Transposing from the laboratory to the classroom to generate authentic research experiences for undergraduates.

Large lecture classes and standardized laboratory exercises are characteristic of introductory biology courses. Previous research has found that these courses do not adequately convey the process of scientific research and the excitement of discovery. Here we propose a model that provides beginning biology students with an inquiry-based, active learning laboratory experience. The Dynamic Genome course replicates a modern research laboratory focused on eukaryotic transposable elements where beginning undergraduates learn key genetics concepts, experimental design, and molecular biological skills. Here we report on two key features of the course, a didactic module and the capstone original research project. The module is a modified version of a published experiment where students experience how virtual transposable elements from rice (Oryza sativa) are assayed for function in transgenic Arabidopsis thaliana. As part of the module, students analyze the phenotypes and genotypes of transgenic plants to determine the requirements for transposition. After mastering the skills and concepts, students participate in an authentic research project where they use computational analysis and PCR to detect transposable element insertion site polymorphism in a panel of diverse maize strains. As a consequence of their engagement in this course, students report large gains in their ability to understand the nature of research and demonstrate that they can apply that knowledge to independent research projects

TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences

Gene families compose a large proportion of eukaryotic genomes. The rapidly expanding genomic sequence database provides a good opportunity to study gene family evolution and function. However, most gene family identification programs are restricted to searching protein databases where data are often lagging behind the genomic sequence data. Here, we report a user-friendly web-based pipeline, named TARGeT (Tree Analysis of Related Genes and Transposons), which uses either a DNA or amino acid ‘seed’ query to: (i) automatically identify and retrieve gene family homologs from a genomic database, (ii) characterize gene structure and (iii) perform phylogenetic analysis. Due to its high speed, TARGeT is also able to characterize very large gene families, including transposable elements (TEs). We evaluated TARGeT using well-annotated datasets, including the ascorbate peroxidase gene family of rice, maize and sorghum and several TE families in rice. In all cases, TARGeT rapidly recapitulated the known homologs and predicted new ones. We also demonstrated that TARGeT outperforms similar pipelines and has functionality that is not offered elsewhere

Observation of plaquette fluctuations in the spin-1/2 honeycomb lattice

Quantum spin liquids are materials that feature quantum entangled spin correlations and avoid magnetic long-range order at T = 0 K. Particularly interesting are two-dimensional honeycomb spin lattices where a plethora of exotic quantum spin liquids have been predicted. Here, we experimentally study an effective S=1/2 Heisenberg honeycomb lattice with competing nearest and next-nearest neighbor interactions. We demonstrate that YbBr$_3$ avoids order down to at least T=100 mK and features a dynamic spin-spin correlation function with broad continuum scattering typical of quantum spin liquids near a quantum critical point. The continuum in the spin spectrum is consistent with plaquette type fluctuations predicted by theory. Our study is the experimental demonstration that strong quantum fluctuations can exist on the honeycomb lattice even in the absence of Kitaev-type interactions, and opens a new perspective on quantum spin liquids.Comment: 32 pages, 7 Figure

Dipolar spin-waves and tunable band gap at the Dirac points in the 2D magnet ErBr3

Topological magnon insulators constitute a growing field of research for their potential use as information carriers without heat dissipation. We report an experimental and theoretical study of the magnetic ground-state and excitations in the van der Waals two-dimensional honeycomb magnet ErBr3. We show that the magnetic properties of this compound are entirely governed by the dipolar interactions which generate a continuously degenerate non-collinear ground-state on the honeycomb lattice with spins confined in the plane. We find that the magnon dispersion exhibits Dirac-like cones when the magnetic moments in the ground-state are related by time-reversal and inversion symmetries associated with a Berry phase \pi as in single-layer graphene. A magnon band gap opens when the dipoles are rotated away from this state, entailing a finite Berry curvature in the vicinity of the K and K' Dirac points. Our results illustrate that the spin-wave dispersion of dipoles on the honeycomb lattice can be reversibly controlled from a magnetic phase with Dirac cones to a topological antiferromagnetic insulator with non-trivial valley Chern number

