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Rxivist combines biology preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 161,564 papers from 674,550 authors.

Most downloaded biology preprints, all time

in category bioengineering

3,330 results found. For more information, click each entry to expand.

1: Paperfuge: An ultra-low cost, hand-powered centrifuge inspired by the mechanics of a whirligig toy
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Posted 30 Aug 2016

Paperfuge: An ultra-low cost, hand-powered centrifuge inspired by the mechanics of a whirligig toy
31,776 downloads bioRxiv bioengineering

M. Saad Bhamla, Brandon Benson, Chew Chai, Georgios Katsikis, Aanchal Johri, Manu Prakash

Sample preparation, including separation of plasma from whole blood or isolation of parasites, is an unmet challenge in many point of care (POC) diagnostics and requires centrifugation as the first key step. From the context of global health applications, commercial centrifuges are expensive, bulky and electricity-powered, leading to a critical bottle-neck in the development of decentralized, electricity-free POC diagnostic devices. By uncovering the fundamental mechanics of an ancient whirligig toy (3300 B.C.E), we design an ultra-low cost (20 cents), light-weight (2 g), human-powered centrifuge that is made out of paper ("paperfuge"). To push the operating limits of this unconventional centrifuge, we present an experimentally-validated theoretical model that describes the paperfuge as a non-linear, non-conservative oscillator system. We use this model to inform our design process, achieving speeds of 125,000 rpm and equivalent centrifugal forces of 30,000 g, with theoretical limits predicting one million rpm. We harness these speeds to separate pure plasma in less than 1.5 minutes and isolate malaria parasites in 15 minutes from whole human blood. By expanding the materials used, we implement centrifugal microfluidics using PDMS, plastic and 3D-printed devices, ultimately opening up new opportunities for electricity-free POC diagnostics, especially in resource-poor settings.

2: Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD
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Posted 20 Mar 2020

Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD
19,529 downloads bioRxiv bioengineering

Genwei Zhang, Sebastian Pomplun, A. R. Loftis, X. Tan, A. Loas, Bradley L. Pentelute

Coronavirus disease 19 (COVID-19) is an emerging global health crisis. With over 7 million confirmed cases to date, this pandemic continues to expand, spurring research to discover vaccines and therapies. SARS-CoV-2 is the novel coronavirus responsible for this disease. It initiates entry into human cells by binding to angiotensin-converting enzyme 2 (ACE2) via the receptor binding domain (RBD) of its spike protein (S). Disrupting the SARS-CoV-2-RBD binding to ACE2 with designer drugs has the potential to inhibit the virus from entering human cells, presenting a new modality for therapeutic intervention. Peptide-based binders are an attractive solution to inhibit the RBD-ACE2 interaction by adequately covering the extended protein contact interface. Using molecular dynamics simulations based on the recently solved cryo-EM structure of ACE2 in complex with SARS-CoV-2-RBD, we observed that the ACE2 peptidase domain (PD) α1 helix is important for binding SARS-CoV-2-RBD. Using automated fast-flow peptide synthesis, we chemically synthesized a 23-mer peptide fragment of the ACE2 PD α1 helix (SBP1) composed entirely of proteinogenic amino acids. Chemical synthesis of SBP1 was complete in 1.5 hours, and after work up and isolation >20 milligrams of pure material was obtained. Bio-layer interferometry (BLI) revealed that SBP1 associates with micromolar affinity to insect-derived SARS-CoV-2-RBD protein obtained from Sino Biological. Association of SBP1 was not observed to an appreciable extent to HEK cell-expressed SARS-CoV-2-RBD proteins and insect-derived variants acquired from other vendors. Moreover, competitive BLI assays showed SBP1 does not outcompete ACE2 binding to Sino Biological insect-derived SARS-CoV-2-RBD. Further investigations are ongoing to gain insight into the molecular and structural determinants of the variable binding behavior to different SARS-CoV-2-RBD protein variants. ### Competing Interest Statement Bradley L. Pentelute is a co-founder of Resolute Bio and Amide Technologies.

