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The temporal and genomic scale of selection following hybridization Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Jeffrey S. Groh, Graham Coop
Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the evolutionary dynamics within hybrid populations that underlie these patterns have been lacking. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of ancestry variation
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Frequent winners explain apparent skewness preferences in experience-based decisions Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Sebastian Olschewski, Mikhail S. Spektor, Gaël Le Mens
Do people’s attitudes toward the (a)symmetry of an outcome distribution affect their choices? Financial investors seek return distributions with frequent small returns but few large ones, consistent with leading models of choice in economics and finance that assume right-skewed preferences. In contrast, many experiments in which decision-makers learn about choice options through experience find the
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Dependence on relative humidity in the formation of reactive oxygen species in water droplets Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Mohammad Mofidfar, Masoud A. Mehrgardi, Yu Xia, Richard N. Zare
Water microdroplets (7 to 11 µm average diameter, depending on flow rate) are sprayed in a closed chamber at ambient temperature, whose relative humidity (RH) is controlled. The resulting concentration of ROS (reactive oxygen species) formed in the microdroplets, measured by the amount of hydrogen peroxide (H 2 O 2 ), is determined by nuclear magnetic resonance (NMR) and by spectrofluorimetric assays
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Transcription-induced active forces suppress chromatin motion Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Sucheol Shin, Guang Shi, Hyun Woo Cho, D. Thirumalai
The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known about the dynamics, especially in the functional states of chromatin. Some experiments have shown that the motility of individual loci in human interphase chromosome decreases during transcription and increases upon inhibiting
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Photo-neuro-immuno-endocrinology: How the ultraviolet radiation regulates the body, brain, and immune system Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Radomir M. Slominski, Jake Y. Chen, Chander Raman, Andrzej T. Slominski
Ultraviolet radiation (UVR) is primarily recognized for its detrimental effects such as cancerogenesis, skin aging, eye damage, and autoimmune disorders. With exception of ultraviolet B (UVB) requirement in the production of vitamin D3, the positive role of UVR in modulation of homeostasis is underappreciated. Skin exposure to UVR triggers local responses secondary to the induction of chemical, hormonal
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A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron-binding protein FutA from Prochlorococcus Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Rachel Bolton, Moritz M. Machelett, Jack Stubbs, Danny Axford, Nicolas Caramello, Lucrezia Catapano, Martin Malý, Matthew J. Rodrigues, Charlotte Cordery, Graham J. Tizzard, Fraser MacMillan, Sylvain Engilberge, David von Stetten, Takehiko Tosha, Hiroshi Sugimoto, Jonathan A. R. Worrall, Jeremy S. Webb, Mike Zubkov, Simon Coles, Eric Mathieu, Roberto A. Steiner, Garib Murshudov, Tobias E. Schrader
The marine cyanobacterium Prochlorococcus is a main contributor to global photosynthesis, whilst being limited by iron availability. Cyanobacterial genomes generally encode two different types of FutA iron-binding proteins: periplasmic FutA2 ABC transporter subunits bind Fe(III), while cytosolic FutA1 binds Fe(II). Owing to their small size and their economized genome Prochlorococcus ecotypes typically
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KCTD10 regulates brain development by destabilizing brain disorder–associated protein KCTD13 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Jianbo Cheng, Zhen Wang, Manpei Tang, Wen Zhang, Guozhong Li, Senwei Tan, Chenjun Mu, Mengyuan Hu, Dan Zhang, Xiangbin Jia, Yangxuan Wen, Hui Guo, Dan Xu, Liang Liu, Jiada Li, Kun Xia, Faxiang Li, Ranhui Duan, Zhiheng Xu, Ling Yuan
KCTD10 belongs to the KCTD (potassiumchannel tetramerization domain) family, many members of which are associated with neuropsychiatric disorders. However, the biological function underlying the association with brain disorders remains to be explored. Here, we reveal that Kctd10 is highly expressed in neuronal progenitors and layer V neurons throughout brain development. Kctd10 deficiency triggers
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A minimal physical model for curvotaxis driven by curved protein complexes at the cell’s leading edge Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Raj Kumar Sadhu, Marine Luciano, Wang Xi, Cristina Martinez-Torres, Marcel Schröder, Christoph Blum, Marco Tarantola, Stefano Villa, Samo Penič, Aleš Iglič, Carsten Beta, Oliver Steinbock, Eberhard Bodenschatz, Benoît Ladoux, Sylvain Gabriele, Nir S. Gov