Elastic Pion Scattering on the Deuteron in a Multiple Scattering Model

Pion elastic scattering on deuterium is studied in the KMT multiple scattering approach developed in momentum space. Using a Paris wave function and the same methods and approximations as commonly used in pion scattering on heavier nuclei excellent agreement with differential cross section data is obtained for a wide range of pion energies. Only for $T_{\pi}>250$ MeV and very backward angles, discrepancies appear that are reminiscent of disagreements in pion scattering on $^3$He, $^3$H, and $^4$He. At low energies the second order corrections have been included. Polarization observables are studied in detail. While tensor analyzing powers are well reproduced, vector analyzing powers exhibit dramatic discrepancies.Comment: 25 pages LATEX and 9 postscript figures in a self-extracting uufile archiv

Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize

Helitrons are a family of mobile elements that were discovered in 2001 and are now known to exist in the entire eukaryotic kingdom. Helitrons, particularly those of maize, exhibit an intriguing property of capturing gene fragments and placing them into the mobile element. Helitron-captured genes are sometimes transcribed, giving birth to chimeric transcripts that intertwine coding regions of different captured genes. Here, we perused the B73 maize genome for high-quality, putative Helitrons that exhibit plus/minus polymorphisms and contain pieces of more than one captured gene. Selected Helitrons were monitored for expression via in silico EST analysis. Intriguingly, expression validation of selected elements by RT–PCR analysis revealed multiple transcripts not seen in the EST databases. The differing transcripts were generated by alternative selection of splice sites during pre-mRNA processing. Selection of splice sites was not random since different patterns of splicing were observed in the root and shoot tissues. In one case, an exon residing in close proximity but outside of the Helitron was found conjoined with Helitron-derived exons in the mature transcript. Hence, Helitrons have the ability to synthesize new genes not only by placing unrelated exons into common transcripts, but also by transcription readthrough and capture of nearby exons. Thus, Helitrons have a phenomenal ability to “display” new coding regions for possible selection in nature. A highly conservative, minimum estimate of the number of new transcripts expressed by Helitrons is ∼11,000 or ∼25% of the total number of genes in the maize genome

Modeling the Excess Cell Surface Stored in a Complex Morphology of Bleb-Like Protrusions

Cells transition from spread to rounded morphologies in diverse physiological contexts including mitosis and mesenchymal-to-amoeboid transitions. When these drastic shape changes occur rapidly, cell volume and surface area are approximately conserved. Consequently, the rounded cells are suddenly presented with a several-fold excess of cell surface whose area far exceeds that of a smooth sphere enclosing the cell volume. This excess is stored in a population of bleb-like protrusions (BLiPs), whose size distribution is shown by electron micrographs to be skewed. We introduce three complementary models of rounded cell morphologies with a prescribed excess surface area. A 2D Hamiltonian model provides a mechanistic description of how discrete attachment points between the cell surface and cortex together with surface bending energy can generate a morphology that satisfies a prescribed excess area and BLiP number density. A 3D random seed-and-growth model simulates efficient packing of BLiPs over a primary rounded shape, demonstrating a pathway for skewed BLiP size distributions that recapitulate 3D morphologies. Finally, a phase field model (2D and 3D) posits energy-based constitutive laws for the cell membrane, nematic F-actin cortex, interior cytosol, and external aqueous medium. The cell surface is equipped with a spontaneous curvature function, a proxy for the cell surface-cortex couple, that is a priori unknown, which the model “learns” from the thin section transmission electron micrograph image (2D) or the “seed and growth” model image (3D). Converged phase field simulations predict self-consistent amplitudes and spatial localization of pressure and stress throughout the cell for any posited stationary morphology target and cell compartment constitutive properties. The models form a general framework for future studies of cell morphological dynamics in a variety of biological contexts