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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 181 records · Page 10Linked to original sources

bioRxiv2017

Chemical-microstructural-nanomechanical variations in the structural units of the cuttlebone of Sepia officinalis

Cuttlebone, the internalized shell found in all members of the cephalopod family Sepiidae, is a sophisticated buoyancy device combining high porosity with considerable strength. Using a complementary suite of characterization tools, we identified significant structural, chemical and mechanical variations across the different structural units of the cuttlebone: the dorsal shield consists of two stiff and hard layers with prismatic mineral organization which encapsulate a more ductile and compliant layer with a lamellar structure, enriched with organic matter. A similar organization is found in the lamellar matrix, which consists of individual chambers separated by septa, and supported by meandering plates ( pillars). Like the dorsal shield, septa contain two layers with lamellar and prismatic organization, respectively, which differ significantly in their mechanical properties: layers with prismatic organization are a factor of three stiffer, and up to a factor of ten harder than those with lamellar organization. The combination of stiff and hard, and compliant and ductile components may serve to reduce the risk of catastrophic failure, and reflect the role of organic matter for the growth process of the cuttlebone. Mechanically weaker units may function as sacrificial structures, ensuring a step-wise failure of the individual chambers in cases of overloading, allowing the animals to retain near-neutral buoyancy even with partially damaged cuttlebones. Our findings have implications for the structure-property-function relationship of cuttlebone, and may help to identify novel bioinspired design strategies for light-weight yet high-strength foams.

bioengineering↗

bioRxiv2017

Genetic-metabolic coupling for targeted metabolic engineering

To produce chemicals, microbes typically employ potent biosynthetic enzymes that interact with native metabolism to affect cell fitness as well as chemical production. However, production optimization largely relies on data collected from wild type strains in the absence of metabolic perturbations, thus limiting their relevance to specific process scenarios. Here, we address this issue by coupling cell fitness to the production of thiamine diphosphate in Escherichia coli using a synthetic RNA biosensor.\n\nWe apply this system to interrogate a library of transposon mutants to elucidate the native gene network influencing both cell fitness and thiamine production. Specifically, we identify uncharacterized effectors of the OxyR-SoxR stress response that limit thiamine biosynthesis via alternative regulation of iron storage and Fe-S-cluster inclusion in enzymes.\n\nOur study represents a new generalizable approach for the reliable high-throughput identification of genetic targets of both known and unknown function that are directly relevant to a specific biosynthetic process.

bioengineering↗

bioRxiv2017

Universal Microfluidic System for Analysis and Control of Cell Dynamics

Dynamical control of the cellular microenvironment is highly desired for quantitative studies of stem cells and immune signaling. Here, we present an automated microfluidic system for high-throughput culture, differentiation and analysis of a wide range of cells in precisely defined dynamic microenvironments recapitulating cellular niches. This system delivers complex, time-varying biochemical signals to 1,500 independently programmable cultures containing either single cells, 2-D populations, or 3-D organoids, and dynamically stimulates adherent or non-adherent cells while tracking and retrieving them for end-point analysis. Using this system, we investigated the signaling landscape of neural stem cell differentiation under combinatorial and dynamic stimulation with growth factors. Experimental and computational analyses identified \"cellular logic rules\" for stem cell differentiation, and demonstrated the importance of signaling sequence and timing in brain development. This universal platform greatly enhances capabilities of microfluidic cell culture, allows dissection of previously hidden aspects of cellular dynamics, and enables accelerated biological discovery.

bioengineering↗

bioRxiv2017

Recapitulating bone development for tissue regeneration through engineered mesenchymal condensations and mechanical cues

Large bone defects cannot heal without intervention and have high complication rates even with the best treatments available. In contrast, bone fractures naturally healing with high success rates by recapitulating the process of bone development through endochondral ossification.1 Endochondral tissue engineering may represent a promising paradigm, but large bone defects are unable to naturally form a callus. We engineered mesenchymal condensations featuring local morphogen presentation (TGF-{beta}1) to mimic the cellular organization and lineage progression of the early limb bud. As mechanical forces are 2,3 critical for proper endochondral ossification during bone morphogenesis2,3 and fracture healing, we hypothesized that mechanical cues would be important for endochondral regeneration.4,5 Here, using fixation plates that modulate ambulatory load transfer through dynamic tuning of axial compliance, we found that in vivo mechanical loading was necessary to restore bone function to large bone defects through endochondral ossification. Endochondral regeneration produced zonal cartilage and primary spongiosa mimetic of the native growth plate. Live human chondrocytes contributed to endochondral regeneration in vivo, while cell devitalization prior to condensation transplantation abrogated bone formation. Mechanical loading induced regeneration comparable to high-dose BMP-2 delivery, but without heterotopic bone formation and with order-of-magnitude greater mechanosensitivity.6-8 In vitro, mechanical loading promoted chondrogenesis, and upregulated pericellular collagen 6 deposition and angiogenic gene expression. Consistently, in vivo mechanical loading regulated cartilage formation and neovascular invasion dependent on load timing. Together, this study represents the first demonstration of the effects of mechanical loading on transplanted cell-mediated bone defect regeneration, and provides a new template for recapitulating developmental programs for tissue engineering.