Cells often migrate on curved surfaces inside the body, such as curved tissues, blood vessels, or highly curved protrusions of other cells. Recent in vitro experiments provide clear evidence that motile cells are affected by the curvature of the substrate on which they migrate, preferring certain curvatures to others, termed “curvotaxis.” The origin and underlying mechanism that gives rise to this
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Changes in spatial self-consciousness elicit grid cell–like representation in the entorhinal cortex Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Hyuk-June Moon, Louis Albert, Emanuela De Falco, Corentin Tasu, Baptiste Gauthier, Hyeong-Dong Park, Olaf Blanke
Grid cells in the entorhinal cortex (EC) encode an individual’s location in space, integrating both environmental and multisensory bodily cues. Notably, body-derived signals are also primary signals for the sense of self. While studies have demonstrated that continuous application of visuo-tactile bodily stimuli can induce perceptual shifts in self-location, it remains unexplored whether these illusory
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Heterogeneous elasticity drives ripening and controls bursting kinetics of transcriptional condensates Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Lingyu Meng, Sheng Mao, Jie Lin
Many biomolecular condensates, including transcriptional condensates, are formed in elastic mediums. In this work, we study the nonequilibrium condensate dynamics in a chromatin-like environment modeled as a heterogeneous elastic medium. We demonstrate that the ripening process in such an elastic medium exhibits a temporal power-law scaling of the average condensate radius, depending on the local stiffness
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SRF transcriptionally regulates the oligodendrocyte cytoskeleton during CNS myelination Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Tal Iram, Miguel A. Garcia, Jérémy Amand, Achint Kaur, Micaiah Atkins, Manasi Iyer, Mable Lam, Nicholas Ambiel, Danielle M. Jorgens, Andreas Keller, Tony Wyss-Coray, Fabian Kern, J. Bradley Zuchero
Myelination of neuronal axons is essential for nervous system development. Myelination requires dramatic cytoskeletal dynamics in oligodendrocytes, but how actin is regulated during myelination is poorly understood. We recently identified serum response factor (SRF)—a transcription factor known to regulate expression of actin and actin regulators in other cell types—as a critical driver of myelination
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Endogenous retrovirus HERVH-derived lncRNA UCA1 controls human trophoblast development Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Xuhui Kong, Ruiqi Li, Manqi Chen, Rongyan Zheng, Jichang Wang, Chuanbo Sun, Yuliang Qu
Endogenous retroviruses (ERVs) are frequently reactivated in mammalian placenta. It has been proposed that ERVs contribute to shaping the gene regulatory network of mammalian trophoblasts, dominantly acting as species- and placental-specific enhancers. However, whether and how ERVs control human trophoblast development through alternative pathways remains poorly understood. Besides the well-recognized
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Molecular and structural basis of the dual regulation of the polycystin-2 ion channel by small-molecule ligands Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Zhifei Wang, Mengying Chen, Qiang Su, Tiago D. C. Morais, Yan Wang, Elianna Nazginov, Akhilraj R. Pillai, Feng Qian, Yigong Shi, Yong Yu
Mutations in the PKD2 gene, which encodes the polycystin-2 (PC2, also called TRPP2) protein, lead to autosomal dominant polycystic kidney disease (ADPKD). As a member of the transient receptor potential (TRP) channel superfamily, PC2 functions as a non-selective cation channel. The activation and regulation of the PC2 channel are largely unknown, and direct binding of small-molecule ligands to this
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Neuronal IL-17 controls Caenorhabditis elegans developmental diapause through CEP-1/p53 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Abhishiktha Godthi, Sehee Min, Srijit Das, Johnny Cruz-Corchado, Andrew Deonarine, Kara Misel-Wuchter, Priya D. Issuree, Veena Prahlad
During metazoan development, how cell division and metabolic programs are coordinated with nutrient availability remains unclear. Here, we show that nutrient availability signaled by the neuronal cytokine, ILC-17.1, switches Caenorhabditis elegans development between reproductive growth and dormancy by controlling the activity of the tumor suppressor p53 ortholog, CEP-1. Specifically, upon food availability
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Identification of a negative-strand RNA virus with natural plant and fungal hosts Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Ruoyin Dai, Shian Yang, Tianxing Pang, Mengyuan Tian, Hao Wang, Dong Zhang, Yunfeng Wu, Hideki Kondo, Ida Bagus Andika, Zhensheng Kang, Liying Sun
The presence of viruses that spread to both plant and fungal populations in nature has posed intriguingly scientific question. We found a negative-strand RNA virus related to members of the family Phenuiviridae , named Valsa mali negative-strand RNA virus 1 (VmNSRV1), which induced strong hypovirulence and was prevalent in a population of the phytopathogenic fungus of apple Valsa canker ( Valsa mali
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Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Allison Judge, Banumathi Sankaran, Liya Hu, Murugesan Palaniappan, André Birgy, B. V. Venkataram Prasad, Timothy Palzkill
