Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat

Background

Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with environmental change as well as respond to different treatments. Although the importance of measuring dynamic growth traits is widely recognised, available open software tools are limited in terms of batch image processing, multiple traits analyses, software usability and cross-referencing results between experiments, making automated phenotypic analysis problematic.

Results

Here, we present Leaf-GP (Growth Phenotypes), an easy-to-use and open software application that can be executed on different computing platforms. To facilitate diverse scientific communities, we provide three software versions, including a graphic user interface (GUI) for personal computer (PC) users, a command-line interface for high-performance computer (HPC) users, and a well-commented interactive Jupyter Notebook (also known as the iPython Notebook) for computational biologists and computer scientists. The software is capable of extracting multiple growth traits automatically from large image datasets. We have utilised it in Arabidopsis thaliana and wheat (Triticum aestivum) growth studies at the Norwich Research Park (NRP, UK). By quantifying a number of growth phenotypes over time, we have identified diverse plant growth patterns between different genotypes under several experimental conditions. As Leaf-GP has been evaluated with noisy image series acquired by different imaging devices (e.g. smartphones and digital cameras) and still produced reliable biological outputs, we therefore believe that our automated analysis workflow and customised computer vision based feature extraction software implementation can facilitate a broader plant research community for their growth and development studies. Furthermore, because we implemented Leaf-GP based on open Python-based computer vision, image analysis and machine learning libraries, we believe that our software not only can contribute to biological research, but also demonstrates how to utilise existing open numeric and scientific libraries (e.g. Scikit-image, OpenCV, SciPy and Scikit-learn) to build sound plant phenomics analytic solutions, in a efficient and effective way.

Conclusions

Leaf-GP is a sophisticated software application that provides three approaches to quantify growth phenotypes from large image series. We demonstrate its usefulness and high accuracy based on two biological applications: (1) the quantification of growth traits for Arabidopsis genotypes under two temperature conditions; and (2) measuring wheat growth in the glasshouse over time. The software is easy-to-use and cross-platform, which can be executed on Mac OS, Windows and HPC, with open Python-based scientific libraries preinstalled. Our work presents the advancement of how to integrate computer vision, image analysis, machine learning and software engineering in plant phenomics software implementation. To serve the plant research community, our modulated source code, detailed comments, executables (.exe for Windows; .app for Mac), and experimental results are freely available at https://github.com/Crop-Phenomics-Group/Leaf-GP/releases.

     

Strategies for the capture and transport of bonefish, Albula vulpes, from tidal creeks to a marine research laboratory for long-term holding

Throughout their circumtropical distribution, bonefish ( Albula spp.) play a vital role in local economies as a highly prized sport fish. Recent interest in stock enhancement to sustain bonefish fisheries has led to the recognition that there currently are no data on how to live capture large numbers of adults (potential broodstock), transport them to captive facilities and how to handle them to ensure high survival. The objective of this study was to develop strategies for the capture and relocation of wild bonefish to a marine research holding facility to enable basic research and explore the potential for culturing bonefish for stock enhancement. Bonefish Albula vulpes (Linnaeus, 1758) were captured as they entered or left tidal creeks on Eleuthera, The Bahamas using seine nets and then transported by boat or truck to the laboratory. The relocation process evoked secondary stress responses at the metabolic, osmoregulatory and haematological levels as indicated by changes in blood glucose, lactate, haematocrit and ion values, relative to control fish. Physical and behavioural disturbances were also observed in bonefish that were unable to acclimate to laboratory conditions. Successful laboratory acclimation and long-term holding of wild bonefish was achieved through an adaptive learning process, whereby we identified a series of strategies and handling techniques to facilitate the acclimation of wild adult bonefish to captivity. This knowledge will enable future laboratory research on bonefish and is a prerequisite to the culture of this highly prized sport fish, and other sub-tropical and tropical marine species.     

The molecular cloning and functional expression of the dog CCR5

Activation of CCR5 by specific chemokines is involved in the regulation of the immunological response of leukocytes at sites of inflammation. In addition, CCR5 serves as a fusion co-factor for macrophage-tropic strains of human immunodeficiency virus type 1 (HIV-1). Consequently, several CCR5 antagonists are currently in development for the treatment of HIV-1 infection. The dog CCR5 gene was cloned in order to characterise the chemokine binding site of the dog receptor for comparison across species. The deduced amino acid sequence of the dog CCR5 has close homology to the human receptor (80% identity). A HEK-293 cell line expressing the dog recombinant receptor was generated and immunoblot analysis with an anti-human CCR5 antibody revealed a 58kDa band in the cell lysate. In functional calcium signalling assays, the CCR5 endogenous ligands MIP-1alpha, MIP-1beta and RANTES evoked a robust response in the dog recombinant CCR5 cells. In a CRE-Luc (cAMP response element-luciferase) reporter gene assay, MIP-1beta (0.01-30nM) produced concentration-dependent inhibition of forskolin induced elevation in cAMP levels, and was equipotent in dog, human and macaque recombinant CCR5 cells (EC(50) 0.4, 0.21 and 0.47nM, respectively). These data suggest that chemokine signalling is conserved in the dog CCR5.     

A species comparison of liver slice synthesis and secretion of triacylglycerol from nonesterified fatty acids in media

The ability of liver slices from eight species to synthesize and secrete triacylglycerol from nonesterified fatty acids contained in media was investigated. Species were grouped according to the relative proportion of lipogenesis occurring in the liver. The rate of liver triacylglycerol synthesis from nonesterified fatty acids in media was similar among species studied. Liver slices from species in which the liver contribution to lipogenesis is minor (sheep, cattle, pig and guinea pig) secreted less triacylglycerol synthesized from nonesterified fatty acids than did liver slices from species in which lipogenesis occurs predominantly in the liver (chicken and fish) or in liver and adipose tissue (rat and rabbit). The results suggest that the ability of liver to secrete triacylglycerol in very low density lipoproteins is proportional to the liver's lipogenic capacity.