A large-scale systematic survey of SARS-CoV-2 antibodies reveals recurring molecular features

In the past two years, the global research in combating COVID-19 pandemic has led to isolation and characterization of numerous human antibodies to the SARS-CoV-2 spike. This enormous collection of antibodies provides an unprecedented opportunity to study the antibody response to a single antigen. Using information derived from 88 research publications and 13 patents, we have assembled a dataset of ~8,000 human antibodies to the SARS-CoV-2 spike from >200 donors. Analysis of antibodies that target different domains of the spike protein reveals a number of common (public) responses to SARS-CoV-2, exemplified via recurring IGHV/IGK(L)V pairs, CDR H3 sequences, IGHD usage, and somatic hypermutation. We further present a proof-of-concept for predicting antigen specificity by using deep learning to differentiate sequences of antibodies to SARS-CoV-2 spike and to influenza hemagglutinin. Overall, this study not only provides an informative resource for antibody research, but fundamentally advances our molecular understanding of public antibody responses.

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Mitochondrial phosphate transport. Large scale isolation and characterization of the phosphate transport protein from beef heart mitochondria.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)47273-5 ◽

1984 ◽

Vol 259 (14) ◽

pp. 9115-9120 ◽

Cited By ~ 11

Author(s):

H V Kolbe ◽

D Costello ◽

A Wong ◽

R C Lu ◽

H Wohlrab

Keyword(s):

Large Scale ◽

Phosphate Transport ◽

Transport Protein ◽

Heart Mitochondria ◽

Beef Heart ◽

Isolation And Characterization ◽

Beef Heart Mitochondria

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Isolation and Characterization of Polyethylene Glycol (PEG)-Modified Glycol Lignin via PEG Solvolysis of Softwood Biomass in a Large-Scale Batch Reactor

ACS Sustainable Chemistry & Engineering ◽

10.1021/acssuschemeng.8b00965 ◽

2018 ◽

Vol 6 (6) ◽

pp. 7841-7848 ◽

Cited By ~ 4

Author(s):

Thi Thi Nge ◽

Yuki Tobimatsu ◽

Shiho Takahashi ◽

Eri Takata ◽

Masaomi Yamamura ◽

...

Keyword(s):

Polyethylene Glycol ◽

Large Scale ◽

Batch Reactor ◽

Isolation And Characterization

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Network-based characterization of disease–disease relationships in terms of drugs and therapeutic targets

Bioinformatics ◽

10.1093/bioinformatics/btaa439 ◽

2020 ◽

Vol 36 (Supplement_1) ◽

pp. i516-i524

Author(s):

Midori Iida ◽

Michio Iwata ◽

Yoshihiro Yamanishi

Keyword(s):

Large Scale ◽

Expression Patterns ◽

Therapeutic Targets ◽

Molecular Networks ◽

Supplementary Information ◽

New Associations ◽

Disease States ◽

Molecular Features ◽

Novel Approach

Abstract Motivation Disease states are distinguished from each other in terms of differing clinical phenotypes, but characteristic molecular features are often common to various diseases. Similarities between diseases can be explained by characteristic gene expression patterns. However, most disease–disease relationships remain uncharacterized. Results In this study, we proposed a novel approach for network-based characterization of disease–disease relationships in terms of drugs and therapeutic targets. We performed large-scale analyses of omics data and molecular interaction networks for 79 diseases, including adrenoleukodystrophy, leukaemia, Alzheimer's disease, asthma, atopic dermatitis, breast cancer, cystic fibrosis and inflammatory bowel disease. We quantified disease–disease similarities based on proximities of abnormally expressed genes in various molecular networks, and showed that similarities between diseases could be explained by characteristic molecular network topologies. Furthermore, we developed a kernel matrix regression algorithm to predict the commonalities of drugs and therapeutic targets among diseases. Our comprehensive prediction strategy indicated many new associations among phenotypically diverse diseases. Supplementary information Supplementary data are available at Bioinformatics online.

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Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms

Science ◽

10.1126/science.abe3354 ◽

2020 ◽

Vol 370 (6519) ◽

pp. 950-957 ◽

Cited By ~ 21

Author(s):

M. Alejandra Tortorici ◽

Martina Beltramello ◽

Florian A. Lempp ◽

Dora Pinto ◽

Ha V. Dang ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Viral Escape ◽

Angiotensin Converting Enzyme 2 ◽

Effector Functions ◽

Human Antibodies ◽

Binding Domains ◽

Isolation And Characterization ◽

Cryo Electron Microscopy ◽

Escape Mutants

Efficient therapeutic options are needed to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has caused more than 922,000 fatalities as of 13 September 2020. We report the isolation and characterization of two ultrapotent SARS-CoV-2 human neutralizing antibodies (S2E12 and S2M11) that protect hamsters against SARS-CoV-2 challenge. Cryo–electron microscopy structures show that S2E12 and S2M11 competitively block angiotensin-converting enzyme 2 (ACE2) attachment and that S2M11 also locks the spike in a closed conformation by recognition of a quaternary epitope spanning two adjacent receptor-binding domains. Antibody cocktails that include S2M11, S2E12, or the previously identified S309 antibody broadly neutralize a panel of circulating SARS-CoV-2 isolates and activate effector functions. Our results pave the way to implement antibody cocktails for prophylaxis or therapy, circumventing or limiting the emergence of viral escape mutants.

