Library

This library presents some publications, presentations, posters and case studies of Noblis’ staff. The research spans diverse subjects — developing cutting-edge whole genome sequence computational tools, biomarkers of anthrax infection, microbiomics and microbial metabolomics — all accretive to productive bioinformatics analysis. Please contact us for more information about the tools, methods and topics.

PRESENTATIONS/POSTERS PUBLICATIONS CASE STUDIES

PRESENTATIONS and Posters


Automated Molecular Clock Analysis of the O-PS Gene Cluster of Vibrio cholerae

Gram-negative bacteria express a lipopolysaccharide (LPS) that stabilizes the outer membrane while promoting host-pathogen interactions. The O-antigen (O-PS) is the external component of this endotoxin and is the basis of subspecies classification via serological methods. Our goal for this project was to test the molecular clock hypothesis and estimate the mutation rate of the O-PS region. In 2019, Noblis presented this research at the 54th US-Japan Cooperative Medical Sciences Program (CMSP) Joint Panel Conference on Cholera and Other Bacterial Enteric Infections in Osaka, Japan.

Related

Microbial Genomics

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BioLaboro: An end-to-end application for detecting molecular assay signature erosion and design of new assays in response to emerging new biothreats

The entire BioLaboro system is driven by a simple graphical user interface that allows users to point-and-click to create analysis pipelines. The system ingests an array of NCBI data sources to perform its analyses and can be customized by a variety of parameters, adjustable on the fly. Using BioLaboro, Noblis is able to quickly identify which currently fielded Ebolavirus assays could potentially detect Bombali ebolavirus today and design a set of potential new assays with perfect in silico detection accuracy for the future. In 2019, Noblis presented this research at the 14th Annual Sequencing, Finishing, and Analysis in the Future (SFAF) Meeting in Santa Fe, New Mexico.

Related

PCR Assay Testing and Development

Tools

BioVelocity PCR Signature Erosion Toolkit (PSET)

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Whole Genome Sequencing Data Obfuscation Using Bloom Cipher

Bloom Cipher is a method of compressing and encoding metagenomics whole genome sequencing read sets for easy transfer and analysis, reduced liability, and increased security. By using the Bloom Cipher, one can compress and encode the read set in a lossy format, which allows for basic analysis while removing some of the liability of finding by using the probabilistic analysis. Future research will further enhance the utility and security of the method. In 2017, Noblis presented this research at the 12th Annual Sequencing, Finishing, and Analysis in the Future (SFAF) Meeting in Santa Fe, New Mexico.

Related

Data Hygiene Engineered Sequences – Reducing the Problem Set

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Whole Genome Sequencing Enhances Food Safety by Rapidly and Accurately Detecting Pathogens in Food Products

Noblis developed a high-speed sequence processing and alignment platform, BioVelocity, to analyze whole genome sequence (WGS) data. During the 2016 Institute of Food Technologists (IFT16) conference, we presented on the use of BioVelocity to characterize a foodborne disease outbreak of Salmonella. Our analysis discriminated the Salmonella outbreak samples to the strain level and linked them to a commercial peanut butter product. Furthermore, simultaneous alignment of WGS data to reference genomes identified single nucleotide polymorphisms (SNPs) that were used to create a phylogenetic tree. Based on this method, we inferred that three unassociated samples were also highly related to the outbreak strain.

Related

Metagenomics Food Safety Visualizations

Tools

BioVelocity PCR Signature Erosion Toolkit (PSET)

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Analysis of the O-antigen of Vibrio cholerae

Noblis co-authored two poster presentations about the phylogenetic analysis of the O-antigen of Vibrio cholerae. There is a lack of fully sequenced V. cholerae genomes, but there are numerous whole genome shotgun sequences from which to extract regions of interest. Noblis developed a pipeline to automatically download and extract the O-antigen region of interest for Basic Local Alignment Search Tool (BLAST) processing and heat-map visualization of the results. The study exploited the presence of conserved junction genes to extract complete regions from contigs and subsequently perform phylogenetic analysis. Results revealed some mixture of the O-antigen serotypes, suggesting that horizontal-gene transfer has occurred.

Related

PCR Assay Testing and Design Visualizations

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In Silico Primer Design

Identification of bacterial organisms and viruses plays an important role in a multitude of areas, such as healthcare, biodefense, research, and food safety. Continually increasing databases of sequence data has made it possible to identify species-specific genomic regions, even serotypes of bacteria, as well as various classes of virus. As a part of an internal research project, Noblis examined the possibility that unique regions of genomes (i.e., signature sequences) could be used to differentiate phylogenetic levels, such as genus, species, and strain from all other known genomes, including those of closely-related organisms. The identified signature regions were evaluated as potential primers using the open source tool Primer 3 and were confirmed for specificity using BLAST. This pipeline supports continual generation of primers, particularly to combat assay degradation occurring over time.