3: Directed evolution of TurboID for efficient proximity labeling in living cells and organisms
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Posted 02 Oct 2017

Directed evolution of TurboID for efficient proximity labeling in living cells and organisms
16,948 downloads bioRxiv bioengineering

Tess C Branon, Justin A Bosch, Ariana D Sanchez, Namrata D Udeshi, Tanya Svinkina, Steven A Carr, Jessica L. Feldman, Norbert Perrimon, Alice Y. Ting

Protein interaction networks and protein compartmentation underlie every signaling process and regulatory mechanism in cells. Recently, proximity labeling (PL) has emerged as a new approach to study the spatial and interaction characteristics of proteins in living cells. However, the two enzymes commonly used for PL come with tradeoffs: BioID is slow, requiring tagging times of 18-24 hours, while APEX peroxidase uses substrates that have limited cell permeability and high toxicity. To address these problems, we used yeast display-based directed evolution to engineer two mutants of biotin ligase, TurboID and miniTurbo, with much greater catalytic efficiency than BioID, and the ability to carry out PL in cells in much shorter time windows (as little as 10 minutes) with non-toxic and easily deliverable biotin. In addition to shortening PL time by 100-fold and increasing PL yield in cell culture, TurboID enabled biotin-based PL in new settings, including yeast, Drosophila, and C. elegans.

4: Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza
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Posted 14 Mar 2020

Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza
14,541 downloads bioRxiv bioengineering

Timothy R. Abbott, Girija Dhamdhere, Yanxia Liu, Xueqiu Lin, Laine Goudy, Leiping Zeng, Augustine Chemparathy, Stephen Chmura, Nicholas S Heaton, Robert Debs, Tara Pande, Drew Endy, Marie La Russa, David B Lewis, Lei S Qi

The outbreak of the coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), has infected more than 100,000 people worldwide with over 3,000 deaths since December 2019. There is no cure for COVID-19 and the vaccine development is estimated to require 12-18 months. Here we demonstrate a CRISPR-Cas13-based strategy, PAC-MAN (Prophylactic Antiviral CRISPR in huMAN cells), for viral inhibition that can effectively degrade SARS-CoV-2 sequences and live influenza A virus (IAV) genome in human lung epithelial cells. We designed and screened a group of CRISPR RNAs (crRNAs) targeting conserved viral regions and identified functional crRNAs for cleaving SARS-CoV-2. The approach is effective in reducing respiratory cell viral replication for H1N1 IAV. Our bioinformatic analysis showed a group of only six crRNAs can target more than 90% of all coronaviruses. The PAC-MAN approach is potentially a rapidly implementable pan-coronavirus strategy to deal with emerging pandemic strains.

5: Potent neutralization of 2019 novel coronavirus by recombinant ACE2-Ig
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Posted 02 Feb 2020

Potent neutralization of 2019 novel coronavirus by recombinant ACE2-Ig
12,322 downloads bioRxiv bioengineering

Changhai Lei, Wenyan Fu, Kewen Qian, Tian Li, Sheng Zhang, Min Ding, Shi Hu

2019-nCoV, which is a novel coronavirus emerged in Wuhan, China, at the end of 2019, has caused at least infected 11,844 as of Feb 1, 2020. However, there is no specific antiviral treatment or vaccine currently. Very recently report had suggested that novel CoV would use the same cell entry receptor, ACE2, as the SARS-CoV. In this report, we generated a novel recombinant protein by connecting the extracellular domain of human ACE2 to the Fc region of the human immunoglobulin IgG1. An ACE2 mutant with low catalytic activity was also used in the study. The fusion proteins were then characterized. Both fusion proteins has high affinity binding to the receptor-binding domain (RBD) of SARS-CoV and 2019-nCoV and exerted desired pharmacological properties. Moreover, fusion proteins potently neutralized SARS-CoV and 2019-nCoV in vitro. As these fusion proteins exhibit cross-reactivity against coronaviruses, they could have potential applications for diagnosis, prophylaxis, and treatment of 2019-nCoV.

