Abstract Background Circumnutation (Darwin et al., Sci Rep 10(1):1–13, 2000) is the side-to-side movement common among growing plant appendages but the purpose of circumnutation is not always clear. Accurately tracking and quantifying circumnutation can help researchers to better study its underlying purpose. Results In this paper, a deep learning-based model is proposed to track the circumnutating flowering apices in the plant Arabidopsis thaliana from time-lapse videos. By utilizing U-Net to segment the apex, and combining it with the model update mechanism, pre- and post- processing steps, the proposed model significantly improves the tracking time and accuracy over other baseline tracking methods. Additionally, we evaluate the computational complexity of the proposed model and further develop a method to accelerate the inference speed of the model. The fast algorithm can track the apices in real-time on a computer without a dedicated GPU. Conclusion We demonstrate that the accuracy of tracking the flowering apices in the plant Arabidopsis thaliana can be improved with our proposed deep learning-based model in terms of both the racking success rate and the tracking error. We also show that the improvement in the tracking accuracy is statistically significant. The time-lapse video dataset of Arabidopsis is also provided which can be used for future studies on Arabidopsis in various takes.

Due to its distinct phenotype and relatively simple inheritance pattern, the phenylthiocarbamide (PTC) loci is frequently utilized in teaching laboratories to demonstrate genetic concepts such as Mendelian inheritance and population genetics. We have developed a next-generation sequencing and bioinformatics approach to analyze the PTC gene locus to reveal single nucleotide polymorphism (SNP) variation at nucleotide position 785 that predicts tasting ability in humans. Here students purify DNA from their own cheek cells, perform polymerase chain reaction (PCR) amplification of the PTC gene followed by cleaved amplified polymorphic sequence (CAPS) testing. Students perform a second PCR on the PTC loci using high-fidelity Taq to create bar-coded amplicons for next-generation sequencing on the Ion Torrent Personal Genome Machine. Bioinformatic verification reveals polymorphic variation by aligning the entire class PTC PCR fragment sequence to the human gene using Bowtie2 and visualizing the results in the Integrated Genome Viewer. This exercise presents a learning opportunity for students to use next-generation sequencing to predict their own PTC taste sensitivity phenotype coupled with the standard CAPS method. This approach brings the PTC teaching method into the genomics era.

Invasive species are the second main cause of biodiversity loss because of their exceptional ability to supplant native species by creating major upheavals in ecosystems. Inexpensive and prevalent time-lapse photography provides an exciting opportunity to better understand the aggressive behavior of invasive species including how they invade and conquer new territory. One of the most pervasive invasive species in the Eastern United States is Japanese stiltgrass, Microstegium vimineum (Trin.) A. Campus, which originated from Southeast Asia. Previous research has examined the conditions that enable Japanese stiltgrass to become invasive, but nothing is known regarding root and shoot behavior. Here time-lapse was used to examine Japanese stiltgrass seedlings, early in their development, as a first step to observe its behavior. Our results demonstrate that Japanese stiltgrass shoots appear to drop or collapse and then resurrect back to an upright stature - sometimes the same plant exhibits this behavior multiple times. We have shown, in addition, that emergent stilt root growth rate increases with increased root length. This and similar kinds of analyses may provide insight into how Japanese stiltgrass thrives aggressively in a non-native environment with the goal of developing better methods of controlling this noxious weed.

Presented here is a simple teaching lab to illustrate the dynamic qualities of plant movement using smartphones to create movies of gravitropism and circumnutation. Within as little as 90 minutes, students can observe dramatic changes in plant position using the easy-to-grow, simple genetic model plant, Arabidopsis thaliana. Student assessment revealed that 64 percent of students stated that this lab increased their interest in plants; and interestingly, 46 percent of students showed their movies to individuals who were not associated with the teaching lab, strongly suggesting that this teaching method can be used to propagate interest in plants to individuals in society at large.

We present a lab that enables students to test the role of genes involved in the regulation of lateral roots growth in the model plant Arabidopsis thaliana. Here, students design an experiment that follows the effects of the hormone auxin on the stimulation of genes involved in the formation of lateral root initials. These genes, known as lateral organ boundary domain containing protein (LBD) genes, are upregulated in the presence of auxin as part of a multistep molecular and biochemically controlled pathway. Depending on which LBD gene is tested, and the stage of root development, expression patterns are localized in a discrete and punctate fashion at the site of lateral root initials (LBD33), or reveal a broader localization pattern (LBD16). Students view expression using the reporter gene GUS (beta-glucuronidase). Before GUS staining, students view root growth in a "pseudo-aseptic" agar-based environment that allows complete visualization of whole root development to determine the proper stage to test molecular expression.

