Browsing by Author "Kalvapalle, Prashant"

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    Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
    (Springer Nature, 2024) Wang, Michael X.; Lou, Esther G.; Sapoval, Nicolae; Kim, Eddie; Kalvapalle, Prashant; Kille, Bryce; Elworth, R. A. Leo; Liu, Yunxi; Fu, Yilei; Stadler, Lauren B.; Treangen, Todd J.; Bioengineering; Civil and Environmental Engineering; Computer Science
    Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 15 million complete SARS-CoV-2 genomes are now publicly available, most sequenced and assembled via tiled amplicon sequencing. While computational tools for tiled amplicon design exist, they require downstream manual optimization both computationally and experimentally, which is slow and costly. Here we present Olivar, a first step towards a fully automated, variant-aware design of tiled amplicons for pathogen genomes. Olivar converts each nucleotide of the target genome into a numeric risk score, capturing undesired sequence features that should be avoided. In a direct comparison with PrimalScheme, we show that Olivar has fewer mismatches overlapping with primers and predicted PCR byproducts. We also compare Olivar head-to-head with ARTIC v4.1, the most widely used primer set for SARS-CoV-2 sequencing, and show Olivar yields similar read mapping rates (~90%) and better coverage to the manually designed ARTIC v4.1 amplicons. We also evaluate Olivar on real wastewater samples and found that Olivar has up to 3-fold higher mapping rates while retaining similar coverage. In summary, Olivar automates and accelerates the generation of tiled amplicons, even in situations of high mutation frequency and/or density. Olivar is available online as a web application at https://olivar.rice.edu and can be installed locally as a command line tool with Bioconda. Source code, installation guide, and usage are available at https://github.com/treangenlab/Olivar.
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    Snapshot ARG Removal Rates across Wastewater Treatment Plants Are Not Representative Due to Diurnal Variations
    (American Chemical Society, 2023) Lou, Esther G.; Ali, Priyanka; Lu, Karen; Kalvapalle, Prashant; Stadler, Lauren B.
    To evaluate the threat of the environmental dissemination of antibiotic resistance associated with wastewater treatment plants (WWTPs), the removal efficiency of antibiotic resistance genes (ARGs) during wastewater treatment needs to be assessed. The sample collection strategy is one factor that is often overlooked in study design and most studies on ARGs in wastewater perform grab sampling. Here, we hypothesized that wastewater sampling (i.e., grab and composite sampling) influences the observed ARG concentrations and calculated removal rates across WWTPs. We compared the removal rates calculated based on the two different sampling methods for several genes, including some clinically relevant ARGs (blaNDM-1, blaOXA-1, MCR-1, MCR-5, MCR-10, and qnrA). We conducted summer and winter 24 h sampling campaigns where grab samples were collected every 2 h from the influent, secondary effluent, and final effluent. The snapshot removal rate of each target gene calculated based on the 12 grab samples fluctuated by 0.5–1.6 log in the winter and 0.9–2.7 log in the summer, indicating diurnal variation. Overall, for each target gene, the removal rates calculated based on 24 h composite samples were approximately equal to the median of the 12 snapshot removal rates. Our study confirms the importance of using composite samples to monitor ARGs in wastewater.
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    Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences
    (Frontiers, 2021) Del Valle, Ilenne; Fulk, Emily M.; Kalvapalle, Prashant; Silberg, Jonathan J.; Masiello, Caroline A.; Stadler, Lauren B.; Bioengineering; Biosciences; Chemical and Biomolecular Engineering; Chemistry; Civil and Environmental Engineering
    The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed.
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    Using cellular fitness to map the structure and function of a major facilitator superfamily effluxer
    (EMBO Press, 2017) Perez, Anisha Maria; Gomez, Marcella M.; Kalvapalle, Prashant; O’Brien-Gilbert, Erin; Bennett, Matthew R.; Shamoo, Yousif; Bioengineering; Biosciences