Christopher J. Love

Source of Sustained Voltage Difference between the Xylem of a Potted Ficus benjamina Tree and Its Soil

It has long been known that there is a sustained electrical potential (voltage) difference between the xylem of many plants and their surrounding soil, but the mechanism behind this voltage has remained controversial. After eliminating any extraneous capacitive or inductive couplings and ground-mediated electric current flows, we have measured sustained differences of 50–200 mV between the xylem region of a Faraday-caged, intact, potted Ficus benjamina tree and its soil, as well as between its cut branches and soils and ionic solutions standardized to various pH values. Using identical platinum electrodes, no correlation between the voltage and time of day, illumination, sap flow, electrode elevation, or ionic composition of soil was found, suggesting no direct connection to simple dissimilar-metal redox reactions or transpirational activity. Instead, a clear relationship between the voltage polarity and magnitude and the pH difference between xylem and soil was observed. We attribute these sustained voltages to a biological concentration cell likely set up by the homeostatic mechanisms of the tree. Potential applications of this finding are briefly explored.

Size-dependent thermal oxidation of copper: single-step synthesis of hierarchical nanostructures

Thermal oxidation of copper is a simple and scalable method to produce copper oxide nanowires. We report for the first time the formation of nanowires on copper powder during thermal oxidation and the resulting nanowire coverage that is dependent on the initial particle size. Systematic thermogravimetric analysis (TGA) and in situ X-ray diffraction (XRD) studies of thermal oxidation of particles of different sizes provide insights into the size-dependent process and evolution of the various phases of copper and copper oxide with time. Furthermore, we find that a large void is formed within these particles after oxidation and propose a mechanism based on the Kirkendall effect. The unique tunability of hierarchical features and hollow interior can be used to create new scalable structures for applications in a variety of areas including thermal management and catalysis.

Abstract LB-136: High concordance of whole-exome sequencing of cell-free DNA and matched biopsies enables genomic discovery in metastatic cancer

Background: Circulating cell-free DNA (cfDNA) has largely been used to monitor blood for specific tumor mutations, but genome-wide discovery from cfDNA has not been well established. Here, we establish a scalable approach for whole-exome sequencing (WES) of cfDNA, making it possible to perform comprehensive genomic characterization of metastatic cancer in a routine and minimally-invasive manner. Comprehensive genomic characterization of metastatic cancer stands to uncover novel alterations of clinical significance. A major challenge is that metastatic tumors are infrequently biopsied. Cell-free DNA is shed abundantly into the bloodstream from metastatic tumors, presenting an opportunity for genomic discovery in advanced cancers that are rarely biopsied in routine clinical care. We report an efficient process to qualify and sequence whole-exomes from cfDNA at scale and systematically compare the somatic mutations, indels, and copy number alterations detected in WES of cfDNA to WES of matched tumor biopsies. Methods: We consented 86 patients with metastatic breast or prostate cancers for blood collection. We isolated cfDNA and germline DNA from blood and performed low coverage sequencing to estimate tumor content based on genome-wide copy number. We screened patient blood samples and prioritized those with higher tumor fractions for WES. In parallel, we analyzed cfDNA and germline DNA from healthy donors to calibrate our methods and assess false positive rate for genomic alterations. Results: We found the vast majority of patients with metastatic prostate or breast cancer to have detectable tumor-derived cfDNA. WES of cfDNA from healthy donors revealed very low false positive rates for somatic mutations, indels and copy number alterations (SCNAs). By analyzing WES of cfDNA and tumor biopsies from dozens of patients with metastatic breast or prostate cancers, we established guidelines for the coverage and tumor fraction required for mutation discovery in WES of cfDNA. We found WES of cfDNA to uncover 91% of the clonal mutations, 59% of the subclonal mutations, and 75% of the SCNAs detected in WES of matched tumor biopsies. In several cases, we observed mutations exclusive to cfDNA that were confirmed in later blood draws, suggesting that cfDNA-exclusive mutations may be derived from unsampled metastases. In some cases, cfDNA revealed clinically actionable mutations that were not detected in matched tumor biopsies. Conclusions: WES of cfDNA uncovers the majority of somatic mutations, indels, and SCNAs found in matched tumor biopsies of metastatic cancer. The high degree of concordance suggests that comprehensive sequencing of cfDNA can be leveraged for genomic discovery in settings where conventional biopsies are difficult to access. Furthermore, the detection of mutations in cfDNA that are not detected in concurrent biopsies suggests that cfDNA may be complementary to tumor biopsies for both translational studies and precision cancer medicine. Citation Format: Viktor A. Adalsteinsson, Gavin Ha, Sam Freeman, Atish D. Choudhury, Daniel G. Stover, Heather A. Parsons, Gregory Gydush, Sarah Reed, Denis Loginov, Dimitri Livitz, Daniel Rosebrock, Ignat Leshchiner, Ofir Cohen, Coyin Oh, Jaegil Kim, Chip Stewart, Mara Rosenberg, Huiming Ding, Maxwell R. Lloyd, Sairah Mahmud, Karla E. Helvie, Margaret S. Merrill, Rebecca A. Santiago, Edward P. O’Connor, Seong H. Jeong, Joseph F. Kramkowski, Jens G. Lohr, Laura Polacek, Nelly Oliver, Lori Marini, Joshua Francis, Lauren C. Harshman, Eliezer M. Van Allen, Eric P. Winer, Nancy U. Lin, Mari Nakabayashi, Mary-Ellen Taplin, Levi A. Garraway, Todd R. Golub, Jesse S. Boehm, Nikhil Wagle, Gad Getz, Matthew Meyerson, Christopher J. Love. High concordance of whole-exome sequencing of cell-free DNA and matched biopsies enables genomic discovery in metastatic cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-136.

