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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 487 records · Page 27Linked to original sources

bioRxiv2018

High-throughput retrieval of physical DNA for NGS-identifiable clones in phage display library

In antibody discovery, in-depth analysis of an antibody library and high-throughput retrieval of clones in the library are crucial to identifying and exploiting rare clones with different properties. However, existing methods have several technical limitations such as low process throughput from laborious cloning process and waste of the phenotypic screening capacity from unnecessary repetitive tests on the dominant clones. To overcome the limitations, we developed a new high-throughput platform for the identification and retrieval of clones in the library, TrueRepertoire. TrueRepertoire provides highly accurate sequences of the clones with linkage information between heavy and light chains of the antibody fragment. Additionally, the physical DNA of clones can be retrieved in high throughput based on the sequence information. We validated the high accuracy of the sequences and demonstrated that there is no platform-specific bias. Moreover, the applicability of TrueRepertoire was demonstrated by a phage-displayed single-chain variable fragment (scFv) library targeting human hepatocyte growth factor (hHGF) protein.

bioengineering↗

bioRxiv2018

A generic widefield topographical and chemical photopatterning method for hydrogels.

3D cell culture aims at reconciliating the simplicity of in vitro models with the human like properties encountered in vivo. Soft permeable hydrogels have emerged as user-friendly materials to grow cells in more physiological conditions. With the intent on turning these homogeneous substrates into biomimetic templates, we introduce a generic solution compatible with the most biologically relevant and often frail materials. Here we take control of the chemical environment driving generic radical reactions to craft common gels with patterned light. In a simple microreactor, we harness the well-known inhibition of radicals by oxygen to enable topographical photopolymerization. Strikingly, by sustaining an oxygen rich environment, we can also induce hydrogel photo-scission which turns out to be a powerful and generic subtractive manufacturing method. We finally introduce a flexible patterned functionalization protocol based on available photo-linkers. Using these common tools on the most popular hydrogels, we tailored soft templates where cells grow or self-organize into standardized structures. The platform we describe has the potential to set a standard in future 3D cell culture experiments.

bioengineering↗

bioRxiv2018

Analysis and Engineering of Substrate Shuttling by the Acyl Carrier Protein (ACP) in Fatty Acid Synthases (FASs)

In the large enzyme complexes of natural biosynthetic pathways, molecules are assembled like in a factory. Carrier domains shuttle substrates and intermediates as covalently attached cargo within the enzyme complex between active sites. The physical confinement of the reaction increases reaction rates and hinders pathway branching. Alternating interactions of substrate-loaded carrier domains with different catalytic domains modulate the chemical environment. In this study, we aim at assessing the impact of domain-domain interactions (DDIs) on the reaction progress of a multienzyme type I fatty acid synthase (FAS) in quantitative terms. We modulate DDIs by single interface mutations, and read out the impact on substrate shuttling by recording fatty acid (FA) chain length product spectra and FAS activities. Our data show that even single interface point mutations can severely affect FA synthesis. With molecular dynamics simulations and modeling, we relate the mutation effects to specific alterations in the molecular interaction networks and domain-domain binding energetics. Some of the presented mutations induce the synthesis of short-chain FAs. These compounds are important commodity products and potent precursors for microbial biofuel production.

bioengineering↗

bioRxiv2018

A comprehensive suite of measures to quantify cell shape and actin organization

A number of recent studies have shown that cell shape and cytoskeletal texture can be used as sensitive readouts of the physiological state of the cell. However, utilization of this information requires the development of quantitative measures that can describe relevant aspects of cell shape. In this paper we develop a toolbox, TISMorph, to calculate set of quantitative measures to address this need. Some of the measures introduced here are used previously and others are new and have desirable properties for shape and texture quantification of cells. These measures, broadly classifiable into the categories of textural, spreading and irregularity measures, are tested by using them to discriminate between osteosarcoma cell lines treated with different cytoskeletal drugs. We find that even though specific classification tasks often rely on a few measures, these are not the same between all classification tasks, thus requiring the use of the entire suite of measures for classification and discrimination. We provide detailed descriptions of the measures, well as TISMorph package to implement them. Image based quantitative analysis has the potential to become a new field of biological data (\"image-omics\"), providing quantitative insight into cellular processes.

