Top 10 Biorxiv Papers Today in Bioengineering


1.998 Mikeys
#1. Discover Stable Expression Hot Spot in Genome of Chinese Hamster Ovary Cells Using Lentivirus based Random Integration Method
Songtao Zhou, Xuefeng Ding, Lei Yang, Yun Chen, Xiaohai Gong, Jian Jin, Huazhong Li
Traditional construction method for stable expression cell line was mainly achieved by using random integration method. However, target gene might be integrated into heterochromatin region or unstable region of chromatin by using this method, and thus required multiple rounds of selection to obtain desirable expression cell lines with stable expression level of target proteins. Rational cell line construction method can overcome this shortcoming by integrating transgenes into stable hot spot within genome specifically. Thus, to discover novel effective hot spot would be critical for this new cell line construction method. Here we reported one practical method to discover new stable hot spot by using lentivirus infection and random integration. One such hot spot located at NW_006880285.1 was thoroughly investigated in this article. The expression stability of this hot spot was verified by detecting Zsgreen1 reporter gene expression for over 50 passages. When cells were adapted to suspension culture, they successfully kept...
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Sample Sizes : None.
Authors: 7
Total Words: 5167
Unqiue Words: 1584

1.996 Mikeys
#2. Polymerization Kinetics Stability, Volumetric Changes, Apatite Precipitation, Strontium Release and Fatigue of Novel Bone Composites for Vertebroplasty
Piyaphong Panpisut, Kirsty Main, Muhammad Adnan Khan, Mayda Arshad, Wendy Xia, Haralampos Petridis, Anne Margaret Young
Purpose: The aim was to determine effects of diluent monomer and monocalcium phosphate monohydrate (MCPM) on polymerization kinetics and volumetric stability, apatite precipitation, strontium release and fatigue of novel dual-paste composites for vertebroplasty. Materials and methods: Polypropylene (PPGDMA) or triethylene (TEGDMA) glycol dimethacrylates (25 wt%) diluents were combined with urethane dimethacrylate (70 wt%) and hydroxyethyl methacrylate (5 wt%). 70 wt% filler containing glass particles, glass fibers (20 wt%) and polylysine (5 wt%) was added. Benzoyl peroxide and MCPM (10 or 20 wt%) or N-tolyglycine glycidyl methacrylate and tristrontium phosphate (15 wt%) were included to give initiator or activator pastes. Commercial PMMA (Simplex) and bone composite (Cortoss) were used for comparison. ATR-FTIR was used to determine thermal activated polymerization kinetics of initiator pastes at 50-80 ?C. Paste stability, following storage at 4-37 ?C, was assessed visually or through mixed paste polymerization kinetics at 25 ?C....
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Sample Sizes : [3, 3, 3, 25, 5, 20, 5, 3, 3, 3, 3, 20, 5]
Authors: 7
Total Words: 11657
Unqiue Words: 4328

0.0 Mikeys
#3. Multiobjective Strain Design: A Framework for Modular Cell Engineering
Sergio Garcia, Cong T Trinh
Diversity of cellular metabolism can be harnessed to produce a large space of molecules. However, development of optimal strains with high product titers, rates, and yields required for industrial production is laborious and expensive. To accelerate the strain engineering process, we have recently introduced a modular cell design concept that enables rapid generation of optimal production strains by systematically assembling a modular cell with an exchangeable production module(s) to produce target molecules efficiently. In this study, we formulated the modular cell design concept as a general multiobjective optimization problem with flexible design objectives derived from mass action. We developed algorithms and an associated software package, named ModCell2 to implement the design. We demonstrated that ModCell2 can systematically identify genetic modifications to design modular cells that can couple with a variety of production modules and exhibit a minimal tradeoff among modularity, performance, and robustness. Analysis of the...
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Sample Sizes : None.
Authors: 2
Total Words: 9497
Unqiue Words: 3055

0.0 Mikeys
#4. Murine bone properties and their relationship to gait during growth
Hyunggwi Song, John David Polk, Mariana Elizabeth Kersh
Allometric relationships have been queried over orders of mammals to understand how bone accommodates the mechanical demands associated with increasing mass. However, less attention has been given to the scaling of bone within a single lifetime. We aimed to determine if bone morphology and apparent density is related to (1) bending and compressive strength, and (2) gait dynamics. Longitudinal in vivo computed tomography and gait data were collected from female rats (n=5, age 8 - 20 weeks). Cross sectional properties and apparent density were measured at the diaphysis, distal, and proximal regions of the tibia and scaling exponents were calculated. Finite-element models were used to simulate four-point bending and axial compression using time-specific ground reaction forces (GRF) to calculate the mean strain energy density (SED) at the midshaft. Second moment of area at the diaphysis followed strain similarity based allometry, while bone area was positively allometric. The average SED at the diaphysis decreased, especially after...
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biorxivpreprint: Murine bone properties and their relationship to gait during growth https://t.co/VheZAC2Bzc #bioRxiv
KershTBL: Woot! Our first @biorxivpreprint - fantastic work by @HyunggwiSong studying the relationship between bone properties and gait during growth. https://t.co/yJsA44adcg https://t.co/ChpEjBi8Ap
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Sample Sizes : [5]
Authors: 3
Total Words: 6901
Unqiue Words: 2242

