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

Shattered Families: The Perilous Intersection of Immigration Enforcement and the Child Welfare System

Examines how systemic biases in government practices, lack of legal protections, and limited expertise on the part of child welfare services exacerbate the trauma of separation following parents' detention and deportation and prevent family reunification

Two key events associated with a transposable element burst occurred during rice domestication

Transposable elements shape genome evolution through periodic bursts of amplification. In this study we exploited knowledge of the components of the mPing/Ping/Pong TE family in four rice strains undergoing mPing bursts to track their copy numbers and distribution in a large collection of genomes from the wild progenitor Oryza rufipogon and domesticated Oryza sativa (rice). We characterized two events that occurred to the autonomous Ping element and appear to be critical for mPing hyperactivity. First, a point mutation near the end of the element created a Ping variant ( Ping16A ) with reduced transposition. The proportion of strains with Ping16A has increased during domestication while the original Ping (Ping16G) has been dramatically reduced. Second, transposition of Ping16A into a Stowaway element generated a locus ( Ping16A_Stow ) whose presence correlates with strains that have high mPing copies. Finally, demonstration that Pong elements have been stably silenced in all strains analyzed indicates that sustained activity of the mPing/Ping family during domestication produced the components necessary for the mPing burst, not the loss of epigenetic regulation

Functional characterization of the active Mutator-like transposable element, Muta1 from the mosquito Aedes aegypti

Yeast transposition assay constructs. (A) Structures of pMuta1_PAG415 and pWL89Ae. AmpR, ampicillin resistance gene; ori, E. coli replication origin; Pgal1, GAL1 promoter; CYC1 ter, terminator; CEN, centromere sequences of yeast chromosomes; ARS, autonomous replication site. Dashed lines indicate the position of nonautonomous element insertions, in the 5’UTR and coding region respectively. Black arrows indicate the positions of primers used for PCR analysis in Figure S3A. (B) Excision from coding region of ADE2. (C) Excision from 5’ UTR of ADE2. (D) Reintegration. In the parental strain, pWL89A carries Muta1HIS in the coding region of ADE2. Reintegration is assayed by selecting cells that retain the HIS marker in Muta1HIS when the parental plasmid is excluded by 5-FOA treatment, which is toxic to Ura+ cells. (TIF 602 kb