Publications

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The threats of disease outbreaks and exposure to biothreat agents, both accidental and intentional, demand field-deployable technology capable of rapid, sensitive, and accurate diagnosis. In order to address these public health concerns, we present a portable centrifugal microfluidic platform and demonstrate sensitive detection protein antigens, host response antibodies, and nucleic acids down to single digit starting copies. The nucleic acid detection utilizes an isothermal amplification via loop-mediated isothermal amplification (LAMP). The platform, which is composed of a compact optical system for laser induced fluorescence (LIF) detection, a quiet brushless motor, and an efficient non-contact heater, offers an easy-to-use system capable of performing sensitive biodetection in a constrained-resource environment.

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Monitoring infections in vectors such as mosquitoes,sand flies, tsetse flies, and ticks to identify human pathogens may serve as an early warning detection system to direct local government disease preventive measures. One major hurdle in detection is the ability to screen large numbers of vectors for human pathogens without the use of genotype-specific molecular techniques. Next generation sequencing (NGS) provides an unbiased platform capable of identifying known and unknown pathogens circulating within a vector population, but utilizing this technology is time-consuming and costly for vector-borne disease surveillance programs. To address this we developed cost-effective Ilumina® RNA-Seq library preparation methodologiesin conjunction with an automated computational analysis pipeline to characterize the microbial populations circulating in Culex mosquitoes (Culex quinquefasciatus, Culex quinquefasciatus/pipiens complex hybrids, and Culex tarsalis) throughout California. We assembled 20 novel and well-documented arboviruses representing members of Bunyaviridae, Flaviviridae, Ifaviridae, Mesoniviridae, Nidoviridae, Orthomyxoviridae, Parvoviridae, Reoviridae, Rhabdoviridae, Tymoviridae, as well as several unassigned viruses. In addition, we mapped mRNA species to divergent species of trypanosoma and plasmodium eukaryotic parasites and characterized the prokaryotic microbial composition to identify bacterial transcripts derived from wolbachia, clostridium, mycoplasma, fusobacterium and campylobacter bacterial species. We utilized these microbial transcriptomes present in geographically defined Culex populations to define spatial and mosquito species-specific barriers of infection. The virome and microbiome composition identified in each mosquito pool provided sufficient resolution to determine both the mosquito species and the geographic region in California where the mosquito pool originated. This data provides insight into the complexity of microbial species circulating in medically important Culex mosquitoes and their potential impact on the transmission of vector-borne human/veterinary pathogens in California.

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We have developed a novel modular automated processing system (MAPS) that enables reliable, high-throughput analysis as well as sample-customized processing. This system is comprised of a set of independent modules that carry out individual sample processing functions: cell lysis, protein concentration (based on hydrophobic, ion-exchange and affinity interactions), interferent depletion, buffer exchange, and enzymatic digestion of proteins of interest. Taking advantage of its unique capacity for enclosed processing of intact bioparticulates (viruses, spores) and complex serum samples, we have used MAPS for analysis of BSL1 and BSL2 samples to identify specific protein markers through integration with the portable microChemLab{trademark} and MALDI.