high positive predictive value of 89%: it predicts with high accuracy the subset of mutations that are deleterious because of stability issues, but is by construction unable of classifying variants that are deleterious for other reasons. Its combination with an evolutionary-based predictor increases the balanced accuracy up to 75%, and allowed predicting more than 1/4 of the deleterious variants with 95% positive predictive value. Our method, called SNPMuSiC, can be used with both experimental and structural models and compares favorably with other prediction tools on several independent test sets. It constitutes a step towards interpreting variant effects at the molecular scale.

bioinformatics↗

bioRxiv2017

Voltage-dependent inward currents in smooth muscle cells of skeletal muscle arterioles

Voltage-dependent inward currents responsible for the depolarizing phase of action potentials were characterized in smooth muscle cells of 4th order arterioles in mouse skeletal muscle. Currents through L-type Ca2+ channels were expected to be dominant; however, action potentials were not eliminated in nominally Ca2+-free bathing solution or by addition of L-type Ca2+ channel blocker nifedipine (10 M). Instead, Na+ channel blocker tetrodotoxin (TTX, 1 M) reduced the maximal velocity of the upstroke at low, but not at normal (2 mM), Ca2+ in the bath. The magnitude of TTX-sensitive currents recorded with 140 mM Na+ was about 20 pA/pF. TTX-sensitive currents decreased five-fold when Ca2+ increased from 2 to 10 mM. The currents reduced three-fold in the presence of 10 mM caffeine, but remained unaltered by 1 mM of isobutylmethylxanthine (IBMX). In addition to L-type Ca2+ currents (15 pA/pF in 20 mM Ca2+), we also found Ca2+ currents that are resistant to 10 M nifedipine (5 pA/pF in 20 mM Ca2+). Based on their biophysical properties, these Ca2+ currents are likely to be through voltage-gated T-type Ca2+ channels. Our results suggest that Na+ and at least two types (T- and L-) of Ca2+ voltage-gated channels contribute to depolarization of smooth muscle cells in skeletal muscle arterioles. Voltage-gated Na+ channels appear to be under a tight control by Ca2+ signaling.

physiology↗

bioRxiv2017

Successful aggregation of Tau protein labelled on its native cysteines

The formation of fibrillar tangles of the Tau protein is crucial in the development of Alzheimers disease. Biophysical methods based on labelling of the cysteines of Tau with fluorescence dyes would allow to study fibril formation with an internal eye. However, the two native cysteines of Tau at positions 291 and 322 are located in the repeat domain, which is involved in forming the fibrils. The contribution of both cysteines to this process is unclear. Here we show that blocking natural cysteines using large fluorescent dyes does not interfere with Tau fibrillation so that FRET can be used to follow structural changes during the process. We anticipate that cysteine-labelled Tau enables following structural rearrangements during fibril formation in detail. This may also allow to monitor the effect of drugs, small molecules and proteins on the process.

biochemistry↗

bioRxiv2017

Firing pattern classification and phenotyping in a knowledge base of hippocampal neuron types