6: Octopi: Open configurable high-throughput imaging platform for infectious disease diagnosis in the field
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Posted 27 Jun 2019

Octopi: Open configurable high-throughput imaging platform for infectious disease diagnosis in the field
10,999 downloads bioRxiv bioengineering

Hongquan Li, Hazel Soto-Montoya, Maxime Voisin, Lucas Fuentes Valenzuela, Manu Prakash

Access to quantitative, robust, yet affordable diagnostic tools is necessary to reduce global infectious disease burden. Manual microscopy has served as a bedrock for diagnostics with wide adaptability, although at a cost of tedious labor and human errors. Automated robotic microscopes are poised to enable a new era of smart field microscopy but current platforms remain cost prohibitive and largely inflexible, especially for resource poor and field settings. Here we present Octopi, a low-cost ($250-$500) and reconfigurable autonomous microscopy platform capable of automated slide scanning and correlated bright-field and fluorescence imaging. Being highly modular, it also provides a framework for new disease-specific modules to be developed. We demonstrate the power of the platform by applying it to automated detection of malaria parasites in blood smears. Specifically, we discovered a spectral shift on the order of 10 nm for DAPI-stained Plasmodium falciparum malaria parasites. This shift allowed us to detect the parasites with a low magnification (equivalent to 10x) large field of view (2.56 mm^2) module. Combined with automated slide scanning, real time computer vision and machine learning-based classification, Octopi is able to screen more than 1.5 million red blood cells per minute for parasitemia quantification, with estimated diagnostic sensitivity and specificity exceeding 90% at parasitemia of 50/ul and 100% for parasitemia higher than 150/μl. With different modules, we further showed imaging of tissue slice and sputum sample on the platform. With roughly two orders of magnitude in cost reduction, Octopi opens up the possibility of a large robotic microscope network for improved disease diagnosis while providing an avenue for collective efforts for development of modular instruments.

7: DNA microscopy: Optics-free spatio-genetic imaging by a stand-alone chemical reaction
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Posted 19 Nov 2018

DNA microscopy: Optics-free spatio-genetic imaging by a stand-alone chemical reaction
9,368 downloads bioRxiv bioengineering

Joshua A. Weinstein, Aviv Regev, Feng Zhang

Analyzing the spatial organization of molecules in cells and tissues is a cornerstone of biological research and clinical practice. However, despite enormous progress in profiling the molecular constituents of cells, spatially mapping these constituents remains a disjointed and machinery-intensive process, relying on either light microscopy or direct physical registration and capture. Here, we demonstrate DNA microscopy, a new imaging modality for scalable, optics-free mapping of relative biomolecule positions. In DNA microscopy of transcripts, transcript molecules are tagged in situ with randomized nucleotides, labeling each molecule uniquely. A second in situ reaction then amplifies the tagged molecules, concatenates the resulting copies, and adds new randomized nucleotides to uniquely label each concatenation event. An algorithm decodes molecular proximities from these concatenated sequences, and infers physical images of the original transcripts at cellular resolution. Because its imaging power derives entirely from diffusive molecular dynamics, DNA microscopy constitutes a chemically encoded microscopy system.