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bioRxiv2018

Information theoretic analysis of hyperspectralimaging systems with applications to fluorescencemicroscopy

We present a general stochastic model for hyperspectral imaging data and derive analytical expressions for the Fisher information matrix for the underlying spectral unmixing problem. We investigate the linear mixing model as a special case and define a linear unmixing performance bound by using the Cramer-Rao inequality. As an application, we consider fluorescence imaging and show how the performance bound provides a spectral resolution limit that predicts how accurately a pair of spectrally similar fluorescent labels can be spectrally unmixed. We also report a novel result that shows how the spectral resolution limit can be overcome by exploiting the phenomenon of anti-Stokes shift fluorescence. In addition, we investigate how photon statistics, channel addition and channel splitting affect the performance bound. Finally by using the performance bound as a benchmark, we compare the performance of the least squares and the maximum likelihood estimators for spectral unmixing. For the imaging conditions tested here, our analysis shows that both estimators are unbiased and that the standard deviation of the maximum likelihood estimator is consistently closer to the performance bound than that of the least squares estimator. The results presented here are based on broad assumptions regarding the underlying data model and are applicable to hyperspectral data acquired with point detectors, sCMOS, CCD and EMCCD imaging detectors.\n\nEDICS: ELI-COL, COI-MCI.

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bioRxiv2018

Microfluidic study of effects of flow velocity and nutrient concentration on biofilm accumulation and adhesive strength in microchannels

AbstractBiofilm accumulation in the porous media can cause plugging and change many physical properties of porous media. Up to now, applications of desired biofilm growth and its subsequent bioplugging have been attempted for various practices. A deeper understanding of the relative influences of hydrodynamic conditions including flow velocity and nutrient concentration, on biofilm growth and detachment is necessary to plan and analyze bioplugging experiments and field trials. The experimental results by means of microscopic imaging over a T-shape microchannel show that flow velocity and nutrient concentrations can have significant impacts on biofilm accumulation and adhesive strength in both flowing and stagnant microchannels. Increase in fluid velocity could facilitate biofilm growth, but that above a velocity threshold, biofilm detachment and inhibition of biofilm formation due to high shear stress were observed. High nutrient concentration prompts the biofilm growth, but was accompanied by a relatively weak adhesive strength. This research provides an overview of biofilm development in a hydrodynamic environment for better predicting and modelling the bioplugging associated with porous system in petroleum industry, hydrogeology, and water purification.\n\nIMPORTANCEIn the recent decade, the use of bacteria has become more and more important in many applications. Bioplugging caused by bacteria growth in porous media has been explored as a viable technique for some applications, such as bioremediation, water purification and microbial enhanced oil recovery (MEOR). In order to control biofilms/biomasses selectively/directionally plugging in desirable places, the role of hydrodynamic conditions on biofilm growth and detachment is essential to investigate. Herein, a T-shape microchannel was prepared to study effects of flow velocity and nutrient concentration on biofilm accumulation and adhesive strength at pore scale. Our results suggest that flow velocity and nutrient concentration could control biofilm accumulation in microchannels. The finding helps explain and predict the engineering bioplugging in porous media, especially for the selective plugging strategy of a MEOR field trial.

bioengineering↗

bioRxiv2018

Balance of Mechanical Forces Drives Endothelial Gap Formation and May Facilitate Cancer and Immune-Cell Extravasation

The formation of gaps in the endothelium is a crucial process underlying both cancer and immune cell extravasation, contributing to the functioning of the immune system during infection, the unfavorable development of chronic inflammation and tumor metastasis. Here, we present a stochastic-mechanical multiscale model of an endothelial cell monolayer and show that the dynamic nature of the endothelium leads to spontaneous gap formation, even without intervention from the transmigrating cells. These gaps preferentially appear at the vertices between three endothelial cells, as opposed to the border between two cells. We quantify the frequency and lifetime of these gaps, and validate our predictions experimentally. Interestingly, we find experimentally that cancer cells also preferentially extravasate at vertices, even when they first arrest on borders. This suggests that extravasating cells, rather than initially signaling to the endothelium, might exploit the autonomously forming gaps in the endothelium to initiate transmigration.