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Virulence Characterization of Puccinia striiformis f. sp. tritici Using a New Set of Yr Single-Gene Line Differentials in the United States in 2010

Plant Disease ◽

10.1094/pdis-01-14-0071-re ◽

2014 ◽

Vol 98 (11) ◽

pp. 1534-1542 ◽

Cited By ~ 89

Author(s):

Anmin Wan ◽

Xianming Chen

Keyword(s):

United States ◽

Stripe Rust ◽

Large Scale ◽

Puccinia Striiformis ◽

Yellow Rust ◽

Single Gene ◽

The United States ◽

The Past ◽

History Of

Puccinia striiformis f. sp. tritici causes stripe rust (yellow rust) of wheat and is highly variable in virulence toward wheat with race-specific resistance. During 2010, wheat stripe rust was the most widespread in the recorded history of the United States, resulting in large-scale application of fungicides and substantial yield loss. A new differential set with 18 yellow rust (Yr) single-gene lines was established and used to differentiate races of P. striiformis f. sp. tritici, which were named as race PSTv in distinction from the PST races identified in the past. An octal system was used to describe the virulence and avirulence patterns of the PSTv races. From 348 viable P. striiformis f. sp. tritici isolates recovered from a total of 381 wheat and grass stripe rust samples collected in 24 states, 41 races, named PSTv-1 to PSTv-41, were identified using the new set of 18 Yr single-gene differentials, and their equivalent PST race names were determined on the previous set of 20 wheat cultivar differentials. The frequencies and distributions of the races and their virulences were determined. The five most predominant races were PSTv-37 (34.5%), PSTv-11 (17.5%), PSTv-14 (7.2%), PSTv-36 (5.2%), and PSTv-34 (4.9%). PSTv-37 was distributed throughout the country while PSTv-11 and PSTv-14 were almost restricted to states west of the Rocky Mountains. The races had virulence to 0 to 13 of the 18 Yr genes. Frequencies of virulences toward resistance genes Yr6, Yr7, Yr8, Yr9, Yr17, Yr27, Yr43, Yr44, YrTr1, and YrExp2 were high (67.0 to 93.7%); those to Yr1 (32.8%) and YrTye (31.3%) were moderate; and those to Yr10, Yr24, Yr32, and YrSP were low (3.4 to 5.7%). All of the isolates were avirulent to Yr5 and Yr15.

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Isolation and characterization of extracellular vesicles

Trillium Exctracellular Vesicles ◽

10.47184/tev.2019.01.02 ◽

2019 ◽

Vol 1 (1) ◽

pp. 18-26

Author(s):

Fabia Fricke ◽

Dominik Buschmann ◽

Michael W. Pfaffl

Keyword(s):

Cell Culture ◽

Extracellular Vesicles ◽

Culture Media ◽

Body Fluids ◽

Cell Culture Media ◽

Advantages And Disadvantages ◽

The Past ◽

Isolation And Characterization ◽

Basic Biology

Research into extracellular vesicles (EVs) gained significant traction in the past decade and EVs have been investigated in a wide variety of studies ranging from basic biology to diagnostic and therapeutic applications. Since EVs are secreted by most, if not all, eukaryotic and prokaryotic cells, they have been detected in body fluids as diverse as blood, urine and saliva as well as in cell culture media. In this chapter, we will provide an overview of EV isolation and characterization strategies and highlight their advantages and disadvantages.

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THE APPARENT FRACTAL CONJECTURE

Fractals ◽

10.1142/s0218348x01000646 ◽

2001 ◽

Vol 09 (03) ◽

pp. 237-240 ◽

Cited By ~ 8

Author(s):

MARCELO B. RIBEIRO

Keyword(s):

Large Scale ◽

Short Communication ◽

Fractal Structure ◽

Average Density ◽

The Past ◽

Standard Cosmology ◽

Geometrical Effect ◽

Theoretical Results ◽

Past Light Cone

This short communication advances the hypothesis that the observed fractal structure of large-scale distribution of galaxies is due to a geometrical effect, which arises when observational quantities relevant for the characterization of a cosmological fractal structure are calculated along the past light cone. If this hypothesis proves, even partially, correct, most, if not all, objections raised against fractals in cosmology may be solved. For instance, under this view the standard cosmology has zero average density, as predicted by an infinite fractal structure, with, at the same time, the cosmological principle remaining valid. The theoretical results which suggest this conjecture are reviewed, as well as possible ways of checking its validity.

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