The importance of living botanical collections for plant biology and the “next generation” of evo-devo research

Living botanical collections include germplasm repositories, long-term experimental plantings, and botanical gardens. We present here a series of vignettes to illustrate the central role that living collections have played in plant biology research, including evo-devo research. Looking toward the future, living collections will become increasingly important in support of future evo-devo research. The driving force behind this trend is nucleic acid sequencing technologies, which are rapidly becoming more powerful and cost-effective, and which can be applied to virtually any species. This allows for more extensive sampling, including non-model organisms with unique biological features and plants from diverse phylogenetic positions. Importantly, a major challenge for sequencing-based evo-devo research is to identify, access, and propagate appropriate plant materials. We use a vignette of the ongoing 1,000 Transcriptomes project as an example of the challenges faced by such projects. We conclude by identifying some of the pinch points likely to be encountered by future evo-devo researchers, and how living collections can help address them

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees.

BackgroundOne of the great advantages of next generation sequencing is the ability to generate large genomic datasets for virtually all species, including non-model organisms. It should be possible, in turn, to apply advanced computational approaches to these datasets to develop models of biological processes. In a practical sense, working with non-model organisms presents unique challenges. In this paper we discuss some of these challenges for ChIP-seq and RNA-seq experiments using the undomesticated tree species of the genus Populus.ResultsWe describe specific challenges associated with experimental design in Populus, including selection of optimal genotypes for different technical approaches and development of antibodies against Populus transcription factors. Execution of the experimental design included the generation and analysis of Chromatin immunoprecipitation-sequencing (ChIP-seq) data for RNA polymerase II and transcription factors involved in wood formation. We discuss criteria for analyzing the resulting datasets, determination of appropriate control sequencing libraries, evaluation of sequencing coverage needs, and optimization of parameters. We also describe the evaluation of ChIP-seq data from Populus, and discuss the comparison between ChIP-seq and RNA-seq data and biological interpretations of these comparisons.ConclusionsThese and other "lessons learned" highlight the challenges but also the potential insights to be gained from extending next generation sequencing-supported network analyses to undomesticated non-model species

Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

BACKGROUND : Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. RESULTS : Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. CONCLUSIONS : In this first genome-wide analysis of a modified histone in a woody tissue, we optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation.Additional file 1: Supplementary Note S1.Additional file 2: Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, Figure S6, Figure S7, Figure S8, Figure S9, Figure S10, Figure S11, Figure S12, Figure S13, Figure S14, Figure S15, Figure S16.Additional file 3: Table S1, Table S2, Table S3, Table S4, Table S5, Table S6, Table S7.Additional file 4: Genomic locations and fragment coverage of significant H3K4me3 peaks.Additional file 5: Genomic locations of annotated genes overlapping with significant H3K4me3 peaks.Additional file 6: Genomic locations of low-confidence gene models overlapping with significant H3K4me3 peaks.SH, EM and AM acknowledge funding from the Department of Science and Technology (DST), South Africa, the National Research Foundation of South Africa (NRF) Incentive Funding for Rated Researchers Grant (UID 81111) and NRF Bioinformatics and Functional Genomics Program (UID 71255, UID 86936), Sappi and Mondi through the Forest Molecular Genetics (FMG) Program at the University of Pretoria (UP), and the Technology and Human Resources for Industry Program (THRIP) (UID 80118). AG acknowledges funding from USDA National Institute of Food and Agriculture and the Office of Science (BER), US Department of Energy.http://www.biomedcentral.com/bmcplantbiolam201

COVID-19 vaccine perceptions and uptake in a national prospective cohort of essential workers