Cooperative interactions between amino acids are critical for protein function. A genetic reflection of cooperativity is epistasis, which is when a change in the amino acid at one position changes the sequence requirements at another position. To assess epistasis within an enzyme active site, we utilized CTX-M β-lactamase as a model system. CTX-M hydrolyzes β-lactam antibiotics to provide antibiotic
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Distinct early role of PTEN regulation during HCMV infection of monocytes Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Liudmila S. Chesnokova, Bailey S. Mosher, Heather L. Fulkerson, Hyung W. Nam, Akhalesh K. Shakya, Andrew D. Yurochko
Human cytomegalovirus (HCMV) infection of monocytes is essential for viral dissemination and persistence. We previously identified that HCMV entry/internalization and subsequent productive infection of this clinically relevant cell type is distinct when compared to other infected cells. We showed that internalization and productive infection required activation of epidermal growth factor receptor (EGFR)
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Predation without direction selectivity Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Jenna Krizan, Xiayingfang Song, Michael J. Fitzpatrick, Ning Shen, Florentina Soto, Daniel Kerschensteiner
Across the animal kingdom, visual predation relies on motion-sensing neurons in the superior colliculus (SC) and its orthologs. These neurons exhibit complex stimulus preferences, including direction selectivity, which is thought to be critical for tracking the unpredictable escape routes of prey. The source of direction selectivity in the SC is contested, and its contributions to predation have not
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Structural transitions modulate the chaperone activities of Grp94 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Yaa S. Amankwah, Yasmeen Fleifil, Erin Unruh, Preston Collins, Yi Wang, Katherine Vitou, Alison Bates, Ikponwmosa Obaseki, Meghana Sugoor, John Paul Alao, Robert M. McCarrick, Daniel T. Gewirth, Indra D. Sahu, Zihai Li, Gary. A. Lorigan, Andrea N. Kravats
Hsp90s are ATP-dependent chaperones that collaborate with co-chaperones and Hsp70s to remodel client proteins. Grp94 is the ER Hsp90 homolog essential for folding multiple secretory and membrane proteins. Grp94 interacts with the ER Hsp70, BiP, although the collaboration of the ER chaperones in protein remodeling is not well understood. Grp94 undergoes large-scale conformational changes that are coupled
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Large nonlinear optical magnetoelectric response in a noncentrosymmetric magnetic Weyl semimetal Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Kentaro Shoriki, Keigo Moriishi, Yoshihiro Okamura, Kohei Yokoi, Hidetomo Usui, Hiroshi Murakawa, Hideaki Sakai, Noriaki Hanasaki, Yoshinori Tokura, Youtarou Takahashi
Weyl semimetals resulting from either inversion ( P ) or time-reversal ( T ) symmetry breaking have been revealed to show the record-breaking large optical response due to intense Berry curvature of Weyl-node pairs. Different classes of Weyl semimetals with both P and T symmetry breaking potentially exhibit optical magnetoelectric (ME) responses, which are essentially distinct from the previously observed
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East Asian summer monsoon delivers large abundances of very-short-lived organic chlorine substances to the lower stratosphere Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Laura L. Pan, Elliot L. Atlas, Shawn B. Honomichl, Warren P. Smith, Douglas E. Kinnison, Susan Solomon, Michelle L. Santee, Alfonso Saiz-Lopez, Johannes C. Laube, Bin Wang, Rei Ueyama, James F. Bresch, Rebecca S. Hornbrook, Eric C. Apel, Alan J. Hills, Victoria Treadaway, Katie Smith, Sue Schauffler, Stephen Donnelly, Roger Hendershot, Richard Lueb, Teresa Campos, Silvia Viciani, Francesco D’Amato
Deep convection in the Asian summer monsoon is a significant transport process for lifting pollutants from the planetary boundary layer to the tropopause level. This process enables efficient injection into the stratosphere of reactive species such as chlorinated very-short-lived substances (Cl-VSLSs) that deplete ozone. Past studies of convective transport associated with the Asian summer monsoon
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On-the-fly Raman microscopy guaranteeing the accuracy of discrimination Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Koji Tabata, Hiroyuki Kawagoe, J. Nicholas Taylor, Kentaro Mochizuki, Toshiki Kubo, Jean-Emmanuel Clement, Yasuaki Kumamoto, Yoshinori Harada, Atsuyoshi Nakamura, Katsumasa Fujita, Tamiki Komatsuzaki
Accelerating the measurement for discrimination of samples, such as classification of cell phenotype, is crucial when faced with significant time and cost constraints. Spontaneous Raman microscopy offers label-free, rich chemical information but suffers from long acquisition time due to extremely small scattering cross-sections. One possible approach to accelerate the measurement is by measuring necessary
