Top 8 Biorxiv Papers Today in Bioengineering


2.002 Mikeys
#1. Genetically encoded phase contrast agents for digital holographic microscopy
Arash Farhadi, Manuel Bedrossian, Justin Lee, Gabrielle H. Ho, Mikhail G. Shapiro, Jay Nadeau
Quantitative phase imaging and digital holographic microscopy have shown great promise for visualizing the motion, structure and physiology of microorganisms and mammalian cells in three dimensions. However, these imaging techniques currently lack molecular contrast agents analogous to the fluorescent dyes and proteins that have revolutionized fluorescence microscopy. Here we introduce the first genetically encodable phase contrast agents based on gas vesicles, a unique class of air-filled protein nanostructures derived from buoyant microbes. The relatively low index of refraction of the air-filled core of gas vesicles results in optical phase advancement relative to aqueous media, making them a positive phase contrast agent easily distinguished from organelles, dyes, or microminerals. We demonstrate this capability by identifying and tracking the motion of gas vesicles and gas vesicle-expressing bacteria using digital holographic microscopy, and by imaging the uptake of engineered gas vesicles by mammalian cells. These results...
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biorxivpreprint: Genetically encoded phase contrast agents for digital holographic microscopy https://t.co/yj2BjpHMGa #bioRxiv
biophotonicat: Genetically encoded phase contrast agents for digital holographic microscopy (relevance: 100%) https://t.co/Jilr5zCpSc #biophotonics #biomedicaloptics https://t.co/T7QFEGSnWd
farhadi_arash: Light, camera, action! Gas vesicles + digital holographic microscopy allows easy 4D imaging of particles and cells. Amazing collaboration with @m_bedrossian, Justin, Gabrielle, Jay and @mikhailshapiro. https://t.co/CR9GlcYRuS @biorxivpreprint https://t.co/4kA08Pei5D
biophotonicat: RT @biophotonicat: Genetically encoded phase contrast agents for digital holographic microscopy (relevance: 100%) https://t.co/Jilr5zCpSc #…
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Sample Sizes : [50, 110, 50, 50, 50, 50]
Authors: 6
Total Words: 6051
Unqiue Words: 2135

1.997 Mikeys
#2. Synthetic soil crusts against green-desert transitions: a spatial model
Blai Vidiella Rocamora, Josep Sardanyes, Ricard Sole
Semiarid ecosystems are threatened by global warming due to longer dehydration times and increasing soil degradation. Mounting evidences indicate that, given the current trends, drylands are likely to expand and possibly experience catastrophic shifts from vegetated to desert states. Here we explore a recent suggestion based on the concept of ecosystem terraformation, where a synthetic organism is used to counterbalance some of the nonlinear effects causing the presence of such tipping points. Using an explicit spatial model incorporating facilitation and considering a simplification of states found in semiarid ecosystems i.e., vegetation, fertile and desert soil, we investigate how engineered microorganisms can shape the fate of these ecosystems. Specifically, two different, but complementary, terraformation strategies are proposed: Cooperation -based: C -terraformation; and Dispersion -based: D -terraformation. The first strategy involves the use of soil synthetic microorganisms to introduce cooperative loops (facilitation) with...