8: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases
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Posted 28 Dec 2017

Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases
8,190 downloads bioRxiv bioengineering

David Welch, Manuela Buonanno, Veljko Grilj, Igor Shuryak, Connor Crickmore, Alan W Bigelow, Gerhard Randers-Pehrson, Gary W Johnson, David J Brenner

Airborne-mediated microbial diseases such as influenza and tuberculosis represent major public health challenges. A direct approach to prevent airborne transmission is inactivation of airborne pathogens, and the airborne antimicrobial potential of UVC ultraviolet light has long been established; however, its widespread use in public settings is limited because conventional UVC light sources are both carcinogenic and cataractogenic. By contrast, we have previously shown that far-UVC light (207-222 nm) efficiently kills bacteria without harm to exposed mammalian skin. This is because, due to its strong absorbance in biological materials, far-UVC light cannot penetrate even the outer (non living) layers of human skin or eye; however, because bacteria and viruses are of micrometer or smaller dimensions, far-UVC can penetrate and inactivate them. We show for the first time that far-UVC efficiently kills airborne aerosolized viruses, a very low dose of 2 mJ/cm2 of 222-nm light inactivating >95% of aerosolized H1N1 influenza virus. Continuous very low dose-rate far-UVC light in indoor public locations is a promising, safe and inexpensive tool to reduce the spread of airborne-mediated microbial diseases.

9: Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing
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Posted 29 Apr 2017

Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing
7,086 downloads bioRxiv bioengineering

Andrew M Smith, Miten Jain, Logan Mulroney, Daniel R Garalde, Mark Akeson

The ribosome small subunit is expressed in all living cells. It performs numerous essential functions during translation, including formation of the initiation complex and proofreading of base-pairs between mRNA codons and tRNA anticodons. The core constituent of the small ribosomal subunit is a ~1.5 kb RNA strand in prokaryotes (16S rRNA) and a homologous ~1.8 kb RNA strand in eukaryotes (18S rRNA). Traditional sequencing-by-synthesis (SBS) of rRNA genes or rRNA cDNA copies has achieved wide use as a "molecular chronometer" for phylogenetic studies [1], and as a tool for identifying infectious organisms in the clinic [2]. However, epigenetic modifications on rRNA are erased by SBS methods. Here we describe direct MinION nanopore sequencing of individual, full-length 16S rRNA absent reverse transcription or amplification. As little as 5 picograms (~10 attomole) of E. coli 16S rRNA was detected in 4.5 micrograms of total human RNA. Nanopore ionic current traces that deviated from canonical patterns revealed conserved 16S rRNA base modifications, and a 7-methylguanosine modification that confers aminoglycoside resistance to some pathological E. coli strains. This direct RNA sequencing technology has promise for rapid identification of microbes in the environment and in patient samples.

10: Exponential fluorescent amplification of individual RNAs using clampFISH probes
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Posted 21 Nov 2017

Exponential fluorescent amplification of individual RNAs using clampFISH probes
6,631 downloads bioRxiv bioengineering

Sara H. Rouhanifard, Ian A Mellis, Margaret Dunagin, Sareh Bayatpour, Orsolya Symmons, Allison Coté, Arjun Raj

Non-enzymatic, high-gain signal amplification methods with single-cell, single-molecule resolution are in great need. We present click-amplifying FISH (clampFISH) for the fluorescent detection of RNA that combines the specificity of oligonucleotides with bioorthogonal click chemistry in order to achieve high specificity and extremely high-gain (>400x) signal amplification. We show that clampFISH signal enables detection with low magnification microscopy and separation of cells by RNA levels via flow cytometry. Additionally, we show that the modular design of clampFISH probes enables multiplexing, that the locking mechanism prevents probe detachment in expansion microscopy, and that clampFISH works in tissue samples.

11: High-throughput, low-cost and rapid DNA sequencing using surface-coating techniques
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Posted 11 Dec 2020

High-throughput, low-cost and rapid DNA sequencing using surface-coating techniques
6,238 downloads bioRxiv bioengineering

Yanzhe Qin, Stephan Koehler, Shengming Zhao, Ruibin Mai, Zhuo Liu, Hao Lu, Chengmei Xing