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bioRxiv2017

The Influence of Aging and Mechanical Stretch in Alveolar Epithelium ER Stress and Inflammation

Ventilator-Induced lung injury (VILI) is a form of acute lung injury that is initiated or exacerbated by mechanical ventilation. The aging lung is more susceptible to lung injury. Harmful mechanical stretch of the alveolar epithelium is a recognized mechanism of VILI, yet little is known about how mechanical stretch affects aged epithelial cells. An activated response known as Endoplasmic Reticulum (ER) Stress occurs at the cellular level, which is increased with aging. The disrupted ER function results in disruption in cellular homeostasis, apoptosis, and inflammation. We hypothesized that age and mechanical stretch increase proinflammatory gene expression that is mediated by ER stress. Type II alveolar epithelial cells (ATII) were harvested from C57Bl6/J mice 8 weeks (young) and 20 months (old) of age. The cells were cyclically mechanically stretched at 15% change in surface area for up to 24 hours. Prior to stretch, groups were administered 4-PBA or vehicle as a control. Mechanical stretch upregulated both ER stress and proinflammatory gene expression in ATIIs. Age-matched and mis-matched monocyte recruitment by ATII conditioned media was quantified. Administration of 4-PBA attenuated both the ER stress and proinflammatory increases from stretch and/or age and significantly reduced monocyte migration to ATII conditioned media. Age increases susceptibility to stretch-induced ER stress and downstream inflammation in a primary ATII epithelial cell model.

bioengineering↗

bioRxiv2017

Sensor location optimization and joint angle prediction in hand postures

1. Sensor selection problem 1. Sensor selection problem Grasping of objects (Mason et al. 2001; Santello et al. 2002) or hand shaping during grasping is of interest in robotics, neuroscience, and biomechanics. In animation industry and biomechanics, tracking body and hand movements are essential. For tracking body movements and hand movements, a sizable number of markers are required. As number of marker increase complexity and cost also increase. Researchers have tried various approaches for selecting a set of minimum no. of markers for accurate reproduction of movements. Data-driven approaches have been proposed for classification of various grasps. Some studies have focussed on prediction of joint angles (Kang et al. 2012; Hoyet et al. 2012; Wheatland et al. 2013). Our objective is to predict joint angles from a reduced set of sensors. For preliminary sorting purpose, we used PCA based sensor ranking which is disc ...

bioengineering↗

bioRxiv2017

Morphology-driven downscaling of Streptomyces lividans to micro-cultivation

Actinobacteria are prolific producers of secondary metabolites and industrially relevant enzymes. Growth of these mycelial microorganisms in small culture volumes is challenging due to their complex morphology. Since morphology and production are typically linked, scaling down culture volumes requires better control over morphogenesis. In larger scale platforms, ranging from shake flasks to bioreactors, the hydrodynamics play an important role in shaping the morphology and determining product formation. Here, we report on the effects of agitation on the mycelial morphology of Streptomyces lividans grown in microtitre plates (MTP). Our work shows that at the proper agitation rates cultures can be scaled down to volumes as small as 100 l while maintaining the same morphology as seen in larger scale platforms. Using image analysis we compared the morphologies of the cultures; when agitated at 1400 rpm the mycelial morphology in microcultures approached that obtained in shake flasks, while product formation was also maintained. Our study shows that the morphology of actinobacteria in microcultures can be controlled in a similar manner as in larger scale cultures by carefully controlling the mixing rate. This could facilitate high-throughput screening and upscaling.