0.0 Mikeys
#5. Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads
Huy Q Nguyen, Jagoree Roy, Bjorn Harink, Nikhil Damle, Brian Baxter, Kara Brower, Tanja Kortemme, Kurt Thorn, Martha Cyert, Polly M Fordyce
Weak, transient binding of globular protein domains to Short Linear Motifs (SLiMs) in disordered regions of other proteins drive cellular signaling. Mapping the energy landscape of such interactions is essential for deciphering signaling networks and developing therapeutic inhibitors, but is complicated by technical challenges associated with quantitatively measuring weak interactions in high-throughput. Here, we synthesize peptide libraries on spectrally encoded beads with each peptide sequence uniquely linked to a spectral code (MRBLE-pep), allowing high-throughput quantification of protein-peptide binding via imaging. Using computational modeling and MRBLE-pep assays, we map the affinity landscape for human calcineurin (CN), a conserved protein phosphatase essential for the immune response and target of immunosuppressants, interacting with a known SLiM (PxIxIT). We find that PxIxIT recognition depends critically on flanking residues and is regulated by post-translational modifications. Using this information, we designed PxIxIT...
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Decoding and analysis software for MRBLEs (Microspheres with Ratiometric Barcode Lanthanide Encoding).

Repository: MRBLEs
User: FordyceLab
Language: Python
Stargazers: 1
Subscribers: 5
Forks: 0
Open Issues: 0
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Sample Sizes : None.
Authors: 10
Total Words: 10604
Unqiue Words: 3412

0.0 Mikeys
#6. Curvature Dependent constraints drive remodeling of epithelia
Florian Maechler, Cedric Allier, Aurelien Roux, Caterina Tomba
Epithelial tissues are essential to keep a proper barrier for the organism. They usually have highly curved shapes, such as tubules or cysts. However, interplays between the environment and cell mechanical properties to set the shape are not known. In this study, we encapsulated two epithelial cell lineages, MDCK and J3B1A, into hollow alginate tubes and grew them under cylindrical confinement. Once formed, the epithelial MDCK layer detached from the alginate shell, while J3B1A layer remained adherent. Detachment resulted from contractile forces within cell layers that pulled cells away from the shell. We concluded that J3B1A cells have lower contractility than MDCK cells. As the pulling forces depend on the radius of the tube, we induced detachment of J3B1A cells by reducing the size of the hollow tube by two. Moreover, in bent tubes, detachment was more pronounced on the outer side of the turn, while extrusion occurred in the inner side, further highlighting the coupling between curvature and cell contractility.
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biorxivpreprint: Curvature Dependent constraints drive remodeling of epithelia https://t.co/Our12jVau5 #bioRxiv
Alexis_Lomakin: RT @biorxivpreprint: Curvature Dependent constraints drive remodeling of epithelia https://t.co/Our12jVau5 #bioRxiv
LeonardoMorsut: RT @biorxivpreprint: Curvature Dependent constraints drive remodeling of epithelia https://t.co/Our12jVau5 #bioRxiv
MorphoLg: RT @biorxivpreprint: Curvature Dependent constraints drive remodeling of epithelia https://t.co/Our12jVau5 #bioRxiv
bulgakova_lab: RT @biorxivpreprint: Curvature Dependent constraints drive remodeling of epithelia https://t.co/Our12jVau5 #bioRxiv
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Sample Sizes : None.
Authors: 4
Total Words: 7899
Unqiue Words: 2367

