Flowers, leaves or both? How to obtain suitable images for automated plant identification

Background: Deep learning algorithms for automated plant identification need large quantities of precisely labelled images in order to produce reliable classification results. Here, we explore what kind of perspectives and their combinations contain more characteristic information and therefore allow for higher identification accuracy. Results: We developed an image-capturing scheme to create observations of flowering plants. Each observation comprises five in-situ images of the same individual from predefined perspectives (entire plant, flower frontal- and lateral view, leaf top- and back side view). We collected a completely balanced dataset comprising 100 observations for each of 101 species with an emphasis on groups of conspecific and visually similar species including twelve Poaceae species. We used this dataset to train convolutional neural networks and determine the prediction accuracy for each single perspective and their combinations via score level fusion. Top-1 accuracies ranged between 77% (entire plant) and 97% (fusion of all perspectives) when averaged across species. Flower frontal view achieved the highest accuracy (88%). Fusing flower frontal, flower lateral and leaf top views yields the most reasonable compromise with respect to acquisition effort and accuracy (96%). The perspective achieving the highest accuracy was species dependent. Conclusions: We argue that image databases of herbaceous plants would benefit from multi organ observations, comprising at least the front and lateral perspective of flowers and the leaf top view

Epiphytic and endophytic bacteria on olive tree phyllosphere: Exploring tissue and cultivar effect

Variation on bacterial communities living in the phyllosphere as epiphytes and endophytes has been attributed to plant host effects. However, there is contradictory or inconclusive evidence regarding the effect of plant genetics (below the species' level) and of plant tissue type on phyllosphere bacterial community assembly, in particular when epiphytes and endophytes are considered simultaneously. Here, both surface and internal bacterial communities of two olive (Olea europaea) cultivars were evaluated in twigs and leaves by molecular identification of cultivable isolates, with an attempt to answer these questions. Overall,Proteobacteria,ActinobacteriaandFirmicuteswere the dominant phyla, being epiphytes more diverse and abundant than endophytes. Host genotype (at cultivar level) had a structuring effect on the composition of bacterial communities and, in a similar way, for both epiphytes and endophytes. Plant organ (leaf vs. twig) control of the bacterial communities was less evident when compared with plant genotype and with a greater influence on epiphytic than on endophytic community structure. Each olive genotype/plant organ was apparently selective towards specific bacterial operational taxonomic units (OTUs), which may lead to specific feedbacks on fitness of plant genotypes. Bacterial recruitment was observed to happen mainly within epiphytes than in endophytes and in leaves as compared with twigs. Such host specificity suggested that the benefits derived from the plant-bacteria interaction should be considered at genetic levels below the species.The authors are grateful to the FEDER and Foundation for Science and Technology (FCT, Portugal) under Programme PT2020 for financial support to CIMO (UID/AGR/00690/2019) and BioISI (UID/MULTI/04046/2013), as well as the Horizon 2020, the European Union’s Framework Programme for Research and Innovation, for financial support the project PRIMA/0002/2018 INTOMED—Innovative tools to combat crop pests in the Mediterranean. D. Mina thanks FCT, POPH-QREN and FSE for SFRH-BD-105341/2014 grant

Transcriptional Regulation: a Genomic Overview

The availability of the Arabidopsis thaliana genome sequence allows a comprehensive analysis of transcriptional regulation in plants using novel genomic approaches and methodologies. Such a genomic view of transcription first necessitates the compilation of lists of elements. Transcription factors are the most numerous of the different types of proteins involved in transcription in eukaryotes, and the Arabidopsis genome codes for more than 1,500 of them, or approximately 6% of its total number of genes. A genome-wide comparison of transcription factors across the three eukaryotic kingdoms reveals the evolutionary generation of diversity in the components of the regulatory machinery of transcription. However, as illustrated by Arabidopsis, transcription in plants follows similar basic principles and logic to those in animals and fungi. A global view and understanding of transcription at a cellular and organismal level requires the characterization of the Arabidopsis transcriptome and promoterome, as well as of the interactome, the localizome, and the phenome of the proteins involved in transcription

