journal
https://read.qxmd.com/read/38484038/sister-chromatid-cohesion-establishment-during-dna-replication-termination
#1
JOURNAL ARTICLE
George Cameron, Dominika T Gruszka, Rhian Gruar, Sherry Xie, Çağla Kaya, Kim A Nasmyth, Jonathan Baxter, Madhusudhan Srinivasan, Hasan Yardimci
Newly copied sister chromatids are tethered together by the cohesin complex, but how sister chromatid cohesion is coordinated with DNA replication is poorly understood. Prevailing models suggest cohesin complexes, bound to DNA before replication, remain behind the advancing replication fork to keep sister chromatids together. By visualizing single replication forks colliding with pre-loaded cohesin complexes, we find that the replisome instead pushes cohesin to where a converging replisome is met. While the converging replisomes are removed during DNA replication termination, cohesin remains on nascent DNA and provides cohesion...
March 14, 2024: Science
https://read.qxmd.com/read/38484037/misconduct-s-forgotten-victims
#2
EDITORIAL
H Holden Thorp
No abstract text is available yet for this article.
March 14, 2024: Science
https://read.qxmd.com/read/38484036/antibacterial-activity-of-nonantibiotics-is-orthogonal-to-standard-antibiotics
#3
JOURNAL ARTICLE
Mariana Noto Guillen, Carmen Li, Brittany Rosener, Amir Mitchell
Numerous nonantibiotic drugs have potent antibacterial activity and can adversely impact the human microbiome. The mechanistic underpinning of this toxicity remains largely unknown. We investigated the antibacterial activity of 200 drugs using genetic screens with thousands of barcoded Escherichia coli knockouts. We analyzed 2 million gene-drug interactions underlying drug-specific toxicity. Network-based analysis of drug-drug similarities revealed that antibiotics clustered into modules consistent with the mode of action of their established classes, while nonantibiotics remained unconnected...
March 14, 2024: Science
https://read.qxmd.com/read/38452048/mechanism-for-feature-learning-in-neural-networks-and-backpropagation-free-machine-learning-models
#4
JOURNAL ARTICLE
Adityanarayanan Radhakrishnan, Daniel Beaglehole, Parthe Pandit, Mikhail Belkin
Understanding how neural networks learn features, or relevant patterns in data, for prediction is necessary for their reliable use in technological and scientific applications. In this work, we presented a unifying mathematical mechanism, known as Average Gradient Outer Product (AGOP), that characterized feature learning in neural networks. We provided empirical evidence that AGOP captured features learned by various neural network architectures, including transformer-based language models, convolutional networks, multi-layer perceptrons, and recurrent neural networks...
March 7, 2024: Science
https://read.qxmd.com/read/38452047/generalized-biomolecular-modeling-and-design-with-rosettafold-all-atom
#5
JOURNAL ARTICLE
Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet, Gyu Rie Lee, Felix S Morey-Burrows, Ivan Anishchenko, Ian R Humphreys, Ryan McHugh, Dionne Vafeados, Xinting Li, George A Sutherland, Andrew Hitchcock, C Neil Hunter, Alex Kang, Evans Brackenbrough, Asim K Bera, Minkyung Baek, Frank DiMaio, David Baker
Deep learning methods have revolutionized protein structure prediction and design but are currently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA) which combines a residue-based representation of amino acids and DNA bases with an atomic representation of all other groups to model assemblies containing proteins, nucleic acids, small molecules, metals, and covalent modifications given their sequences and chemical structures. By fine tuning on denoising tasks we obtain RFdiffusionAA, which builds protein structures around small molecules...
March 7, 2024: Science
https://read.qxmd.com/read/38422185/induction-of-durable-remission-by-dual-immunotherapy-in-shiv-infected-art-suppressed-macaques
#6
JOURNAL ARTICLE
So-Yon Lim, Jina Lee, Christa E Osuna, Pratik Vikhe, Dane R Schalk, Elsa Chen, Emily Fray, Mithra Kumar, Nancy Schultz-Darken, Eva Rakasz, Saverio Capuano, Ruby A Ladd, Hwi Min Gil, David T Evans, Emily K Jeng, Michael Seaman, Malcolm Martin, Christiaan Van Dorp, Alan S Perelson, Hing C Wong, Janet D Siliciano, Robert Siliciano, Jeffrey T Safrit, Douglas F Nixon, Patrick Soon-Shiong, Michel Nussenzweig, James B Whitney
The eradication of the viral reservoir represents the major obstacle to the development of a clinical cure for established HIV-1 infection. Here, we demonstrate that the administration of Anktiva (N-803) and broadly neutralizing antibodies (bNAbs) resulted in sustained viral control after discontinuation of antiretroviral therapy (ART) in SHIV-AD8-infected, ART-suppressed rhesus macaques. N-803+bNAbs treatment induced immune activation and transient viremia, but only limited reductions in the SHIV reservoir...