Systematically organizing the anatomical, molecular, and physiological properties of cortical neurons is important for understanding their computational functions. Hippocampome.org defines 122 neuron types in the rodent hippocampal formation (dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex) based on their somatic, axonal, and dendritic locations, putative excitatory/inhibitory outputs, molecular marker expression, and biophysical properties such as time constant and input resistance. Here we augment the electrophysiological data of this knowledge base by collecting, quantifying, and analyzing the firing responses to depolarizing current injections for every hippocampal neuron type from available published experiments. We designed and implemented objective protocols to classify firing patterns based on both transient and steady-state activity. Specifically, we identified 5 transients (delay, adapting spiking, rapidly adapting spiking, transient stuttering, and transient slow-wave bursting) and 4 steady states (non-adapting spiking, persistent stuttering, persistent slow-wave bursting, and silence). By characterizing the set of all firing responses reported for hippocampal neurons, this automated classification approach revealed 9 unique families of firing pattern phenotypes while distinguishing potential new neuronal subtypes. Several novel statistical associations also emerged between firing responses and other electrophysiological properties, morphological features, and molecular marker expression. The firing pattern parameters, complete experimental conditions (including solution and stimulus details), digitized spike times, exact reference to the original empirical evidence, and analysis scripts are released open-source through Hippocampome.org for all neuron types, greatly enhancing the existing search and browse capabilities. This information, collated online in human-and machine-accessible form, will help design and interpret both experiments and hippocampal model simulations.\n\nSignificance StatementComprehensive characterization of nerve cells is essential for understanding signal processing in biological neuronal networks. Firing patterns are important identification characteristics of neurons and play crucial roles in information coding in neural systems. Building upon the comprehensive knowledge base Hippocampome.org, we developed and implemented automated protocols to classify all known firing responses exhibited by each neuron type of the rodent hippocampus based on analysis of transient and steady-state activity. This approach identified the most distinguishing elements of every firing phenotype and revealed previously unnoticed statistical associations of firing responses with other electrophysiological, morphological, and molecular properties. The resulting data, freely released online, constitute a powerful resource for designing and interpreting experiments as well as developing and testing hippocampal models.

neuroscience↗

bioRxiv2017

Coherent olfactory bulb gamma oscillations arise from coupling independent columnar oscillators

Spike timing-based representations of sensory information depend on embedded dynamical frameworks within neuronal networks that establish the rules of local computation and interareal communication. Here, we investigated the dynamical properties of olfactory bulb circuitry in mice of both sexes using microelectrode array recordings from slice and in vivo preparations. Neurochemical activation or optogenetic stimulation of sensory afferents evoked persistent gamma oscillations in the local field potential. These oscillations arose from slower, GABA(A) receptor-independent intracolumnar oscillators coupled by GABA(A)-ergic synapses into a faster, broadly coherent network oscillation. Consistent with the theoretical properties of coupled-oscillator networks, the spatial extent of zero-phase coherence was bounded in slices by the reduced density of lateral interactions. The intact in vivo network, however, exhibited long-range lateral interactions that suffice in simulation to enable zero-phase gamma coherence across the olfactory bulb. The timing of action potentials in a subset of principal neurons was phase-constrained with respect to evoked gamma oscillations. Coupled-oscillator dynamics in olfactory bulb thereby enable a common clock, robust to biological heterogeneities, that is capable of supporting gamma-band spike synchronization and phase coding across the ensemble of activated principal neurons. New & NoteworthyOdor stimulation evokes rhythmic gamma oscillations in the field potential of the olfactory bulb, but the dynamical mechanisms governing these oscillations have remained unclear. Establishing these mechanisms is important, as they determine the biophysical capacities of the bulbar circuit to, for example, maintain zero-phase coherence across a spatially extended network, or coordinate the timing of action potentials in principal neurons. These properties in turn constrain and suggest hypotheses of sensory coding.

neuroscience↗

bioRxiv2017

Quantitative methods to investigate the 4D dynamics of heterochromatic repair sites in Drosophila cells

Heterochromatin is mostly composed of long stretches of repeated DNA sequences prone to ectopic recombination during double-strand break (DSB) repair. In Drosophila, safe homologous recombination (HR) repair of heterochromatic DSBs relies on a striking relocalization of repair sites to the nuclear periphery. Central to understanding heterochromatin repair is the ability to investigate the 4D dynamics (movement in space and time) of repair sites. A specific challenge of these studies is preventing phototoxicity and photobleaching effects while imaging the sample over long periods of time, and with sufficient time points and Z-stacks to track repair foci over time. Here we describe an optimized approach for high-resolution live imaging of heterochromatic DSBs in Drosophila cells, with a specific emphasis on the fluorescent markers and imaging setup used to capture the motion of repair foci over long time periods. We detail approaches that minimize photobleaching and phototoxicity with a DeltaVision widefield deconvolution microscope, and image-processing techniques for signal recovery post-imaging using SoftWorX and Imaris software. We present a method to derive mean square displacement (MSD) curves revealing some of the biophysical properties of the motion. Finally, describe a method in R to identify tracts of directed motions in mixed trajectories. These approaches enable a deeper understanding of the mechanisms of heterochromatin dynamics and genome stability in the three-dimensional context of the nucleus, and have broad applicability in the field of nuclear dynamics.