INTRODUCTION: In a multi-center prospective cohort of essential workers, we assessed knowledge, attitudes, and practices (KAP) by vaccine intention, prior SARS-CoV-2 positivity, and occupation, and their impact on vaccine uptake over time. METHODS: Initiated in July 2020, the HEROES-RECOVER cohort provided socio-demographics and COVID-19 vaccination data. Using two follow-up surveys approximately three months apart, COVID-19 vaccine KAP, intention, and receipt was collected; the first survey categorized participants as reluctant, reachable, or endorser. RESULTS: A total of 4,803 participants were included in the analysis. Most (70%) were vaccine endorsers, 16% were reachable, and 14% were reluctant. By May 2021, 77% had received at least one vaccine dose. KAP responses strongly predicted vaccine uptake, particularly positive attitudes about safety (aOR = 5.46, 95% CI: 1.4-20.8) and effectiveness (aOR = 5.0, 95% CI: 1.3-19.1). Participants' with prior SARS-CoV-2 infection were 22% less likely to believe the COVID-19 vaccine was effective compared with uninfected participants (aOR 0.78, 95% CI: 0.64-0.96). This was even more pronounced in first responders compared with other occupations, with first responders 42% less likely to believe in COVID-19 vaccine effectiveness (aOR = 0.58, 95% CI 0.40-0.84). Between administrations of the two surveys, 25% of reluctant, 56% reachable, and 83% of endorser groups received the COVID-19 vaccine. The reachable group had large increases in positive responses for questions about vaccine safety (10% of vaccinated, 34% of unvaccinated), and vaccine effectiveness (12% of vaccinated, 27% of unvaccinated). DISCUSSION: Our study demonstrates attitudes associated with COVID-19 vaccine uptake and a positive shift in attitudes over time. First responders, despite potential high exposure to SARS-CoV-2, and participants with a history of SARS-CoV-2 infection were more vaccine reluctant. CONCLUSIONS: Perceptions of the COVID-19 vaccine can shift over time. Targeting messages about the vaccine's safety and effectiveness in reducing SARS-CoV-2 virus infection and illness severity may increase vaccine uptake for reluctant and reachable participants

Uncertainty evaluation associated with versatile automated gauging influenced by process variations through design of experiments approach

Recent advances in versatile automated gauging have enabled accurate geometric tolerance assessment on the shop floor. This paper is concerned with the uncertainty evaluation associated with comparative coordinate measurement using the design of experiments (DOE) approach. It employs the Renishaw Equator which is a software-driven comparative gauge based on the traditional comparison of production parts to a reference master part. The fixturing requirement of each production part to the master part is approximately ±1 mm for a comparison process with an uncertainty of ±2 μm. Therefore, a number of experimental designs are applied with the main focus on the influence of part misalignment from rotation between master and measure coordinate frames on the comparator measurement uncertainty. Other factors considered include measurement mode mainly in scanning and touch-trigger probing (TTP) and alignment procedure used to establish the coordinate reference frame (CRF) with respect to the number of contact points used for each geometric feature measured. The measurement uncertainty analysis of the comparator technique used by the Equator gauge commences with a simple measurement task using a gauge block to evaluate the three-dimensional (3D) uncertainty of length comparative coordinate measurement influenced by an offset by tilt in one direction (two-dimensional angular misalignment). Then, a specific manufactured measurement object is employed so that the comparator measurement uncertainty can be assessed for numerous measurement tasks within a satisfactory range of the working volume of the versatile gauge. Furthermore, in the second case study, different types of part misalignment including both 2D and 3D angular misalignments are applied. The time required for managing the re-mastering process is also examined. A task specific uncertainty evaluation is completed using DOE. Also, investigating the effects of process variations that might be experienced by such a device in workshop environments. It is shown that the comparator measurement uncertainties obtained by all the experiments agree with system features under specified conditions. It is also demonstrated that when the specified conditions are exceeded, the comparator measurement uncertainty is associated with the measurement task, the measurement strategy used, the feature size, and the magnitude and direction of offset angles in relation to the reference axes of the machine. In particular, departures from the specified part fixturing requirement of Equator have a more significant effect on the uncertainty of length measurement in comparator mode and a less significant effect on the diameter measurement uncertainty for the specific Equator and test conditions