Measurement of plant growth in view of an integrative analysis of regulatory networks

As the regulatory networks of growth at the cellular level are elucidated at a fast pace, their complexity is not reduced; on the contrary, the tissue, organ and even whole-plant level affect cell proliferation and expansion by means of development-induced and environment-induced signaling events in growth regulatory processes. Measurement of growth across different levels aids in gaining a mechanistic understanding of growth, and in defining the spatial and temporal resolution of sampling strategies for molecular analyses in the model Arabidopsis thaliana and increasingly also in crop species. The latter claim their place at the forefront of plant research, since global issues and future needs drive the translation from laboratory model-acquired knowledge of growth processes to improvements in crop productivity in field conditions

The role of the anaphase-promoting complex/cyclosome in plant growth

The anaphase-promoting complex/cyclosome (APC/C) is a multi-subunit E3 ubiquitin ligase that plays a major role in the progression of the eukaryotic cell cycle. This unusual protein complex targets key cell cycle regulators, such as mitotic cyclins and securins, for degradation via the 26S proteasome by ubiquitination, triggering the metaphase-to-anaphase transition and exit from mitosis. Because of its essential role in cell cycle regulation, the APC/C has been extensively studied in mammals and yeasts, but relatively less in plants. Evidence shows that, besides its well-known role in cell cycle regulation, the APC/C also has functions beyond the cell cycle. In metazoans, the APC/C has been implicated in cell differentiation, disease control, basic metabolism and neuronal survival. Recent studies also have shed light on specific functions of the APC/C during plant development. Plant APC/C subunits and activators have been reported to play a role in cellular differentiation, vascular development, shoot branching, female and male gametophyte development and embryogenesis. Here, we discuss our current understanding of the APC/C controlling plant growth

Functional characterization of two plant type I MADS-box genes in Arabidopsis thaliana : AGL40 and AGL62 : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Plant Biology at Massey University, Palmerston North, New Zealand

MADS-box transcription factors (TF) are a family of evolutionary conserved genes found across various eukaryotic species. Characterized by the conserved DNA binding MADS-box domain. MADS-box TF has been shown to play various roles in developmental processes. MADS-box genes can be based on MADS-box structural motifs divided into type I and type II lineages. In plants very limited functional characterization have been achieved with type I genes MADS-box genes. In this project we attempted to functionally characterize 2 closely related members of the type I lineage MADS-box genes AGL40 and AGL62 and give further support to the hypothesis that plant type I MADS-box genes are also crucial to normal plant development. Based on our expression domain characterization assay using AGL62: GUS fusion construct, we have shown expression of AGL62 in various tissues but especially strong in developing seeds, pollen and seedling roots and shoots. The web based microarray data suggesting that AGL62 may have a function in seed, pollen and seedling development backed up this result. Interestingly when we carried out PCR based genotyping with segregating population of heterozygous AGL62 T-DNA insertion lines (agl62/+) to identify the homozygous T-DNA insertion lines we detected no homozygous T-DNA insertion line indicating loss-of-function of AGL62 may be lethal to plant. With reference to the AGL62 expression in pollen, seed and seedling root and shoot, we carried out phenotypic assay on each of these tissues in agl62/+ background to investigate whether there was any phenotypic defect observed. Significant reduction in number of seeds was observed in agl62/+ indicating possible role of AGL62 in seed development. Our microscopic observation of seeds from agl62/+ plants showed defective embryos and confirmed that AGL62 plays a role in seed development. Our data on AGL62 is the first report that confirms AGL62's involvement in plant development and can be a ground work for further works on functional characterization of other members of plant type I MADS-box genes

