Elizabeth Vitalis

• Biomedical Sciences at Inscripta

Genes conferring antibiotic resistance to groups of bacterial pathogens are cause for considerable concern, as many once-reliable antibiotics continue to see a reduction in efficacy. The recent discovery of the metallo β-lactamase blaNDM-1 gene, which appears to grant antibiotic resistance to a variety of Enterobacteriaceae via a mobile plasmid, is...

B1_MBL_active_site_measurements.csv--(Comma-separated values file) Measurements for active sites of selected MBLs. Each row-wise record of this file contains information regarding the active site of the PDB entry noted in the first column. This data includes: the B1 type, the area and volume of the active site (as estimated by CASTp), an indicator...

MBL_library.csv--(Comma-seprated values file) Enumeration of MBL folds comprising the comparative analysis library. This file contains a list of all structures included in the described MBL library (see 2.1), as well as their type classification.

3q6x_A_StralSV_w90_5.txt--(Text file) StralSV output for NDM-1 structure 3q6x_A. This file contains the raw output of the StralSV algorithm run on 3q6x_A using the entire PDB (release 2011/08/02). The header of the file contains structural matches (by region) of various PDB templates to NDM-1, followed by the annotations of the templates. The main...

Whole_chain_clustering--(Portable document format file) Whole-chain clustering of B1 MBL library using StralCP. This supplemental figure is the whole chain dendrogram for the B1 library, and is depicted in similar form and labeling as Figure 4.

This chapter addresses issues associated with the identification of signatures based on genomic DNA/RNA, which can be used to identify and characterize pathogens for biodefense and microbial forensic goals. Genomic signature-based identification techniques have the advantage of being precise, highly sensitive, and relatively fast in comparison to b...

We developed an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs. LAVA identifies combinations of six primer regions for basic LAMP signatures, or combinations of eight primer regi...

Multiplex RT-PCR suspension array assays provide a powerful tool for identifying the causative agent(s) of respiratory infections. These assays are time consuming and laborious on a time-per-sample basis if only a few samples require processing. To address this shortcoming and provide an automated solution for fast detection and identification of v...

Good progress has been made on both bacterial and viral sequencing by the TMTI centers. While access to appropriate samples is a limiting factor to throughput, excellent progress has been made with respect to getting agreements in place with key sources of relevant materials. Sharing of sequenced genomes funded by TMTI has been extremely limited to...

The Lawrence Livermore National Lab Bioinformatics group has recently taken on a role in DTRA's Transformation Medical Technologies Initiative (TMTI). The high-level goal of TMTI is to accelerate the development of broad-spectrum countermeasures. To achieve those goals, TMTI has a near term need to obtain more sequence information across a large ra...

Finding the amino acid mutations that affect the severity of influenza infections remains an open and challenging problem. Of special interest is better understanding how current circulating influenza strains could evolve into a new pandemic strain. Influenza proteomes from distinct viral phenotype classes were searched for class specific amino aci...

A nucleic acid-based multiplexed assay was developed that combines detection of foot-and-mouth disease virus (FMDV) with rule-out assays for two other foreign animal diseases and four domestic animal diseases that cause vesicular or ulcerative lesions indistinguishable from FMDV infection in cattle, sheep and swine. The FMDV "look-alike" diagnostic...

A high-throughput multiplexed assay was developed for the differential laboratory detection of foot-and-mouth disease virus (FMDV) from viruses that cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses by using multiplexed reverse transcription-PCR (mRT-PCR) amplification coupled with a...

Human disease likely attributable to variola virus (VARV), the etiologic agent of smallpox, has been reported in human populations for >2,000 years. VARV is unique among orthopoxviruses in that it is an exclusively human pathogen. Because VARV has a large, slowly evolving DNA genome, we were able to construct a robust phylogeny of VARV by analyzing...

Described herein is the identification of nucleotide sequences specific to Francisella tularensis that serves as a marker or signature for identification of this bacterium. In addition, forward and reverse primers and hybridization probes derived from these nucleotide sequences that are used in nucleotide detection methods to detect the presence of...