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ricard_sole: Unless something is done, many drylands will experience a green-desert catastrophic transition. Is there a way to avoid it? Our approach is "terraforming" these ecosystems using synthetic biology. Our paper with @JosepSardanyes and @BlaiVidiella is out: https://t.co/9vqrscU7Cs https://t.co/cDkmxNvUbT
JosepSardanyes: Dynamical systems theory helps to study changes between states (green-desert) and their dependence on climate crisis or ecosystem's degradation. Here's our new scientific article on synthetic terraformation of arid ecosystems @ricard_sole @BlaiVidiella https://t.co/HtXoJuMaeq https://t.co/3nPCQDpk76
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1.997 Mikeys
#3. Surface Modification Effects on Single-Walled Carbon Nanotubes for Multimodal Optical Applications
Linda Chio, Rebecca L Pinals, Natalie S Goh, Aishwarya Murali, Markita P Landry
Optical nanoscale technologies often implement covalent or noncovalent strategies for the modification of nanoparticles, whereby both functionalizations can affect the intrinsic fluorescence of nanoparticles. Specifically, single-walled carbon nanotubes (SWCNTs) can enable real-time imaging and cellular delivery, however, the introduction of SWCNT sidewall functionalizations attenuates SWCNT fluorescence. Herein, we leverage recent advances in SWCNT covalent functionalization chemistries that preserve the SWCNT's pristine surface lattice and intrinsic fluorescence, and demonstrate that such covalently-functionalized SWCNT can enable fluorescence-based molecular recognition of neurotransmitter and protein analytes. We show that the covalently-modified SWCNT nanosensor fluorescence signal towards its analyte can be preserved only for certain nanosensors, presumably dependent on the steric hindrance of the SWCNT noncovalent coating. We further demonstrate these SWCNT nanosensors can be functionalized via their covalent handles to...
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biophotonicat: Surface Modification Effects on Single-Walled Carbon Nanotubes for Multimodal Optical Applications (relevance: 86%) https://t.co/oe6zhOKMIJ #biophotonics #biomedicaloptics https://t.co/4XGOrDL0R4
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Authors: 5
Total Words: 5062
Unqiue Words: 1707

1.997 Mikeys
#4. An enzymatic assay to measure long-term adherence to pre-exposure prophylaxis and antiretroviral therapy
Ayokunle O. Olanrewaju, Benjmain P Sullivan, Jane Y Zhang, Andrew T Bender, Derin Sevenler, Tiffany J Lo, Marta Fernandez-Suarez, Paul K Drain, Jonathan D Posner
Poor adherence to pre-exposure prophylaxis (PrEP) and antiretroviral therapy (ART) can lead to human immunodeficiency virus (HIV) acquisition and emergence of drug resistant infections, respectively. Measurement of antiviral drug levels provides objective adherence information that may help prevent adverse health outcomes. Gold standard drug-level measurement by liquid chromatography/mass spectrometry is centralized, heavily instrumented, and expensive and is thus unsuitable and unavailable for routine use in clinical settings. We developed the REverse TranscrIptase Chain Termination (RESTRICT) assay as a rapid and accessible measurement of drug levels indicative of long term adherence to PrEP and ART. The assay uses designer single stranded DNA templates and intercalating fluorescent dyes to measure complementary DNA (cDNA) formation by reverse transcriptase in the presence of nucleotide reverse transcriptase inhibitor drugs. We developed a probabilistic model for the RESTRICT assay by calculating the likelihood of incorporation...
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Authors: 9
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1.997 Mikeys
#5. OpenSim Moco: Musculoskeletal optimal control
Christopher L Dembia, Nicholas A Bianco, Antoine Falisse, Jennifer L Hicks, Scott L Delp
Musculoskeletal simulations of movement can provide insights needed to help humans regain mobility after injuries and design robots that interact with humans. Here, we introduce OpenSim Moco, a software toolkit for optimizing the motion and control of musculoskeletal models built in the OpenSim modeling and simulation package. OpenSim Moco uses the direct collocation method, which is often faster and can handle more diverse problems than other methods for musculoskeletal simulation but requires extensive technical expertise to implement. Moco frees researchers from implementing direct collocation themselves, allowing them to focus on their scientific questions. The software can handle the wide range of problems that interest biomechanists, including motion tracking, motion prediction, parameter optimization, model fitting, electromyography-driven simulation, and device design. Moco is the first musculoskeletal direct collocation tool to handle kinematic constraints, which are common in musculoskeletal models. To show Moco's...