0.0 Mikeys
#7. Real-time three-dimensional MRI for the assessment of dynamic carpal instability
Calvin B Shaw, Brent H Foster, Marissa Borgese, Robert D Boutin, Cyrus Bateni, Christopher O Bayne, Robert M Szabo, Krishna S Nayak, Abhijit Chaudhari
Carpal instability is defined as a condition where wrist motion or loading creates mechanical dysfunction, resulting in weakness, pain and decreased function. Often the diagnosis is made late when malalignment is visualized on static radiography, CT, or MRI. When conventional imaging methods do not identify the instability patterns, yet clinical signs associated with instability exist, the diagnosis of dynamic instability is often suggested to describe carpal derangement manifested only during the wrist's active motion or stress. We addressed the question: can advanced MRI techniques provide quantitative measures for evaluating dynamic carpal instability and supplement standard static MRI acquisition? Our objectives were to [1] develop a real-time, three-dimensional MRI method to image the carpal joints during their active, uninterrupted motion; and [2] demonstrate feasibility of the method for assessing metrics relevant to dynamic carpal instability, thus overcoming limitations of conventional MRI. Twenty wrists (bilateral wrists...
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Sample Sizes : None.
Authors: 9
Total Words: 7592
Unqiue Words: 2389

0.0 Mikeys
#8. Estimation of in vivo constitutive parameters of the aortic wall: a machine learning approach
Minliang Liu, Liang Liang, Wei Sun
The patient-specific biomechanical analysis of the aorta demands the in vivo mechanical properties of individual patients. Current inverse approaches have shown the feasibility of estimating the nonlinear, anisotropic material parameters from in vivo image data using certain optimization schemes. However, since such inverse methods are dependent on iterative nonlinear optimization, these methods are highly computation-intensive, which may take weeks to complete for only a single patient, inhibiting rapid feedback for clinical use. Recently, machine learning (ML) techniques have led to revolutionary breakthroughs in many applications. A potential paradigm-changing solution to the bottleneck associated with patient-specific computational modeling is to incorporate ML algorithms to expedite the procedure of in vivo material parameter identification. In this paper, we developed a ML-based approach to identify the material parameters from three-dimensional aorta geometries obtained at two different blood pressure levels, namely...
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Sample Sizes : None.
Authors: 3
Total Words: 7495
Unqiue Words: 2286

0.0 Mikeys
#9. Multi-stage chemical heating for instrument-free biosensing
John P Goertz, Kenya M Colvin, Andrew B Lippe, John L Daristotle, Peter Kofinas, Ian M White
Improving the portability of diagnostic medicine is crucial to alleviating global access-to-care deficiencies. This requires not only designing devices that are small and lightweight but also autonomous and independent of electricity. Here, we present a strategy for conducting automated multi-step diagnostic assays using chemically generated, passively regulated heat. Ligation and polymerization reagents for Rolling Circle Amplification of nucleic acids are separated by melt-able phase-change partitions, thus replacing precise manual reagent additions with automated partition melting. To actuate these barriers and individually initiate the various steps of the reaction, field ration heaters exothermically generate heat in a thermos while fatty acids embedded in a carbonaceous matrix passively buffer the temperature around their melting points. Achieving multi-stage temperature profiles extends the capability of instrument-free diagnostic devices and improves the portability of reaction automation systems built around phase-change...
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Authors: 6
Total Words: 4528
Unqiue Words: 1831

0.0 Mikeys
#10. Mesenchymal stem cell derived exosomes enhance lymphangiogenesis via exosomal transfer of Ang-2/Tie2
Ting Zhao, Zhixin Yan, Jinwen Liu, Hui Sun, Yifei Chen, Yan Tao, Wenrong Xu, Hui Qian, Yongmin Yan
Mesenchymal stem cell derived exosomes (MSC-Ex) are nanosized membrane-bound extracellular vesicles found in MSC conditioned medium, that have yielded beneficial effects in several experimental models of organ injury. However, the therapeutic value and mechanism of MSC-Ex in lymphedema is poorly understood. Here we find that human umbilical cord MSCs derived exosomes (hucMSC-Ex) treatment contributed to the regeneration of LYVE-1 positive lymphatic vessels and reduction of lymphedema in a mouse model of tail lymphedema. Following uptake, exosomal lymphangiogenic factors (angiopoietin (Ang)-2 and Tie2) are taken up by HDLECs and promoted HDLECs proliferation, migration, and tube formation in vitro. We also find that exosomal Ang-2 and Tie2 exert a prolymphangiogenic effect on HDLECs through upregulating Prox1 and VEGFR3/p-Akt expression. In conclusion, our result unravel a previously unappreciated prolymphangiogenic role of hucMSC-Ex in lymphedema therapy and provide a new mechanism of Ang-2 in therapeutic lymphangiogenesis.
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biorxivpreprint: Mesenchymal stem cell derived exosomes enhance lymphangiogenesis via exosomal transfer of Ang-2/Tie2 https://t.co/DcJkVx9JSf #bioRxiv
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Sample Sizes : [6, 6, 6]
Authors: 9
Total Words: 9133
Unqiue Words: 2446

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