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1. Learning the Helix Topology of Musical Pitch

   https://doi.org/10.1109/ICASSP40776.2020.9053644  

   Lostanlen, Vincent; Sridhar, Sripathi; McFee, Brian; Farnsworth, Andrew; Bello, Juan Pablo (May 2020, ICASSP 2020 - 2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP))

   null (Ed.)

   To explain the consonance of octaves, music psychologists represent pitch as a helix where azimuth and axial coordinate correspond to pitch class and pitch height respectively. This article addresses the problem of discovering this helical structure from unlabeled audio data. We measure Pearson correlations in the constant-Q transform (CQT) domain to build a K-nearest neighbor graph between frequency subbands. Then, we run the Isomap manifold learning algorithm to represent this graph in a three-dimensional space in which straight lines approximate graph geodesics. Experiments on isolated musical notes demonstrate that the resulting manifold resembles a helix which makes a full turn at every octave. A circular shape is also found in English speech, but not in urban noise. We discuss the impact of various design choices on the visualization: instrumentarium, loudness mapping function, and number of neighbors K. 

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2. Evolution and diversification of the ACT-like domain associated with plant basic helix–loop–helix transcription factors

   https://doi.org/10.1073/pnas.2219469120  

   Lee, Yun Sun; Shiu, Shin-Han; Grotewold, Erich (May 2023, Proceedings of the National Academy of Sciences)

   Basic helix–loop–helix (bHLH) proteins are one of the largest families of transcription factor (TF) in eukaryotes, and ~30% of all flowering plants’ bHLH TFs contain the aspartate kinase, chorismate mutase, and TyrA (ACT)-like domain at variable distances C-terminal from the bHLH. However, the evolutionary history and functional consequences of the bHLH/ACT-like domain association remain unknown. Here, we show that this domain association is unique to the plantae kingdom with green algae (chlorophytes) harboring a small number of bHLH genes with variable frequency of ACT-like domain’s presence. bHLH-associated ACT-like domains form a monophyletic group, indicating a common origin. Indeed, phylogenetic analysis results suggest that the association of ACT-like and bHLH domains occurred early in Plantae by recruitment of an ACT-like domain in a common ancestor with widely distributed ACT DOMAIN REPEAT ( ACR ) genes by an ancestral bHLH gene. We determined the functional significance of this association by showing that Chlamydomonas reinhardtii ACT-like domains mediate homodimer formation and negatively affect DNA binding of the associated bHLH domains. We show that, while ACT-like domains have experienced faster selection than the associated bHLH domain, their rates of evolution are strongly and positively correlated, suggesting that the evolution of the ACT-like domains was constrained by the bHLH domains. This study proposes an evolutionary trajectory for the association of ACT-like and bHLH domains with the experimental characterization of the functional consequence in the regulation of plant-specific processes, highlighting the impacts of functional domain coevolution. 

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3. Structure, function and evolution of the Helix-hairpin-Helix DNA glycosylase superfamily: Piecing together the evolutionary puzzle of DNA base damage repair mechanisms

   https://doi.org/10.1016/j.dnarep.2021.103231  

   Trasviña-Arenas, C.H.; Demir, Merve; Lin, Wen-Jen; David, Sheila S. (December 2021, DNA Repair)

   null (Ed.)
4. Combing a double helix

   https://doi.org/10.1039/d1sm01533h  

   Plumb-Reyes, Thomas B.; Charles, Nicholas; Mahadevan, L. (April 2022, Soft Matter)

   Combing hair involves brushing away the topological tangles in a collective curl, defined as a bundle of interacting elastic filaments. Using a combination of experiment and computation, we study this problem that naturally links topology, geometry and mechanics. Observations show that the dominant interactions in hair are those of a two-body nature, corresponding to a braided homochiral double helix. This minimal model allows us to study the detangling of an elastic double helix driven by a single stiff tine that moves along it and leaves two untangled filaments in its wake. Our results quantify how the mechanics of detangling correlates with the dynamics of a topological quantity, the link density, that propagates ahead of the tine and flows out the free end as a link current. This in turn provides a measure of the maximum characteristic length of a single combing stroke in the many-body problem on a head of hair, producing an optimal combing strategy that balances trade-offs between comfort, efficiency and speed of combing in hair curls of varying geometrical and topological complexity. 

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5. Phosphatidylserine Asymmetry Promotes the Membrane Insertion of a Transmembrane Helix

   https://doi.org/10.1016/j.bpj.2019.03.003  

   Scott, Haden L.; Heberle, Frederick A.; Katsaras, John; Barrera, Francisco N. (April 2019, Biophysical Journal)