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Thermodynamic properties and enhancement of diamagnetism in nitrogen doped lutetium hydride synthesized at high pressure Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Yifeng Han, Yunbo Ou, Hualei Sun, Jan Kopaczek, Gerson J. Leonel, Xin Guo, Benjamin L. Brugman, Kurt Leinenweber, Hongwu Xu, Meng Wang, Sefaattin Tongay, Alexandra Navrotsky
Nitrogen doped lutetium hydride has drawn global attention in the pursuit of room-temperature superconductivity near ambient pressure and temperature. However, variable synthesis techniques and uncertainty surrounding nitrogen concentration have contributed to extensive debate within the scientific community about this material and its properties. We used a solid-state approach to synthesize nitrogen
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Structural insights reveal interplay between LAG-3 homodimerization, ligand binding, and function Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 John L. Silberstein, Jasper Du, Kun-Wei Chan, Jessica A. Frank, Irimpan I. Mathews, Yong Bin Kim, Jia You, Qiao Lu, Jia Liu, Elliot A. Philips, Phillip Liu, Eric Rao, Daniel Fernandez, Grayson E. Rodriguez, Xiang-Peng Kong, Jun Wang, Jennifer R. Cochran
Lymphocyte activation gene-3 (LAG-3) is an inhibitory receptor expressed on activated T cells and an emerging immunotherapy target. Domain 1 (D1) of LAG-3, which has been purported to directly interact with major histocompatibility complex class II (MHCII) and fibrinogen-like protein 1 (FGL1), has been the major focus for the development of therapeutic antibodies that inhibit LAG-3 receptor-ligand
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Epidermal growth factor receptor (EGFR) is a target of the tumor-suppressor E3 ligase FBXW7 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Matteo Boretto, Maarten H. Geurts, Shashank Gandhi, Ziliang Ma, Nadzeya Staliarova, Martina Celotti, Sangho Lim, Gui-Wei He, Rosemary Millen, Else Driehuis, Harry Begthel, Lidwien Smabers, Jeanine Roodhart, Johan van Es, Wei Wu, Hans Clevers
FBXW7 is an E3 ubiquitin ligase that targets proteins for proteasome-mediated degradation and is mutated in various cancer types. Here, we use CRISPR base editors to introduce different FBXW7 hotspot mutations in human colon organoids. Functionally, FBXW7 mutation reduces EGF dependency of organoid growth by ~10,000-fold. Combined transcriptomic and proteomic analyses revealed increased EGFR protein
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Multiple retinal isomerizations during the early phase of the bestrhodopsin photoreaction Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Spyridon Kaziannis, Matthias Broser, Ivo H. M. van Stokkum, Jakub Dostal, Wayne Busse, Arno Munhoven, Cesar Bernardo, Miroslav Kloz, Peter Hegemann, John T. M. Kennis
Bestrhodopsins constitute a class of light-regulated pentameric ion channels that consist of one or two rhodopsins in tandem fused with bestrophin ion channel domains. Here, we report on the isomerization dynamics in the rhodopsin tandem domains of Phaeocystis antarctica bestrhodopsin, which binds all-trans retinal Schiff-base (RSB) absorbing at 661 nm and, upon illumination, converts to the meta-stable
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RN7SL1 may be translated under oncogenic conditions Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Tomoaki Hara, Sikun Meng, Yoshiko Tsuji, Yasuko Arao, Yoshiko Saito, Hiromichi Sato, Daisuke Motooka, Shizuka Uchida, Hideshi Ishii
RN7SL1 (RNA component of signal recognition particle 7SL1), a component of the signal recognition particle, is a non-coding RNA possessing a small ORF (smORF). However, whether it is translated into peptides is unknown. Here, we generated the RN7SL1-Green Fluorescent Protein (GFP) gene, in which the smORF of RN7SL1 was replaced by GFP, introduced it into 293T cells, and observed cells emitting GFP
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A type I interferon regulatory network for human plasmacytoid dendritic cells based on heparin, membrane-bound and soluble BDCA-2 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Francisco Venegas-Solis, Laura Staliunaite, Elisa Rudolph, Carina Chan-Song Münch, Philipp Yu, Sven-A. Freibert, Takahiro Maeda, Christine L. Zimmer, Christian Möbs, Christian Keller, Andreas Kaufmann, Stefan Bauer
Plasmacytoid dendritic cells (pDCs) produce type I interferons (IFNs) after sensing viral/bacterial RNA or DNA by toll-like receptor (TLR) 7 or TLR9, respectively. However, aberrant pDCs activation can cause adverse effects on the host and contributes to the pathogenesis of type I IFN-related autoimmune diseases. Here, we show that heparin interacts with the human pDCs-specific blood dendritic cell
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Grain boundary plasticity initiated by excess volume Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Qi Zhu, Qingkun Zhao, Qishan Huang, Yingbin Chen, Subra Suresh, Wei Yang, Ze Zhang, Haofei Zhou, Huajian Gao, Jiangwei Wang
Grain boundaries (GBs) serve not only as strong barriers to dislocation motion, but also as important carriers to accommodate plastic deformation in crystalline solids. During deformation, the inherent excess volume associated with loose atomic packing in GBs brings about a microscopic degree of freedom that can initiate GB plasticity, which is beyond the classic geometric description of GBs. However
