Top 10 Biorxiv Papers Today in Bioengineering


2.037 Mikeys
#1. Versatile multi-transgene expression using improved BAC TG-EMBED toolkit, novel BAC episomes, and BAC-MAGIC
Binhui Zhao, Pankaj Chaturvedi, David L. Zimmerman, Andrew S. Belmont
Achieving reproducible, stable, and high-level transgene expression in mammalian cells remains problematic. Previously, we attained copy-number-dependent, chromosome-position-independent expression of reporter minigenes by embedding them within a BAC containing the mouse Msh3-Dhfr locus (DHFR BAC). Here we extend this 'BAC TG-EMBED' approach. First, we report a toolkit of endogenous promoters capable of driving transgene expression over a 0.01-5 fold expression range relative to the CMV promoter, allowing fine-tuning of relative expression levels of multiple reporter genes expressed on a single BAC. Second, we show small variability in both the expression level and long-term expression stability of a reporter gene embedded in BACs containing either transcriptionally active or inactive genomic regions, making choice of BACs more flexible. Third, we describe an intriguing phenomenon in which BAC transgenes are maintained as episomes in a large fraction of stably selected clones. Finally, we demonstrate the utility of BAC TG-EMBED by...
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biorxivpreprint: Versatile multi-transgene expression using improved BAC TG-EMBED toolkit, novel BAC episomes, and BAC-MAGIC https://t.co/fnMKg9LFWG #bioRxiv
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Authors: 4
Total Words: 0
Unqiue Words: 0

2.019 Mikeys
#2. Investigation of a New Superhydrophobic, Oleophobic-Coated Biliary Duct Stent and its Preventive Effect on Biliary Mud in Vitro
Xin Jian Wan, Wei Xing Zhang, Ya Li Ji, Yue Qin Qian, Zheng Jie Xu
Background and Aim A new type of superhydrophobic, oleophobic-coated biliary stent was created, and its characteristics and preventive effect on biliary mud deposition in vitro are studied herein. Methods The observational experiment included a bare stent group and coated stent group, with 10 stents per group. The groups were used in a model of the extracorporeal biliary perfusion system with bacterial infection, and the experiment was terminated when the stent was completely blocked. Changes of bile characteristics before and after the experiment, patency time, and amount of bile sludge deposition were compared between the groups. The t-test and analysis of variance were used to analyze the data. Results In the bare stent group, contact angles of bile were about 80.4 degrees and 79.8 degrees before and after the experiment, respectively. There was no change in the effect of bile aversion after the experiment between the groups (P < 0.05). In the coated stent group, contact angles of bile changed from 143.3 degrees before the...
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biorxivpreprint: Investigation of a New Superhydrophobic, Oleophobic-Coated Biliary Duct Stent and its Preventive Effect on Biliary Mud in Vitro https://t.co/XugJ3c2GHs #bioRxiv
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Authors: 5
Total Words: 0
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2.013 Mikeys
#3. Visual speed compensation of pitch-constrained blue-bottle flies under retinal-image velocity perturbation in a flight mill
Shih-Jung Hsu, Bo Cheng
Flies regulate speed to maintain a constant retinal-image velocity primarily by adjusting their body pitch, despite they can change speed via only the wing motion modulation. To determine whether and to what extent this behavior holds under a fixed body pitch condition, we investigated the speed regulation of semi-tethered blue-bottle flies ( Calliphora vomitoria ) flying in a magnetically levitated flight mill. The flies were perturbed with different spatial frequencies and retinal-image motions. Results showed that flies compensated retinal-image velocity perturbations by adjusting their airspeed up to 20%, thereby maintaining a relatively constant retinal-image velocity, similar to those observed in free-flight. However, when the retinal-image velocity perturbation became large, the compensation weakened as airspeed plateaued, suggesting that flies reached their biomechanical limits. The compensation gain, i.e., the ratio of airspeed compensation and retinal-image velocity perturbation, depended on the spatial frequency of the...
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biorxivpreprint: Visual speed compensation of pitch-constrained blue-bottle flies under retinal-image velocity perturbation in a flight mill https://t.co/jH0XCpYPoA #bioRxiv
biophotonicat: Visual speed compensation of pitch-constrained blue-bottle flies under retinal-image velocity perturbation in a flight mill (relevance: 71%) https://t.co/q613NiVbH3 #biophotonics #biomedicaloptics https://t.co/lmK5EERPgW
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Authors: 2
Total Words: 5323
Unqiue Words: 1707