February 29, 2024: Science
https://read.qxmd.com/read/38422184/vocal-learning-associated-convergent-evolution-in-mammalian-proteins-and-regulatory-elements
#7
JOURNAL ARTICLE
Morgan E Wirthlin, Tobias A Schmid, Julie E Elie, Xiaomeng Zhang, Amanda Kowalczyk, Ruby Redlich, Varvara A Shvareva, Ashley Rakuljic, Maria B Ji, Ninad S Bhat, Irene M Kaplow, Daniel E Schäffer, Alyssa J Lawler, Andrew Z Wang, BaDoi N Phan, Siddharth Annaldasula, Ashley R Brown, Tianyu Lu, Byung Kook Lim, Eiman Azim, Nathan L Clark, Wynn K Meyer, Sergei L Kosakovsky Pond, Maria Chikina, Michael M Yartsev, Andreas R Pfenning, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Vocal production learning is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical and neurophysiological data from the Egyptian fruit-bat with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal-motor cortical region in the Egyptian fruit-bat, an emergent vocal learner, and leveraged that knowledge to identify active cis -regulatory elements in the motor cortex of vocal learners...
February 29, 2024: Science
https://read.qxmd.com/read/38359104/attosecond-pump-attosecond-probe-x-ray-spectroscopy-of-liquid-water
#8
JOURNAL ARTICLE
Shuai Li, Lixin Lu, Swarnendu Bhattacharyya, Carolyn Pearce, Kai Li, Emily T Nienhuis, Gilles Doumy, R D Schaller, S Moeller, M-F Lin, G Dakovski, D J Hoffman, D Garratt, Kirk A Larsen, J D Koralek, C Y Hampton, D Cesar, Joseph Duris, Z Zhang, Nicholas Sudar, James P Cryan, A Marinelli, Xiaosong Li, Ludger Inhester, Robin Santra, Linda Young
Attosecond-pump/attosecond-probe experiments have long been sought as the most straightforward method to observe electron dynamics in real time. Although numerous successes have been achieved with overlapped near infrared femtosecond and extreme ultraviolet attosecond pulses combined with theory, true attosecond-pump/attosecond-probe experiments have been limited. We used a synchronized attosecond x-ray pulse pair from an x-ray free electron laser to study the electronic response to valence ionization in liquid water via all x-ray attosecond transient absorption spectroscopy (AX-ATAS)...
February 15, 2024: Science
https://read.qxmd.com/read/38349746/passion-is-not-misconduct
#9
EDITORIAL
H Holden Thorp
No abstract text is available yet for this article.
February 13, 2024: Science
https://read.qxmd.com/read/38330140/fracturing-and-tectonic-stress-drives-ultrarapid-magma-flow-into-dikes
#10
JOURNAL ARTICLE
Freysteinn Sigmundsson, Michelle Parks, Halldór Geirsson, Andrew Hooper, Vincent Drouin, Kristín S Vogfjörd, Benedikt G Ófeigsson, Sonja H M Greiner, Yilin Yang, Chiara Lanzi, Gregory P De Pascale, Kristín Jónsdóttir, Sigrún Hreinsdóttir, Valentyn Tolpekin, Hildur María Friðriksdóttir, Páll Einarsson, Sara Barsotti
Many examples of exposed giant dike swarms can be found where lateral magma flow exceeded hundreds of kilometers. We show that massive magma flow into dikes can be established with only modest overpressure in a magma body, if a large enough pathway opens at its boundary, and gradual build-up of high tensile stress has occurred along the dike pathway prior to onset of diking. This explains rapid initial magma flow rates, modeled up to about 7400 m3 /s into a dike approximately 15 km long, propagating under the town of Grindavík, Southwest Iceland, in November 2023...
February 8, 2024: Science
https://read.qxmd.com/read/38305685/transition-of-human-%C3%AE-tubulin-ring-complex-into-a-closed-conformation-during-microtubule-nucleation
#11
JOURNAL ARTICLE
Cláudia Brito, Marina Serna, Pablo Guerra, Oscar Llorca, Thomas Surrey
Microtubules are essential for intracellular organization and chromosome segregation. They are nucleated by the γ-tubulin ring complex (γTuRC). However, isolated vertebrate γTuRC adopts an open conformation that deviates from the microtubule structure, raising the question of the nucleation mechanism. Here we determine cryo-electron microscopy structures of human γTuRC bound to a nascent microtubule. Structural changes of the complex into a closed conformation ensure that γTuRC templates the 13-protofilament microtubules that exist in human cells...