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Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Sylvain Legrand, Asma Saifudeen, Hélène Bordelet, Julien Vernerey, Arnaud Guille, Amaury Bignaud, Agnès Thierry, Laurent Acquaviva, Maxime Gaudin, Aurore Sanchez, Dominic Johnson, Anne Friedrich, Joseph Schacherer, Matthew J. Neale, Valérie Borde, Romain Koszul, Bertrand Llorente
Meiotic recombination shows broad variations across species and along chromosomes and is often suppressed at and around genomic regions determining sexual compatibility such as mating type loci in fungi. Here, we show that the absence of Spo11-DSBs and meiotic recombination on Lakl0C-left, the chromosome arm containing the sex locus of the Lachancea kluyveri budding yeast, results from the absence
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Harmonizing the cyano-group and Na to enhance selective photocatalytic O 2 activation on carbon nitride for refractory pollutant degradation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Mingkai Xu, Ruizhao Wang, Haoyang Fu, Yanbiao Shi, Lan Ling
Manipulating exciton dissociation and charge-carrier transfer processes to selectively generate free radicals of more robust photocatalytic oxidation capacity for mineralizing refractory pollutants remains challenging. Herein, we propose a strategy by simultaneously introducing the cyano-group and Na into graphitic carbon nitride (CN) to obtain CN-Cy-Na, which makes the charge-carrier transfer pathways
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A tale of two topological isomers: Uptuning [Fe IV (O)(Me 4 cyclam)] 2+ for olefin epoxidation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Bittu Chandra, Faiza Ahsan, Yuan Sheng, Marcel Swart, Lawrence Que
TMC- anti and TMC- syn, the two topological isomers of [Fe IV (O)(TMC)(CH 3 CN)] 2+ (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane, or Me 4 cyclam), differ in the orientations of their Fe IV =O units relative to the four methyl groups of the TMC ligand framework. The Fe IV =O unit of TMC- anti points away from the four methyl groups, while that of TMC- syn is surrounded by the methyl
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4D microvelocimetry reveals multiphase flow field perturbations in porous media Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Tom Bultreys, Sharon Ellman, Christian M. Schlepütz, Matthieu N. Boone, Gülce Kalyoncu Pakkaner, Shan Wang, Mostafa Borji, Stefanie Van Offenwert, Niloofar Moazami Goudarzi, Wannes Goethals, Chandra Widyananda Winardhi, Veerle Cnudde
Many environmental and industrial processes depend on how fluids displace each other in porous materials. However, the flow dynamics that govern this process are still poorly understood, hampered by the lack of methods to measure flows in optically opaque, microscopic geometries. We introduce a 4D microvelocimetry method based on high-resolution X-ray computed tomography with fast imaging rates (up
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Interpreting chemisorption strength with AutoML-based feature deletion experiments Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Zhuo Li, Changquan Zhao, Haikun Wang, Yanqing Ding, Yechao Chen, Philippe Schwaller, Ke Yang, Cheng Hua, Yulian He
The chemisorption energy of reactants on a catalyst surface, E ads , is among the most informative characteristics of understanding and pinpointing the optimal catalyst. The intrinsic complexity of catalyst surfaces and chemisorption reactions presents significant difficulties in identifying the pivotal physical quantities determining E ads . In response to this, the study proposes a methodology, the
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Balance and imbalance in biogeochemical cycles reflect the operation of closed, exchange, and open sets Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Preston Cosslett Kemeny, Mark A. Torres, Woodward W. Fischer, Clara L. Blättler
Biogeochemical reactions modulate the chemical composition of the oceans and atmosphere, providing feedbacks that sustain planetary habitability over geological time. Here, we mathematically evaluate a suite of biogeochemical processes to identify combinations of reactions that stabilize atmospheric carbon dioxide by balancing fluxes of chemical species among the ocean, atmosphere, and geosphere. Unlike
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Predictive phage therapy for Escherichia coli urinary tract infections: Cocktail selection for therapy based on machine learning models Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Marianne Keith, Alba Park de la Torriente, Antonia Chalka, Adriana Vallejo-Trujillo, Sean P. McAteer, Gavin K. Paterson, Alison S. Low, David L. Gally
This study supports the development of predictive bacteriophage (phage) therapy: the concept of phage cocktail selection to treat a bacterial infection based on machine learning (ML) models. For this purpose, ML models were trained on thousands of measured interactions between a panel of phage and sequenced bacterial isolates. The concept was applied to Escherichia coli associated with urinary tract
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H 2 S preconditioning induces long-lived perturbations in O 2 metabolism Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 David A. Hanna, Jutta Diessl, Arkajit Guha, Roshan Kumar, Anthony Andren, Costas Lyssiotis, Ruma Banerjee