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Authors: 5
Total Words: 11827
Unqiue Words: 2980

1.997 Mikeys
#6. Feasibility analysis of semiconductor voltage nanosensors for neuronal membrane potential sensing
Anastasia Ludwig, Pablo Serna, Lion Morgenstein, Gaoling Yang, Omri Bar-Elli, Gloria Ortiz, Evan Miller, Dan Oron, Asaf Grupi, Shimon Weiss, Antoine Triller
In the last decade, optical imaging methods have significantly improved our understanding of the information processing principles in the brain. Although many promising tools have been designed, sensors of membrane potential are lagging behind the rest. Semiconductor nanoparticles are an attractive alternative to classical voltage indicators, such as voltage-sensitive dyes and proteins. Such nanoparticles exhibit high sensitivity to external electric fields via the quantum-confined Stark effect. Here we report the development of lipid-coated semiconductor voltage-sensitive nanorods (vsNRs) that self-insert into the neuronal membrane. We describe a workflow to detect and process the photoluminescent signal of vsNRs after wide-field time-lapse recordings. We also present data indicating that vsNRs are feasible for sensing membrane potential in neurons at a single-particle level. This shows the potential of vsNRs for detection of neuronal activity with unprecedentedly high spatial and temporal resolution.
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biophotonicat: Feasibility analysis of semiconductor voltage nanosensors for neuronal membrane potential sensing (relevance: 77%) https://t.co/YxreGKovqO #biophotonics #biomedicaloptics https://t.co/eYSTQmIAQW
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Authors: 11
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1.994 Mikeys
#7. Pre-Innervated Tissue Engineered Muscle Promotes a Pro-Regenerative Microenvironment Following Volumetric Muscle Loss
SURADIP DAS, KEVIN D BROWNE, FRANCO A LAIMO, JOSEPH C MAGGIORE, Halimulati Kaisaier, Carlos Andres Aguilar, ZARINA S ALI, FOTEINI MOURKIOTI, DANIEL KACY CULLEN
Volumetric Muscle Loss (VML) is defined as traumatic or surgical loss of skeletal muscle tissue beyond the inherent regenerative capacity of the body, generally leading to a severe functional deficit. Autologous muscle grafts remain the prevalent method of treatment whereas recent muscle repair techniques using biomaterials and tissue engineering are still at a nascent stage and have multiple challenges to address to ensure functional recovery of the injured muscle. Indeed, appropriate somato-motor innervations remain one of the biggest challenges for both autologous muscle grafts as well as tissue engineered muscle constructs. We aim to address this challenge by developing Pre-Innervated Tissue Engineered Muscle comprised of long aligned networks of spinal motor neurons and skeletal myocytes. Here, we developed methodology to biofabricate long fibrils of pre-innervated tissue engineered muscle using a co-culture of myocytes and motor neurons on aligned nanofibrous scaffolds. Motor neurons lead to enhanced differentiation and...
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1.994 Mikeys
#8. Anthropomorphic left ventricular mesh phantom: a framework to investigate the accuracy of SQUEEZ using Coherent Point Drift for the detection of regional wall motion abnormalities
Ashish Manohar, Gabrielle M Colvert, Andrew Schluchter, Francisco J Contijoch, Elliot R McVeigh
We present an anthropomorphically accurate left ventricular (LV) phantom derived from human CT data to serve as the ground truth for the optimization and the spatial resolution quantification of a CT-derived regional strain metric (SQUEEZ) for the detection of regional wall motion abnormalities. Displacements were applied to the mesh points of a clinically derived end-diastolic LV mesh to create analytical end-systolic poses with physiologically accurate endocardial strains. Normal function as well as regional dysfunction of four sizes (1, 2/3, 1/2, and 1/3 AHA (American Heart Association) segments as core diameter), each exhibiting hypokinesia (70% reduction in strain) and subtle hypokinesia (40% reduction in strain), were simulated. Regional shortening (RSCT) estimates were obtained by registering the end-diastolic mesh to each simulated end-systolic mesh condition using a non-rigid registration algorithm. Ground-truth models of normal function and of hypokinesia were used to identify the optimal parameters in the registration...
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