Cristina E. Davis

Advanced methods of plant disease detection. A review

Plant diseases are responsible for major economic losses in the agricultural industry worldwide. Monitoring plant health and detecting pathogen early are essential to reduce disease spread and facilitate effective management practices. DNA-based and serological methods now provide essential tools for accurate plant disease diagnosis, in addition to the traditional visual scouting for symptoms. Although DNA-based and serological methods have revolutionized plant disease detection, they are not very reliable at asymptomatic stage, especially in case of pathogen with systemic diffusion. They need at least 1–2 days for sample harvest, processing, and analysis. Here, we describe modern methods based on nucleic acid and protein analysis. Then, we review innovative approaches currently under development. Our main findings are the following: (1) novel sensors based on the analysis of host responses, e.g., differential mobility spectrometer and lateral flow devices, deliver instantaneous results and can effectively detect early infections directly in the field; (2) biosensors based on phage display and biophotonics can also detect instantaneously infections although they can be integrated with other systems; and (3) remote sensing techniques coupled with spectroscopy-based methods allow high spatialization of results, these techniques may be very useful as a rapid preliminary identification of primary infections. We explain how these tools will help plant disease management and complement serological and DNA-based methods. While serological and PCR-based methods are the most available and effective to confirm disease diagnosis, volatile and biophotonic sensors provide instantaneous results and may be used to identify infections at asymptomatic stages. Remote sensing technologies will be extremely helpful to greatly spatialize diagnostic results. These innovative techniques represent unprecedented tools to render agriculture more sustainable and safe, avoiding expensive use of pesticides in crop protection.

Transcriptome Profiling of Citrus Fruit Response to Huanglongbing Disease

Huanglongbing (HLB) or “citrus greening” is the most destructive citrus disease worldwide. In this work, we studied host responses of citrus to infection with Candidatus Liberibacter asiaticus (CaLas) using next-generation sequencing technologies. A deep mRNA profile was obtained from peel of healthy and HLB-affected fruit. It was followed by pathway and protein-protein network analysis and quantitative real time PCR analysis of highly regulated genes. We identified differentially regulated pathways and constructed networks that provide a deep insight into the metabolism of affected fruit. Data mining revealed that HLB enhanced transcription of genes involved in the light reactions of photosynthesis and in ATP synthesis. Activation of protein degradation and misfolding processes were observed at the transcriptomic level. Transcripts for heat shock proteins were down-regulated at all disease stages, resulting in further protein misfolding. HLB strongly affected pathways involved in source-sink communication, including sucrose and starch metabolism and hormone synthesis and signaling. Transcription of several genes involved in the synthesis and signal transduction of cytokinins and gibberellins was repressed while that of genes involved in ethylene pathways was induced. CaLas infection triggered a response via both the salicylic acid and jasmonic acid pathways and increased the transcript abundance of several members of the WRKY family of transcription factors. Findings focused on the fruit provide valuable insight to understanding the mechanisms of the HLB-induced fruit disorder and eventually developing methods based on small molecule applications to mitigate its devastating effects on fruit production.

Overcoming the challenges of studying conservation physiology in large whales: a review of available methods

A description and comparison of the four major methods available for studying conservation physiology of large whales, namely analysis of faecal, respiratory vapour, and skin/blubber biopsy samples, and photographs.

Avian influenza in birds and mammals

The disease syndromes caused by avian influenza viruses are highly variable depending on the host species infected, its susceptibility and response to infection and the virulence of the infecting viral strain. Although avian influenza viruses have a broad host range in general, it is rare for an individual strain or subtype to infect more than one species. The H5N1 highly pathogenic avian influenza virus (HPAIV) lineages of viruses that descended from A/goose/Guandong/96 (H5N1 HPAIV) are unusual in the diversity of species they have infected worldwide. Although the species affected by H5N1 HPAI in the field and those that have been experimentally studied are diverse, their associated disease syndromes are remarkably similar across species. In some species, multi-organ failure and death are rapid and no signs of the disease are observed. Most prominently in this category are chickens and other avian species of the order Galliformes. In other species, neurologic signs develop resulting in the death of the host. This is what has been reported in domestic cats (Carnivora), geese (Anseriformes), ratites (Struthioniformes), pigeons inoculated with high doses (Columbiformes) and ducks infected with H5N1 HPAIV isolated since 2002 (Anseriformes). In some other species, the disease is more prolonged and although multi-organ failure and death are the eventual outcomes, the signs of disease are more extensive. Predominantly, these species include humans (Primates) and the laboratory models of human disease, the ferret (Carnivora), mouse (Rodentia) and cynamologous macaques (Primates). Finally, some species are more resistant to infection with H5N1 HPAIV and show few or no signs of disease. These species include pigeons in some studies (Columbiformes), ducks inoculated with pre-2002 isolates (Anseriformes), and pigs (Artiodactyla).