Hydrogen sulfide exposure in moderate doses can induce profound but reversible hypometabolism in mammals. At a cellular level, H 2 S inhibits the electron transport chain (ETC), augments aerobic glycolysis, and glutamine-dependent carbon utilization via reductive carboxylation; however, the durability of these changes is unknown. We report that despite its volatility, H 2 S preconditioning increases
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Unsupervised identification of significant lineages of SARS-CoV-2 through scalable machine learning methods Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Roberto Cahuantzi, Katrina A. Lythgoe, Ian Hall, Lorenzo Pellis, Thomas House
Since its emergence in late 2019, SARS-CoV-2 has diversified into a large number of lineages and caused multiple waves of infection globally. Novel lineages have the potential to spread rapidly and internationally if they have higher intrinsic transmissibility and/or can evade host immune responses, as has been seen with the Alpha, Delta, and Omicron variants of concern. They can also cause increased
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High-throughput measurement of elastic moduli of microfibers by rope coiling Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Yuan Liu, Jack H. Y. Lo, Janine K. Nunes, Howard A. Stone, Ho Cheung Shum
There are many fields where it is of interest to measure the elastic moduli of tiny fragile fibers, such as filamentous bacteria, actin filaments, DNA, carbon nanotubes, and functional microfibers. The elastic modulus is typically deduced from a sophisticated tensile test under a microscope, but the throughput is low and limited by the time-consuming and skill-intensive sample loading/unloading. Here
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Aerosolization of viable Mycobacterium tuberculosis bacilli by tuberculosis clinic attendees independent of sputum-Xpert Ultra status Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Benjamin Patterson, Ryan Dinkele, Sophia Gessner, Anastasia Koch, Zeenat Hoosen, Vanessa January, Bryan Leonard, Andrea McKerry, Ronnett Seldon, Andiswa Vazi, Sabine Hermans, Frank Cobelens, Digby F. Warner, Robin Wood
Potential Mycobacterium tuberculosis ( Mtb ) transmission during different pulmonary tuberculosis (TB) disease states is poorly understood. We quantified viable aerosolized Mtb from TB clinic attendees following diagnosis and through six months’ follow-up thereafter. Presumptive TB patients (n=102) were classified by laboratory, radiological, and clinical features into Group A: Sputum-Xpert Ultra-positive
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The training process of many deep networks explores the same low-dimensional manifold Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Jialin Mao, Itay Griniasty, Han Kheng Teoh, Rahul Ramesh, Rubing Yang, Mark K. Transtrum, James P. Sethna, Pratik Chaudhari
We develop information-geometric techniques to analyze the trajectories of the predictions of deep networks during training. By examining the underlying high-dimensional probabilistic models, we reveal that the training process explores an effectively low-dimensional manifold. Networks with a wide range of architectures, sizes, trained using different optimization methods, regularization techniques
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Weaker land–atmosphere coupling in global storm-resolving simulation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Junhong Lee, Cathy Hohenegger
The debate on the sign of the soil moisture–precipitation feedback remains open. On the one hand, studies using global coarse-resolution climate models have found strong positive feedback. However, such models cannot represent convection explicitly. On the other hand, studies using km-scale regional climate models and explicit convection have reported negative feedback. Yet, the large-scale circulation
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A diterpene synthase from the sandfly Lutzomyia longipalpis produces the pheromone sobralene Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Charles Ducker, Cameron Baines, Jennifer Guy, Antônio Euzébio Goulart Santana, John A. Pickett, Neil J. Oldham
The phlebotomine sandfly, Lutzomyia longipalpis , a major vector of the Leishmania parasite, uses terpene pheromones to attract conspecifics for mating. Examination of the L. longipalpis genome revealed a putative terpene synthase (TPS), which—upon heterologous expression in, and purification from, Escherichia coli —yielded a functional enzyme. The TPS, termed Ll TPS, converted geranyl diphosphate
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Gondwanan flood basalts linked seismically to plume-induced lithosphere instability Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Yanan Shi, Jason P. Morgan
Delamination of the continental lithospheric mantle is well recorded beneath several continents. However, the fate of the removed continental lithosphere has been rarely noted, unlike subducted slabs reasonably well imaged in the upper and mid mantle. Beneath former Gondwana, recent seismic tomographic models indicate the presence of at least 5 horizontal fast-wavespeed anomalies at ~600 km depths
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Collective neural network behavior in a dynamically driven disordered system of superconducting loops Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Uday S. Goteti, Shane A. Cybart, Robert C. Dynes
