• A modular hierarchical array camera

      Yuan, X.; Ji, M.; Wu, J.; Brady, D.J.; Dai, Q.; Fang, L.; College of Optical Sciences, University of Arizona (Springer Nature, 2021)
      Array cameras removed the optical limitations of a single camera and paved the way for high-performance imaging via the combination of micro-cameras and computation to fuse multiple aperture images. However, existing solutions use dense arrays of cameras that require laborious calibration and lack flexibility and practicality. Inspired by the cognition function principle of the human brain, we develop an unstructured array camera system that adopts a hierarchical modular design with multiscale hybrid cameras composing different modules. Intelligent computations are designed to collaboratively operate along both intra- and intermodule pathways. This system can adaptively allocate imagery resources to dramatically reduce the hardware cost and possesses unprecedented flexibility, robustness, and versatility. Large scenes of real-world data were acquired to perform human-centric studies for the assessment of human behaviours at the individual level and crowd behaviours at the population level requiring high-resolution long-term monitoring of dynamic wide-area scenes. © 2021, The Author(s).
    • Assembly of multicomponent structures from hundreds of micron-scale building blocks using optical tweezers

      Melzer, J.E.; McLeod, E.; Wyant College of Optical Sciences, The University of Arizona (Springer Nature, 2021)
      The fabrication of three-dimensional (3D) microscale structures is critical for many applications, including strong and lightweight material development, medical device fabrication, microrobotics, and photonic applications. While 3D microfabrication has seen progress over the past decades, complex multicomponent integration with small or hierarchical feature sizes is still a challenge. In this study, an optical positioning and linking (OPAL) platform based on optical tweezers is used to precisely fabricate 3D microstructures from two types of micron-scale building blocks linked by biochemical interactions. A computer-controlled interface with rapid on-the-fly automated recalibration routines maintains accuracy even after placing many building blocks. OPAL achieves a 60-nm positional accuracy by optimizing the molecular functionalization and laser power. A two-component structure consisting of 448 1-µm building blocks is assembled, representing the largest number of building blocks used to date in 3D optical tweezer microassembly. Although optical tweezers have previously been used for microfabrication, those results were generally restricted to single-material structures composed of a relatively small number of larger-sized building blocks, with little discussion of critical process parameters. It is anticipated that OPAL will enable the assembly, augmentation, and repair of microstructures composed of specialty micro/nanomaterial building blocks to be used in new photonic, microfluidic, and biomedical devices. © 2021, The Author(s).
    • Drivers and implications of distance decay differ for ectomycorrhizal and foliar endophytic fungi across an anciently fragmented landscape

      Bowman, Elizabeth A.; Arnold, A. Elizabeth; School of Plant Sciences, The University of Arizona; Department of Ecology and Evolutionary Biology, The University of Arizona (Springer Nature, 2021-06-07)
      Fungal communities associated with plants often decrease in similarity as the distance between sampling sites increases (i.e., they demonstrate distance decay). In the southwestern USA, forests occur in highlands separated from one another by warmer, drier biomes with plant and fungal communities that differ from those at higher elevations. These disjunct forests are broadly similar in climate to one another, offering an opportunity to examine drivers of distance decay in plant-associated fungi across multiple ecologically similar yet geographically disparate landscapes. We examined ectomycorrhizal and foliar endophytic fungi associated with a dominant forest tree (Pinus ponderosa) in forests across ca. 550 km of geographic distance from northwestern to southeastern Arizona (USA). Both guilds of fungi showed distance decay, but drivers differed for each: ectomycorrhizal fungi are constrained primarily by dispersal limitation, whereas foliar endophytes are constrained by specific environmental conditions. Most ectomycorrhizal fungi were found in only a single forested area, as were many endophytic fungi. Such regional-scale perspectives are needed for baseline estimates of fungal diversity associated with forest trees at a landscape scale, with attention to the sensitivity of different guilds of fungal symbionts to decreasing areas of suitable habitat, increasing disturbance, and related impacts of climate change.
    • Endocytosis regulates TDP-43 toxicity and turnover

