Search

The ability to perform laboratory testing near the patient and with smaller blood volumes would benefit patients and physicians alike. We describe our design of a miniaturized clinical laboratory system with three components: a hardware platform (ie, the miniLab) that performs preanalytical and analytical processing steps using miniaturized sample manipulation and detection modules, an assay-configurable cartridge that provides consumable materials and assay reagents, and a server that communicates bidirectionally with the miniLab to manage assay-specific protocols and analyze, store, and report results (i.e., the virtual analyzer). The miniLab can detect analytes in blood using multiple methods, including molecular diagnostics, immunoassays, clinical chemistry, and hematology. Analytical performance results show that our qualitative Zika virus assay has a limit of detection of 55 genomic copies/ml. For our anti-herpes simplex virus type 2 immunoglobulin G, lipid panel, and lymphocyte subset panel assays, the miniLab has low imprecision, and method comparison results agree well with those from the United States Food and Drug Administration-cleared devices. With its small footprint and versatility, the miniLab has the potential to provide testing of a range of analytes in decentralized locations.

Halogenated organic solvents such as chlorobenzenes (CBs) are frequent groundwater contaminants due to legacy spills. When contaminated anaerobic groundwater discharges into surface water through wetlands and other transition zones, aeration can occur from various physical and biological processes at shallow depths, resulting in oxic-anoxic interfaces (OAIs). This study investigated the potential for 1,2,4-trichlorobenzene (1,2,4-TCB) biodegradation at OAIs. A novel upflow column system was developed to create stable anaerobic and aerobic zones, simulating a natural groundwater OAI. Two columns containing (1) sand and (2) a mixture of wetland sediment and sand were operated continuously for 295 days with varied doses of 0.14–1.4 mM sodium lactate (NaLac) as a model electron donor. Both column matrices supported anaerobic reductive dechlorination and aerobic degradation of 1,2,4-TCB spatially separated between anaerobic and aerobic zones. Reductive dechlorination produced a mixture of di- and monochlorobenzene daughter products, with estimated zero-order dechlorination rates up to 31.3 μM/h. Aerobic CB degradation, limited by available dissolved oxygen, occurred for 1,2,4-TCB and all dechlorinated daughter products. Initial reductive dechlorination did not enhance the overall observed extent or rate of subsequent aerobic CB degradation. Increasing NaLac dose increased the extent of reductive dechlorination, but suppressed aerobic CB degradation at 1.4 mM NaLac due to increased oxygen demand. 16S-rRNA sequencing of biofilm microbial communities revealed strong stratification of functional anaerobic and aerobic organisms between redox zones including the sole putative reductive dechlorinator detected in the columns, Dehalobacter. The sediment mixture column supported enhanced reductive dechlorination compared to the sand column at all tested NaLac doses and growth of Dehalobacter populations up to 4.1 × 108 copies/g (51% relative abundance), highlighting the potential benefit of sediments in reductive dechlorination processes. Results from these model systems suggest both substantial anaerobic and aerobic CB degradation can co-occur along the OAI at contaminated sites where bioavailable electron donors and oxygen are both present.

Sustainable mass production of algal biofuels requires a reduction in nutrient demand and efficient conversion into fuels of all biomass including lipid-extracted algal residues (LEA). This study evaluated methane production, nutrient recovery and recycling from untreated and enzymatically pretreated Nannochloropsis LEA using semi-continuous anaerobic digestion (AD). Additionally, this process was compared to methane generation from whole Nannochloropsis alga (WA) and thermally pretreated WA. The methane production from untreated LEA and WA reached up to 0.22 L and 0.24 L per gram of biomass volatile solids (VS), respectively, corresponding to only 36–38% of the theoretical potential. Additionally, observed VS reduction was only 40–50% confirming biomass recalcitrance to biodegradation. While enzymatic treatment hydrolyzed up to 65% of the LEA polysaccharides, the methane production increased by only 15%. Alternatively, WA thermal pretreatment at 150–170 °C enhanced methane production up to 40%. Overall, an integrated process of lipid conversion into biodiesel coupled with LEA conversion into methane generates nearly 40% more energy compared to methane production from WA, and about 100% more energy than from biodiesel alone. Additionally, the AD effluent contained up to 60–70% of the LEA phosphorus content, 30–50% of the nitrogen, sulfur, calcium and boron, 20% of the iron and cobalt, and 10% of manganese, zinc and copper, which can partially replace chemical fertilizers during algal cultivation. Consequently, supplementation of Nannochloropsis cultures with 5% AD effluent was optimal for a high algal growth rate. Therefore, coupling biodiesel and methane production provides significant energy advantages along with sustainability and economic benefits from nutrient recycling.