An Extension of the Plant Ontology Project Supporting Wood Anatomy and Development Research

A wealth of information on plant anatomy and morphology is available in the current and historical literature, and molecular biologists are producing massive amounts of transcriptome and genome data that can be used to gain better insights into the development, evolution, ecology, and physiological function of plant anatomical attributes. Integrating anatomical and molecular data sets is of major importance to the field of wood science, but this is often hampered by the lack of a standardized, controlled vocabulary that allows for cross-referencing among disparate data types. One approach to overcome this obstacle is through the annotation of data using a common controlled vocabulary or “ontology” (Ashburner et al. 2000; Smith et al. 2007). An ontology is a way of representing knowledge in a given domain that includes a set of terms to describe the classes in that domain, as well as the relationships among terms. Each term can be associated with an array of data such as names, definitions, identification numbers, and genes involved. Ontologies are fundamental for unifying diverse terminologies and are increasingly used by scientists, philosophers, the military and online web search engines. In an ontology, terms are carefully defined, allowing a wide array of researchers to (1) use terms consistently in scientific publications or standardized handbooks on quality/trait evaluations, and (2) search for and integrate data linked to these terms in anatomical, genetic, genomic, and other types of biological databases.This is the publisher’s final pdf. The published article is copyrighted by the International Association of Wood Anatomists and can be found at: http://science.naturalis.nl/media/337871/lens%20et%20al-2012%20iawa%20j%20plant%20ontology.pdf)

A Cilia-inspired Closed-loop Sensor-actuator Array

© 2018, Jilin University. Cilia are finger-like cell-surface organelles that are used by certain varieties of aquatic unicellular organisms for motility, sensing and object manipulation. Initiated by internal generators and external mechanical and chemical stimuli, coordinated undulations of cilia lead to the motion of a fluid surrounding the organism. This motion transports micro-particles towards an oral cavity and provides motile force. Inspired by the emergent properties of cilia possessed by the pond organism P. caudatum, we propose a novel smart surface with closed-loop control using sensor-actuators pairings that can manipulate objects. Each vibrating motor actuator is controlled by a localised microcontroller which utilises proximity sensor information to initiate actuation. The circuit boards are designed to be plug-and-play and are infinitely up-scalable and reconfigurable. The smart surface is capable of moving objects at a speed of 7.2 millimetres per second in forward or reverse direction. Further development of this platform will include more anatomically similar biomimetic cilia and control

First steps in studying the origins of secondary woodiness in Begonia (Begoniaceae): Combining anatomy, phylogenetics, and stem transcriptomics

Since Darwin’s observation that secondary woodiness is common on islands, the evolution of woody plants fromherbaceous ancestors has been documented in numerous angiosperm groups. However, the evolutionary processesthat give rise to this phenomenon are poorly understood. To begin addressing this we have used a range ofapproaches to study the anatomical and genetic changes associated with the evolution and development ofsecondary woodiness in a tractable group. Begonia is a large, mainly herbaceous, pantropical genus that showsmultiple shifts towards secondarily woody species inhabiting mainly tropical montane areas throughout the world.Molecular phylogenies, including only a sample of the woody species in Begonia, indicated at least eight instancesof a herbaceous–woody transition within the genus. Wood anatomical observations of the five woody speciesstudied revealed protracted juvenilism that further support the secondary derived origin of wood within Begonia.To identify potential genes involved in shifts towards secondary woodiness, stem transcriptomes of wooddevelopment in B. burbidgei were analysed and compared with available transcriptome datasets for the non-woodyB. venustra, B. conchifolia, and Arabidopsis, and with transcriptome datasets for wood development in Populus.Results identified a number of potential regulatory genes as well as variation in expression of key biosyntheticenzymes. </div

Editorial: Evolution of Gene Regulatory Networks in Plant Development

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