Acharya, N. | Search bioRxiv

bioRxiv2018

Getting there and staying there: supporting and enabling persistent human life on Mars using synthetic natural rubber, self-healing materials, and biological batteries.

Planetary exploration requires a balance between preemptive planning and financial feasibility. The risk of mid-mission equipment failure, power shortages, or supply depletion incentivizes precautionary measures, but the financial strain of sending unnecessary mass into space limits this practice.\n\nTo balance the two, our team explored the advantages of biological solutions, namely the self-sustaining abilities of low-mass organisms, to make planetary exploration more self-sufficient and economical. Prioritizing repair over replacement, we are developing self-healing materials embedded with Bacillus subtilis. For longer-lasting energy, we are designing a \"biobactery\" using linearly oriented Escherichia coli to generate power. For renewable materials, we are engineering bacteria to synthesize and degrade rubber. Individually, these projects offer sustainable alternatives for repair, power, and materials. But when combined, these consolidated insights can provide us with the power to get to Mars and resources to sustain us while were there.

synthetic biology↗

bioRxiv2017

Metagenomic DNA sequencing for the diagnosis of intraocular infections

PurposeTo compare the performance of unbiased high-throughput sequencing with pathogen directed PCR using DNA isolated from archived ocular fluid, approaches that are compatible with the current sample handling practice of ophthalmologists.\n\nDesignRetrospective molecular study of banked vitreous samples.\n\nMethodsWe evaluated a metagenomic DNA sequencing-based approach (DNA-seq) using archived positive (n = 31) and negative (n=36) vitreous specimens as determined by reference pathogen-specific PCR assays (herpes simplex virus 1 and 2, cytomegalovirus, varicella-zoster virus, and Toxoplasma gondii). Pathogens were identified using a rapid computational pipeline to analyze the non-host sequences obtained from DNA-seq. Clinical samples were de-identified and laboratory personnel handling the samples and interpreting the data were masked.\n\nResultsMetagenomic DNA sequencing detected 87% of positive reference samples. In the presumed negative reference samples, DNA-seq detected an additional 6 different pathogens in 8 samples (22% of negative samples) that were either not detected or not targeted with pathogen-specific PCR assays. Infectious agents identified only with DNA-seq were Candida dubliniensis, Klebsiella pneumoniae, human herpesvirus 6 (HHV-6), and human T-cell leukemia virus type 1 (HTLV-1). Discordant samples were independently verified in CLIA-certified laboratories. CMV sequences were compared against the antiviral mutation database and 3 of the samples were found to have mutations conferring ganciclovir resistance.\n\nConclusionsMetagenomic DNA sequencing was highly concordant with pathogen-directed PCRs. The unbiased nature of metagenomics DNA sequencing allowed an expanded scope of pathogen detection, including bacteria, fungal species, and viruses, resolving 22% of cases that had previously escaped detection by routine pathogen-specific PCRs. The detection of drug resistance mutations highlights the potential for unbiased sequencing to provide clinically actionable information beyond pathogen species detection.

genomics↗