Detection of biological and chemical agents using differential mobility spectrometry (DMS) technology

With international concern growing over the potential for chemical and biological terrorism, there is an urgent need for a sensor that can quickly and accurately detect chemical and biological agents. Such a sensor needs to be portable, robust, and sensitive, with fast sample analysis time. We will demonstrate the use of a micromachined differential mobility spectrometer (DMS) with these characteristics that can detect multiple agents simultaneously on a time scale of seconds. In this study, we have demonstrated the ability of the DMS to detect Bacillus subtilis spores, a surrogate for Bacillus anthracis spores, the causative agent of anthrax. Pyrolysis was used as the sample introduction method to volatilize the spores before introducing material into the DMS. Additionally, we examined the effect of pyrolysis on B. subtilis spores suspended in sterile water using SDS-PAGE. These experiments showed that the spores must be heated at 650/spl deg/C or greater for 5 s or at 550/spl deg/C for at least 10 s to be fragmented into particles considerably smaller than 10 kDa, which the DMS can detect. Several major biomarkers can be easily distinguished above the background of the sterile water in which the spores are suspended, and we hypothesize that additional biomarkers could be liberated by further optimizing conditions. The DMS also has shown promise as a detector for chemical weapon agents, and we have demonstrated the ability of the DMS to detect nerve and blister agent simulants at clinically relevant levels.

Gene regulatory networks elucidating huanglongbing disease mechanisms.

Next-generation sequencing was exploited to gain deeper insight into the response to infection by Candidatus liberibacter asiaticus (CaLas), especially the immune disregulation and metabolic dysfunction caused by source-sink disruption. Previous fruit transcriptome data were compared with additional RNA-Seq data in three tissues: immature fruit, and young and mature leaves. Four categories of orchard trees were studied: symptomatic, asymptomatic, apparently healthy, and healthy. Principal component analysis found distinct expression patterns between immature and mature fruits and leaf samples for all four categories of trees. A predicted protein – protein interaction network identified HLB-regulated genes for sugar transporters playing key roles in the overall plant responses. Gene set and pathway enrichment analyses highlight the role of sucrose and starch metabolism in disease symptom development in all tissues. HLB-regulated genes (glucose-phosphate-transporter, invertase, starch-related genes) would likely determine the source-sink relationship disruption. In infected leaves, transcriptomic changes were observed for light reactions genes (downregulation), sucrose metabolism (upregulation), and starch biosynthesis (upregulation). In parallel, symptomatic fruits over-expressed genes involved in photosynthesis, sucrose and raffinose metabolism, and downregulated starch biosynthesis. We visualized gene networks between tissues inducing a source-sink shift. CaLas alters the hormone crosstalk, resulting in weak and ineffective tissue-specific plant immune responses necessary for bacterial clearance. Accordingly, expression of WRKYs (including WRKY70) was higher in fruits than in leaves. Systemic acquired responses were inadequately activated in young leaves, generally considered the sites where most new infections occur.

Continuous Droplet Removal upon Dropwise Condensation of Humid Air on a Hydrophobic Micropatterned Surface

Combination of two physical phenomena, capillary pressure gradient and wettability gradient, allows a simple two-step fabrication process that yields a reliable hydrophobic self-cleaning condenser surface. The surface is fabricated with specific microscopic topography and further treatment with a chemically inert low-surface-energy material. This process does not require growth of nanofeatures (nanotubes) or hydrophilic–hydrophobic patterning of the surface. Trapezoidal geometry of the microfeatures facilitates droplet transfer from the Wenzel to the Cassie state and reduces droplet critical diameter. The geometry of the micropatterns enhances local coalescence and directional movement for droplets with diameter much smaller than the radial length of the micropatterns. The hydrophobic self-cleaning micropatterned condenser surface prevents liquid film formation and promotes continuous dropwise condensation cycle. Upon dropwise condensation, droplets follow a designed wettability gradient created with micropatterns from the most hydrophobic to the least hydrophobic end of the surface. The surface has higher condensation efficiency, due to its directional self-cleaning property, than a plain hydrophobic surface. We explain the self-actuated droplet collection mechanism on the condenser surface and demonstrate experimentally the creation of an effective wettability gradient over a 6 mm radial distance. In spite of its fabrication simplicity, the fabricated surface demonstrates self-cleaning property, enhanced condensation performance, and reliability over time. Our work enables creation of a hydrophobic condenser surface with the directional self-cleaning property that can be used for collection of biological (chemical, environmental) aerosol samples or for condensation enhancement.