February 2, 2024: Science
https://read.qxmd.com/read/38305684/structural-basis-for-sugar-perception-by-drosophila-gustatory-receptors
#12
JOURNAL ARTICLE
Demin Ma, Meiqin Hu, Xiaotong Yang, Qiang Liu, Fan Ye, Weijie Cai, Yong Wang, Ximing Xu, Shenghai Chang, Ruiying Wang, Wei Yang, Sheng Ye, Nannan Su, Minrui Fan, Haoxing Xu, Jiangtao Guo
Insects rely on a family of seven-transmembrane proteins called gustatory receptors (GRs) to encode different taste modalities such as sweet and bitter. Here we report structures of Drosophila sweet taste receptors GR43a and GR64a in the apo and sugar-bound states. Both GRs form tetrameric sugar-gated cation channels, composed of one central pore domain (PD) and four peripheral ligand-binding domains (LBDs). Whereas GR43a is specifically activated by the monosaccharide fructose that binds to a narrow pocket in LBD, disaccharides sucrose and maltose selectively activate GR64a by binding to a larger and flatter pocket in LBD...
February 2, 2024: Science
https://read.qxmd.com/read/38127809/dealuminated-beta-zeolite-reverses-ostwald-ripening-for-durable-copper-nanoparticle-catalysts
#13
JOURNAL ARTICLE
Lujie Liu, Jiaye Lu, Yahui Yang, Wolfgang Ruettinger, Xinhua Gao, Ming Wang, Hao Lou, Zhandong Wang, Yifeng Liu, Xin Tao, Lina Li, Yong Wang, Hangjie Li, Hang Zhou, Chengtao Wang, Qingsong Luo, Huixin Wu, Kaidi Zhang, Jiabi Ma, Xiaoming Cao, Liang Wang, Feng-Shou Xiao
Copper nanoparticle-based catalysts have been extensively applied in industry, but the nanoparticles tend to sinter into larger ones in the chemical atmospheres, which is detrimental to catalyst performance. Herein we used dealuminated Beta zeolite to support Cu nanoparticles (Cu/Beta-deAl) and showed that these particles become smaller in methanol vapor at 200°C, decreasing from ~5.6 to ~2.4 nanometers, which is opposite to the general sintering phenomenon. A reverse Ostwald ripening process was discovered, where migratable copper sites activated by methanol were trapped by silanol nests, and the copper species in the nests acted as new nucleation sites for forming small nanoparticles...
December 21, 2023: Science
https://read.qxmd.com/read/38484084/erratum-for-the-research-article-aminative-suzuki-miyaura-coupling-by-p-onnuch-et-al
#14
JOURNAL ARTICLE
(no author information available yet)
No abstract text is available yet for this article.
March 15, 2024: Science
https://read.qxmd.com/read/38484083/erratum-for-the-research-article-the-huanan-seafood-wholesale-market-in-wuhan-was-the-early-epicenter-of-the-covid-19-pandemic-by-m-worobey-et-al
#15
JOURNAL ARTICLE
(no author information available yet)
No abstract text is available yet for this article.
March 15, 2024: Science
https://read.qxmd.com/read/38484082/biden-s-lean-science-budget-doesn-t-fund-all-his-priorities
#16
Jeffrey Mervis
White House faces tight spending cap in 2025 request.
March 15, 2024: Science
https://read.qxmd.com/read/38484081/new-legal-aid-fund-for-sleuths
#17
Holly Else
Investor pledges $1 million for science whistleblowers.
March 15, 2024: Science
https://read.qxmd.com/read/38484080/big-data-in-earth-science-emerging-practice-and-promise
#18
REVIEW
Tiffany C Vance, Thomas Huang, Kevin A Butler
Improvements in the number and resolution of Earth- and satellite-based sensors coupled with finer-resolution models have resulted in an explosion in the volume of Earth science data. This data-rich environment is changing the practice of Earth science, extending it beyond discovery and applied science to new realms. This Review highlights recent big data applications in three subdisciplines-hydrology, oceanography, and atmospheric science. We illustrate how big data relate to contemporary challenges in science: replicability and reproducibility and the transition from raw data to information products...
March 15, 2024: Science
https://read.qxmd.com/read/38484079/-i-m-not-tony-anthony-fauci-s-heir-vows-new-direction-at-niaid
#19
Jon Cohen
Jeanne Marrazzo, an HIV prevention researcher, sees need for more "holistic" approach to community health problems.
March 15, 2024: Science
https://read.qxmd.com/read/38484078/generalized-fear-after-acute-stress-is-caused-by-change-in-neuronal-cotransmitter-identity
#20
JOURNAL ARTICLE
Hui-Quan Li, Wuji Jiang, Li Ling, Marta Pratelli, Cong Chen, Vaidehi Gupta, Swetha K Godavarthi, Nicholas C Spitzer
Overgeneralization of fear to harmless situations is a core feature of anxiety disorders resulting from acute stress, yet the mechanisms by which fear becomes generalized are poorly understood. In this study, we show that generalized fear in mice results from a transmitter switch from glutamate to γ-aminobutyric acid (GABA) in serotonergic neurons of the lateral wings of the dorsal raphe. Similar change in transmitter identity was found in the postmortem brains of individuals with posttraumatic stress disorder (PTSD)...
March 15, 2024: Science
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