cell biology↗

bioRxiv2017

Regulation of Eag by calcium/calmodulin controls presynaptic excitability in Drosophila

Drosophila ether-a-go-go (eag) is the founding member of a large family of voltage-gated K+ channels, the KCNH family, which includes Kv10, 11 and 12, (Ganetzky et al. 1999). Concurrent binding of calcium/calmodulin (Ca2+/CaM) to N-and C-terminal sites inhibits mammalian EAG1 channels at sub-micromolar Ca2+ concentrations (Schonherr et al. 2000), likely by causing pore constriction (Whicher and MacKinnon 2016). Although the Drosophila EAG channel was believed to be Ca2+-insensitive (Schonherr et al. 2000), both the N-and C-terminal sites are conserved. Here we show that Drosophila EAG is inhibited by high Ca2+ concentrations that are only present at plasma membrane Ca2+ channel microdomains. To test the role of this regulation in vivo, we engineered mutations that block CaM-binding to the major C-terminal site of the endogenous eag locus, disrupting Ca2+-dependent inhibition. eag CaMBD mutants have reduced evoked release from larval motor neuron presynaptic terminals and show decreased Ca2+ influx in stimulated adult projection neuron presynaptic terminals, consistent with an increase in K+ conductance. These results are predicted by a conductance-based multi-compartment model of the presynaptic terminal in which some fraction of EAG is localized to the Ca2+ channel microdomains that control neurotransmitter release. The reduction of release in the larval neuromuscular junction drives a compensatory increase in motor neuron somatic excitability. This misregulation of synaptic and somatic excitability has consequences for systems-level processes and leads to defects in associative memory formation in adults.\n\nNew and NoteworthyRegulation of excitability is critical to tuning the nervous system for complex behaviors. We demonstrate here that the EAG family of voltage-gated K+ channels exhibit conserved gating by Ca2+/CaM. Disruption of this inhibition in Drosophila results in decreased evoked neurotransmitter release due to truncated Ca2+ influx in presynaptic terminals. In adults, disrupted Ca2+ dynamics cripples memory formation. These data demonstrate that the biophysical details of channels have important implications for cell function and behavior.

neuroscience↗

bioRxiv2017

Differential polarization of cortical pyramidal neuron dendrites through weak extracellular fields

The rise of transcranial current stimulation (tCS) techniques have sparked an increasing interest in the effects of weak extracellular electric fields on neural activity. These fields modulate ongoing neural activity through polarization of the neuronal membrane. While the somatic polarization has been investigated experimentally, the frequency-dependent polarization of the dendritic trees in the presence of alternating (AC) fields has received little attention yet. Using a biophysically detailed model with experimentally constrained active conductances, we analyze the subthreshold response of cortical pyramidal cells to weak AC fields, as induced during tCS. We observe a strong frequency resonance around 10-20 Hz in the apical dendrites sensitivity to polarize in response to electric fields but not in the basal dendrites nor the soma. To disentangle the relative roles of the cell morphology and active and passive membrane properties in this resonance, we perform a thorough analysis using simplified models, e.g. a passive pyramidal neuron model, simple passive cables and reconstructed cell model with simplified ion channels. We attribute the origin of the resonance in the apical dendrites to (i) a locally increased sensitivity due to the morphology and to (ii) the high density of h-type channels. Our systematic study provides an improved understanding of the subthreshold response of cortical cells to weak electric fields and, importantly, allows for an improved design of tCS stimuli.

