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1. An autoregulatory poison exon in Smndc1 is conserved across kingdoms and influences organism growth

   https://doi.org/10.1371/journal.pgen.1011363  

   Belleville, Andrea E; Thomas, James D; Tonnies, Jackson; Gabel, Austin M; Borrero_Rossi, Andrea; Singh, Priti; Queitsch, Christine; Bradley, Robert K (August 2024, PLOS Genetics)

   Copenhaver, Gregory P (Ed.)

   Many of the most highly conserved elements in the human genome are “poison exons,” alternatively spliced exons that contain premature termination codons and permit post-transcriptional regulation of mRNA abundance through induction of nonsense-mediated mRNA decay (NMD). Poison exons are widely assumed to be highly conserved due to their presumed importance for organismal fitness, but this functional importance has never been tested in the context of a whole organism. Here, we report that a poison exon inSmndc1is conserved across mammals and plants and plays a molecular autoregulatory function in both kingdoms. We generated mouse andA.thalianamodels lacking this poison exon to find its loss leads to deregulation of SMNDC1 protein levels, pervasive alterations in mRNA processing, and organismal size restriction. Together, these models demonstrate the importance of poison exons for both molecular and organismal phenotypes that likely explain their extraordinary conservation. 

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2. Investigating Sk-3 Based Spore Killing in Neurospora crassa Through Deletion Analysis of DNA Intervals i383 And i394

   Paulikas, Paulina (January 2025, ISU ReD)

   Neurospora fungi are found around the world. The species N. crassa is a popular model for use in genetics research. N. crassa produces sexual spores, called ascospores, during mating between strains of opposite mating types. N. crassa also produces spore sacs called asci, and each ascus typically contains eight viable ascospores. However, some Neurospora fungi carry selfish genetic elements called Spore killers, and when a strain carrying a Spore killer mates with a spore killing-susceptible strain, asci contain four black viable ascospores and four white inviable ascospores. In this project, I investigated a Spore killer called Sk-3. To act as a selfish genetic element, Sk-3 is thought to require at least two genes, a poison gene and an antidote gene. The Sk-3 antidote gene (rsk) has been identified, but the poison gene has not. The purpose of this study is to help identify the location of the poison gene. To do this, I deleted two DNA intervals (i383 and i394) from a location of the Neurospora genome that may harbor the poison gene. My results indicate that deletion of i383 eliminates spore killing while deletion of i394 has no effect on spore killing. The possibility that i394 overlaps with the poison gene is discussed. 

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3. Phonon downconversion to suppress correlated errors in superconducting qubits

   https://doi.org/10.1038/s41467-022-33997-0  

   Iaia, V.; Ku, J.; Ballard, A.; Larson, C. P.; Yelton, E.; Liu, C. H.; Patel, S.; McDermott, R.; Plourde, B. L. (December 2022, Nature Communications)

   Abstract Quantum error correction can preserve quantum information in the presence of local errors, but correlated errors are fatal. For superconducting qubits, high-energy particle impacts from background radioactivity produce energetic phonons that travel throughout the substrate and create excitations above the superconducting ground state, known as quasiparticles, which can poison all qubits on the chip. We use normal metal reservoirs on the chip back side to downconvert phonons to low energies where they can no longer poison qubits. We introduce a pump-probe scheme involving controlled injection of pair-breaking phonons into the qubit chips. We examine quasiparticle poisoning on chips with and without back-side metallization and demonstrate a reduction in the flux of pair-breaking phonons by over a factor of 20. We use a Ramsey interferometer scheme to simultaneously monitor quasiparticle parity on three qubits for each chip and observe a two-order of magnitude reduction in correlated poisoning due to background radiation. 

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4. Tissue-specific in vivo transformation of plasmid DNA in Neotropical tadpoles using electroporation

   https://doi.org/10.1371/journal.pone.0289361  

   Delia, Jesse; Gaines-Richardson, Maiah; Ludington, Sarah C.; Akbari, Najva; Vasek, Cooper; Shaykevich, Daniel; O’Connell, Lauren A. (August 2023, PLOS ONE)

   Schubert, Michael (Ed.)

   Electroporation is an increasingly common technique used for exogenous gene expression in live animals, but protocols are largely limited to traditional laboratory organisms. The goal of this protocol is to testin vivoelectroporation techniques in a diverse array of tadpole species. We explore electroporation efficiency in tissue-specific cells of five species from across three families of tropical frogs: poison frogs (Dendrobatidae), cryptic forest/poison frogs (Aromobatidae), and glassfrogs (Centrolenidae). These species are well known for their diverse social behaviors and intriguing physiologies that coordinate chemical defenses, aposematism, and/or tissue transparency. Specifically, we examine the effects of electrical pulse and injection parameters on species- and tissue-specific transfection of plasmid DNA in tadpoles. After electroporation of a plasmid encoding green fluorescent protein (GFP), we found strong GFP fluorescence within brain and muscle cells that increased with the amount of DNA injected and electrical pulse number. We discuss species-related challenges, troubleshooting, and outline ideas for improvement. Extendingin vivoelectroporation to non-model amphibian species could provide new opportunities for exploring topics in genetics, behavior, and organismal biology. 

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5. Evidence for individual vocal recognition in a pair-bonding poison frog, Ranitomeya imitator

   https://doi.org/10.1242/jeb.246753  

   Podraza, Molly E; Moss, Jeanette B; Fischer, Eva K (February 2024, Journal of Experimental Biology)

   ABSTRACT Individually distinctive vocalizations are widespread in nature, although the ability of receivers to discriminate these signals has only been explored through limited taxonomic and social lenses. Here, we asked whether anuran advertisement calls, typically studied for their role in territory defense and mate attraction, facilitate recognition and preferential association with partners in a pair-bonding poison frog (Ranitomeya imitator). Combining no- and two-stimulus choice playback experiments, we evaluated behavioral responses of females to male acoustic stimuli. Virgin females oriented to and approached speakers broadcasting male calls independent of caller identity, implying that females are generally attracted to male acoustic stimuli outside the context of a pair bond. When pair-bonded females were presented with calls of a mate and a stranger, they showed significant preference for calls of their mate. Moreover, behavioral responses varied with breeding status: females with eggs were faster to approach stimuli than females that were pair bonded but did not currently have eggs. Our study suggests a potential role for individual vocal recognition in the formation and maintenance of pair bonds in a poison frog and raises new questions about how acoustic signals are perceived in the context of monogamy and biparental care. 

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