Collective properties of complex systems composed of many interacting components such as neurons in our brain can be modeled by artificial networks based on disordered systems. We show that a disordered neural network of superconducting loops with Josephson junctions can exhibit computational properties like categorization and associative memory in the time evolution of its state in response to information
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Increased methane emissions from oil and gas following the Soviet Union’s collapse Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Tai-Long He, Ryan J. Boyd, Daniel J. Varon, Alexander J. Turner
Global atmospheric methane concentrations rose by 10 to 15 ppb/y in the 1980s before abruptly slowing to 2 to 8 ppb/y in the early 1990s. This period in the 1990s is known as the “methane slowdown” and has been attributed in part to the collapse of the former Soviet Union (USSR) in December 1991, which may have decreased the methane emissions from oil and gas operations. Here, we develop a methane
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Electronic diffusion in a normal state of high-Tc cuprate YBa 2 Cu 3 O 6+x Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Jure Kokalj
The bad metallic phase with resistivity above the Mott–Ioffe–Regel (MIR) limit, which appears also in cuprate superconductors, was recently understood by cold atom and computer simulations of the Hubbard model via charge susceptibility and charge diffusion constant. However, since reliable simulations can be typically done only at temperatures above the experimental temperatures, the question for cuprate
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Individual differences in human gaze behavior generalize from faces to objects Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Maximilian Davide Broda, Benjamin de Haas
Individuals differ in where they fixate on a face, with some looking closer to the eyes while others prefer the mouth region. These individual biases are highly robust, generalize from the lab to the outside world, and have been associated with social cognition and associated disorders. However, it is unclear, whether these biases are specific to faces or influenced by domain-general mechanisms of
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Heritability within groups is uninformative about differences among groups: Cases from behavioral, evolutionary, and statistical genetics Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Joshua G. Schraiber, Michael D. Edge
Without the ability to control or randomize environments (or genotypes), it is difficult to determine the degree to which observed phenotypic differences between two groups of individuals are due to genetic vs. environmental differences. However, some have suggested that these concerns may be limited to pathological cases, and methods have appeared that seem to give—directly or indirectly—some support
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The effects of mnemonic variability and spacing on memory over multiple timescales Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Emily T. Cowan, Yiwen Zhang, Benjamin M. Rottman, Vishnu P. Murty
The memory benefit that arises from distributing learning over time rather than in consecutive sessions is one of the most robust effects in cognitive psychology. While prior work has mainly focused on repeated exposures to the same information, in the real world, mnemonic content is dynamic, with some pieces of information staying stable while others vary. Thus, open questions remain about the efficacy
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Resistivity detection of perfluoroalkyl substances with fluorous polyaniline in an electrical lateral flow sensor Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Sohyun Park, Collette T. Gordon, Timothy M. Swager
Perfluoroalkyl substances (PFAS), known as “forever chemicals,” are a growing concern in the sphere of human and environmental health. In response, rapid, reproducible, and inexpensive methods for PFAS detection in the environment and home water supplies are needed. We have developed a simple and inexpensive perfluoroalkyl acid detection method based on an electrically read lateral flow assay (e-LFA)
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Motor “laziness” constrains fixation selection in real-world tasks Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Charlie S. Burlingham, Naveen Sendhilnathan, Oleg Komogortsev, T. Scott Murdison, Michael J. Proulx
Humans coordinate their eye, head, and body movements to gather information from a dynamic environment while maximizing reward and minimizing biomechanical and energetic costs. However, such natural behavior is not possible in traditional experiments employing head/body restraints and artificial, static stimuli. Therefore, it is unclear to what extent mechanisms of fixation selection discovered in
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Higher-order homophily on simplicial complexes Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Arnab Sarker, Natalie Northrup, Ali Jadbabaie
Higher-order network models are becoming increasingly relevant for their ability to explicitly capture interactions between three or more entities in a complex system at once. In this paper, we study homophily, the tendency for alike individuals to form connections, as it pertains to higher-order interactions. We find that straightforward extensions of classical homophily measures to interactions of