bioengineering↗

bioRxiv2017

Invasion and migration of self-limiting gene drives: a comparative analysis

Recent advances in research on gene drives have produced genetic constructs that could theoretically spread a desired gene (payload) into all populations of a species, with a single release in one place. This attribute has advantages, but also comes with risks and ethical concerns. There has been a call for research on gene drive systems that are spatially and/or temporally self-limiting. Here we use a population genetics model to compare the expected characteristics of three spatially self-limiting gene drive systems: one-locus underdominance, two-locus underdominance, and daisy-chain drives. We find large differences between these gene drives in the minimum release size required for successfully driving a payload into a population. The daisy-chain system is the most efficient, requiring the smallest release, followed by the two-locus underdominance system, and then the one-locus underdominance system. However, when the target population exchanges migrants with a non-target population, the gene drives requiring smaller releases suffer from higher risks of unintended spread. For payloads that incur relatively low fitness costs (up to 30%), a simple daisy-chain drive is practically incapable of remaining localized, even with migration rates as low as 0.5% per generation. The two-locus underdominance system can achieve localized spread under a broader range of migration rates and of payload fitness costs, while the one-locus underdominance system largely remains localized. We also find differences in the extent of population alteration and in the permanence of the alteration achieved by the three gene drives. The two-locus underdominance system does not always spread the payload to fixation, even after successful drive, while the daisy-chain system can, for a small set of parameter values, achieve a temporally-limited spread of the payload. These differences could affect the suitability of each gene drive for specific applications. Note: This manuscript has been accepted for publication in the journal Evolutionary Applications and is pending publication. We suggest that any reference to or quotation of this article should be made with this recognition.

bioengineering↗

bioRxiv2017

Classifying smartphone-based accelerometer data to obtain validated measures of subject activity status, step count, and gait speed

BackgroundThe ubiquitous spread of smartphone technology throughout global societies offers an unprecedented opportunity to ethically obtain long-term, highly accurate measurements of individual physical activity. For example, the smartphone intrinsic 3-D accelerometer can be queried during normal phone operation to save time series of acceleration magnitudes (in each of the component directions) for near-real time or post processing.\n\nObjectiveWe describe simple, straightforward algorithms (based on windowed Fourier analysis) for accelerometer data quality control and behavioral classification.\n\nMethodsTo maximize the clinical utility of our classifications, we focused on differentiating the following conditions: forgotten phone, subject resting, low physical activity, high physical activity. We further differentiated high physical activity into epochs of walking and climbing stairs, and further quantified walking to infer step count and gait speed.\n\nResultsWe validated these algorithms in 75 individuals, in both laboratory (treadmill) and naturalistic settings. Our algorithm performance was quite satisfactory, with accuracies of 92-99% for all behavioral categories, and 87-90% for gait metrics in naturalistic settings.\n\nConclusionsWe conclude that smartphones are valid and accurate platforms for measuring day-to-day physical activity in ambulatory, community dwelling individuals.

bioengineering↗

bioRxiv2017

A dual-mode mobile phone microscope using integrated and ambient light

Mobile phone microscopes are a natural platform for point-of-care imaging, but current solutions require an externally powered illumination source, thereby adding bulk and cost. We present a mobile phone microscope that uses the internal flash or sunlight as the illumination source, thereby reducing complexity whilst maintaining functionality and performance. The microscope is capable of both brightfield and darkfield imaging modes, enabling microscopic visualization of samples ranging from plant to mammalian cells. We describe the microscope design principles, assembly process, and demonstrate its imaging capabilities through the visualization of unlabelled cell nuclei to observing the motility of cattle sperm.

bioengineering↗

bioRxiv2017

Rapid Detection of Norovirus Using Paper-based Microfluidic Device

Noroviruses (NoV) are the leading cause of outbreak of acute gastroenteritis worldwide. A substantial effort has been made in the development of analytical devices for rapid and sensitive food safety monitoring via the detection of foodborne bacteria, viruses and parasites. Conventional analytical approaches for noroviruses suffer from some critical weaknesses: labor-intensive, time-consuming, and relatively low sensitivity. In this study, we developed a rapid and highly sensitive biosensor towards point-of-care device for noroviruses based on 6-carboxyfluorescein (6-FAM) labeled aptamer and nanomaterials, multi-walled carbon nanotubes (MWCNTs) and graphene oxide (GO). In an assay, the fluorescence of 6-FAM labeled aptamer was quenched by MWCNTs or GO via fluorescence resonance energy transfer (FRET). In the presence of norovirus, the fluorescence would be recovered due to the release of the 6-FAM labeled aptamer from MWCNTs or GO. An easy-to-make paper-based microfluidic platform made by nitrocellulose membrane was used to conduct the assay. The quantitative detection of norovirus virus-like particles (NoV VLPs) was successfully performed. A linear range of 0-12.9 g/mL with a detection limit of 40 pM and 30 pM was achieved for the MWCNTs and GO based paper sensors, respectively. The results suggested the developed paper-based microfluidic device is simple, cost-effective and holds the potential of rapid in situ visual determination for noroviruses with remarkable sensitivity and specificity, which provides a new way for early identification of NoV and thereby an early intervention for preventing the spread of an outbreak.

