PHENOS: a high-throughput and flexible tool for microorganism growth phenotyping on solid media

Abstract Background Microbial arrays, with a large number of different strains on a single plate printed with robotic precision, underpin an increasing number of genetic and genomic approaches. These include Synthetic Genetic Array analysis, high-throughput Quantitative Trait Loci (QTL) analysis and 2-hybrid techniques. Measuring the growth of individual colonies within these arrays is an essential part of many of these techniques but is useful for any work with arrays. Measurement is typically done using intermittent imagery fed into complex image analysis software, which is not especially accurate and is challenging to use effectively. We have developed a simple and fast alternative technique that uses a pinning robot and a commonplace microplate reader to continuously measure the thickness of colonies growing on solid agar, complemented by a technique for normalizing the amount of cells initially printed to each spot of the array in the first place. We have developed software to automate the process of combining multiple sets of readings, subtracting agar absorbance, and visualizing colony thickness changes in a number of informative ways. Results The “PHENOS” pipeline (PHENotyping On Solid media), optimized for Saccharomyces yeasts, produces highly reproducible growth curves and is particularly sensitive to low-level growth. We have empirically determined a formula to estimate colony cell count from an absorbance measurement, and shown this to be comparable with estimates from measurements in liquid. We have also validated the technique by reproducing the results of an earlier QTL study done with conventional liquid phenotyping, and found PHENOS to be considerably more sensitive. Conclusions “PHENOS” is a cost effective and reliable high-throughput technique for quantifying growth of yeast arrays, and is likely to be equally very useful for a range of other types of microbial arrays. A detailed guide to the pipeline and software is provided with the installation files at https://github.com/gact/phenos

Genetic and epidemiological characterization of Stretch Lagoon orbivirus, a novel orbivirus isolated from Culex and Aedes mosquitoes in northern Australia

Stretch Lagoon orbivirus (SLOV) was isolated in 2002 from pooled Culex annulirostris mosquitoes collected at Stretch Lagoon, near the Wolfe Creek national park in the Kimberley region of Western Australia. Conventional serological tests were unable to identify the isolate, and electron microscopy indicated a virus of the genus Orbivirus, family Reoviridae. Here, a cDNA subtraction method was used to obtain approximately one-third of the viral genome, and further sequencing was performed to complete the sequences of segment 1 (viral polymerase) and segment 2 (conserved inner-core protein). Phylogenetic analysis showed that SLOV should be considered a new species within the genus Orbivirus. A real-time RT-PCR test was designed to study the epidemiology of SLOV in the field. Six additional isolates of SLOV were identified, including isolates from four additional locations and two additional mosquito species. Horses, donkeys and goats were implicated as potential vertebrate hosts in a serological survey

Environmental and Organismal Predictors of Intraspecific Variation in the Stoichiometry of a Neotropical Freshwater Fish

The elemental composition of animals, or their organismal stoichiometry, is thought to constrain their contribution to nutrient recycling, their interactions with other animals, and their demographic rates. Factors that affect organismal stoichiometry are generally poorly understood, but likely reflect elemental investments in morphological features and life history traits, acting in concert with the environmental availability of elements. We assessed the relative contribution of organismal traits and environmental variability to the stoichiometry of an insectivorous Neotropical stream fish, Rivulus hartii. We characterized the influence of body size, life history phenotype, stage of maturity, and environmental variability on organismal stoichiometry in 6 streams that differ in a broad suite of environmental variables. The elemental composition of R. hartii was variable, and overlapped with the wide range of elemental composition documented across freshwater fish taxa. Average %P composition was ∼3.2%(±0.6), average %N∼10.7%(±0.9), and average %C∼41.7%(±3.1). Streams were the strongest predictor of organismal stoichiometry, and explained up to 18% of the overall variance. This effect appeared to be largely explained by variability in quality of basal resources such as epilithon N∶P and benthic organic matter C∶N, along with variability in invertebrate standing stocks, an important food source for R. hartii. Organismal traits were weak predictors of organismal stoichiometry in this species, explaining when combined up to 7% of the overall variance in stoichiometry. Body size was significantly and positively correlated with %P, and negatively with N∶P, and C∶P, and life history phenotype was significantly correlated with %C, %P, C∶P and C∶N. Our study suggests that spatial variability in elemental availability is more strongly correlated with organismal stoichiometry than organismal traits, and suggests that the stoichiometry of carnivores may not be completely buffered from environmental variability. We discuss the relevance of these findings to ecological stoichiometry theory

Importance of Preserved Tricuspid Valve Function for Effective Soft Robotic Augmentation of the Right Ventricle in Cases of Elevated Pulmonary Artery Pressure

Purpose: In clinical practice, many patients with right heart failure (RHF) have elevated pulmonary artery pressures and increased afterload on the right ventricle (RV). In this study, we evaluated the feasibility of RV augmentation using a soft robotic right ventricular assist device (SRVAD), in cases of increased RV afterload. Methods: In nine Yorkshire swine of 65-80 kg, a pulmonary artery band was placed to cause RHF and maintained in place to simulate an ongoing elevated afterload on the RV. The SRVAD was actuated in synchrony with the ventricle to augment native RV output for up to one hour. Hemodynamic parameters during SRVAD actuation were compared to baseline and RHF levels. Results: Median RV cardiac index (CI) was 1.43 (IQR, 1.37-1.80) L/min/m(2) and 1.26 (IQR 1.05-1.57) L/min/m(2) at first and second baseline. Upon PA banding RV CI fell to a median of 0.79 (IQR 0.63-1.04) L/min/m(2). Device actuation improved RV CI to a median of 0.87 (IQR 0.78-1.01), 0.85 (IQR 0.64-1.59) and 1.11 (IQR 0.67-1.48) L/min/m(2) at 5 min (p = 0.114), 30 min (p = 0.013) and 60 (p = 0.033) minutes respectively. Statistical GEE analysis showed that lower grade of tricuspid regurgitation at time of RHF (p = 0.046), a lower diastolic pressure at RHF (p = 0.019) and lower mean arterial pressure at RHF (p = 0.024) were significantly associated with higher SRVAD effectiveness. Conclusions: Short-term augmentation of RV function using SRVAD is feasible even in cases of elevated RV afterload. Moderate or severe tricuspid regurgitation were associated with reduced device effectiveness

Acceleration of relativistic beams using laser-generated terahertz pulses

Dielectric structures driven by laser-generated terahertz (THz) pulses may hold the key to overcoming the technological limitations of conventional particle accelerators and with recent experimental demonstrations of acceleration, compression and streaking of low-energy (sub-100 keV) electron beams, operation at relativistic beam energies is now essential to realize the full potential of THz-driven structures. We present the first THz-driven linear acceleration of relativistic 35 MeV electron bunches, exploiting the collinear excitation of a dielectric-lined waveguide driven by the longitudinal electric field component of polarization-tailored, narrowband THz pulses. Our results pave the way to unprecedented control over relativistic electron beams, providing bunch compression for ultrafast electron diffraction, energy manipulation for bunch diagnostics, and ultimately delivering high-field gradients for compact THz-driven particle acceleration.Comment: 8 pages, 4 figure