neuroscience↗

bioRxiv2017

AptaBlocks: Accelerating the Design of RNA-based Drug Delivery Systems

Synthetic RNA molecules are increasingly used to alter cellular functions. These successful applications indicate that RNA-based therapeutics might be able to target currently undruggable genes. However, to achieve this promise, an effective method for delivering therapeutic RNAs into specific cells is required. Recently, RNA aptamers emerged as promising delivery agents due to their ability of binding specific cell receptors. Crucially, these aptamers can frequently be internalized into the cells expressing these receptors on their surfaces. This property is leveraged in aptamer based drug delivery systems by combining such receptor-specific aptamers with a therapeutic \"cargo\" such that the aptamer facilitates the internalization of the cargo into the cell. The advancement of this technology however is contingent on an efficient method to produce stable molecular complexes that include specific aptamers and cargoes. A recently proposed experimental procedure for obtaining such complexes relies on conjugating the aptamer and the cargo with complementary RNA strands so that when such modified molecules are incubated together, the complementary RNA strands hybridize to form a double-stranded \"sticky bridge\" connecting the aptamer with its cargo. However, designing appropriate sticky bridge sequences guaranteeing the formation and stability of the complex while simultaneously not interfering with the aptamer or the cargo as well as not causing spurious aggregation of the molecules during incubation has proven highly challenging. To fill this gap, we developed AptaBlocks, a computational method to design sticky bridges to connect RNA-based molecules (blocks). AptaBlocks relies on a biophysically inspired theoretical model capturing the complex objectives of the design and yet is simple enough to allow for efficient parameter estimation. Given this model, the sticky bridge sequence is optimized using a Monte Carlo algorithm based on heat-bath transitions. The effectiveness of the algorithm has been verified computationally and experimentally. AptaBlocks can be used in variety of experimental settings and its preliminary version has already been leveraged to design an aptamer based delivery system for a cytotoxic drug targeting Pancreatic ductal adenocarcinoma cells. It is thus expected that AptaBlocks will play a substantial role in accelerating RNA-based drug delivery design.\n\nAptaBlocks is available at https://github.com/wyjhxq/AptaBlocks.

bioinformatics↗

bioRxiv2017

Molecular basis of hemoglobin adaptation in the high-flying bar-headed goose

During adaptive phenotypic evolution, some selectively fixed mutations may be directly causative and others may be purely compensatory. The relative contribution of these two classes of mutation depends on the form and prevalence of mutational pleiotropy. To investigate the nature of adaptive substitutions and their pleiotropic effects, we used a protein engineering approach to characterize the molecular basis of hemoglobin (Hb) adaptation in the bar-headed goose (Anser indicus), a hypoxia-tolerant species renowned for its trans-Himalayan migratory flights. We synthesized and tested all possible mutational intermediates in the line of descent connecting the wildtype bar-headed goose genotype with the most recent common ancestor of bar-headed goose and its lowland relatives. Site-directed mutagenesis experiments revealed effect-size distributions of causative mutations and biophysical mechanisms underlying changes in function. Trade-offs between alternative functional properties revealed the importance of compensating deleterious pleiotropic effects in the adaptive evolution of protein function.

genomics↗

bioRxiv2017

Investigating on relationship between effective quantum efficiency and irradiance

AbstractModels describing the relationship between effective quantum efficiency of PS II ({Phi}PSII) and irradiance (I) are routinely used to determine how irradiance influences effective quantum efficiency and photosynthetic electron transport rate (ETR). However, with no single model one can accurately describe the relationship between{Phi} PSII and I, and explain the interdependence between{Phi} PSII and biophysical properties of photosynthetic pigments, especially in plants growing under low level irradiances. Basing on the mechanistic model of photosynthetic electron transport rate we have developed the model of the relationship between{Phi} PSII and I. The new model reveals that{Phi} PSII increases with photochemistry (kP) and heat dissipation (kD). Furthermore, the values of key parameters calculated using the new model were compared with the values calculated with two other empirical models. The new model was perfectly fitted to the light-response curves of{Phi} PSII. The key calculated photosynthetic parameters: maximum{Phi} PSII, maximum ETR and their corresponding saturation irradiance were close to the measured values. In addition, our model associates{Phi} PSII with intrinsic features of photosynthetic pigments. We concluded that{Phi} PSII decreased with increasing I due to the decrease in the effective absorption cross-section of photosynthetic pigments molecules.\n\nHighlightA model of the relationship between effective quantum efficiency of PS II ({Phi}PSII) and irradiance (I) has been developed. Using this new model it was found that{Phi} PSII decreased with increasing I due to the decrease in the effective absorption cross-section of photosynthetic pigments molecules.\n\nAbbreviations

plant biology↗

bioRxiv2017

LRX Proteins play a crucial role in pollen grain and pollen tube cell wall development