The ability to perform laboratory testing near the patient and with smaller blood volumes would benefit patients and physicians alike. We describe our design of a miniaturized clinical laboratory system with three components: a hardware platform (ie, the miniLab) that performs preanalytical and analytical processing steps using miniaturized sample manipulation and detection modules, an assay‐configurable cartridge that provides consumable materials and assay reagents, and a server that communicates bidirectionally with the miniLab to manage assay‐specific protocols and analyze, store, and report results (i.e., the virtual analyzer). The miniLab can detect analytes in blood using multiple methods, including molecular diagnostics, immunoassays, clinical chemistry, and hematology. Analytical performance results show that our qualitative Zika virus assay has a limit of detection of 55 genomic copies/ml. For our anti‐herpes simplex virus type 2 immunoglobulin G, lipid panel, and lymphocyte subset panel assays, the miniLab has low imprecision, and method comparison results agree well with those from the United States Food and Drug Administration‐cleared devices. With its small footprint and versatility, the miniLab has the potential to provide testing of a range of analytes in decentralized locations.

Introduction: The challenge in precision medicine has been improving the understanding of cancer heterogeneity and clonal evolution, which has major implications in targeted therapy selection and disease monitoring. However, current bulk sequencing methods are unable to unambiguously identify rare pathogenic or drug-resistant cell populations and determine whether mutations co-occur within the same cell. Single-cell sequencing has the potential to provide unique insights on the cellular and genetic composition, drivers, and signatures of cancer at unparalleled sensitivity. Methods: Previously we have developed a high-throughput single-cell DNA analysis platform (TapestriTM) that leverages droplet microfluidics and a multiplex-PCR based targeted DNA sequencing approach, and demonstrated the generation of high-resolution maps of clonal architecture from acute myeloid leukemia (AML) tumors. Here we present an update to the Tapestri Platform which employs new biochemistry and features improved firmware, software, workflow, and data analysis solution resulting in higher throughput, better sensitivity, specificity and unprecedented flexibility. Results: From cell prep to sequencing-ready libraries, the workflow can be completed within 2 days, and new modifications have doubled the throughput to up to 20,000 genotyped cells per run from 10,000 shown previously. We have validated the performance of an AML (19 genes, 50 amplicons) and a CLL (chronic lymphocytic leukemia) (34 genes, 286 amplicons) panel. We also developed a robust web-based design portal for custom targets. The updated biochemistry enables easy addition of new gene and loci targets into existing panels for improved coverage and updated studies. Using longitudinal AML and CLL samples, we were able to detect rare subclones of Conclusion: We demonstrate that single-cell DNA sequencing can reveal the heterogeneity of blood cancers and map the clonal architecture and clonal evolution with higher sensitivity than bulk NGS methods. This is critical in patient stratification and drug selection over the entire course of treatment. Besides the catalog AML and CLL panels, the flexibility of system allows for analyzing SNV and indel mutations of any custom cancer DNA targets. Additionally, the system provides capabilities for quality control of gene edited cells, further advancing research into cancer therapies. Citation Format: Nianzhen Li, Daniel Mendoza, Adam Sciambi, Mani Manivannan, Jacob Ho, Kaustubh Gokhale, Jacqueline Marin, Kathryn Thompson, Jamie Yates, Vasu Sharma, Steven Chow, Sombeet Sahu, Shu Wang, Dennis Eastburn, Keith Jones. High-throughput single-cell targeted DNA sequencing using an updated TapestriTM Platform reveals rare clones and clonal evolution for multiple blood cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4696.

The report on climate change and health commissioned by University College London and the Lancet concludes: “Climate change is the biggest global health threat of the 21st century.”1 In this report, the authors emphasise not only the immediacy and gravity of this threat but also the directness: while the poorest in the world will be …