bioengineering↗

bioRxiv2017

Self-assembled Star-shaped Chiroplasmonic Gold Nanoparticles for Ultrasensitive Chiro-immunosensor of Viruses

Near field optics and optical tunneling light-matter interaction in the superstructure of chiral nanostructures and semiconductor quantum dots exhibit strong optical rotation activity that may open a new window for chiral-based bioanalytes detection. Herein we report an ultrasensitive, chiro-immunosensor using superstructure of chiral gold nanohybrids (CAu NPs) and quantum dots (QDs). Self-assembling techniques were employed to create asymmetric plasmonic chiral nanostructures for extending the spectral range of circular dichroism (CD) response for obtaining superior plasmonic resonant coupling with the QDs excitonic state; this may help to achieve lower the limit of detection (LOD) values. As a result, the designed probe exhibited avian influenza A (H5N1) viral concentration at picomolar level, a significant improvement in sensitivity in comparison to a non-assembled CAu NPs based chiroassay. The practicability of the proposed sensing system was successfully demonstrated on several virus cultures including, avian influenza A (H4N6) virus, fowl adenovirus and coronavirus in blood samples. The results of our study highlights that exciton-plasmon interaction changes chirality and the self-assembled nanostructures are an efficient strategy for enhancing the sensitivity of plasmonic nanosensors.

bioengineering↗

bioRxiv2017

Paper based microfluidic aptasensor for food safety

Food analysis is requiring rapid, accurate, sensitive and cost-effective methods to monitor and guarantee the safety and quality to fulfill the strict food legislation and consumer demands. In our study, a nano-materials enhanced multipurpose paper based microfluidic aptasensor was demonstrated as a sensing tool for accurate detection of food allergens and food toxins. Graphene oxide (GO) and specific aptamer-functionalized quantum dots (QDs) were employed as probes, the fluorescence quenching and recovering of the QDs caused by the interaction among GO, aptamer-functionalized QDs and the target protein were investigated to quantitatively analyze the target concentration. The homogenous assay was performed on the paper based microfluidic chip, which significantly decreased the sample and reagent consumptions and reduced the assay time. Egg white lysozyme, {beta}-conglutin lupine and food toxins, okadaic acid and brevetoxin standard solutions and spiked food samples were successfully assayed by the presented aptasensor. Dual-target assay was completed within 5 min, and superior sensitivities were achieved when testing the samples with commercial ELISA kits side by side.

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bioRxiv2017

Chitozyme: First Peroxidase-like Activity of Chitosan for Multiplexed Visual Detection of H2O2, Glucose and Lactate on Paper-based Device

Visual read-out diagnostics tools are promising candidates for field applicable medical devices. Current colorimetric biosensors require introduction of natural enzymes or nanozymes, which has some serious drawbacks for practical applications. Chitosan, a natural polymer, provides safe and efficient compound in medical and pharmaceutical technology. Herein, we report on a simple, cost-efficient, field-portable, environmental friendly and ultra-sensitive multiplex detection platform based on peroxidase-like activity of chitosan in the presence of 3,3,5,5-Tetramethylbenzidine (TMBZ) and H2O2. This straight forward signal amplification strategy was successfully applied to detect H2O2, glucose and lactate with the limit of detection (LOD) of 2.64 pM, 0.104 M and 2.8 nM respectively, represents the lowest LOD of H2O2, glucose and lactate with visual read-out. The chitosan-based assay performance was also retained in complex biological media for glucose and lactate detection. Furthermore, the proposed assay was successfully demonstrated as a paper-based colorimetric biosensor. Most importantly, the simplicity, biocompatibility and sensitivity of the proposed assay will open new doors for instrument free naked eye visual detection of H2O2, glucose and lactate detection.

bioengineering↗

bioRxiv2017

Comparing Caenorhabditis elegans gentle and harsh touch response behavior using a multiplexed hydraulic microfluidic device

