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Shen, Yang

Publications and source records attributed to Shen, Yang.

11 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Current and future directions in network biology

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Osmosensor-mediated control of Ca 2+ spiking in pollen germination

Higher plants survive terrestrial water deficiency and fluctuation by arresting cellular activities (dehydration) and resuscitating processes (rehydration). However, how plants monitor water availability during rehydration is unknown. Although increases in hypo-osmolarity-induced cytosolic Ca 2+ concentration (HOSCA) have long been postulated to be the mechanism for sensing hypo-osmolarity in rehydration, the molecular basis remains unknown. Because osmolarity triggers membrane tension and the osmosensing specificity of osmosensing channels can only be determined in vivo, these channels have been classified as a subtype of mechanosensors. Here we identify bona fide cell surface hypo-osmosensors in Arabidopsis and find that pollen Ca 2+ spiking is controlled directly by water through these hypo-osmosensors—that is, Ca 2+ spiking is the second messenger for water status. We developed a functional expression screen in Escherichia coli for hypo-osmosensitive channels and identified OSCA2.1, a member of the hyperosmolarity-gated calcium-permeable channel (OSCA) family of proteins. We screened single and high-order OSCA mutants, and observed that the osca2.1/osca2.2 double-knockout mutant was impaired in pollen germination and HOSCA. OSCA2.1 and OSCA2.2 function as hypo-osmosensitive Ca 2+ -permeable channels in planta and in HEK293 cells. Decreasing osmolarity of the medium enhanced pollen Ca 2+ oscillations, which were mediated by OSCA2.1 and OSCA2.2 and required for germination. OSCA2.1 and OSCA2.2 convert extracellular water status into Ca 2+ spiking in pollen and may serve as essential hypo-osmosensors for tracking rehydration in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Machine learning-assisted elucidation of CD81–CD44 interactions in promoting cancer stemness and extracellular vesicle integrity

Tumor-initiating cells with reprogramming plasticity or stem-progenitor cell properties (stemness) are thought to be essential for cancer development and metastatic regeneration in many cancers; however, elucidation of the underlying molecular network and pathways remains demanding. Combining machine learning and experimental investigation, here we report CD81, a tetraspanin transmembrane protein known to be enriched in extracellular vesicles (EVs), as a newly identified driver of breast cancer stemness and metastasis. Using protein structure modeling and interface prediction-guided mutagenesis, we demonstrate that membrane CD81 interacts with CD44 through their extracellular regions in promoting tumor cell cluster formation and lung metastasis of triple negative breast cancer (TNBC) in human and mouse models. In-depth global and phosphoproteomic analyses of tumor cells deficient with CD81 or CD44 unveils endocytosis-related pathway alterations, leading to further identification of a quality-keeping role of CD44 and CD81 in EV secretion as well as in EV-associated stemness-promoting function. CD81 is coexpressed along with CD44 in human circulating tumor cells (CTCs) and enriched in clustered CTCs that promote cancer stemness and metastasis, supporting the clinical significance of CD81 in association with patient outcomes. Our study highlights machine learning as a powerful tool in facilitating the molecular understanding of new molecular targets in regulating stemness and metastasis of TNBC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Presence of Delocalized Ti 3d Electrons in Ultrathin Single-Crystal SrTiO 3

Strontium titanate (STO), with a wide spectrum of emergent properties such as ferroelectricity and superconductivity, has received significant attention in the community of strongly correlated materials. In the strain-free STO film grown on the SrRuO 3 buffer layer, the existing polar nanoregions can facilitate room-temperature ferroelectricity when the STO film thickness approaches 10 nm. Here we show that around this thickness scale, the freestanding STO films without the influence of a substrate show the tetragonal structure at room temperature, contrasting with the cubic structure seen in bulk form. Further, the spectroscopic measurements reveal the modified Ti-O orbital hybridization that causes the Ti ion to deviate from its nominal 4+ valency (3d o configuration) with excess delocalized 3d electrons. Additionally, the Ti ion in TiO 6 octahedron exhibits an off-center displacement. The inherent symmetry lowering in ultrathin freestanding films offers an alternative way to achieve tunable electronic structures that are of paramount importance for future technological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Circulating ACE2-expressing extracellular vesicles block broad strains of SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of the coronavirus induced disease 2019 (COVID-19) with evolving variants of concern. It remains urgent to identify novel approaches against broad strains of SARS-CoV-2, which infect host cells via the entry receptor angiotensin-converting enzyme 2 (ACE2). Herein, we report an increase in circulating extracellular vesicles (EVs) that express ACE2 (evACE2) in plasma of COVID-19 patients, which levels are associated with severe pathogenesis. Importantly, evACE2 isolated from human plasma or cells neutralizes SARS-CoV-2 infection by competing with cellular ACE2. Compared to vesicle-free recombinant human ACE2 (rhACE2), evACE2 shows a 135-fold higher potency in blocking the binding of the viral spike protein RBD, and a 60- to 80-fold higher efficacy in preventing infections by both pseudotyped and authentic SARS-CoV-2. Consistently, evACE2 protects the hACE2 transgenic mice from SARS-CoV-2-induced lung injury and mortality. Furthermore, evACE2 inhibits the infection of SARS-CoV-2 variants (α, β, and δ) with equal or higher potency than for the wildtype strain, supporting a broad-spectrum antiviral mechanism of evACE2 for therapeutic development to block the infection of existing and future coronaviruses that use the ACE2 receptor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