      Liu, Guangbo; Coyne, Alyssa N.; Pei, Fen; Vaughan, Spencer; Chaung, Matthew; Zarnescu, Daniela C.; Buchan, J. Ross; Univ Arizona, Dept Mol & Cellular Biol (Springer Nature, 2017)
      Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron degenerative disease. ALS-affected motor neurons exhibit aberrant localization of a nuclear RNA binding protein, TDP-43, into cytoplasmic aggregates, which contributes to pathology via unclear mechanisms. Here, we demonstrate that TDP-43 turnover and toxicity depend in part upon the endocytosis pathway. TDP-43 inhibits endocytosis, and co-localizes strongly with endocytic proteins, including in ALS patient tissue. Impairing endocytosis increases TDP-43 toxicity, aggregation, and protein levels, whereas enhancing endocytosis reverses these phenotypes. Locomotor dysfunction in a TDP-43 ALS fly model is also exacerbated and suppressed by impairment and enhancement of endocytic function, respectively. Thus, endocytosis dysfunction may be an underlying cause of ALS pathology.
    • Evaluation of fireground exposures using urinary PAH metabolites

      Hoppe-Jones, Christiane; Griffin, Stephanie C.; Gulotta, John J.; Wallentine, Darin D.; Moore, Paul K.; Beitel, Shawn C.; Flahr, Leanne M.; Zhai, Jing; Zhou, Jin J.; Littau, Sally R.; et al. (Springer Nature, 2021-03-02)
      Background: Firefighters have increased cancer incidence and mortality rates compared to the general population, and are exposed to multiple products of combustion including known and suspected carcinogens. Objective: The study objective was to quantify fire response exposures by role and self-reported exposure risks. Methods: Urinary hydroxylated metabolites of polycyclic aromatic hydrocarbons (PAH-OHs) were measured at baseline and 2–4 h after structural fires and post-fire surveys were collected. Results: Baseline urine samples were collected from 242 firefighters. Of these, 141 responded to at least one of 15 structural fires and provided a post-fire urine. Compared with baseline measurements, the mean fold change of post-fire urinary PAH-OHs increased similarly across roles, including captains (2.05 (95% CI 1.59–2.65)), engineers (2.10 (95% CI 1.47–3.05)), firefighters (2.83 (95% CI 2.14–3.71)), and paramedics (1.84 (95% CI 1.33–2.60)). Interior responses, smoke odor on skin, and lack of recent laundering or changing of hoods were significantly associated with increased post-fire urinary PAH-OHs. Significance: Ambient smoke from the fire represents an exposure hazard for all individuals on the fireground; engineers and paramedics in particular may not be aware of the extent of their exposure. Post-fire surveys identified specific risks associated with increased exposure. © 2021, The Author(s).
    • Experimental identification and in silico prediction of bacterivory in green algae

      Bock, Nicholas A.; Charvet, Sophie; Burns, John; Gyaltshen, Yangtsho; Rozenberg, Andrey; Duhamel, Solange; Kim, Eunsoo; Department of Molecular and Cellular Biology, The University of Arizona (Springer Nature, 2021-03-02)
      While algal phago-mixotrophs play a major role in aquatic microbial food webs, their diversity remains poorly understood. Recent studies have indicated several species of prasinophytes, early diverging green algae, to be able to consume bacteria for nutrition. To further explore the occurrence of phago-mixotrophy in green algae, we conducted feeding experiments with live fluorescently labeled bacteria stained with CellTracker Green CMFDA, heat-killed bacteria stained with 5-(4,6-dichlorotriazin-2-yl) aminofluorescein (DTAF), and magnetic beads. Feeding was detected via microscopy and/or flow cytometry in five strains of prasinophytes when provided with live bacteria: Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, and Dolichomastix tenuilepis CCMP3274. No feeding was detected when heat-killed bacteria or magnetic beads were provided, suggesting a strong preference for live prey in the strains tested. In parallel to experimental assays, green algal bacterivory was investigated using a gene-based prediction model. The predictions agreed with the experimental results and suggested bacterivory potential in additional green algae. Our observations underline the likelihood of widespread occurrence of phago-mixotrophy among green algae, while additionally highlighting potential biases introduced when using prey proxy to evaluate bacterial ingestion by algal cells. © 2021, The Author(s).
    • Genome sequence and evolution of Betula platyphylla