Abstract 5538A: Cell size-specific intracellular delivery

Among the many methods of intracellular delivery, cell size-selective delivery is particularly applicable to cancer research and therapeutics where tumor cells tend to be larger than blood cells and selective manipulation of a single cell-type while minimally affecting the other cells in a heterogeneous mixture is important. In this study, cell size-selective delivery is achieved using a novel microfluidic device with 75 parallel channels through which cells are pushed under nitrogen pressure. The cells undergo deformation as they transit through the channels, which results in temporary disruption of the cell membrane to facilitate delivery of material into the cytoplasm. For each cell size, there is a specific channel width for which optimal cell viability and fluorophore delivery is achieved, with smaller cells requiring narrower channels. When two cells of different sizes are mixed in solution, the channel width for optimal cell viability and fluorophore delivery for each cell type remains the same, and larger cells can achieve fluorophore delivery at a significantly higher percentage than smaller cells at the former9s optimal channel width. One possible application for this technology is tagging circulating tumor cells, and we have been able to selectively deliver fluorophores into tumor cells when spiked into whole human blood with 91% specificity. We were also able to isolate pancreatic tumors cells from a patient9s blood sample that matched the genotype of the patient9s primary pancreatic tumor. Intracellular delivery of materials has become increasingly important as we delve deeper into understanding cellular processes and developing targeted therapies, and with this device, selective delivery can be achieved in a vector-free environment and without dependence on cell-surface receptors. Citation Format: May Tun Saung, Armon Sharei, Viktor Adalsteinsson, Andrew Liss, Nahyun Cho, Tushar Kamath, Camilo Ruiz, Jesse Kirkpatrick, Robert Langer, Christopher Love, Klavs Jensen. Cell size-specific intracellular delivery. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5538A. doi:10.1158/1538-7445.AM2015-5538A

Scalable manufacturing of hierarchical nanostructures for thermal management

Thermal oxidation of copper is a simple and scalable method to produce copper oxide nanowires. We report for the first time the formation of nanowires on copper powder during thermal oxidation and the resulting nanowire coverage that is dependent on initial particle size. Systematic thermogravimetric analysis (TGA) and in-situ x-ray diffraction (XRD) studies of thermal oxidation of particles of different sizes provide insights into the size-dependent process and evolution of the various phases of copper and copper oxide with time. Furthermore, we find that a large void is formed within these particles after oxidation and propose a mechanism based on the Kirkendall effect. Using this new size-dependent oxidation process, we demonstrate the simple and scalable creation of new hierarchical structures for applications in thermal management, including electronics cooling and boiling.