Here we present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.

protein complexes↗
DOE OSTI2021

Prediction and observation of intermodulation sidebands from anharmonic phonons in NaBr

A quantum Langevin model, like models from optomechanics, was developed for phonons. It predicts intermodulation phonon sidebands (IPSs) in anharmonic crystals. Ab initio calculations of anharmonic phonons in rock-salt NaBr showed these spectral features as many-body effects. Modern inelastic neutron scattering measurements on a crystal of NaBr at 300 K revealed diffuse intensity at high phonon energy from a predicted upper IPS. The transverse optical (TO) part of the new features originates from phonon intermodulation between the transverse acoustic (TA) and TO phonons. The longitudinal optical spectral features originate from three-phonon coupling between the TA modes and the TO lattice modes. The partner lower IPS proves to be an intrinsic localized mode. Interactions with the thermal bath broaden and redistribute the spectral weight of the IPS pair. These sidebands are a probe of the anharmonicity and quantum noise of phonons in NaBr and suggest novel interactions between photons and phonons.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Toroidal polar topology in strained ferroelectric polymer

Polar topological texture has become an emerging research field for exotic phenomena and potential applications in reconfigurable electronic devices. Here, we report toroidal topological texture self-organized in a ferroelectric polymer, poly(vinylidene fluoride-ran-trifluoroethylene) [P(VDF-TrFE)], that exhibits concentric topology with anticoupled chiral domains. The interplay among the elastic, electric, and gradient energies results in continuous rotation and toroidal assembly of the polarization perpendicular to polymer chains, whereas relaxor behavior is induced along polymer chains. Such toroidal polar topology gives rise to periodic absorption of polarized far-infrared (FIR) waves, enabling the manipulation of the terahertz wave on a mesoscopic scale. Our observations should inform design principles for flexible ferroic materials toward complex topologies and provide opportunities for multistimuli conversions in flexible electronics.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Anharmonic Origin of the Giant Thermal Expansion of NaBr

ll phonons in a single crystal of NaBr are measured by inelastic neutron scattering at temperatures of 10, 300, and 700 K. Even at 300 K, the phonons, especially the longitudinal-optical phonons, show large shifts in frequencies and show large broadenings in energy owing to anharmonicity. Ab initio computations are first performed with the quasiharmonic approximation (QHA) in which the phonon frequencies depend only on V and on T only insofar as it alters V by thermal expansion. This QHA is an unqualified failure for predicting the temperature dependence of phonon frequencies, even 300 K, and the thermal expansion is in error by a factor of 4. Ab initio computations that include both anharmonicity and quasiharmonicity successfully predict both the temperature dependence of phonons and the large thermal expansion of NaBr. The frequencies of longitudinal-optical phonon modes decrease significantly with temperature owing to the real part of the phonon self-energy from explicit anharmonicity originating from the cubic anharmonicity of nearest-neighbor NaBr bonds. Anharmonicity is not a correction to the QHA predictions of thermal expansion and thermal phonon shifts but dominates the behavior.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1996

Chiral Bosonization of Superconformal Ghosts

We explain the difference of the Hilbert space of the superconformal ghosts (beta,gamma) system from that of its bosonized fields phi and chi. We calculate the chiral correlation functions of phi, chi fields by inserting appropriate projectors.

Shi, Deheng↗