Reidunn Birgitta Aalen Javier Abadia Ibrokhim Y. Abdurakhmonov Ikuro Abe Steffen Abel Gian Paolo Accotto Jose Luis Acebes Keith L. Adams Joshua Adams Ahmed Afzal Khairulmazmi Ahmad Elizabeth Ainsworth Eduard Akhunov Kiba Akinori Emre Aksoy Emidio Albertini Veronica Albrecht-Borth Ruben Alcazar Jameel Al-Haddad Karine Alix James William Allwood Tancrède Alméras Maria Elena Alvarez Iraida Amaya Anna Amtmann Gynheung An Anne J. Anderson Louise E. Anderson James V. Anderson Charles T. Anderson Jill T. Anderson Mats X. Andersson John Andralojc Gerco C. Angenent Klaus Apel Miguel A. Aranda Jose Luis Araus Cris M. Argueso Shin-ichi Arimura Idoia Ariz Charles L. Armstrong Susan J. Armstrong Eva-Mari Aro Han Asard Motoyuki Ashikari Sarah M. Assmann Brian J. Atwell Sylvain Aubry Kris Audenaert Koichiro Awai Michael Axtell Thomas J. Bach Tony Bacic Eric Badel Murray Badger Stephen Baenziger Scott Baerson Sacha Baginsky Harsh Pal Bais Soren Bak Neil R. Baker Ian T. Baldwin Steven G. Ball Marilyn C. Ball Carlos L. Ballare Jennifer Baltzer Frantisek Baluska Roberto Barbato Marie Barberon Margaret M. Barbour Gianni Barcaccia Alice Barkan Fredy Barneche Cornelius Barry Bonnie Bartel Dorothea Bartels Madelaine Bartlett Kathy Barton Vitthal T. Barvkar Dudy Bar-Zvi George Bassel Gilles Basset Alfred Batschauer Petra Bauer David Baum Hermann Bauwe Ivan R. Baxter Martin Bayer Michael H. Beale Nathalie Beaudoin Frederic Beaudoin Ulrike Bechtold Dirk Becker Jörg D. Becker Diane M. Beckles Philip W. Becraft Sebastian Bednarek Pawel Bednarek Tom Beeckman Gerrit T.S. Beemster Eric P. Beers Christophe Belin Catherine Bellini Philip N. Benfey Eva Benkova Malcolm J. Bennett Tom Bennett Frederic Berger Susanne Berger John A. Berges Gerald Berkowitz Oliver Berkowitz Thomas Berleth Carl Bernacchi Mark A. Bernards Christine A. Beveridge Rishikesh Bhalerao Hongwu Bian Tatiana N. Bibikova Brad Binder James A. Birchler Kenneth D. Birnbaum Sherryl R. Bisgrove Crysten Blaby Ian Blaby Elison B. Blancaflor Mike R. Blatt Andreas Blennow Claudia Blindauer Arnold Bloom Yaroslav B. Blume Leonor C. Boavida Jens Boch Laszlo Bogre Joerg Bohlmann Cordelia Bolle Vera Bonardi Atle M. Bones Paola Bonfante Anne M. Borland Frederik Börnke Jan-Willem Borst Paul K. Boss Rebecca S. Boston Firas Bou Daher Marie Boudsocq Frédéric Bourgaud Ralph Bours Yohann Boutte Mondher Bouzayen John L. Bowman Caroline Bowsher Nanette R. Boyle Janet Braam Kent J. Bradford Siobhan M. Brady Peter M. Bramley Federica Brandizzi Benjamin Brandt Hans-Peter Braun David M. Braun Melissa Brazier-Hicks Volker Brendel Oliver Brendel Eric D. Brenner Jean-Francois Briat Winslow R. Briggs Anne Bagg Britt Myron Bruce Robert Brueggeman David A. Brummell Glenn J. Bryan Bretislav Brzobhaty Bob Buchanan Peter Buchner Thomas Buckhout Thomas N. Buckley

It is commonly believed that gene duplications provide the raw material for morphological evolution. Both the number of genes and size of gene families have increased during the diversification of land plants. Several small proteins that regulate transcription factors have recently been identified in plants, including the LITTLE ZIPPER (ZPR) proteins. ZPRs are post-translational negative regulators, via heterodimerization, of class III Homeodomain Leucine Zipper (C3HDZ) proteins that play a key role in directing plant form and growth. We show that ZPR genes originated as a duplication of a C3HDZ transcription factor paralog in the common ancestor of euphyllophytes (ferns and seed plants). The ZPRs evolved by degenerative mutations resulting in loss all of the C3HDZ functional domains, except the leucine zipper that modulates dimerization. ZPRs represent a novel regulatory module of the C3HDZ network unique to the euphyllophyte lineage, and their origin correlates to a period of rapid morphological changes and increased complexity in land plants. The origin of the ZPRs illustrates the significance of gene duplications in creating developmental complexity during land plant evolution that likely led to morphological evolution.