Design-of-experiment optimization of exhaled breath condensate analysis using a miniature differential mobility spectrometer (DMS).

Analytical instruments that can measure small amounts of chemicals in complicated biological samples are often useful as diagnostic tools. However, it can be challenging to optimize these sensors using actual clinical samples, given the heterogeneous background and composition of the test materials. Here we use gas chromatography-differential mobility spectrometry (GC/DMS) to analyze the chemical content of human exhaled breath condensate (EBC). Ultimately, this system can be used for non-invasive disease diagnostics. Many parameters can be adjusted within this instrument system, and we implemented a factorial design-of-experiments to systematically test several combinations of parameter settings while concurrently analyzing effects and interactions. We examined four parameters that affect sensitivity and detection for our instrument, requiring a 2(4) factorial design. We optimized sensor function using EBC samples spiked with acetone, a known clinical biomarker in breath. Two outputs were recorded for each experiment combination: number of chemicals detected, and the amplitude of acetone signal. Our goal is to find the best parameter combination that yields the highest acetone peak while also preserving the largest number of other chemical peaks in the spectra. By optimizing the system, we can conduct further clinical experiments with our sensor more efficiently and accurately.

Fluorescence emission spectral shift measurements of membrane potential in single cells.

Previous measurements of transmembrane potential using the electrochromic probe di-8-ANEPPS have used the excitation spectral shift response by alternating excitation between two wavelengths centered at voltage-sensitive portions of the excitation spectrum and recording at a single wavelength near the peak of the emission spectrum. Recently, the emission spectral shift associated with the change in transmembrane potential has been used for continuous membrane potential monitoring. To characterize this form of the electrochromic response from di-8-ANEPPS, we have obtained fluorescence signals from single cells in response to step changes in transmembrane potentials set with a patch electrode, using single wavelength excitation near the peak of the dye absorption spectrum. Fluorescence changes at two wavelengths near voltage-sensitive portions of the emission spectrum and shifts in the complete emission spectrum were determined for emission from plasma membrane and internal membrane. We found that the fluorescence ratio from either dual-wavelength recordings, or from opposite sides of the emission spectrum, varied linearly with the amplitude of the transmembrane potential step between -80 and +60 mV. Voltage dependence of difference spectra exhibit a crossover point near the peak of the emission spectra with approximately equal gain and loss of fluorescence intensity on each side of the spectrum and equal response amplitude for depolarization and hyperpolarization. These results are consistent with an electrochromic mechanism of action and demonstrate how the emission spectral shift response can be used to measure the transmembrane potential in single cells.

Characterization of Volatile Organic Compounds in Human Leukocyte Antigen Heterologous Expression Systems: A Cell's "Chemical Odor Fingerprint"

The major histocompatibility complex (MHC), or human leukocyte antigen (HLA) gene‐coding region in humans, plays a significant role in infectious disease response, autoimmunity, and cellular recognition. This super locus is essential in mate selection and kin recognition because of the organism‐specific odor which can be perceived by other individuals. However, how the unique MHC genetic combination of an organism correlates with generation of the organism‐specific odor is not well understood. In the present work, we have shown that human B‐cells produce a set of volatile organic compounds (VOCs) that can be measured by GC‐MS. More importantly, our results show that specific HLA alleles are related to production of selected VOCs, and that this leads to a cell‐specific odor “fingerprint”. We used a C1R HLA class I A and B locus negative cell line, along with C1R cell lines that were stably transfected with specific A and B alleles. Our work demonstrates for the first time that HLA alleles can directly influence production of specific odor compounds at the cellular level. Given that the resulting odor fingerprint depends on expression of specific HLA sequences, it may yield information on unique human scent profiles, composition of exhaled breath, as well as immune response states in future studies.