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bioRxiv2018

Cardiac myocyte microtissue aggregates broadcast local field potentials

Muscle tissue has been exploited as a living biopotential amplifier to facilitate transduction of peripheral nerve signals into prosthetic control in patients with limb amputation. Here we sought to address the question of whether microscopically small volumes of muscle tissue could effectively broadcast field potentials to electrodes not immediately in contact with that tissue. Cardiac myocytes were grown as three-dimensional aggregates containing 105 cells comprising a volume of approximately 0.065 mm3 (~500 m in diameter) atop multi-electrode arrays. In addition to the expected spontaneous contraction potentials detected using electrodes in direct contact with the myocytes, potentials could also be detected on distant electrodes not contacting the aggregates. Specifically, while both dissociated and aggregated cardiac myocyte cultures generated spontaneous contractions that could easily be recorded from underlying multi-electrode arrays, only aggregated myocyte cultures generated signals detectable several millimeters away by the electrode grid floating in media. This confirmed the ability of micro-volumes of aggregated muscle tissue to broadcast readily detectible signals. The amplitude of the potentials generated by the aggregates decreased exponentially with distance. The aggregates were sensitive to pharmacologic modification with isoproterenol increasing contraction rate. Simultaneous recordings with electrodes in physical contact to the aggregate and with electrodes several millimeters away revealed that the aggregates function as amplifiers and low-pass filters. This study lays the groundwork for forging myocyte aggregates as \"living amplifiers\" for long-term neural recording in brain-computer interfaces to treat neurological disease and injury.

bioengineering↗

bioRxiv2018

Towards an autologous iPSC-derived patient-on-a-chip

Microphysiological systems are fundamental for progressing towards a global paradigm shift in drug development through the generation of patient-on-a-chip models. An increasing number of single- and multi-organ systems have been adopted by the pharmaceutical and cosmetic industries for predictive substance testing. These models run on heterogeneous tissues and cell types from different donors. However, a patient is an individual. Therefore, patient-on-a-chip systems need to be built from tissues from one autologous source. Individual on-chip organ differentiation from a single induced pluripotent stem cell source could provide a solution to this challenge.\n\nWe designed a four-organ chip based on human physiology. It enables the interconnection of miniaturized human intestine, liver, brain and kidney equivalents. All four organ models were predifferentiated from induced pluripotent stem cells from the same healthy donor and integrated into the microphysiological system. The cross talk led to further differentiation over a 14-day cultivation period under pulsatile blood flow conditions in one common medium deprived of growth factors. This model platform will pave the way for disease induction and subsequent drug testing.

bioengineering↗

bioRxiv2018

PABA Release from Chitosan-PCL with Induced Electric Current

Controlled drug delivery systems such as the stimulation-based biomaterial scaffolds for sequestration and release of drugs offer safety and regulated therapeutic approach. In this study, the drug: para-aminobenzoic acid (PABA) was absorbed into a crosslinked chitosan and poly(caprolactone) (PCL) hydrogel and its release kinetics quantified under different conditions. It was experimentally-observed that the higher the pH (or the more basic the pH), the slower the PABA saturation release trended over time. At the acidic environment of pH 4, PABA was released the fastest, and enhanced by the degradation of chitosan-PCL gel. When a constant electric current of 0.6 mA sa applied, PABA release was induced at pH 10. However, at pH 7, PABA was stably-bound to the chitosan-PCL matrix, with or without the external current. The selective sequestration of PABA at basic pH and its stimulated release via electric current application can be further explored for clinical translatability.

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bioRxiv2018

COMPASS: An Open-Source, General-Purpose Software Toolkit for Computational Psychiatry

Mathematical modeling of behavior during psychophysical tasks, referred to as \"computational psychiatry\", could greatly improve our understanding of mental disorders. One barrier to broader adoption of computational methods is that they often require advanced programming skills. We developed the Computational Psychiatry Adaptive State-Space (COMPASS) toolbox, an open-source MATLAB-based software package. After specifying a few parameters in a small set of user-friendly functions, COMPASS allows the user to efficiently fit of a wide range of computational behavioral models. The model output can be analyzed as an experimental outcome or used as a regressor for neural data, and can be tested using goodness-of-fit methods. Here, we demonstrate that COMPASS can replicate two computational behavior analyses from different groups. COMPASS replicates and, in one case, slightly improves on the original modeling results. This flexible, general-purpose toolkit should accelerate the use of computational modeling in psychiatric neuroscience.

bioengineering↗

bioRxiv2018

In Vitro Assay for the Detection of Network Connectivity in Embryonic Stem Cell-Derived Cultures