The speed, expense and throughput of genomic sequencing impose limitations on its use for time-sensitive acute cases, such as rare or antibiotic resistant infections, and large-scale testing that is necessary for containing COVID-19 outbreaks using source-tracing. The major bottleneck for increasing the bandwidth and decreasing operating costs of next-generation sequencers (NGS) is the flow cell that supplies reagents for the biochemical processes; this subsystem has not significantly improved since 2005. Here we report a new method for sourcing reagents based on surface coating technology (SCT): the DNA adhered onto the biochip is directly contacted by a reagent-coated polymeric strip. Compared with flow cells the reagent layers are an order of magnitude thinner while both the reagent exchange rate and biochip area are orders of magnitude greater. These improvements drop the turn-around time from days to twelve hours and the cost for whole genome sequencing (WGS) from about $1000 to $15, as well as increase data production by several orders of magnitude. This makes NGS more affordable than many blood tests while rapidly providing detailed genomic information about microbial and viral pathogens, cancers and genetic disorders for targeted treatments and personalized medicine. This data can be pooled in population-wide databases for accelerated research and development as well providing detailed real-time data for tracking and containing outbreaks, such as the current COVID-pandemic.

12: Corrigendum and follow-up: Whole genome sequencing of multiple CRISPR-edited mouse lines suggests no excess mutations.
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Posted 23 Jun 2017

Corrigendum and follow-up: Whole genome sequencing of multiple CRISPR-edited mouse lines suggests no excess mutations.
6,176 downloads bioRxiv bioengineering

Kellie A. Schaefer, Benjamin W. Darbro, Diana F. Colgan, Stephen H. Tsang, Alexander G. Bassuk, Vinit B. Mahajan

Our previous publication suggested CRISPR-Cas9 editing at the zygotic stage might unexpectedly introduce a multitude of subtle but unintended mutations, an interpretation that not surprisingly raised numerous questions. The key issue is that since parental lines were not available, might the reported variants have been inherited? To expand upon the limited available whole genome data on whether CRISPR-edited mice show more genetic variation, whole-genome sequencing was performed on two other mouse lines that had undergone a CRISPR-editing procedure. Again, parents were not available for either the Capn5 nor Fblim1 CRISPR-edited mouse lines, so strain controls were examined. Additionally, we also include verification of variants detected in the initial mouse line. Taken together, these whole-genome-sequencing-level results support the idea that in specific cases, CRISPR-Cas9 editing can precisely edit the genome at the organismal level and may not introduce numerous, unintended, off-target mutations.

13: Deep learning achieves super-resolution in fluorescence microscopy
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Posted 27 Apr 2018

Deep learning achieves super-resolution in fluorescence microscopy
5,918 downloads bioRxiv bioengineering

Hongda Wang, Yair Rivenson, Yiyin Jin, Zhensong Wei, Ronald Gao, Harun Günaydin, Laurent A. Bentolila, Aydogan Ozcan

We present a deep learning-based method for achieving super-resolution in fluorescence microscopy. This data-driven approach does not require any numerical models of the imaging process or the estimation of a point spread function, and is solely based on training a generative adversarial network, which statistically learns to transform low resolution input images into super-resolved ones. Using this method, we super-resolve wide-field images acquired with low numerical aperture objective lenses, matching the resolution that is acquired using high numerical aperture objectives. We also demonstrate that diffraction-limited confocal microscopy images can be transformed by the same framework into super-resolved fluorescence images, matching the image resolution acquired with a stimulated emission depletion (STED) microscope. The deep network rapidly outputs these super-resolution images, without any iterations or parameter search, and even works for types of samples that it was not trained for.

14: Glycoengineering of NK cells with glycan ligands of CD22 and selectins for B-cell lymphoma therapy
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Posted 25 Mar 2020

Glycoengineering of NK cells with glycan ligands of CD22 and selectins for B-cell lymphoma therapy
5,859 downloads bioRxiv bioengineering

Senlian Hong, Chenhua Yu, Peng Wang, Yujie Shi, Bo Cheng, Mingkuan Chen, Digantkumar G. Chapla, Natalie Reigh, Yoshiki Narimatsu, Xing Chen, Henrik Clausen, Kelly W. Moremen, Matthew Scott Macauley, James C. Paulson, Peng Wu

