Search bioRxivSearch

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 559 records · Page 31Linked to original sources

Microbial Cells Harboring a Mitochondrial Gene Are Capable of CO2 Capture

Global warming is escalating with increased temperatures reported worldwide. Given the enormous land mass on the planet, biological capture of CO2 remains a viable approach to mitigate the crisis as it is economical and easy to implement. In this study, a gene capable of CO2 capture was identified via selection in minimal media. This mitochondrial gene named as OG1 encodes the OK/SW-CL.16 protein and shares homology with cytochrome oxidase subunit III of various species and PII uridylyl-transferase from Loktanella vestfoldensis SKA53. CO2 capture experiments indicate that {delta}13C was substantially higher in the cells harboring the gene OG1 than the control in the nutrition-poor media. This study suggests that CO2 capture using engineered microorganisms in barren land can be exploited to address the soaring CO2 level in the atmosphere, opening up vast land resources to cope with global warming.\n\nIMPORTANCEGlobal warming crisis is deteriorating with increased CO2 levels in the atmosphere each year. Action must be taken before catastrophic consequences occur in the not-so-distant future. Biological capture of CO2 is a feasible approach to alleviate the current crisis. We have identified a mitochondrial gene which demonstrated CO2 utilization capability. Data presented in this study suggest that CO2 capture using engineered microorganisms can be harnessed to address the ever-rising CO2 level in the atmosphere.

bioengineering

Imaging breast cancer using a dual-ligand nanochain particle

Nanoparticles often only exploit the upregulation of a receptor on cancer cells to enhance intratumoral deposition of therapeutic and imaging agents. However, a single targeting moiety assumes that a tumor is homogenous and static. Tumoral microenvironments are both heterogenous and dynamic, often displaying variable spatial and temporal expression of targetable receptors throughout disease progression. Here, we evaluated the in vivo performance of an iron oxide nanoparticle in terms of targeting and imaging of orthotropic mouse models of aggressive breast tumors. The nanoparticle, a multi-component nanochain, was comprised of 3-5 iron oxide nanoparticles chemically linked in a linear chain. The nanoparticles surface was decorated with two types of ligands each targeting two different upregulated biomarkers on the tumor endothelium, P-selectin and fibronectin. The nanochain exhibited improved tumor deposition not only through vascular targeting but also through its elongated structure. A single-ligand nanochain exhibited a [~]2.5-fold higher intratumoral deposition than a spherical nanoparticle variant. Furthermore, the dual-ligand nanochain exhibited higher consistency in generating detectable MR signals compared to a single-ligand nanochain. Using a 7T MRI, the dual-ligand nanochains exhibited highly detectable MR signal within 3h after injection in two different animal models of breast cancer.

bioengineering

Establishment and Characterization of a Multi-Purpose Large Animal Exposure Chamber for Investigating Health Effects

Air pollution poses a significant threat to the environment and human health. Most in-vivo health studies conducted regarding air pollutants, including particulate matter (PM) and gas phase pollutants, have been either through traditional medical intranasal treatment or using a tiny chamber, which limit animal activities. In this study, we designed and tested a large, whole-body, multiple animal exposure chamber with uniform dispersion and exposure stability for animal studies. The chamber simultaneously controls particle size distribution and PM mass concentration. Two different methods were used to generate aerosol suspension through either soluble material (Alternaria extract), liquid particle suspension (Nanosilica solution) or dry powder (silica powder). We demonstrate that the chamber system provides well controlled and characterized whole animal exposures, where dosage is by inhalation of particulate matter.

bioengineering

Plantarflexor fiber length and tendon slack length are the strongest determinates of simulated single-leg heel raise function

AbstractAchilles tendon ruptures lead to reduced ankle function and often limits recreational activity. Single-leg heel raises are often used clinically to characterize patient function. However, it is unclear how the structure of the Achilles tendon and plantarflexor muscles affects single-leg heel raise function. Therefore, the purpose of this study was to develop a musculoskeletal model in order to simulate the effects of muscle-tendon unit (MTU) parameters on peak plantarflexion during this clinically-relevant task. The ankle joint was plantarflexed by two MTUs that represented the soleus and gastrocnemius muscles. The optimal fiber length, maximal muscle force, muscle pennation, tendon stiffness, and resting ankle angle - a surrogate measure of tendon slack length - were iteratively adjusted to test the combined effects of each of these MTU parameters. Single-leg heel raises were simulated by maximally exciting the two plantarflexor MTUs for each model configuration (N = 161,051 simulations). Optimal muscle fiber and tendon slack lengths had the greatest effect on peak plantarflexion during simulated single-leg heel raises. Simulations that were unable to produce at least 30 degrees of plantarflexion had muscle fibers that were shorter than healthy muscle and longer tendon slack lengths. These findings highlight the importance of preserving muscle fascicle and tendon length following Achilles tendon injuries.\n\nFunding no funding has been provided for this research\n\nAcknowledgements the Authors have no acknowledgements\n\nConflict of interest the Authors have no conflicts of interest that are relevant to this work

bioengineering

Design and Analysis of a Whole Body Non-Contact Electromagnetic Stimulation Device with Field Modulation