      Chen, Su; Wang, Yucheng; Yu, Lili; Zheng, Tao; Wang, Sui; Yue, Zhen; Jiang, Jing; Kumari, Sapna; Zheng, Chunfang; Tang, Haibao; et al. (Springer Nature, 2021-02-11)
      Betula L. (birch) is a pioneer hardwood tree species with ecological, economic, and evolutionary importance in the Northern Hemisphere. We sequenced the Betula platyphylla genome and assembled the sequences into 14 chromosomes. The Betula genome lacks evidence of recent whole-genome duplication and has the same paleoploidy level as Vitis vinifera and Prunus mume. Phylogenetic analysis of lignin pathway genes coupled with tissue-specific expression patterns provided clues for understanding the formation of higher ratios of syringyl to guaiacyl lignin observed in Betula species. Our transcriptome analysis of leaf tissues under a time-series cold stress experiment revealed the presence of the MEKK1–MKK2–MPK4 cascade and six additional mitogen-activated protein kinases that can be linked to a gene regulatory network involving many transcription factors and cold tolerance genes. Our genomic and transcriptome analyses provide insight into the structures, features, and evolution of the B. platyphylla genome. The chromosome-level genome and gene resources of B. platyphylla obtained in this study will facilitate the identification of important and essential genes governing important traits of trees and genetic improvement of B. platyphylla. © 2021, The Author(s).
    • Longitudinal evaluation of whole blood miRNA expression in firefighters

      Jung, Alesia M.; Zhou, Jin; Beitel, Shawn C.; Littau, Sally R.; Gulotta, John J.; Wallentine, Darin D.; Moore, Paul K.; Burgess, Jefferey L.; Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona; Department of Community, Environment and Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona (Springer Nature, 2021-02-18)
      Background: Dysregulated microRNA (miRNA) expression could provide a mechanism linking firefighter exposure to increased cancer risk. Objective: To determine if changes in longitudinal miRNA expression in firefighters are associated with occupational exposures. Methods: Whole blood MiRNA was evaluated in 52 new recruits prior to live-fire training and 20–37 months later. Linear mixed effects models adjusted for age, ethnicity, BMI, and batch effects were used to determine associations separately for all fires and structure fires only between employment duration, cumulative fire-hours and fire-runs, and time since most recent fire with (1) nine a priori and (2) the full array of 799 miRNAs. Results: For multivariable models including all fires, two a priori miRNAs were associated with employment duration and four with time since most recent fire. For multivariable models restricted to structure fires, three a priori miRNAs were associated with employment duration and one with fire-runs. Additional miRNAs from the full array were associated with employment duration for all fires and/or structure fires. In general, tumor suppressive miRNAs decreased and oncogenic miRNAs increased with exposure. Significance: Changes in miRNAs may serve as biomarkers of exposure effects and a mechanism for increased cancer risk in firefighters. © 2021, The Author(s).
    • Wireless, battery-free, and fully implantable electrical neurostimulation in freely moving rodents

      Burton, A.; Won, S.M.; Sohrabi, A.K.; Stuart, T.; Amirhossein, A.; Kim, J.U.; Park, Y.; Gabros, A.; Rogers, J.A.; Vitale, F.; et al. (Springer Nature, 2021)
      Implantable deep brain stimulation (DBS) systems are utilized for clinical treatment of diseases such as Parkinson’s disease and chronic pain. However, long-term efficacy of DBS is limited, and chronic neuroplastic changes and associated therapeutic mechanisms are not well understood. Fundamental and mechanistic investigation, typically accomplished in small animal models, is difficult because of the need for chronic stimulators that currently require either frequent handling of test subjects to charge battery-powered systems or specialized setups to manage tethers that restrict experimental paradigms and compromise insight. To overcome these challenges, we demonstrate a fully implantable, wireless, battery-free platform that allows for chronic DBS in rodents with the capability to control stimulation parameters digitally in real time. The devices are able to provide stimulation over a wide range of frequencies with biphasic pulses and constant voltage control via low-impedance, surface-engineered platinum electrodes. The devices utilize off-the-shelf components and feature the ability to customize electrodes to enable broad utility and rapid dissemination. Efficacy of the system is demonstrated with a readout of stimulation-evoked neural activity in vivo and chronic stimulation of the medial forebrain bundle in freely moving rats to evoke characteristic head motion for over 36 days. © 2021, The Author(s).