Stem cell transplantation holds great promise as a repair strategy following spinal cord injury. Embryonic stem cell (ESC) transplantation therapies have elicited encouraging though limited improvement in motor and sensory function with the use of heterogeneous mixtures of spinal cord neural progenitors and ESCs. Recently, transgenic lines of ESCs have been developed to allow for purification of specific candidate populations prior to transplantation, but the functional network connectivity of these populations and its relationship to recovery is difficult to examine with current technological limitations. In this study, we combine an ESC differentiation protocol, multi-electrode arrays (MEAs), and previously developed neuronal connectivity detection algorithms to develop an in vitro high-throughput assay of network connectivity in ESC-derived populations of neurons. Neuronal aggregation results in more consistent detection of individual neuronal activity than dissociated cultures. Both aggregated and dissociated culture types exhibited synchronized bursting behaviors at days 17 and 18 on MEAs, and thousands of statistically significance functional connections were detected in both culture types. Aggregate cultures, however, demonstrate a tight linear relationship between the inter-neuron distance of neuronal pairs and the time delay of the neuronal pair functional connections, whereas dissociated cultures do not. These results suggest that ESC-derived aggregated cultures may reflect some of the spatiotemporal connectivity characteristics of in vivo tissue and prove to be useful models of investigating potentially therapeutic populations of ESC-derived neurons in vitro.\n\nNOVELTY AND SIGNIFICANCEPrevious investigations of stem cell-derived network connectivity on multi-electrode arrays (MEAs) have been limited to characterizations of bursting activity or broad averages of overall temporal network correlations, both of which overlook neuronal level interactions. The use of spike-sorting and short-time cross-correlation histograms along with statistical techniques developed specifically for MEAs allows for the characterization of functional connections between individual stem cell-derived neurons. This high-throughput connectivity assay will open doors for future examinations of the differences in functional network formation between various candidate stem cell-derived populations for spinal cord injury transplantation therapies--a critical inquiry into their therapeutic viability.

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bioRxiv2018

Mobility in Osteogenesis Imperfecta: A Multicenter North American Study

BackgroundOsteogenesis imperfecta (OI) is a genetic connective tissue disorder characterized by increased bone fragility and recurrent fractures. The phenotypic severity of OI has a significant influence on the ability to walk but little is known about the ambulatory characteristics, strength, or functional abilities in individuals with OI, especially in the more severe forms. To advance clinical research in OI, the Linked Clinical Research Centers, network of clinical centers in North America with significant experience in treating patients with OI, was established in 2009. The purpose of this work was to characterize mobility in OI using standard clinical assessment tools. and determine if any patient characteristics could be used to predict mobility outcomes.\n\nMethodsData were collected at five clinical sites and included age, gender, ethnicity, height, weight, use of assistive device, and bisphosphonate use and mobility metrics (age at first walk, Gillette Functional Assessment Questionnaire, Functional Mobility Scale, and distance walked in the 6 minute walk test). Linear mixed models were developed to explore the relationships between subject demographics and mobility metrics.\n\nResultsThe study identified 491 individuals age 3 and older. In general, the results showed minor limitations in the type I group while the more severe types showed more significant limitations in all mobility metrics analyzed. Height and weight were shown to be the most significant predictors of mobility metrics. Relationships with mobility and bisphosphonates varied with OI type and whether oral or IV was used.\n\nConclusionThis paper is the most comprehensive report of mobility in individuals with OI to date. These results are vital to understanding the mobility limitations of specific types of OI and beneficial when developing rehabilitation protocols for this population. It is important for physicians, patients, and caregivers to gain insight into severity and classification of the disease and the influence of disease-related characteristics on the prognosis for mobility.

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bioRxiv2018

Sagittal Subtalar and Talocrural Joint Assessment Between Barefoot and Shod Walking: A Fluoroscopic Study

INTRODUCTION INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION REFERENCES Despite the fact that shoes are routinely worn during typical daily activities [1, 2], intra-foot kinematic models are usually developed and reported in the barefoot condition [3-5]. Understanding shod foot kinematics requires the description of foot/bone position inside footwear. This description has proven challenging using standard stereophotogrammetry techniques. Most external marker based studies in the current literature that report on shod foot mechanics use sandals [6-9], remove shoe material to expose the underlying anatomic area for marker placement [6, 10, 11], or place mark ...

bioengineering↗

bioRxiv2018

Identifying Gait Phases from Joint Kinematics during Walking with Switched Linear Dynamical Systems