CD22, a member of Siglec family of sialic acid binding proteins, has restricted expression on B cells. Antibody-based agents targeting CD22 or CD20 (RituxanTM) on B lymphoma and leukemia cells exhibit clinical efficacy for treating these malignancies, but also attack normal B cells leading to immune deficiency. Here, we report a chemoenzymatic glycocalyx editing strategy to introduce high-affinity and specific CD22 ligands onto NK-92MI and cytokine-induced killer (CIK) cells to achieve tumor-specific CD22 targeting. These CD22-ligand modified cells exhibited significantly enhanced tumor cell binding and killing in vitro without harming healthy B cells. For effective lymphoma cell killing in vivo we further functionalized CD22 ligand-modified NK-92MI cells with the E-selectin ligand sialyl Lewis X to promote trafficking to bone marrow. The cells containing the ligands of both CD22 and selectins resulted in the efficient suppression of B lymphoma in a xenograft model. Our results suggest that NK cells modified with glycan ligands to CD22 and selectins promote both targeted killing of B lymphoma cells and improved trafficking to sites where the cancer cells reside, respectively.

15: A rapid and tunable method to temporally control Cas9 expression enables the identification of essential genes and the interrogation of functional gene interactions in vitro and in vivo.
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Posted 28 Jul 2015

A rapid and tunable method to temporally control Cas9 expression enables the identification of essential genes and the interrogation of functional gene interactions in vitro and in vivo.
5,737 downloads bioRxiv bioengineering

Serif Senturk, Nitin H Shirole, Dawid D. Nowak, Vincenzo Corbo, Alexander Vaughan, David A. Tuveson, Lloyd C. Trotman, Adam Kepecs, Frank Stegmeier, Raffaella Sordella

The Cas9/CRISPR system is a powerful tool for studying gene function. Here we describe a method that allows temporal control of Cas9/CRISPER activity based on conditional CAS9 destabilization. We demonstrate that fusing an FKBP12-derived destabilizing domain to Cas9 enables conditional rapid and reversible Cas9 expression in vitro and efficient gene-editing in the presence of a guide RNA. Further, we show that this strategy can be easily adapted to co-express, from the same promoter, DD-Cas9 with any other gene of interest, without the latter being co-modulated. In particular, when co-expressed with inducible Cre-ERT2, our system enables parallel, independent manipulation of alleles targeted by Cas9 and traditional recombinase with single-cell specificity. We anticipate this platform will be used for the systematic identification of essential genes and the interrogation of genes functional interactions.

16: DeepImageJ: A user-friendly environment to run deep learning models in ImageJ
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Posted 16 Oct 2019

DeepImageJ: A user-friendly environment to run deep learning models in ImageJ
5,600 downloads bioRxiv bioengineering

Estibaliz Gómez-de-Mariscal, Carlos García-López-de-Haro, Wei Ouyang, Laurène Donati, Emma Lundberg, Michael Unser, Arrate Muñoz-Barrutia, Daniel Sage

DeepImageJ is a user-friendly solution that enables the generic use of pre-trained deep learning (DL) models for biomedical image analysis in ImageJ. The deepImageJ environment gives access to the largest bioimage repository of pre-trained DL models (BioImage Model Zoo). Hence, non-experts can easily perform common image processing tasks in life-science research with DL-based tools including pixel and object classification, instance segmentation, denoising or virtual staining. DeepImageJ is compatible with existing state-of-the-art solutions and it is equipped with utility tools for developers to add new models. Very recently, several training frameworks have adopted the deepImageJ format to deploy their work in one of the most used software in the field (ImageJ). Beyond its direct use, we expect deepImageJ to contribute to the broader dissemination and reuse of DL models in life-sciences applications and bioimage informatics.

