bluuebunny/crossref_metadata_2025 huggingface dataset:
Phosphorylation of PLPPR3 membrane proteins as signaling integrator at neuronal synapses
Authors: Kroon Cristina , Bareesel Shannon , Kirchner Marieluise , Gimber Niclas , Ranti Dimitra , Brosig Annika , Textoris-Taube Kathrin , Zolnik Timothy A. , Mertins Philipp , Schmoranzer Jan , Leondaritis George , Eickholt Britta J.
Published: March 2024

Phospholipid-phosphatase related protein 3 (PLPPR3, previously known as Plasticity Related Gene 2 or PRG2) belongs to a family of transmembrane proteins, highly expressed in neuronal development, which regulate critical growth processes in neurons. Prior work established crucial functions of PLPPR3 in axon guidance, filopodia formation and axon branching. However, little is known regarding the signaling events regulating PLPPR3 function. We identify here 26 high-confidence phosphorylation sites in the intracellular domain of PLPPR3 using mass spectrometry. Biochemical characterization established one of these – S351 – as abona fidephosphorylation site of PKA. Experiments in neuronal cell lines suggest that phosphorylation of S351 does not regulate filopodia formation. Instead, it regulates binding to BASP1, a signaling molecule previously implicated in axonal growth and regeneration. Interestingly, both PLPPR3 intracellular domain and BASP1 enrich in presynapses in primary neurons. We propose that the presynaptic PLPPR3-BASP1 complex may function as novel signaling integrator at neuronal synapses.
Insights into Cellular Evolution: Temporal Deep Learning Models and Analysis for Cell Image Classification
Authors: Zhao Xinran , de Perez Alexander Ruys , Dimitrova Elena S. , Kemp Melissa , Anderson Paul E.
Published: March 2024

I.

Abstract

Understanding the temporal evolution of cells poses a significant challenge in developmental biology. This study embarks on a comparative analysis of various machine-learning techniques to classify sequences of cell colony images, thereby aiming to capture dynamic transitions of cellular states. Utilizing transfer learning with advanced classification networks, we achieved high accuracy in single-timestamp image categorization. We introduce temporal models—LSTM, R-Transformer, and ViViT—to explore the effectiveness of integrating temporal features in classification, comparing their performance against non-temporal models. This research benchmarks various machine learning approaches in understanding cellular dynamics, setting a foundation for future studies to enhance our understanding of cellular developments with computational methods, contributing significantly to biological research advancements.
Reduced Filaggrin expression induces dysregulated intracellular signalling in atopic eczema
Authors: Hughes AJ , Coppock L , Tachie-Menson T , Thomas BR , Dewan P , Doykov I , Mills K , O’Toole EA , O’Shaughnessy RFL
Published: March 2024

Atopic eczema (AE) is the most common inflammatory dermatosis, affecting up to 20% of children. Loss of function mutations in the Filaggrin (FLG) gene are the most strongly implicated genetic risk factor for AE, but little is known about the signalling pathways altered in response to loss ofFLG.To explore the downstream effects of loss of FLG on the cellular environment, we combined RNAseq analysis of siRNA knockdown of normal human keratinocytes and analysis of tape strip (TS) samples from AE patients who were clinically phenotyped and genotyped forFLGmutation status.

RNA-seq analysis revealed an increase in BMP signalling following FLG KD, which we validatedin vivousing TS samples and biopsies. Recombinant BMP2 or BMP6 increased FLG and suprabasal keratin expression in vitro. Phosphoproteomic analysis identified 237 significantly differentially phosphorylated proteins following FLG KD. Kinase enrichment analysis identified downregulation of ERK1/2 and AKT1 signalling which was confirmed in AE biopsies. cFOS was downregulated following FLG KD and correlated with FLG expression in repository datasets. cFOS was downregulated following BMP6 treatment, implying that cFOS may be an important link between FLG and BMP signalling. Finally, proteomic analysis of TS samples identified altered desmosomal expression and phosphorylation following either loss of FLG or increased BMP signalling. Therefore, we have identified a SMAD1/Filaggrin/AKT axis as a potential therapeutic avenue in AE.
Epidemiological inference at the threshold of data availability: an influenza A(H1N2)v spillover event in the United Kingdom
Authors: Fozard John A. , Thomson Emma C. , Illingworth Christopher J. R.
Published: March 2024