Related

PCR Assay Testing and Design

Tools

BioVelocity PCR Signature Erosion Toolkit (PSET)

PDF

PUBLICATIONS


Courts Have a Significant Role to Play in the Whole-of-Government Approach (WGA) to Our Safety and Security

As technology continues to expand and diversify the potential for Chemical, Biological, Radiological, Nuclear, and Explosives (CBRNE) attacks, cyberattacks, and other threats to homeland security, a broad Whole-of-Government Approach (WGA) is needed. In the lead article in the online, quarterly publication of the National Association for Court Management (NACM) Court Manager Vol. 34 #4 – Winter 2019, we contend that complex 21st century threats defy solutions by individual government entities. Rather interagency coordination across all three branches of government and engagement of non-governmental agencies are key to countering threats to our public health, safety, security, way of life and democratic values. To ensure a successful WGA, we argue for the active judicial participation in advanced planning, education and coordination to anticipate the future need for court decision making. The purpose of the article is to promote serious conversation about the roles of court administrators, judges and policymakers in the face of natural and manmade disasters, epidemics and pandemics, CBRNE attacks, and cyberattacks.

Related

Noblis Website Data Hygiene

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Lassa Virus Circulating in Liberia: A Retrospective Genomic Characterization

Noblis scientists and other scientists and researchers contributed to a paper entitled “Lassa virus circulating in Liberia: a retrospective genomic characterization” which appeared in the Lancet Infectious Diseases October 4, 2019 issue. The purpose of the paper was to compare published and recent Lassa virus genomes to assess the ability of currently deployed diagnostic assays to detect circulating Lassa virus. Our scientists used in silico bioinformatics methods, including Noblis’ PCR Signature Erosion Tool (PSET), to provide data visualizations and insights for the genome relationships.

Lancet Infectious Diseases: DOI 10.1016/S1473-3099(19)30486-4, 2019.

Related

PCR Assay Testing and Design

Tools

PCR Signature Erosion Toolkit (PSET)

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Evaluation of Signature Erosion in Ebola Virus Due to Genomic Drift and Its Impact on the Performance of Diagnostic Assays

Evaluation of Signature Erosion in Ebola Virus Due to Genomic Drift and Its Impact on the Performance of Diagnostic Assays demonstrates the use of BioVelocity and PCR Signature Erosion Tool (PSET) to evaluate polymerase chain reaction (PCR) assays deployed during the West African Ebola epidemic and other Ebola PCR assays available. PSET evaluated the assays’ effectiveness against the strain circulating in West Africa during the epidemic, while BioVelocity identified optimal sequence target for future assay design and compared its findings to classical techniques.

Viruses 7: 3130-3154, 2015.

Related

PCR Assay Testing and Design

Tools

BioVelocity PCR Signature Erosion Toolkit (PSET)

PDF

Microbiome in the Urinary System – a Review

Urine was considered sterile in healthy individuals for many years, and the presence of bacteria signified a urinary tract infection. With Expanded Quantitative Urine Culture and molecular techniques, the previous clinical dogma is no longer valid. Healthy people harbor a considerable microbial community—or microbiota—in their urinary systems. Similar to other physiological niches, microbiota also play a crucial role in urinary health of individuals. Understanding the urinary microbiome allows a more holistic approach in the diagnosis, treatment, and prevention of diseases in the urinary system. This review provides an overview of current findings in urinary microbiome research and discusses gaps for future research.

AIMS Microbiology 3(2): 143-154, 2017.

Related

Metagenomics

Tools

BioVelocity

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Probiotics in Personal Care Products

Knowledge gained from the Human Microbiome Project supports using probiotics to achieve a balanced microbial community and potentially reduce or alleviate certain disorders. Most research studies and commercial probiotic products have focused on the human gastrointestinal tract. Recently, interests and applications have extended to other physiological systems. Personal care products are used widely every day, and potential uses of probiotics in this market sector are being explored. This review summarizes recent findings of microbial communities in the skin and oral cavity—where personal care products are mostly applied—and discusses opportunities and challenges of probiotics in these products.

Microbiology Discovery 3(5), 2015.

Related

Metagenomics

Tools

BioVelocity

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Microbial Metabolomics

Microbial metabolomics constitutes an integrated component of systems biology. By studying the complete set of metabolites within a microorganism and monitoring the global outcome of interactions between its development processes and the environment, metabolomics can potentially provide a more accurate snap shot of the actual physiological state of the cell. Recent advancements of technologies and post-genomic developments enable the study and analysis of the metabolome. This unique contribution resulted in many scientific disciplines incorporating metabolomics as one of their “-omics” platforms. This review focuses on metabolomics in microorganisms and uses selected topics to illustrate its impact on the understanding of systems microbiology.

Current Genomics 12:391-403, 2011.