17: Scaling up DNA data storage and random access retrieval
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Posted 07 Mar 2017

Scaling up DNA data storage and random access retrieval
5,448 downloads bioRxiv bioengineering

Lee Organick, Siena Dumas Ang, Yuan-Jyue Chen, Randolph Lopez, Sergey Yekhanin, Konstantin Makarychev, Miklos Z. Racz, Govinda Kamath, Parikshit Gopalan, Bichlien Nguyen, Christopher Takahashi, Sharon Newman, Hsing-Yeh Parker, Cyrus Rashtchian, Kendall Stewart, Gagan Gupta, Robert Carlson, John Mulligan, Douglas Carmean, Georg Seelig, Luis Ceze, Karin Strauss

Current storage technologies can no longer keep pace with exponentially growing amounts of data. Synthetic DNA offers an attractive alternative due to its potential information density of ~ 1018B/mm3, 107 times denser than magnetic tape, and potential durability of thousands of years. Recent advances in DNA data storage have highlighted technical challenges, in particular, coding and random access, but have stored only modest amounts of data in synthetic DNA. This paper demonstrates an end-to-end approach toward the viability of DNA data storage with large-scale random access. We encoded and stored 35 distinct files, totaling 200MB of data, in more than 13 million DNA oligonucleotides (about 2 billion nucleotides in total) and fully recovered the data with no bit errors, representing an advance of almost an order of magnitude compared to prior work. Our data curation focused on technologically advanced data types and historical relevance, including the Universal Declaration of Human Rights in over 100 languages, a high-definition music video of the band OK Go, and a CropTrust database of the seeds stored in the Svalbard Global Seed Vault. We developed a random access methodology based on selective amplification, for which we designed and validated a large library of primers, and successfully retrieved arbitrarily chosen items from a subset of our pool containing 10.3 million DNA sequences. Moreover, we developed a novel coding scheme that dramatically reduces the physical redundancy (sequencing read coverage) required for error-free decoding to a median of 5x, while maintaining levels of logical redundancy comparable to the best prior codes. We further stress-tested our coding approach by successfully decoding a file using the more error-prone nanopore-based sequencing. We provide a detailed analysis of errors in the process of writing, storing, and reading data from synthetic DNA at a large scale, which helps characterize DNA as a storage medium and justify our coding approach. Thus, we have demonstrated a significant improvement in data volume, random access, and encoding/decoding schemes that contribute to a whole-system vision for DNA data storage.

18: Applicability of Drug Response Metrics for Cancer Studies using Biomaterials
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Posted 07 Sep 2018

Applicability of Drug Response Metrics for Cancer Studies using Biomaterials
5,202 downloads bioRxiv bioengineering

Elizabeth A. Brooks, Sualyneth Galarza, Maria F. Gencoglu, R. Chase Cornelison, Jennifer M Munson, Shelly R Peyton

Bioengineers have built increasingly sophisticated models of the tumor microenvironment in which to study cell-cell interactions, mechanisms of cancer growth and metastasis, and to test new potential therapies. These models allow researchers to culture cells in conditions that include features of the in vivo tumor microenvironment (TME) implicated in regulating cancer progression, such as ECM stiffness, integrin binding to the ECM, immune and stromal cells, growth factor and cytokine depots, and a 3D geometry more representative of the TME than tissue culture polystyrene (TCPS). These biomaterials could be particularly useful for drug screening applications to make better predictions of efficacy, offering better translation to preclinical in vivo models and clinical trials. However, it can be challenging to compare drug response reports across different platforms and conditions in the current literature. This is, in part, as a result of inconsistent reporting and use of drug response metrics, and vast differences in cell growth rates across a large variety of biomaterial design. This perspective paper attempts to clarify the definitions of drug response measurements used in the field, and presents examples in which these measurements can and cannot be applied. We suggest as best practice to include appropriate controls, always measure the growth rate of cells in the absence of drug, and follow our provided decision tree matrix when reporting drug response metrics.

