The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents

BACKGROUND: Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. RESULTS: We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. CONCLUSION: The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases

Rapid Identification of Emerging Pathogens: Coronavirus

New surveillance approach can analyze >900 polymerase chain reactions per day

Phase-Transfer Deracemization, Development of Reagents for Electrophilic Trifluoromethylation, and Hydrogen-Mediated Deoxydehydration

AbstractPhase-Transfer Deracemization, Development of Reagents for Electrophilic Trifluoromethylation, and Hydrogen-Mediated DeoxydehydrationbyAndrew Vivek SamantDoctor of Philosophy in ChemistryUniversity of California, BerkeleyProfessor F. Dean Toste, Chair As is often the case in the chemical sciences, the research presented here represents a path that followed naturally from one step to the next in the laboratory while ending up in seemingly disparate areas of focus at the end of each project. Chapter 1 describes the development of a purely chemical deracemization system. Typical asymmetric reactions fall into two categories: those where the starting material must be transformed into a new compound, and those where enantioenriched starting materials can be recovered in a maximum of 50% yield. Deracemization is an alternate strategy which can generate enantioenriched starting material in 100% maximum yield. The major challenge to implementing a successful chemical deracemization is that, on its own, solution-phase deracemization is always thermodynamically unfavorable. In order to circumvent this, we developed a system where the deracemization process could be chemically pumped by coupling it to the quenching of a strong oxidant and a strong reductant. In particular, we used a phase-transfer strategy to promote selective reaction of the substrate with both a cationic, water-soluble oxidant and a highly insoluble reductant, rather than having the oxidant and reductant react directly with one another. An interest in cationic reagents similar to the oxidant used to accomplish deracemization led (albeit quite indirectly) to the development of the reagents described in Chapter 2. Widely used iodine(III)-based electrophilic trifluoromethyling agents (e.g. Togni reagents) are typically neutral species, which require activation by a Lewis acid in order to trifluoromethylate nucleophiles such as alcohols and imidazoles. In contrast, we have developed a new class of trifluoromethyliodonium chlorides, which possess a high degree of cationic character and are capable of accomplishing these trifluoromethylations in the absence of an activator. Furthermore, we have demonstrated that these iodonium chlorides serve as good surrogates for reactive intermediates produced during acid-mediated trifluoromethylation. This equivalence has allowed us to gain a better understanding of these systems and has led to observations that could aid in the development of even more effective classes of reagent in the future. Chapter 3 describes a new and promising method for the conversion of biomass into commodity chemicals. Most modern commercial biomass conversion relates to the transformation of lipids (e.g. triglycerides) into chemically simple biofuels. Carbohydrate-based feedstocks, which include abundant natural resources such as glucose and cellulose, have the potential to be converted into more complex monomers and fine chemicals. In the course of our research, we developed a system capable of reducing sugar-derived compounds, such as glucaric acid and its derivates, directly to commercially relevant starting materials such as adipate esters using hydrogen gas as the reductant. This dual-catalytic system uses palladium on carbon to activate hydrogen gas and high-valent soluble rhenium catalysts to deoxygenate polyols. Additionally, we have investigated the unusual alpha,beta-selectivity that this deoxydhydration system provides, and used to selectively convert ribonolactone and gluconolactone into compounds which retain a high degree of chemical complexity but are less highly oxygenated than the starting materials

Dosimetry and treatment planning of Occu-Prosta I-125 seeds for intraocular lesions

Intraocular malignant lesions are frequently encountered in clinical practice. Plaque brachytherapy represents an effective means of treatment for intraocular lesions. Recently Radiopharmaceutical Division, BARC, Mumbai, has indigenously fabricated reasonable-cost I-125 sources. Here we are presenting the preliminary experience of dosimetry of sources, configuration of treatment planning system (TPS) and quality assurance (QA) for eye plaque therapy with Occu-Prosta I-125 seeds, treated in our hospital, for a patient with ocular lesions. I-125 seeds were calibrated using well-type chamber. BrachyVision TPS was configured with Monte Carlo computed radial dose functions and anisotropy functions for I-125 sources. Dose calculated by TPS at different points in central axis and off axis was compared with manually calculated dose. Eye plaque was fabricated of 17 karat pure gold, locally. The seeds were arranged in an outer ring near the edge of the plaque and in concentric rings throughout the plaque. The sources were manually digitized on the TPS, and dose distribution was calculated in three dimensions. Measured activity using cross-calibrated well-type chamber was within ±10% of the activity specified by the supplier. Difference in TPS-calculated dose and manually calculated dose was within 5%. Treatment time calculated by TPS was in concordance with published data for similar plaque arrangement

Dosimetry and treatment planning of Occu-Prosta I-125 seeds for intraocular lesions

Intraocular malignant lesions are frequently encountered in clinical practice. Plaque brachytherapy represents an effective means of treatment for intraocular lesions. Recently Radiopharmaceutical Division, BARC, Mumbai, has indigenously fabricated reasonable-cost I-125 sources. Here we are presenting the preliminary experience of dosimetry of sources, configuration of treatment planning system (TPS) and quality assurance (QA) for eye plaque therapy with Occu-Prosta I-125 seeds, treated in our hospital, for a patient with ocular lesions. I-125 seeds were calibrated using well-type chamber. BrachyVision TPS was configured with Monte Carlo computed radial dose functions and anisotropy functions for I-125 sources. Dose calculated by TPS at different points in central axis and off axis was compared with manually calculated dose. Eye plaque was fabricated of 17 karat pure gold, locally. The seeds were arranged in an outer ring near the edge of the plaque and in concentric rings throughout the plaque. The sources were manually digitized on the TPS, and dose distribution was calculated in three dimensions. Measured activity using cross-calibrated well-type chamber was within ±10% of the activity specified by the supplier. Difference in TPS-calculated dose and manually calculated dose was within 5%. Treatment time calculated by TPS was in concordance with published data for similar plaque arrangement

The Ibis T5000 Universal Biosensor: An Automated Platform for Pathogen Identification and Strain Typing

We describe a new approach to the sensitive and specific identification of bacteria, viruses, fungi, and protozoa based on broad-range PCR and high-performance mass spectrometry. The Ibis T5000 is based on technology developed for the Department of Defense known as T.I.G.E.R. (Triangulation Identification for the Genetic Evaluation of Risks) for pathogen surveillance. The technology uses mass spectrometry—derived base composition signatures obtained from PCR amplification of broadly conserved regions of the pathogen genomes to identify most organisms present in a sample. The process of sample analysis has been automated using a combination of commercially available and custom instrumentation. A software system known as T-Track manages the sample flow, signal analysis, and data interpretation and provides simplified result reports to the user. No specialized expertise is required to use the instrumentation. In addition to pathogen surveillance, the Ibis T5000 is being applied to reducing health care—associated infections (HAIs), emerging and pandemic disease surveillance, human forensics analysis, and pharmaceutical product and food safety, and will be used eventually in human infectious disease diagnosis. In this review, we describe the automated Ibis T5000 instrument and provide examples of how it is used in HAI control