Leucine-rich repeat extensins (LRXs) are chimeric proteins containing an N-terminal leucine-rich repeat (LRR) and a C-terminal extensin domain. LRXs are involved in cell wall formation in vegetative tissues and required for plant growth. However, the nature of their role in these cellular processes remains to be elucidated. Here, we used a combination of molecular techniques, light microscopy, and transmission electron microscopy to characterize mutants of pollen-expressed LRXs in Arabidopsis thaliana. Mutations in multiple pollen-expressed lrx genes causes severe defects in pollen germination and pollen tube (PT) growth, resulting in a reduced seed set. Physiological experiments demonstrate that manipulating Ca2+ availability partially suppresses the PT growth defects, suggesting that LRX proteins influence Ca2+-related processes. Furthermore, we show that LRX protein localizes to the cell wall, and its LRR-domain (which likely mediates protein-protein interactions) is associated with the plasma membrane. Mechanical analyses by cellular force microscopy and finite element method-based modelling revealed significant changes in the material properties of the cell wall and the fine-tuning of cellular biophysical parameters in the mutants compared to the wild type. The results indicate that LRX proteins might play a role in cell wall-plasma membrane communication, influencing cell wall formation and cellular mechanics.

plant biology↗

bioRxiv2017

The structure of SALM5 suggests a dimeric assembly for the presynaptic RPTP ligand recognition

Synaptic adhesion molecules play a crucial role in the regulation of synapse development and maintenance. Recently several families of leucine rich repeat domain containing neuronal adhesion molecules have been characterized, including netrin G-ligands, LRRTMs, and the SALM family proteins. Most of these are expressed at the excitatory glutamatergic synapses, and dysfunctions of these genes are genetically linked with cognitive disorders, such as autism spectrum disorders and schizophrenia. The SALM family proteins SALM3 and SALM5, similar to SLITRKs, have been shown to bind to the presynaptic receptor protein tyrosine phosphatase (RPTP) family ligands. Here we present the 3 [A] crystal structure of the SALM5 LRR-Ig domain construct, and biophysical studies that verify the crystallographic results. We show that both SALM3 and SALM5 extracellular domains form similar dimeric structures, in which the LRR domains form the dimer interface. Both proteins bind to the RPTP lg-domains with micromolar affinity. SALM3 shows a clear preference for RPTP-ligands with the meB splice insert. This is in accordance with previous results showing that the LRR domain is also required for the ligand binding. Our structural studies and sequence conservation analysis suggests a ligand binding site and mechanism for RPTP binding via the dimeric LRR domain region.

biochemistry↗

bioRxiv2017

Biofilm Lithography: High-resolution cell patterning via optogenetic adhesin expression

Bacterial biofilms represent a promising opportunity for engineering of microbial communities. However our ability to control spatial structure in biofilms remains limited. Here we engineer Escherichia coli with a light-activated transcriptional promoter to optically regulate adhesin gene expression. When illuminated with patterned blue light, long-term viable biofilms with spatial resolution down to 25m can be formed on a variety of substrates and inside enclosed culture chambers without the need for surface pretreatment. A biophysical model suggests the patterning mechanism involves stimulation of transiently surface-adsorbed cells, lending new evidence to a previously proposed role of adhesin expression during natural biofilm maturation. Overall, this tool - termed Biofilm Lithography - has distinct advantages over existing cell-depositing and patterning methods and provides the ability to grow structured biofilms, with applications towards an improved understanding natural biofilm communities, as well as the engineering of living biomaterials and bottom-up approaches to microbial consortia design.

synthetic biology↗