Subject to environmental changes and recurrent isolation in the last ca. 250 Ma, cycads are often described as relicts of a previously common lineage, with populations characterized by low genetic variation and restricted gene flow. We found that on the island of Guam, the endemic Cycas micronesica has most of the genetic variation of 14 EST-microsatellites distributed within each of 18 genetic populations, from 24 original sampling sites. There were high levels of genetic variation in terms of total number of alleles and private alleles, and moderate levels of inbreeding. Restricted but ongoing gene flow among populations within Guam reveals a genetic mosaic, probably more typical of cycads than previously assumed. Contiguous cycad populations in the north of Guam had higher self-recruitment rates compared to fragmented populations in the south, with no substantial connection between them except for one population. Guam's genetic mosaic may be explained by the influence of forest continuity, seed size, edaphic differences, and human transport of cycads. Also important are the extent of synchrony among flushes of reproductive female seed-bearing sporophylls and restricted pollen movement by an obligate mutualist and generalist insects. An NADH EST-locus under positive selection may reflect pressure from edaphic differences across Guam. This and three other loci are ideal candidates for ecological genomic studies. Given this species' vulnerability due to the recent introduction of the cycad aulacaspis scale, we also identify priority populations for ex situ conservation, and provide a genetic baseline for understanding the effects of invasive species on cycads in the Western Pacific, and islands in general.

BMAA is a cycad-derived glutamate receptor agonist that causes a two- to three-fold increase in hypocotyl elongation on Arabidopsis seedlings grown in the light. To probe the role of plant glutamate receptors and their downstream mediators, we utilized a previously described genetic screen to identify a novel, BMAA insensitive morphology (bim) mutant, bim409. The normal BMAA-induced hypocotyl elongation response observed on wild-type seedlings grown in the light is impaired in the bim409 mutant. This BMAA-induced phenotype is light-specific, as the bim409 mutant exhibits normal hypocotyl elongation in etiolated (dark grown) plants (+ or − BMAA). The mutation in bim409 was identified to be in a gene encoding the Proteosomal Regulatory Particle AAA-ATPase-3 (RPT3). Possible roles of the proteosome in Glu-mediated signaling in plants is discussed.

Background Genome level analyses have enhanced our view of phylogenetics in many areas of the tree of life. With the production of whole genome DNA sequences of hundreds of organisms and large-scale EST databases a large number of candidate genes for inclusion into phylogenetic analysis have become available. In this work, we exploit the burgeoning genomic data being generated for plant genomes to address one of the more important plant phylogenetic questions concerning the hierarchical relationships of the several major seed plant lineages (angiosperms, Cycadales, Gingkoales, Gnetales, and Coniferales), which continues to be a work in progress, despite numerous studies using single, few or several genes and morphology datasets. Although most recent studies support the notion that gymnosperms and angiosperms are monophyletic and sister groups, they differ on the topological arrangements within each major group. Methodology We exploited the EST database to construct a supermatrix of DNA sequences (over 1,200 concatenated orthologous gene partitions for 17 taxa) to examine non-flowering seed plant relationships. This analysis employed programs that offer rapid and robust orthology determination of novel, short sequences from plant ESTs based on reference seed plant genomes. Our phylogenetic analysis retrieved an unbiased (with respect to gene choice), well-resolved and highly supported phylogenetic hypothesis that was robust to various outgroup combinations. Conclusions We evaluated character support and the relative contribution of numerous variables (e.g. gene number, missing data, partitioning schemes, taxon sampling and outgroup choice) on tree topology, stability and support metrics. Our results indicate that while missing characters and order of addition of genes to an analysis do not influence branch support, inadequate taxon sampling and limited choice of outgroup(s) can lead to spurious inference of phylogeny when dealing with phylogenomic scale data sets. As expected, support and resolution increases significantly as more informative characters are added, until reaching a threshold, beyond which support metrics stabilize, and the effect of adding conflicting characters is minimized.

We developed a set of 12 EST-microsatellite markers (EST-STRs) from Cycas rumphii Miq. and tested them on an ex situ collection of the endangered Cycas micronesica K.D. Hill. The number of alleles per locus in both species ranged from 1 to 15. Observed and expected heterozygosities ranged from 0.000 to 0.842, and 0.000 to 0.883, respectively. All primers amplified in four additional Cycas species. These markers are the first genome-enabled tools for cycad population level studies, and are now available to inform conservation efforts and disentangle the biogeographic history of the genus.