This study describes a whole-body, non-contact electromagnetic stimulation device based on the concept of a conventional MRI Radio Frequency (RF) resonating coil, but at a much lower resonant frequency (100-150 kHz), with a field modulation option (0.5-100 Hz) and with an input power of up to 3 kW. Its unique features include a high electric field level within the biological tissue due to the resonance effect and a low power dissipation level, or a low Specific Absorption Rate (SAR), in the body itself. Because of its large resonator volume together with non-contact coupling, the subject may be located anywhere within the coil over a longer period at moderate and safe electric field levels. The electric field effect does not depend on body position within the resonator. However, field penetration is deep anywhere within the body, including the extremities where muscles, bones, and peripheral tissues are mostly affected. A potential clinical application of this device is treatment of chronic pain. Substantial attention is paid to device safety; this includes both AC power safety and exposure of human subjects to electromagnetic fields. In the former case, we employ inductive coupling which eliminates a direct current path from AC power to the coil. Our design enhances overall device safety at any power level, even when operated under higher-power conditions. Human exposure to electromagnetic fields within the coil is evaluated by performing modeling with two independent numerical methods and with an anatomically realistic multi-tissue human phantom. We show that SAR levels within the body correspond to International Electrotechnical Commission (IEC) safety standards when the input power level of the amplifier driver does not exceed 3 kW. We also show that electric field levels generally comply with International Commission on Non-Ionizing Radiation Protection safety standards if the input power level does not exceed 1.5 kW.

bioengineering

High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq

Yeasts can be engineered into \"living foundries\" for non-natural chemical production by reprogramming their genome using a synthetic biology \"design-build-test\" cycle. While methods for \"design\" and \"build\" are scalable and efficient, \"test\" remains a labor-intensive bottleneck, limiting the effectiveness of the genetic reprogramming results. Here we describe Isogenic Colony Sequencing (ICO-seq), a massively-parallel strategy to assess the gene expression, and thus engineered pathway efficacy, of large numbers of genetically distinct yeast colonies. We use the approach to characterize opaque-white switching in 658 C. albicans colonies. By profiling transcriptomes of 1642 engineered S. cerevisiae strains, we use it to assess gene expression heterogeneity in a protein mutagenesis library. Our approach will accelerate synthetic biology by allowing facile and cost-effective transcriptional profiling of large numbers of genetically distinct yeast strains.

bioengineering

Synthetic Metabolic Pathway for the Production of 1-Alkenes from Lignin-derived Molecules

Integration of synthetic metabolic pathways to catabolically diverse chassis provides new opportunities for sustainable production. One attractive scenario is the use of abundant waste material to produce readily collectable product, minimizing production costs. Towards that end, we established the production of semivolatile medium-chain -olefins from lignin-derived monomers: we constructed 1-undecene synthesis pathway in Acinetobacter baylyi ADP1 using ferulate as the sole carbon source. In order to overcome the toxicity of ferulate, we first applied adaptive laboratory evolution, resulting in a highly ferulate-tolerant strain. Next, we demonstrated the 1-undecene production from glucose by heterologously expressing a fatty acid decarboxylase UndA and a thioesterase TesA in the wild type strain. Finally, we constructed the alkene synthesis pathway in the ferulate-tolerant strain. We were able to produce 1-undecene from ferulate and collect the product from the culture headspace without downstream processing. This study demonstrates the potential of bacterial lignin upgradation into value-added products.

bioengineering

Multi-laminate Annulus Fibrosus Repair Scaffold with an Interlamellar Matrix Enhances Impact Resistance, Prevents Herniation and Assists in Restoring Spinal Kinematics

