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1. Morphology and molecular phylogenetics of the rockpens

   Ni, Ethan; Williams, Gary (October 2023, Society for the Advancement of Chicanos/Hispanics and Native Americans in Science - 2023 NDiSTEM)

   Previous research supports the idea that all sea pens anchor to soft sediment using a long, basal, peduncle. The discovery of several pennatulacean sea pen species (rockpens) with an adaptation to bind to rocky substrata alters this understanding. The evolutionary history of octocorals, including these sea pens, has long been poorly understood due to a slow rate of mitochondrial gene evolution and a consequent lack of phylogenetically informative molecular markers to distinguish species. The objective of this project is to analyze three species of rockpens (Calibelemnon francei, Anthoptilum gowlettholmesae, Anthoptilum sp. Alaska) and other octocorals to construct a phylogeny to better understand the evolutionary relationships between these taxa. Using preserved specimens from the California Academy of Sciences' Department of Invertebrate Zoology, the genes of ten octocoral species were analyzed. This project sequenced three protein-coding mitochondrial genes, ND2, ND6, and msh1, and phylogenetic tree construction and analysis were done using Geneious and R Studio. Additionally, SEM photographs of the sclerites were used to morphologically characterize the taxa. We hypothesize that all rockpens actually belong to the genus Anthoptilum and form a monophyletic clade with other species of the genus that do not inhabit rocky substrata. Future research will require investigating how other non-rock inhabiting species in the genus Anthoptilum are phylogenetically related to the rockpens. 

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2. SELFIES and the future of molecular string representations

   https://doi.org/10.1016/j.patter.2022.100588  

   Krenn, Mario; Ai, Qianxiang; Barthel, Senja; Carson, Nessa; Frei, Angelo; Frey, Nathan C.; Friederich, Pascal; Gaudin, Théophile; Gayle, Alberto Alexander; Jablonka, Kevin Maik; et al (October 2022, Patterns)
3. The Physics and Physical Chemistry of Molecular Machines

   https://doi.org/10.1002/cphc.201600184  

   Astumian, R. Dean; Mukherjee, Shayantani; Warshel, Arieh (June 2016, ChemPhysChem)
4. Considerations of the biosynthesis and molecular diversity of tolyporphins

   https://doi.org/10.1039/d1nj01761f  

   Lindsey, Jonathan S. (July 2021, New Journal of Chemistry)

   null (Ed.)

   Tolyporphins A–R constitute fundamentally distinct members of the tetrapyrrole pigments of life family. The 18 members present diversity at multiple levels including the chromophore (dioxobacteriochlorin, oxochlorin, porphyrin); composition of the pyrroline substituents (hydroxy, acetoxy, or one of four C -glycosides); and stereochemical configuration of the pyrroline substituents. Eleven of the 18 tolyporphins contain at least one C -glycoside; each C -glycoside has a β, d configuration and lacks a 6′-hydroxy group: 3′,6′-dideoxygalactose (common name abequose), 2′- O -acetyl-3′,6′-dideoxygalactose (2′- O -acetylabequose), 6′-deoxygalactose ( d -fucose), or 6′-deoxygulose (antiarose). Rare are such glycosides outside of tolyporphins: (2′- O -acetyl)abequose is reported only in the glycan polymer attached to the cell wall of two strains of Gram-negative bacteria, and antiarose is reported in one bacterial natural product and ∼50 plant cardiac glycosides. Eight of the 18 tolyporphins are bis( C -glycosides), an exceptionally uncommon motif in natural products. The biosynthetic pathways to the family of tolyporphins remain unknown. Regardless of such diversity, each tolyporphin member shares a common pattern of perimeter methyl substituents that coheres with derivation from uroporphyrinogen III, the universal precursor in the established pathway to native tetrapyrroles. Here, transformations required to convert uroporphyrinogen III to all 18 tolyporphins are considered in the context of plausible biosynthetic pathways. Heme d 1 , perhaps the closest relative (yet still a distant cousin) of tolyporphins, and for which key biosynthetic transformations remain undeciphered, provides a point of reference. Taken together, the work provides the foundation for bioinformatic searching for enzymes associated with the biosynthesis and diversification of tolyporphins. 

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5. Thermosalient Amphidynamic Molecular Machines: Motion at the Molecular and Macroscopic Scales

   https://doi.org/10.1016/j.matt.2019.06.018  

   Colin-Molina, Abraham; Karothu, Durga Prasad; Jellen, Marcus J.; Toscano, Rubén A.; Garcia-Garibay, Miguel A.; Naumov, Panče; Rodríguez-Molina, Braulio (October 2019, Matter)