Assay for free secretory component and methods for monitoring organ rejection

Methods of monitoring and detecting the early onset of organ injury incident rejection of a organ rejection in an animal are disclosed. The described methods are capable of distinguishing organ rejection injury from other organ tissue damage in the animal. Free secretory component levels in an animal biological fluid (e.g., bile, urine, blood, amniotic fluid) may be used to identify organ rejection in an animal. Multiple and single organ transplant patients may be monitored and diagnosed according to the claimed methods. Biological fluids, such as blood, (serum) or urine, are analyzed immunologically using a particularly adapted ELISA which are then compared to an FSC control concentration to identify elevated FSC values. Animals with test FSC above FSC control concentrations are diagnosed as having an ongoing organ rejection episode. The detection of congenital renal dysfunction in utero is also provided according to the present invention through the measurement of FSC in the amniotic fluid. The described methods are specific for indicating organ rejection tissue injury, and distinguish kidney rejection tissue injury, in particular, from other causes of kidney injury, such as cyclosporin toxicity, urinary tract infection, and urinary obstruction and toxicity (incident to immunosuppressive therapy with cyclosporin). A kit for use in the identification of an organ rejection episode in a patient through measurement of FSC in a biological sample is also provided.Board of Regents, University of Texas Syste

Preliminary Functional-Structural Modeling on Poplar (Salicaceae)

Poplar is one of the best fast-growing trees in the world, widely used for windbreak and wood product. Although architecture of poplar has direct impact on its applications, it has not been descried in previous poplar models, probably because of the difficulties raised by measurement, data processing and parameterization. In this paper, the functional-structural model GreenLab is calibrated by using poplar data of 3, 4, 5, 6 years old. The data was acquired by simplifying measurement. The architecture was also simplified by classifying the branches into several types (physiological age) using clustering analysis, which decrease the number of parameters. By multi-fitting the sampled data of each tree, the model parameters were identified and the plant architectures at different tree ages were simulated

Olfaction in mosquitoes

Female mosquitoes are vectors of diseases, affecting both livestock and humans. The host-seeking and identification behaviors of mosquitoes are mediated mainly by olfactory cues. The peripheral olfactory organs of mosquitoes which perceive olfactory cues are the antennae and maxillary palps. These appendages bear numerous hair shaped structures, sensilla, in which olfactory receptor neurons (ORNs) are housed. The ORNs detect and discriminate various odorant molecules and send information regarding odor quality, quantity and spatio-temporal patterns to the central olfactory system in the brain for further analysis. The first goal of this study was to investigate the neuroanatomy of the mosquito central olfactory system. Using different staining techniques, the neuronal architecture of the deutocerebrum as well as 3D reconstructions of antennal lobe (AL) glomeruli were depicted for both sexes of the Afrcian malaria mosquito, Anopheles gambiae and the yellow fever mosquito, Aedes aegypti. To study how mosquitoes detect olfactory cues, single sensillum recordings (SSRs) were performed, which allowed me to investigate electrophysiological properties of individual ORNs housed in four morphological types of the most abundant olfactory sensilla, s. trichodea. I was able to identify 11 functional types which their ORNs displayed distinct responses to a set of compounds. As part of this study, axons of functionally defined ORNs were traced by neurobiotin to indicate which glomeruli they targeted. This resulted in a functional map of AL glomeruli. The map indicated that different functional types of ORNs converged onto different spatially fixed glomeruli. My next step was to identify novel biologically active compounds for the ORNs using gas chromatography coupled SSRs (GC-SSRs). Headspace odors from different human body parts, i.e. armpit, feet and trunk regions as well as from a plant used as a mosquito repellent (Nepeta faassenii) were collected, extracted and eventually injected onto the GC-column. I found that some of the extract components elicited responses in previously defined ORNs as well as in ORNs of the intermediate sensilla. Some of the compounds, which were subsequently identified by using GC-mass spectrometry (GC-MS) were heptanal, octanal, nonanal and decanal