Focal defects in the annulus fibrosus (AF) of the intervertebral disc (IVD) from herniation or surgical injury have detrimental impacts on IVD mechanical function. Thus, biomaterial-based repair strategies, which can restore the mechanical integrity of the AF and support long-term tissue regeneration are needed. Accordingly, a collagen-based multi-laminate scaffold with an underlying \"angle-ply\" architecture has been previously reported demonstrating similar mechanical properties to native AF tissue. The objectives of this work were to: 1) enhance the biomaterials impact strength, 2) define its contribution to spinal kinematics, and 3) assess its ability to prevent IVD herniation. First, AFRPs were enriched with a glycosaminoglycan-based (GAG) interlamellar matrix (ILM), and then tested for its radially-directed impact resistance under physiological stresses. Subsequent kinematic testing was conducted using a characterized GAG-enriched AFRP as an AF focal defect closure device. In summary, AFRPs demonstrated 1) incorporation of a GAG-based ILM significantly increased radial impact strength, 2) restoration of axial FSU kinematics and 3) ability to prevent herniation of native IVD tissues. Together, these results suggest that the AFRP demonstrates the mechanical robustness and material properties to restore an IVDs physiological mechanical function through the adequate closure of an AF focal defect.

bioengineering

The effect of physiological and measurement noise on the estimate of individual muscle force from indirect measurements of muscle activity

Several forward dynamics estimators have been proposed to quantify individual muscle force using non-invasive measurements of muscle activity. None of them, however, addresses the inaccuracy that arises when measurements are available only from a subset of the muscles involved in the movement under analysis. We present a novel estimator that integrates a forward dynamics estimation approach with knowledge of the optimal contraction strategy to obtain accurate estimates of individual muscle force when measurements of muscle activity are not available for all muscles. A following in-silico characterization showed that when trying to estimate forces form the forearm muscles acting around the wrist joint, our novel estimator is able to decrease the mean estimation bias by about 25% of the true value of muscle force. With a sensitivity analysis, we show that the model-based estimator is robust against physiological variability in muscle co-contraction strategy.

bioengineering

Proving Osteoinductive Potential of a Decellularized Xenograft Bone Substitute

BackgroundLarge bone defects remain a major clinical challenge for orthopaedic surgeons. Tissue engineered bone grafts have garnered increased attention as a solution to this problem. One ideal property of any bone graft is osteoinductivity or the ability to stimulate progenitor cell differentiation into a bone forming lineage.\n\nQuestionsO_LIIs the osteoinductive potential of a porcine bone xenograft maintained in vitro after undergoing a novel decellularization and oxidation process?\nC_LIO_LIAre porcine bone scaffolds osteoinductive in an in vivo animal model?\nC_LI\n\nMethodsO_LIIn Vitro - C2C12 pre-osteoblasts were seeded on the scaffold or a commercial grade demineralized bone matrix (DBM) to study osteogenic differentiation and compare osteoinductive potential. MC3T3-E1 pre-osteoblasts were seeded on the scaffold and compared to a control monolayer to identify early markers of osteogenic differentiation.\nC_LIO_LIIn Vivo - MC3T3-E1-seeded scaffolds were implanted subcutaneously in mice and assessed for markers of early osteogenic differentiation, new bone formation (micro-computed tomography and histological assessment), and vascular infiltration (histology).\nC_LI\n\nResultsOsteoinductive potential was demonstrated in in vitro experiments by similar osteogenic marker expression compared to DBM and significantly greater expression than a control monolayer.\n\nOsteoinductivity was confirmed with in vivo experiments showing both new bone formation and vascular infiltration.\n\nConclusionPorcine bone maintains osteoinductive properties after decellularization and oxidation.\n\nClinical RelevanceThis construct could potentially serve as a bone graft substitute maintaining the osteoinductive potential of native bone. The unrestricted supply and controlled donor biology may satisfy a large clinical need for orthopaedic cases requiring bone grafting.

bioengineering

HIGH-CONTENT, CELL-BY-CELL ASSESSMENT OF HER2 OVEREXPRESSION AND AMPLIFICATION FOR HETEROGENEITY DETECTION IN BREAST CANCER

Immunohistochemistry and fluorescence in situ hybridization are the two standard methods for Human Epidermal Growth Factor Receptor 2 (HER2) assessment. However, they have severe limitations to assess quantitatively intratumoral heterogeneity (ITH) when multiple subclones of tumor cells co-exist. We develop here a high-content, quantitative analysis of breast cancer tissues based on microfluidic experimentation and image processing, to characterize both HER2 protein overexpression and HER2 gene amplification at the cell level. The technique consists of performing sequential steps on the same tissue slide: an immunofluorescence (IF) assay using a microfluidic protocol, an elution step for removing the IF staining agents, a standard FISH staining protocol, followed by automated quantitative cell-by-cell image processing. Moreover, ITH is accurately detected in both cluster and mosaic form using an analysis of spatial association and a mathematical model that allows discriminating true heterogeneity from artifacts due to the use of thin tissue sections. This study paves the way to evaluate ITH with high accuracy and content while requiring standard staining methods.