19: Designing Peptides on a Quantum Computer
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Posted 02 Sep 2019

Designing Peptides on a Quantum Computer
5,040 downloads bioRxiv bioengineering

Vikram Khipple Mulligan, Hans Melo, Haley Irene Merritt, Stewart Slocum, Brian D. Weitzner, Andrew M Watkins, P. Douglas Renfrew, Craig Pelissier, Paramjit S Arora, Richard Bonneau

Although a wide variety of quantum computers are currently being developed, actual computational results have been largely restricted to contrived, artificial tasks. Finding ways to apply quantum computers to useful, real-world computational tasks remains an active research area. Here we describe our mapping of the protein design problem to the D-Wave quantum annealer. We present a system whereby Rosetta, a state-of-the-art protein design software suite, interfaces with the D-Wave quantum processing unit to find amino acid side chain identities and conformations to stabilize a fixed protein backbone. Our approach, which we call the QPacker , uses a large side-chain rotamer library and the full Rosetta energy function, and in no way reduces the design task to a simpler format. We demonstrate that quantum annealer-based design can be applied to complex real-world design tasks, producing designed molecules comparable to those produced by widely adopted classical design approaches. We also show through large-scale classical folding simulations that the results produced on the quantum annealer can inform wet-lab experiments. For design tasks that scale exponentially on classical computers, the QPacker achieves nearly constant runtime performance over the range of problem sizes that could be tested. We anticipate better than classical performance scaling as quantum computers mature.

20: Rapid generation of potent antibodies by autonomous hypermutation in yeast
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Posted 11 Nov 2020

Rapid generation of potent antibodies by autonomous hypermutation in yeast
5,025 downloads bioRxiv bioengineering

Alon Wellner, Conor McMahon, Morgan S.A. Gilman, Jonathan R. Clements, Sarah Clark, Kianna M. Nguyen, Ming H. Ho, Jung-Eun Shin, Jared Feldman, Blake M. Hauser, Timothy M. Caradonna, Laura M. Wingler, Aaron G. Schmidt, Debora S Marks, Jonathan Abraham, Andrew C. Kruse, Chang C Liu

The predominant approach for antibody generation remains animal immunization, which can yield exceptionally selective and potent antibody clones owing to the powerful evolutionary process of somatic hypermutation. However, animal immunization is inherently slow, has poor compatibility with certain antigens (e.g., integral membrane proteins), and suffers from self-tolerance and immunodominance, which limit the functional spectrum of antibodies that can be obtained. Here, we describe Autonomous Hypermutation yEast surfAce Display (AHEAD), a synthetic recombinant antibody generation technology that imitates somatic hypermutation inside engineered yeast. In AHEAD, antibody fragments are encoded on an error-prone orthogonal DNA replication system, resulting in Saccharomyces cerevisiae populations that continuously mutate surface-displayed antibody repertoires. Simple cycles of yeast culturing and enrichment for antigen binding drive the evolution of high-affinity antibody clones in a readily parallelizable process that takes as little as 2 weeks. We applied AHEAD to generate nanobodies against the SARS-CoV-2 S glycoprotein, a GPCR, and other targets. The SARS-CoV-2 nanobodies, concurrently evolved from an open-source naive nanobody library in 8 independent experiments, reached subnanomolar affinities through the sequential fixation of multiple mutations over 3-8 AHEAD cycles that saw ~580-fold and ~925-fold improvements in binding affinities and pseudovirus neutralization potencies, respectively. These experiments highlight the defining speed, parallelizability, and effectiveness of AHEAD and provide a template for streamlined antibody generation at large with salient utility in rapid response to current and future viral outbreaks. ### Competing Interest Statement Provisional patents have been filed on this work, with A.W., C.M., A.C.K., and C.C.L. as co-inventors. A.C.K. is a co-founder and advisor of Tectonic Therapeutic, Inc., and of the Institute for Protein Innovation. C.C.L. is a co-founder of K2 Biotechnologies, Inc., which focuses on the use of continuous evolution technologies applied to antibody engineering.

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