TY - JOUR AB - Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group. AU - Elkrewi, Marwan N AU - Moldovan, Mikhail A. AU - Picard, Marion A L AU - Vicoso, Beatriz ID - 10167 JF - Molecular Biology and Evolution KW - sex chromosomes KW - evolutionary strata KW - W-linked gene KW - sex determining gene KW - schistosome parasites SN - 0737-4038 TI - Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination ER - TY - JOUR AB - The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay. AU - Appel, Lisa-Marie AU - Franke, Vedran AU - Bruno, Melania AU - Grishkovskaya, Irina AU - Kasiliauskaite, Aiste AU - Kaufmann, Tanja AU - Schoeberl, Ursula E. AU - Puchinger, Martin G. AU - Kostrhon, Sebastian AU - Ebenwaldner, Carmen AU - Sebesta, Marek AU - Beltzung, Etienne AU - Mechtler, Karl AU - Lin, Gen AU - Vlasova, Anna AU - Leeb, Martin AU - Pavri, Rushad AU - Stark, Alexander AU - Akalin, Altuna AU - Stefl, Richard AU - Bernecky, Carrie A AU - Djinovic-Carugo, Kristina AU - Slade, Dea ID - 10163 IS - 1 JF - Nature Communications KW - general physics and astronomy KW - general biochemistry KW - genetics and molecular biology KW - general chemistry TI - PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC VL - 12 ER - TY - JOUR AB - With the wider availability of full-color 3D printers, color-accurate 3D-print preparation has received increased attention. A key challenge lies in the inherent translucency of commonly used print materials that blurs out details of the color texture. Previous work tries to compensate for these scattering effects through strategic assignment of colored primary materials to printer voxels. To date, the highest-quality approach uses iterative optimization that relies on computationally expensive Monte Carlo light transport simulation to predict the surface appearance from subsurface scattering within a given print material distribution; that optimization, however, takes in the order of days on a single machine. In our work, we dramatically speed up the process by replacing the light transport simulation with a data-driven approach. Leveraging a deep neural network to predict the scattering within a highly heterogeneous medium, our method performs around two orders of magnitude faster than Monte Carlo rendering while yielding optimization results of similar quality level. The network is based on an established method from atmospheric cloud rendering, adapted to our domain and extended by a physically motivated weight sharing scheme that substantially reduces the network size. We analyze its performance in an end-to-end print preparation pipeline and compare quality and runtime to alternative approaches, and demonstrate its generalization to unseen geometry and material values. This for the first time enables full heterogenous material optimization for 3D-print preparation within time frames in the order of the actual printing time. AU - Rittig, Tobias AU - Sumin, Denis AU - Babaei, Vahid AU - Didyk, Piotr AU - Voloboy, Alexey AU - Wilkie, Alexander AU - Bickel, Bernd AU - Myszkowski, Karol AU - Weyrich, Tim AU - Křivánek, Jaroslav ID - 9547 IS - 2 JF - Computer Graphics Forum SN - 0167-7055 TI - Neural acceleration of scattering-aware color 3D printing VL - 40 ER - TY - JOUR AB - Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials. AU - Martín-Sánchez, Javier AU - Duan, Jiahua AU - Taboada-Gutiérrez, Javier AU - Álvarez-Pérez, Gonzalo AU - Voronin, Kirill V. AU - Prieto Gonzalez, Ivan AU - Ma, Weiliang AU - Bao, Qiaoliang AU - Volkov, Valentyn S. AU - Hillenbrand, Rainer AU - Nikitin, Alexey Y. AU - Alonso-González, Pablo ID - 10177 IS - 41 JF - Science Advances TI - Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas VL - 7 ER - TY - JOUR AB - The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain. AU - Vercellino, Irene AU - Sazanov, Leonid A ID - 10146 IS - 7880 JF - Nature SN - 0028-0836 TI - Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV VL - 598 ER -