bioengineering

Functional retinal imaging using adaptive optics swept-source OCT at 1.6MHz

Objective optical assessment of photoreceptor function may permit earlier diagnosis of retinal disease than current methods such as perimetry, electrophysiology, and clinical imaging. In this work, we describe an adaptive optics (AO) optical coherence tomography (OCT) system designed to measure functional responses of single cones to visible stimuli. The OCT subsystem consisted of a raster-scanning Fourier-domain mode-locked laser that acquires A-scans at 1.64MHz with a center wavelength of 1063nm, and an AO subsystem providing diffraction-limited imaging. Analysis of serial volumetric images revealed phase changes of cone photoreceptors consistent with outer segment elongation and proportional to stimulus intensity, as well as other morphological changes in the outer segment and retinal pigment epithelium.

bioengineering

Crowdsourced MRI quality metrics and expert quality annotations for training of humans and machines

The neuroimaging community is steering towards increasingly large sample sizes, which are highly heterogeneous because they can only be acquired by multi-site consortia. The visual assessment of every imaging scan is a necessary quality control step, yet arduous and time-consuming. A sizeable body of evidence shows that images of low quality are a source of variability that may be comparable to the effect size under study. We present the MRIQC Web-API, an open crowdsourced database that collects image quality metrics extracted from MR images and corresponding manual assessments by experts. The database is rapidly growing, and currently contains over 100,000 records of image quality metrics of functional and anatomical MRIs of the human brain, and over 200 expert ratings. The resource is designed for researchers to share image quality metrics and annotations that can readily be reused in training human experts and machine learning algorithms. The ultimate goal of the database is to allow the development of fully automated quality control tools that outperform expert ratings in identifying subpar images.

bioengineering

Can machine learning assess trunk alignment directly from raw video?

BackgroundThe Segmental Assessment of Trunk Control (SATCo) evaluates sitting control at seven separate trunk segments, making a judgement based on their position in space relative to a defined, aligned posture. SATCo is in regular clinical and research use and is a Recommended Instrument for Cerebral Palsy and Spinal Cord Injury-Paediatric by The National Institute of Neurological Disorders and Stroke (US). However, SATCo remains a subjective assessment.\n\nResearch questionThis study tests the feasibility of providing an objective, automated identification of frames containing the aligned, reference trunk posture using deep convolutional neural network (DCNN) analysis of raw high definition and depth (HD+D) images.\n\nMethodsA SATCo was conducted on sixteen healthy male adults and recorded using a Kinect V2. For each of seven segments tested, two different trials were collected (control and no-control) to simulate a range of alignment configurations. For all images, classification of alignment obtained from a trained and validated DCNN was compared to expert clinicians labelling.\n\nResultsUsing leave-one-out testing, at the optimal operating threshold, the DCNN correctly classified individual images (alignment v misaligned) with average precision 92.7{+/-}16% (mean{+/-}SD).\n\nSignificanceThese results show for the first time, automation of a key component of the SATCo test, namely identification of aligned trunk posture directly from raw images (HD+D). This demonstrates the potential of machine learning to provide a fully automated, objective SATCo test to enhance assessment of trunk control in children and adults for research and treatment of various conditions including neurodisability and stroke.

bioengineering

Complex human gut microbiome cultured in anaerobic human intestine chips

The diverse bacterial populations that comprise the commensal microbiota of the human intestine play a central role in health and disease, yet no method is available to sustain these complex microbial communities in direct contact with living human intestinal cells and their overlying mucus layer in vitro. Here we describe a human Organ-on-a-Chip (Organ Chip) microfluidic platform that permits control and real-time assessment of physiologically-relevant oxygen gradients, and which enables co-culture of living human intestinal epithelium with stable communities of aerobic and anaerobic human gut microbiota. When compared to aerobic co-culture conditions, establishment of a transluminal hypoxia gradient sustained higher microbial diversity with over 200 unique operational taxonomic units (OTUs) from 11 different genera, and an abundance of obligate anaerobic bacteria with ratios of Firmicutes and Bacteroidetes similar to those observed in human feces, in addition to increasing intestinal barrier function. The ability to culture human intestinal epithelium overlaid by complex human gut microbial communities within microfluidic Intestine Chips may enable investigations of host-microbiome interactions that were not possible previously, and serve as a discovery tool for development of new microbiome-related therapeutics, probiotics, and nutraceuticals.

