Characterization of ribonucleotide reductases of emerging pathogens Elizabethkingia anophelis and Elizabethkingia meningoseptica and streptonigrin as their inhibitor: a computational study

Abstract The paper on hand approaches the classical makespan minimization problem on identical parallel machines from a rather theoretical point of view. Using an approach similar to the idea behind inverse optimization, we identify a general structural pattern of optimal multiprocessor schedules. We also show how to derive new dominance rules from the characteristics of optimal solutions. Results of our computational study attest to the efficacy of the new rules. They are particularly useful in limiting the search space when each machine processes only a few jobs on average.

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Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses

PLoS Pathogens ◽

10.1371/journal.ppat.1009315 ◽

2021 ◽

Vol 17 (3) ◽

pp. e1009315

Author(s):

Marylee L. Kapuscinski ◽

Nicholas A. Bergren ◽

Brandy J. Russell ◽

Justin S. Lee ◽

Erin M. Borland ◽

...

Keyword(s):

Plant Pathogens ◽

Reference Sequence ◽

Large Sample Size ◽

Emerging Pathogens ◽

Genome Sequences ◽

Pathogenic Potential ◽

Genomic Characterization ◽

Response Decisions ◽

Rapid Characterization

Bunyaviruses (Negarnaviricota: Bunyavirales) are a large and diverse group of viruses that include important human, veterinary, and plant pathogens. The rapid characterization of known and new emerging pathogens depends on the availability of comprehensive reference sequence databases that can be used to match unknowns, infer evolutionary and pathogenic potential, and make response decisions in an evidence-based manner. In this study, we determined the coding-complete genome sequences of 99 bunyaviruses in the Centers for Disease Control and Prevention’s Arbovirus Reference Collection, focusing on orthonairoviruses (family Nairoviridae), orthobunyaviruses (Peribunyaviridae), and phleboviruses (Phenuiviridae) that either completely or partially lacked genome sequences. These viruses had been collected over 66 years from 27 countries from vertebrates and arthropods representing 37 genera. Many of the viruses had been characterized serologically and through experimental infection of animals but were isolated in the pre-sequencing era. We took advantage of our unusually large sample size to systematically evaluate genomic characteristics of these viruses, including reassortment, and co-infection. We corroborated our findings using several independent molecular and virologic approaches, including Sanger sequencing of 197 genome segments, and plaque isolation of viruses from putative co-infected virus stocks. This study contributes to the described genetic diversity of bunyaviruses and will enhance the capacity to characterize emerging human pathogenic bunyaviruses.

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Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality

10.1101/2021.04.07.438849 ◽

2021 ◽

Author(s):

Jimmy D Gollihar ◽

Jason S McLellan ◽

Daniel R Boutz ◽

Jule Goike ◽

Andrew Horton ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Surface Display ◽

Functional Characterization ◽

Yeast Surface Display ◽

Spike Protein ◽

Emerging Pathogens ◽

Effective Interventions ◽

Yeast Surface

The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence, together with increased genomic surveillance, methods to rapidly develop and assess effective interventions are critically needed. Here we report the discovery of SARS-CoV-2 neutralizing antibodies isolated from COVID-19 patients using a high-throughput platform. Antibodies were identified from unpaired donor B-cell and serum repertoires using yeast surface display, proteomics, and public light chain screening. Cryo-EM and functional characterization of the antibodies identified N3-1, an antibody that binds avidly (Kd,app = 68 pM) to the receptor binding domain (RBD) of the spike protein and robustly neutralizes the virus in vitro. This antibody likely binds all three RBDs of the trimeric spike protein with a single IgG. Importantly, N3-1 equivalently binds spike proteins from emerging SARS-CoV-2 variants of concern, neutralizes UK variant B.1.1.7, and binds SARS-CoV spike with nanomolar affinity. Taken together, the strategies described herein will prove broadly applicable in interrogating adaptive immunity and developing rapid response biological countermeasures to emerging pathogens.