Related

Microbial Genomics

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A rare Presentation of Community-Acquired Pneumonia Caused by Corynebacterium pseudodiptheriticum: A Case Report

A normal flora in the upper respiratory tract, Corynebacterium pseudodiptheriticum is not often considered as the causative bacterium for community-acquired pneumonia. A patient with bronchiectasis was initially suspected as being infected with Mycobacterium avium. When antibiotic treatment was not successful, bronchial alveolar lavage was obtained for microbiological culturing. Once C. pseudodiptheriticum was recovered, its antibiotic susceptibility profile allowed appropriate antimicrobial intervention to arrest the infection. The patient experienced full recovery. This case report shows the importance of considering non-routine--at times invasive--clinical specimens for diagnosis. Furthermore, commensal microbes should not be dismissed as possible etiological agents in pulmonary infections.

Translational Biomedicine 2010. Doi:10:3823/408.

Related

Antibiotic Resistance Using BioVelocity to Detect Pathogens in Human Clinical Samples

Tools

BioVelocity

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Discovery of Infectious Disease Biomarkers in Murine Anthrax Model Using Mass Spectrometry of the Low-Molecular-Mass Serum Proteome

A novel mass-spectrometry–based approach to identify host-derived, low-molecular mass biomarkers in the blood proteome was tested in a murine model. Mice were challenged with Bacillus anthracis Sterne (toxigenic) or delta Sterne (non-virulent) spores. Serum samples obtained at multiple time points yielded more than 200 proteins, displaying low-variance differential abundances between lethal and non-lethal challenges. Six serum proteins strongly coincided with established anthrax disease and mortality, making them potential candidates for host-derived anthrax-disease–associated biomarkers. Furthermore, their abundance levels in sera of doxycycline-treated mice can serve as useful tools for monitoring treatment efficacies.

J. Proteomics & Bioinformatics 2009. Doi: 10.4172/jpb.1000101.

Related

Virulence Factors Structure-Based Protein Engineering and Design

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Microbial Extremophiles at the Limits of Life

Prokaryotic extremophiles were the first representatives of life on Earth and likely contributed to the geological structures of currently known ecosystems. Their genome flexibility allowed adaptation to a wide spectrum of extreme environments. Modern extremophiles consisted of thermophilic, psychrophilic, acidophilic, alkaliphilic, halophilic, barophilic, and radio-resistant species. Since one organism often overlaps several extreme conditions, it reflects multiple interactions between different environmental factors. This review discusses the current status of extremophile research and summarizes the limits of life for different species. Also mentioned are extremophiles from unusual places and recent studies of microfossils in meteorites, with a focus on their significance to astrobiology.

Critical Reviews in Microbiology 33: 183-209, 2007.

Related

Microbial Genomics

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Case Studies


Identifing Unique Genetic Sequences of the International Wuhan Coronavirus

Scientists from Noblis and the Defense Biological Product Assurance Office (DBPAO), a component of the Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense (JPEO-CBRND), are continuously evaluating polymerase chain reaction (PCR) assays (tests) for detection of the new Wuhan coronavirus. The research was done using BioLaboro, a Noblis application developed for rapidly designing de novo (new) assays and validating existing PCR detection assays.

Read the full news release on noblis.org.

Related

PCR Assay Testing and Design

Tools

BioVelocity

Bacterial Strain Detection with BioVelocity

Noblis collaborated with BEI Resources, operated by the American Type Culture Collection (ATCC), on a study to more quickly and accurately identify strains using Noblis’ high-speed sequence processing and analysis platform, BioVelocity. We queried blinded samples of raw reads against several large, public bacterial and viral genome databases using BioVelocity. The samples included a mix of bacterial species that are difficult for ATCC to identify using traditional 16S ribosomal RNA (rRNA) techniques. The results demonstrated a marked improvement over ATCC’s current technology with respect to difficult strains and demonstrates the potential for technologies like BioVelocity to provide new solutions for strain identification in the future.

Related

Metagenomics

Tools

BioVelocity

Rapid and Portable Genome Classification System

Noblis developed a novel method to compact large genome sequence datasets and raw genome sequence read sets for rapid analysis on portable devices. The Rapid and Portable Genome Classification System (RPGCS) is a technical approach that balances accuracy and speed with an intuitive user interface and greatly reduced computational demand. The system combines modern genomics techniques, statistical modeling, data analytics, and machine learning algorithms. The main goals of the RPGCS are to filter out potential organism matches in a sequenced sample and to determine a most-likely organism identity based on the matches found in the data structure without the need for high-performance computing power.

Related

Engineered Sequences

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Pathogen Detection in Human DNA Samples

Noblis collaborated with the National Institutes of Health (NIH) National Institute of Neurological Disorders and Stroke (NINDS) to demonstrate BioVelocity’s ability to detect pathogens in metagenomics samples mixed with human DNA. Noblis was given RNA-Seq data as FASTQ raw reads and tasked to discover pathogens. The case study included three rounds of blinded data that were intentionally spiked with a variety of pathogenic bacteria, viruses, and parasites. Noblis collaborated with the NIH researchers to fine tune our metagenomic algorithm so that by round 3, BioVelocity, with Noblis subject matter expert (SME) input, correctly identified 32 of 33 spiked in pathogens by general type, 26 of which were to the exact correct stain.

Related

Using BioVelocity to Detect Pathogens in Human Clinical Samples

Tools

BioVelocity