2.003 Mikeys
#4. μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells
Nicolas Altemose, Annie Maslan, Andre Lai, Jonathan A. White, Aaron M. Streets
Genome regulation depends on carefully programmed protein-DNA interactions that maintain or alter gene expression states, often by influencing chromatin organization. Most studies of these interactions to date have relied on bulk methods, which in many systems cannot capture the dynamic single-cell nature of these interactions as they modulate cell states. One method allowing for sensitive single-cell mapping of protein-DNA interactions is DNA adenine methyltransferase identification (DamID), which records a protein's DNA-binding history by methylating adenine bases in its vicinity, then selectively amplifies and sequences these methylated regions. These interaction sites can also be visualized using fluorescent proteins that bind to methyladenines. Here we combine these imaging and sequencing technologies in an integrated microfluidic platform (μDamID) that enables single-cell isolation, imaging, and sorting, followed by DamID. We apply this system to generate paired single-cell imaging and sequencing data from a human cell line,...
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biophotonicat: μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells (relevance: 61%) https://t.co/WEsOkQEAG5 #biophotonics #biomedicaloptics https://t.co/v4TpD1bhfp
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Authors: 5
Total Words: 0
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2.002 Mikeys
#5. Elasticity and Topography-Controlled Collagen Hydrogels Mimicking Native Cellular Milieus
Tomoko Gowa Oyama, Kotaro Oyama, Atsushi Kimura, Fumiya Yoshida, Ryo Ishida, Masashi Yamazaki, Hiromi Miyoshi, Mitsumasa Taguchi
Accumulating evidence demonstrates that the elasticity and topography of a cell culture substrate influence cell behavior, in addition to its chemical composition. However, cellular responses to in vivo extracellular matrix (ECM), a hydrogel of proteins (mainly collagen) with various elasticity and a nanometer-to micrometer-scale topography, remain to be elucidated owing to a lack of substrate that provides such complex cues. This study introduces novel collagen hydrogels that can combine, for the first time, elastic, topographic, and compositional cues that recapitulate native ECM. A simple and reagent-free method based on radiation crosslinking alters ECM-derived collagen solutions into hydrogels with a well-defined and tunable elastic modulus covering the broad range of soft tissues (1−236 kPa) and microtopographies while ensuring intrinsic biological functionality of collagen. These collagen hydrogels enabled investigating cell responses to soft topographic cues such as those encountered in vivo , revealing that topography...
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biophotonicat: Elasticity and Topography-Controlled Collagen Hydrogels Mimicking Native Cellular Milieus (relevance: 72%) https://t.co/pTwcf1LbCZ #biophotonics #biomedicaloptics https://t.co/NzE0Jsx5KB
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Authors: 8
Total Words: 5780
Unqiue Words: 1904

1.997 Mikeys
#6. CRISPR-Cas9 modified bacteriophage for treatment of Staphylococcus aureus induced osteomyelitis and soft tissue infection
Leah K. Horstemeyer, JooYoun Park, Elizabeth A. Swanson, Mary Catherine Beard, Emily M. McCabe, Anna S. Rourke, Keun Seok Seo, Lauren Beatty Priddy
Osteomyelitis, or bone infection, is often induced by antibiotic resistant Staphylococcus aureus strains of bacteria. Although debridement and long-term administration of antibiotics are the gold standard for osteomyelitis treatment, the increase in prevalence of antibiotic resistant bacterial strains limits the ability of clinicians to effectively treat infection. Bacteriophages (phages), viruses that effectively lyse bacteria, have gained recent attention for their high specificity, non-toxicity, and the low likelihood of resistance development by pathogens. Previously, we have shown that CRISPR-Cas9 genomic editing techniques could be utilized to expand bacteriophage host range and enhance bactericidal activity through modification of the tail fiber protein, as well as improve safety with removal of major virulence genes. In a dermal infection study, these CRISPR-Cas9 phages reduced bacterial load relative to unmodified phage. Thus, we hypothesized this bacteriophage would be effective to mitigate infection from a biofilm...
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Authors: 8
Total Words: 10123
Unqiue Words: 3511