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Characterization of Protease Produced by Elizabethkingia meningoseptica CS2-1 and Optimization of Cultural Conditions for Amino Acid Production

Journal of Applied Biological Chemistry ◽

10.3839/jabc.2011.023 ◽

2011 ◽

Vol 54 (2) ◽

pp. 135-142

Author(s):

Se-Jong Kim ◽

Chun-Hwi Cho ◽

Kyung-Sook Whang

Keyword(s):

Amino Acid ◽

Acid Production ◽

Amino Acid Production ◽

Cultural Conditions ◽

Elizabethkingia Meningoseptica

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Characterization of Light Weight Heat Sink Materials for Thermal Management of Electronics

ASME 2007 InterPACK Conference, Volume 1 ◽

10.1115/ipack2007-33216 ◽

2007 ◽

Cited By ~ 2

Author(s):

Tunc Icoz ◽

Mehmet Arik ◽

John T. Dardis

Keyword(s):

Thermal Management ◽

Heat Sink ◽

High Efficiency ◽

Computational Study ◽

Heat Sinks ◽

Advanced Materials ◽

Air Cooling ◽

Thermal Management Of Electronics ◽

Thermal Solution

Thermal management of electronics is a critical part of maintaining high efficiency and reliability. Adequate cooling must be balanced with weight and volumetric requirements, especially for passive air-cooling solutions in electronics applications where space and weight are at a premium. It should be noted that there are systems where thermal solution takes more than 95% of the total weight of the system. Therefore, it is necessary to investigate and utilize advanced materials to design low weight and compact systems. Many of the advanced materials have anisotropic thermal properties and their performances depend strongly on taking advantage of superior properties in the desired directions. Therefore, control of thermal conductivity plays an important role in utilization of such materials for cooling applications. Because of the complexity introduced by anisotropic properties, thermal performances of advanced materials are yet to be fully understood. Present study is an experimental and computational study on characterization of thermal performances of advanced materials for heat sink applications. Numerical simulations and experiments are performed to characterize thermal performances of four different materials. An estimated weight savings in excess of 75% with lightweight materials are observed compared to the traditionally used heat sinks.

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Systematic Characterization of Gas Phase Binary Pre-Nucleation Complexes Containing H2SO4 + X, [ X = NH3, (CH3)NH2, (CH3)2NH, (CH3)3N, H2O, (CH3)OH, (CH3)2O, HF, CH3F, PH3, (CH3)PH2, (CH3)2PH, (CH3)3P, H2S, (CH3)SH, (CH3)2S, HCl, (CH3)Cl)]. A Computational Study

The Journal of Physical Chemistry A ◽

10.1021/acs.jpca.7b10205 ◽

2018 ◽

Vol 122 (8) ◽

pp. 2116-2128 ◽

Cited By ~ 3

Author(s):

Paolo Sebastianelli ◽

Pablo M. Cometto ◽

Rodolfo G. Pereyra

Keyword(s):

Gas Phase ◽

Computational Study

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Molecular Characterization of the sucB Gene Encoding the Immunogenic Dihydrolipoamide Succinyltransferase Protein of Bartonella vinsonii subsp. berkhoffii and Bartonella quintana

Infection and Immunity ◽

10.1128/iai.71.8.4818-4822.2003 ◽

2003 ◽

Vol 71 (8) ◽

pp. 4818-4822 ◽

Cited By ~ 10

Author(s):

Robert D. Gilmore, ◽

Amber M. Carpio ◽

Michael Y. Kosoy ◽

Kenneth L. Gage

Keyword(s):

Q Fever ◽

Clinical Manifestations ◽

Cross Reactivity ◽

Emerging Pathogens ◽

Expression Library ◽

Gene Encoding ◽

Bartonella Quintana ◽

Genomic Expression ◽

Dihydrolipoamide Succinyltransferase

ABSTRACT Members of the genus Bartonella have historically been connected with human disease, such as cat scratch disease, trench fever, and Carrion's disease, and recently have been recognized as emerging pathogens causing other clinical manifestations in humans. However, because little is known about the antigens that elicit antibody production in response to Bartonella infections, this project was undertaken to identify and molecularly characterize these immunogens. Immunologic screening of a Bartonella vinsonii subsp. berkhoffii genomic expression library with anti-Bartonella antibodies led to the identification of the sucB gene, which encodes the enzyme dihydrolipoamide succinyltransferase. Antiserum from a mouse experimentally infected with live Bartonella was reactive against recombinant SucB, indicating the mounting of an anti-SucB response following infection. Antigenic cross-reactivity was observed with antiserum against other Bartonella spp. Antibodies against Coxiella burnetti, Francisella tularensis, and Rickettsia typhi also reacted with our recombinant Bartonella SucB. Potential SucB antigenic cross-reactivity presents a challenge to the development of serodiagnostic tests for other intracellular pathogens that cause diseases such as Q fever, rickettsioses, brucelloses, tularemia, and other bartonelloses.

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