Human-robot interaction (HRI) for gait rehabilitation could benefit from data-driven, subject-specific gait models that account for gait phases and gait dynamics. Here we address the current limitation in gait models driven by averaged kinematic data, which do not model interlimb gait dynamics and have not been shown to precisely identify gait events. We used Switched Linear Dynamical Systems (SLDS) to model joint angle kinematic data from healthy individuals walking on a treadmill during normal gait and during gait perturbed by electrical muscle stimulation. We compared model-inferred gait phases to gait phases measured independently via a force plate. We found that SLDS models accounted for over 88% of the variation in each joint angle and labeled the joint kinematics with the correct gait phase with 84% precision on average. The transitions between hidden states matched measured gait events, with a median absolute difference of 25ms. To our knowledge, this is the first time that SLDS inferred gait phases have been validated by an external measure of gait, instead of against pre-defined gait phase durations. SLDS provide individual-specific representations of gait that incorporate both gait phases and gait dynamics. SLDS may be useful for developing control policies for HRI aimed at improving gait by allowing for changes in control to be precisely timed to different gait phases.

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bioRxiv2018

Mechanical Behavior Of Axonal Microtubules; The Effect Of Fluid On The Rupture Of Axonal Microtubules

Axonal microtubules are dynamically instable bundles in the interior part of the axon. The dynamics of these bundles are of vital importance in the behavior of axon such as their degeneration. Each axon typically contains 10~100 microtubule bundles with average length of 4m. These bundles are coated with cytoplasm and are cross linked with random number of tau proteins. In some circumstances such as acceleration or deceleration of head in space or during the strike, they are placed in tension which may cause rupture of these bundles or disconnection of tau protein cross links. Mechanical behavior and rupture modality of microtubule bundles are becoming more and more important recently. In our model, viscoelastic microtubule bundles constituted from several discrete masses connected to the neighboring mass with a standard linear solid (SLS), a spring damper model. In addition we take into account the effect of cytoplasm by Dissipative Particle Dynamic (DPD) to investigate the rupture nature and mechanical behavior of these bundles and the effect of cytoplasm on their mechanical behavior. We obtain these results for various amounts of suddenly applied end forces to the group of axonal microtubule bundles.

bioengineering↗

bioRxiv2018

The permeabilized SecY protein-translocation channel can serve as a nonspecific sugar transporter

As the initial step in carbohydrate catabolism in cells, the substrate-specific transporters via active transport and facilitated diffusion play a decisive role in passage of sugars through the plasma membrane into the cytoplasm. The SecY complex (SecYEG) in bacteria forms a membrane channel responsible for protein translocation. This work demonstrates that weakening the sealability of the SecY channel allowed free diffusion of sugars, including glucose, fructose, mannose, xylose, arabinose, and lactose, into the engineered cells, facilitating its rapid growth on a wide spectrum of monosaccharides and bypassing/reducing stereospecificity, transport saturation, competitive inhibition, and carbon catabolite repression (CCR), which are usually encountered with the specific sugar transporters. The SecY channel is structurally conserved in prokaryotes, thus it may be engineered to serve as a unique and universal transporter for bacteria to passage sugars as demonstrated in Escherichia coli and Clostridium acetobutylicum.

bioengineering↗

bioRxiv2018

3D-Printed Biodegradable Microswimmer for Drug Delivery and Targeted Cell Labeling

Miniaturization of interventional medical devices can leverage minimally invasive technologies by enabling operational resolution at cellular length scales with high precision and repeatability. Untethered micron-scale mobile robots can realize this by navigating and performing in hard-to-reach, confined and delicate inner body sites. However, such a complex task requires an integrated design and engineering strategy, where powering, control, environmental sensing, medical functionality and biodegradability need to be considered altogether. The present study reports a hydrogel-based, biodegradable microrobotic swimmer, which is responsive to the changes in its microenvironment for theranostic cargo delivery and release tasks. We design a double-helical magnetic microswimmer of 20 m length, which is 3D-printed with complex geometrical and compositional features. At normal physiological concentrations, matrix metalloproteinase-2 (MMP-2) enzyme can entirely degrade the microswimmer body in 118 h to solubilized non-toxic products. The microswimmer can respond to the pathological concentrations of MMP-2 by swelling and thereby accelerating the release kinetics of the drug payload. Anti-ErbB 2 antibody-tagged magnetic nanoparticles released from the degraded microswimmers serve for targeted labeling of SKBR3 breast cancer cells to realize the potential of medical imaging of local tissue sites following the therapeutic intervention. These results represent a leap forward toward clinical medical microrobots that are capable of sensing, responding to the local pathological information, and performing specific therapeutic and diagnostic tasks as orderly executed operations using their smart composite material architectures.

bioengineering↗