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Exposing omitted moderators: Explaining why effect sizes differ in the social sciences Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-11 Antonia Krefeld-Schwalb, Eli Rosen Sugerman, Eric J. Johnson
Policymakers increasingly rely on behavioral science in response to global challenges, such as climate change or global health crises. But applications of behavioral science face an important problem: Interventions often exert substantially different effects across contexts and individuals. We examine this heterogeneity for different paradigms that underlie many behavioral interventions. We study the
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Intergenomic signatures of coevolution between Tasmanian devils and an infectious cancer Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-11 Dylan G. Gallinson, Christopher P. Kozakiewicz, Rhett M. Rautsaw, Marc A. Beer, Manuel Ruiz-Aravena, Sebastien Comte, David G. Hamilton, Douglas H. Kerlin, Hamish I. McCallum, Rodrigo Hamede, Menna E. Jones, Andrew Storfer, Ryan McMinds, Mark J. Margres
Coevolution is common and frequently governs host–pathogen interaction outcomes. Phenotypes underlying these interactions often manifest as the combined products of the genomes of interacting species, yet traditional quantitative trait mapping approaches ignore these intergenomic interactions. Devil facial tumor disease (DFTD), an infectious cancer afflicting Tasmanian devils ( Sarcophilus harrisii
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Hominin population bottleneck coincided with migration from Africa during the Early Pleistocene ice age transition Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-11 Giovanni Muttoni, Dennis V. Kent
Two recently published analyses make cases for severe bottlenecking of human populations occurring in the late Early Pleistocene, one case at about 0.9 Mya based on a genomic analysis of modern human populations and the low number of hominin sites of this age in Africa and the other at about 1.1 Mya based on an age inventory of sites of hominin presence in Eurasia. Both models point to climate change
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Cold seep formation from salt diapir–controlled deep biosphere oases Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-11 Anirban Chowdhury, Gregory T. Ventura, Yaisa Owino, Ellen J. Lalk, Natasha MacAdam, John M. Dooma, Shuhei Ono, Martin Fowler, Adam MacDonald, Robbie Bennett, R. Andrew MacRae, Casey R. J. Hubert, Jeremy N. Bentley, Mitchell J. Kerr
Deep sea cold seeps are sites where hydrogen sulfide, methane, and other hydrocarbon-rich fluids vent from the ocean floor. They are an important component of Earth’s carbon cycle in which subsurface hydrocarbons form the energy source for highly diverse benthic micro- and macro-fauna in what is otherwise vast and spartan sea scape. Passive continental margin cold seeps are typically attributed to
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Anthropogenic short-lived halogens increase human exposure to mercury contamination due to enhanced mercury oxidation over continents Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-11 Xiao Fu, Xianyi Sun, Oleg Travnikov, Qinyi Li, Chuang Qin, Carlos A. Cuevas, Rafael P. Fernandez, Anoop S. Mahajan, Shuxiao Wang, Tao Wang, Alfonso Saiz-Lopez
Mercury (Hg) is a contaminant of global concern, and an accurate understanding of its atmospheric fate is needed to assess its risks to humans and ecosystem health. Atmospheric oxidation of Hg is key to the deposition of this toxic metal to the Earth’s surface. Short-lived halogens (SLHs) can provide halogen radicals to directly oxidize Hg and perturb the budget of other Hg oxidants (e.g., OH and O
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Sea-surface temperature pattern effects have slowed global warming and biased warming-based constraints on climate sensitivity Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-11 Kyle C. Armour, Cristian Proistosescu, Yue Dong, Lily C. Hahn, Edward Blanchard-Wrigglesworth, Andrew G. Pauling, Robert C. Jnglin Wills, Timothy Andrews, Malte F. Stuecker, Stephen Po-Chedley, Ivan Mitevski, Piers M. Forster, Jonathan M. Gregory
The observed rate of global warming since the 1970s has been proposed as a strong constraint on equilibrium climate sensitivity (ECS) and transient climate response (TCR)—key metrics of the global climate response to greenhouse-gas forcing. Using CMIP5/6 models, we show that the inter-model relationship between warming and these climate sensitivity metrics (the basis for the constraint) arises from
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Sexual stage–specific A-to-I mRNA editing is mediated by tRNA-editing enzymes in fungi Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-11 Zhuyun Bian, Zeyi Wang, Diwen Wang, Jin-Rong Xu
A-to-I RNA editing catalyzed by adenosine-deaminase-acting-on-RNA (ADARs) was assumed to be unique to metazoans because fungi and plants lack ADAR homologs. However, genome-wide messenger RNA (mRNA) editing was found to occur specifically during sexual reproduction in filamentous ascomycetes. Because systematic characterization of adenosine/cytosine deaminase genes has implicated the involvement of