A nucleic acid-based multiplexed assay was developed that combines detection of foot-and-mouth disease virus (FMDV) with rule-out assays for two other foreign animal diseases and four domestic animal diseases that cause vesicular or ulcerative lesions indistinguishable from FMDV infection in cattle, sheep and swine. The FMDV 'look-alike' diagnostic...

A high-throughput multiplexed assay was developed for the differential laboratory diagnosis of foot-and-mouth disease virus (FMDV) from viruses which cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses using multiplexed reverse transcription PCR (mRT-PCR) amplification coupled with a mi...

The emergence of severe acute respiratory syndrome (SARS) in 2002 and 2003 affected global health and caused major economic disruption. Adequate animal models are required to study the underlying pathogenesis of SARS-associated coronavirus (SARS-CoV) infection and to develop effective vaccines and therapeutics. We report the first findings of measu...

Line Graphs of Serum Chemistry Results Serum chemistry results from cynomolgus macaques infected with SARS-CoV on day 0. Included are results for alkaline phosphatase (alk phos) (A–C); alanine aminotransferase (ALT) (D–F); albumin (G–I); blood urea nitrogen (BUN) (J–L), and creatinine (M–O). Results are grouped by route of infection: group I, intra...

Line Graphs of Complete Blood Count Results Hematology results from cynomolgus macaques infected with SARS-CoV on day 0. Included are results for WBC count (A–C); absolute lymphocyte count (D–F); percent lymphocytes (G–I); hematocrit (J–L); and platelet count (M–O). Results are grouped by route of infection: group I, intrabronchial + intranasal (A,...

Electron Micrograph of SARS-CoV from Cell Culture Transmission electron micrograph of Vero cell infected with SARS-CoV isolate recovered from sample from infected nonhuman primates shows sphere-shaped virions on the surface of the cell as well as maturing virions budding into smooth-walled vesicles. (3.3 MB PSD)

Primer and Probe Sequences for SARS-CoV-Specific Q-PCR Primer and probe names, sequences, and final concentrations for two SARS-CoV specific Q-PCR assays developed to detect SARS-CoV genome in infected NHPs. (31 KB DOC)

Testing of SARS Real-Time PCR Assays Results of POL-minor binding groove (MGB) and SMP-MGB assays for samples spiked with SARS coronavirus versus samples spiked with non-SARS coronaviruses. (34 KB DOC)

Development of SARS-CoV-Specific Q-PCR Assays (38 KB DOC)

MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the compu...

Rapid advances in the genomic sequencing of bacteria and viruses over the past few years have made it possible to consider sequencing the genomes of all pathogens that affect humans and the crops and livestock upon which our lives depend. Recent events make it imperative that full genome sequencing be accomplished as soon as possible for pathogens...

Recent events illustrate the imperative to rapidly and accurately detect and identify pathogens during disease outbreaks, whether they are natural or engineered. Particularly for our primary goal of detecting bioterrorist releases, detection techniques must be both species-wide (capable of detecting all known strains of a given species) and species...

We studied the signaling pathways coupling gonadotropin-releasing hormone (GnRH) secretion to elevations in cAMP levels in the GT1 GnRH-secreting neuronal cell line. We hypothesized that increased cAMP could be acting directly by means of cyclic nucleotide-gated (CNG) cation channels or indirectly by means of activation of cAMP-dependent protein ki...

The type II cAMP-dependent protein kinase (PKA) is localized to specific subcellular environments through binding of dimeric regulatory subunits (RII) to anchoring proteins. Cytoskeletal localization occurs through RII dimer interaction with the PKA substrate molecule microtubule-associated protein 2 (MAP2). RII alpha deletion mutants and RII alpha...

A large number of GE techniques can be adapted from other microorganisms to biothreat bacteria and viruses. Detection of GE in a microorganism increases in difficulty as the size of the genetic change decreases. In addition to the size of the engineered change, the consensus genomic sequence of the microorganism can impact the difficulty of detecti...

MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the compu...