1.997 Mikeys
#7. Isolation of a putative S-layer protein from anammox biofilm extracellular matrix using ionic liquid extraction
Wong Lan Li, Gayatri NATARAJAN, Marissa Boleij, Sara Swi Thi, Fernaldo Richtia Winnerdy, Sudarsan Mugunthan, Yang Lu, Jong-Min Lee, Yuemei Lin, Mark van Loosdrecht, Yingyu Law, Staffan Kjelleberg, Thomas W Seviour
Anaerobic ammonium oxidation (anammox) performing bacteria self-assemble into compact biofilms by expressing extracellular polymeric substances (EPS). Anammox EPS are poorly characterized, largely due to their low solubility in typical aqueous solvents. Pronase digestion achieved 19.5 +- 0.9 and 41.4 +- 1.4% (w/w) more solubilization of Candidatus Brocadia sinica-enriched anammox granules than DNase and amylase respectively. Nuclear magnetic resonance profiling of the granules confirmed that proteins were dominant. We applied ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate and N,N- dimethylacetamide (EMIM-Ac/DMAc) mixture to extract the major structural proteins. Further treatment by anion exchange chromatography isolated homologous S/T-rich proteins BROSI\_A1236 and UZ01\_01563, which were major components of the extracted proteins and sequentially highly similar to putative anammox surface-layer (S-layer) protein KUSTD1514. EMIM-Ac/DMAc extraction enriched for these putative S-layer proteins against all other major...
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Authors: 13
Total Words: 9822
Unqiue Words: 3727

1.997 Mikeys
#8. An antibody-tumor necrosis factor fusion protein that synergizes with oxaliplatin for treatment of colorectal cancer
Davor Bajic, Kerry Ann Chester, Dario Neri
We have cloned and characterized a novel fusion protein (Sm3E-TNF), consisting of the monoclonal antibody Sm3E in single-chain Fv fragment format, fused to murine tumor necrosis factor. The protein, which was expressed in mammalian cells and purified as a non-covalent stable homotrimer, bound to the cognate carcinoembryonic antigen (CEA) and retained tumor necrosis factor activity. A quantitative biodistribution experiment, performed in immunocompetent mice with CT26 colon carcinomas transfected with human CEA, revealed that Sm3E-TNF was able to preferentially accumulate in the tumors with excellent selectivity (tumor:blood ratio = 56:1, twenty-four hours after intravenous administration). The fusion protein mediated a rapid hemorrhagic necrosis of a large portion of the tumor mass, but a rim survived and eventually regrew. Surprisingly, the combination of Sm3E-TNF with 5-fluorouracil led to a reduction of therapeutic activity, while a combination with oxaliplatin led to a prolonged stabilization, with complete tumor eradication...
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Sample Sizes : [5]
Authors: 3
Total Words: 8012
Unqiue Words: 2697

1.994 Mikeys
#9. Gut-Liver physiomimetics reveal paradoxical modulation of IBD-related inflammation by short-chain fatty acids
Martin Trapecar, Catherine Communal, Jason Velazquez, Christian Alexander Maass, Yu-Ja Huang, Kirsten Schneider, Charles W. Wright, David L. Trumper, Linda G. Griffith
Association between the microbiome, IBD and liver diseases are known, yet cause and effect remain elusive. By connecting human microphysiological systems of the gut, liver and circulating Treg/Th17 cells, we modeled progression of ulcerative colitis (UC) ex vivo. We show that microbiome-derived short-chain fatty acids (SCFA) may either improve or worsen disease severity, depending on the activation state of CD4 T cells. Employing multiomics, we found SCFA reduced innate activation of the UC gut and increased hepatic metabolism. However, during acute T cell-mediated inflammation, SCFA exacerbate CD4 T cell effector function leading to gut barrier disruption and liver damage. These paradoxical findings underscore the emerging utility of human physiomimetic technology to study causality and temporal facets of gut-liver axis related diseases where animal models leave ambiguity.
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Authors: 9
Total Words: 0
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1.955 Mikeys
#10. Validating Minimally Invasive Laser Doppler Flowmetry for Serial Bone Perfusion Measurements in Mice
Nicholas J. Hanne, Elizabeth D. Easter, Jacqueline H. Cole
In vivo laser Doppler flowmetry (LDF) has previously been used to quantify blood perfusion accurately at a single timepoint in the murine tibial metaphysis. However, this procedure entailed substantial disruption to soft tissues overlying the bone and caused notable localized inflammation for several weeks after the procedure, impeding serial measurements in the same mouse. In this study, we tested a less invasive technique to measure perfusion in the tibia with LDF and validated that it can be used serially in the same mouse without causing inflammation or gait perturbations. Twenty 14-week-old C57Bl/6J mice were evenly divided into groups that either had daily treadmill exercise or remained sedentary. Within these activity groups, mice were evenly subdivided into groups that received LDF measurements either weekly or only once at the study endpoint. Bone perfusion was measured with LDF in the anteromedial region of the right tibial metaphysis. Serum concentrations of interleukin 6, incision site wound area, and interlimb...
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Authors: 3
Total Words: 0
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