bioengineering

Detection of arterial wall abnormalities via Bayesian model selection

Patient-specific modeling of hemodynamics in arterial networks has so far relied on parameter estimation for inexpensive or small-scale models. We describe here a Bayesian uncertainty quantification framework which makes two major advances: an efficient parallel implementation, allowing parameter estimation for more complex forward models, and a system for practical model selection, allowing evidence-based comparison between distinct physical models. We demonstrate the proposed methodology by generating simulated noisy flow velocity data from a branching arterial tree model in which a structural defect is introduced at an unknown location; our approach is shown to accurately locate the abnormality and estimate its physical properties even in the presence of significant observational and systemic error. As the method readily admits real data, it shows great potential in patient-specific parameter fitting for hemodynamical flow models.

bioengineering

Isolation and Characterization of a Novel Alkaline Lipase/Esterase Lip-1420 from a Metagenomic Library

A novel lipase gene, Lip-1420, was isolated from a metagenomics library constructed from soil samples from reed marshes and from Mt. Jumbong in Korea consisting of 112,500 recombinant plasmids. A selected recombinant plasmid, Lip-1420, was further analyzed which exhibited the maximum lipolytic activity among 18 recombinant fosmids that showed lipolytic activity. Among them, DNA sequence analysis of a 5,513 bp subclone in pUC119 Lip-1420-sub revealed that 11 ORFs were included in the gene according to the blast search from GenBank. The transformant of Lip-1420-ORF3 exhibited lipolytic activity, and plasmid pET21a(+)-Lipase-6H was constructed and transferred to the expression host E. coli BL21(DE3). Finally, the lipase Lip1420 was purified from a FPLC system, and the recombinant enzyme was kept in a -70 {o}C freezer at a concentration of 1 mg/mL in a buffer solution (50 mM Tris-HCl and 0.15 M NaCl, pH 7.4). The Lip-1420 gene was registered in GenBank (MH628529), and the purified enzyme had an optimal activity at 40 {degrees}C and pH 8.0. Kinetic analysis of the Lip-1420 lipase with the substrate p-nitrophenyl palmitate was performed at 40 {degrees}C and pH 8.0, and the Km and Vmax values of the protein were determined to be 0.268 mM and 1.821 units, respectively. The purified Lip-1420 exhibited the maximum enzymatic activity towards p-nitrophenyl palmitate, indicating that it is an esterase.\n\nIMPORTANCEThis study provides the knowledge to develop a new lipase from the metagenomics library of rhizosphere in Korea using an activity-based method. In addition, the knowledge gained from this study has allowed us to understand that the natural ecosystems are still an unknown genetic material storage report in relation to industrially useful biocatalysts, which are still rich in biodiversity. Moreover, alkaline lipase has great potential for applications in the detergent industry. Especially in the major part of the global industrial enzyme market with high growth potential. It is used, for example, in detergent additives, biopolymer synthesis, and biodiesel production, synthesis of optically pure compounds and food additives as well as in the paper industry, perfume and fragrance blends, biological purification and waste treatment.

bioengineering

Combating viral contaminants in CHO cells by engineering STAT1 mediated innate immunity

Viral contamination in biopharmaceutical manufacturing can lead to shortages in the supply of critical therapeutics. To facilitate the protection of bioprocesses, we explored the basis for the susceptibility of CHO cells, the most commonly used cell line in biomanufacturing, to RNA virus infection. Upon infection with certain ssRNA and dsRNA viruses, CHO cells fail to generate a significant interferon (IFN) response. Nonetheless, the downstream machinery for generating IFN responses and its antiviral activity is intact in these cells: treatment of cells with exogenously-added type I IFN or poly I:C prior to infection limited the cytopathic effect from Vesicular stomatitis virus (VSV), Encephalomyocarditis virus (EMCV), and Reovirus-3 virus (Reo-3) in a STAT1-dependent manner. To harness the intrinsic antiviral mechanism, we used RNA-Seq to identify two upstream repressors of STAT1: Gfi1 and Trim24. By knocking out these genes, the engineered CHO cells exhibited increased resistance to the prototype RNA viruses tested. Thus, omics-guided engineering of mammalian cell culture can be deployed to increase safety in biotherapeutic protein production among many other biomedical applications.

bioengineering