The roundworm Caenorhabditis elegans is an important model system for understanding the genetics and physiology of touch. Classical assays for C. elegans touch, which involve manually touching the animal with a probe and observing its response, are limited by their low throughput and qualitative nature. We developed a microfluidic device in which several dozen animals are subject to spatially localized mechanical stimuli with variable amplitude. The device contains 64 sinusoidal channels through which worms crawl, and hydraulic valves that deliver touch stimuli to the worms. We used this assay to characterize the behavioral responses to gentle touch stimuli and the less well studied harsh (nociceptive) touch stimuli. First, we measured the relative response thresholds of gentle and harsh touch. Next, we quantified differences in the receptive fields between wild type worms and a mutant with non-functioning posterior touch receptor neurons. We showed that under gentle touch the receptive field of the anterior touch receptor neurons extends into the posterior half of the body. Finally, we found that the behavioral response to gentle touch does not depend on the locomotion of the animal immediately prior to the stimulus, but does depend on the location of the previous touch. Responses to harsh touch, on the other hand, did not depend on either previous velocity or stimulus location. Differences in gentle and harsh touch response characteristics may reflect the different innervation of the respective mechanosensory cells. Our assay will facilitate studies of mechanosensation, sensory adaptation, and nociception.

bioengineering↗

bioRxiv2017

Platform for Closed Loop Neuromodulation Based on Dual Mode Biosignals

Closed loop neuromodulation, where the stimulation is controlled autonomously based on physiological events, has been more effective than open loop techniques. In the few existing closed loop implementations which have a feedback, indirect non-neurophysiological biomarkers have been typically used (e.g. heart rate, stomach distension). Although these biomarkers enable automatic initiation of neural stimulation, they do not enable intelligent control of stimulation dosage. In this paper, we present a novel closed loop neuromodulation platform based on a dual signal mode that is detecting electrical and chemical signatures of neural activity. We demonstrated it on a case of vagus nerve stimulation (VNS). Vagal chemical (pH) signal is detected and used for initiatisng VNS and vagal compound action potential (CAP) signals are used to determine the stimulation dosage and pattern. Although we used the paradigm of appetite control and neurometabolic therapies, the platform developed here can be utilised for prototyping closed loop neuromodulation systems before adapting the final System-on-Chip (SoC) design.

bioengineering↗

bioRxiv2017

Three-dimensional single cell patterning for mid- to high-throughput studies of tumor cell and extracellular matrix heterogeneity

Cancer heterogeneity includes cancer cell genetic heterogeneity and heterogeneity in the tumor microenvironment (TME)--both stromal cells and extracellular matrix (ECM). Determining which combinations of the vast array of possibly interacting heterogeneities drive tumor progression presents a major multi-disciplinary challenge in cancer research. To make effective treatment decisions this challenge must be addressed. The practical challenge is assessing cellular heterogeneity in a statistically powerful way with respect to targeted TME characteristics. Here we present a simple, but extensible, and low-cost method for conducting mid- to high-throughput and long-term studies of heterogeneous cell responses to various biomechanical stimuli in 3D models mimicking the biomechanical properties of the ECM. Using a platform we term \"the drop-patterning chip\" thousands of cells are simultaneously transferred from microwells and fully embedded, only using the force of gravity, in precise patterns in 3D. This method allows for throughputs approaching flow-through methods, which lack phenotypic information on cell-matrix interactions, and does not rely on expensive or harsh patterning forces, which often times also result in a proximal stiff surface.

bioengineering↗

bioRxiv2017

Tissue Folding by Mechanical Compaction of the Mesenchyme

Many tissues fold during development into complex shapes. Engineering this process in vitro would represent an important advance for tissue engineering. We use embryonic tissue explants, finite element modeling, and 3D cell patterning techniques to show that a mechanical compaction of the ECM during mesenchymal condensation can drive tissue folding along programmed trajectories. The process requires cell contractility, generates strains at nearby tissue interfaces, and causes specific patterns of collagen alignment around and between condensates. Aligned collagen fibers support elevated tensions that promote the folding of interfaces along paths that can be predicted by finite element modeling. We demonstrate the robustness and versatility of this strategy for sculpting tissue interfaces by directing the morphogenesis of a variety of folded tissue forms from engineered patterns of mesenchymal condensates. These studies provide insight into the active mechanical properties of the embryonic mesenchyme and establish entirely new strategies for more robustly directing tissue morphogenesis ex vivo, without genetic engineering.

bioengineering↗