Viruses which infect animals regularly spill over into the human population, but individual events may lead to anything from a single case to a novel pandemic. Rapidly gaining an understanding of a spillover event is critical to calibrating a public health response. We here propose a novel method, using likelihood free rejection sampling to evaluate the properties of an outbreak of swine-origin influenza A(H1N2)v in the United Kingdom, detected in November 2023. From the limited data available we generate historical estimates of the probability that the outbreak had died out in the days following the detection of the first case. Our method suggests that the outbreak could have been said to be over with 95% certainty between 19 and 29 days after the first case was detected, depending upon the probability of a case being detected. We further estimate the number of undetected cases conditional upon the outbreak still being live, the epidemiological parameter R0, and the date on which the spillover event itself occurred. Our method requires minimal data to be effective. While our calculations were performed after the event, the real-time application of our method has potential value for public health responses to cases of emerging viral infection.
Phenylphenalenones and Linear Diarylheptanoid Derivatives are Biosynthesized via Parallel Routes inMusella lasiocarpa, the Chinese Dwarf Banana
Authors: Lyu Hui , Ernst Lukas , Nakamura Yoko , Okamura Yu , Köllner Tobias G. , Luck Katrin , Liu Benye , Chen Yu , Beerhues Ludger , Gershenzon Jonathan , Paetz Christian
Published: March 2024

Phenylphenalenones (PPs) are complex polycyclic natural products that play an important role in the chemical defense system of banana and plantain (Musaceae). Although suggestions for how plants synthesize the PP scaffold were first proposed more than 50 years ago, no biosynthetic information is yet available at the enzyme level. Here, we use transcriptomic data from seeds ofMusella lasiocarpa, the Chinese dwarf banana, to identify five biosynthetic genes involved in the formation of dihydrocurcuminoids. Characterization of the substrate specificities of the enzymes reveals two distinct dihydrocurcuminoid pathways leading to the two types of major aromatic seed metabolites, the PPs and the linear diarylheptanoid derivatives. Furthermore, through multiple rounds of feeding potential intermediates toM. lasiocarparoot protein extract, followed by high-resolution mass spectrometry profiling, product isolation, and NMR-based elucidation, we demonstrate the stepwise conversion of a dihydrocurcumin-type precursor to the PP 4’-hydroxylachnanthocarpone. In contrast to the commonly hypothesized Diels–Alder cyclization mechanism, we propose an unexpected two-step cyclization route to the PP scaffold.
Polyglutamylation of microtubules drives neuronal remodeling
Authors: Gavoci Antoneta , Zhiti Anxhela , Rusková Michaela , Magiera Maria M. , Wang Mengzhe , Ziegler Karin A. , Hausrat Torben Johann , Engelhardt Stefan , Kneussel Matthias , Balastik Martin , Janke Carsten , Misgeld Thomas , Brill Monika S.
Published: March 2024

Developmental remodeling shapes neural circuits via activity-dependent pruning of synapses and axons. The cytoskeleton is critical for this process, as microtubule loss via enzymatic severing is an early step of pruning across many circuits and species. However, how microtubule-severing enzymes, such as spastin, are activated in specific neuronal compartments remains unknown. Here, we reveal that polyglutamylation, a posttranslational tubulin modification that is enriched in neurons, plays an instructive role in developmental remodeling by tagging microtubules for severing. Motor neuron-specific gene deletion of enzymes that add or remove tubulin polyglutamylation—TTLL glutamylases vs. CCP deglutamylases—accelerates or delays neuromuscular synapse remodeling in a neurotransmission-dependent manner. This mechanism is not specific to peripheral synapses but also operates in central circuits, e.g., the hippocampus. Thus, tubulin polyglutamylation acts as an activity-dependent rheostat of remodeling and shapes neuronal morphology and connectivity.
A cellular assay to determine the fusion capacity of MFN2 variants linked to Charcot-Marie-Tooth type 2A
Authors: Barsa Chloe , Perrin Julian , David Claudine , Mourier Arnaud , Rojo Manuel
Published: March 2024

Charcot-Marie-Tooth Disease (CMT) is an inherited peripheral neuropathy with two main forms: demyelinating CMT1 and axonal CMT2. The most frequent subtype of CMT2 (CMT2A) is linked to mutations ofMFN2, encoding a membrane-anchored GTP-binding protein essential for mitochondrial outer membrane fusion. The use of Next-Generation Sequencing for genetic analysis has led to the identification of increasing numbers ofMFN2variants, but a majority of them remain variants of unknown significance, depriving patients of a clear diagnosis. In this work, we establish a cellular assay allowing to assess the impact ofMFN2variants linked to CMT2A on the fusion capacity of MFN2. The analysis of 12MFN2variants revealed that five abolish fusion, one induces an important reduction and six retain a fusion capacity similar to that of wild-type MFN2. Their analysis with computational variant effect predictors demonstrated a remarkable correlation of our results with predictions based on protein sequence analysis. This work develops novel tools to determine the functional impact of known and novelMFN2variants and identifies computational tools allowing to predict their possible consequences and pathogenicity.
FlhE functions as a chaperone to prevent formation of periplasmic flagella in Gram-negative bacteria
Authors: Halte Manuel , Andrianova Ekaterina P. , Goosmann Christian , Chevance Fabienne F.V. , Hughes Kelly T. , Zhulin Igor B. , Erhardt Marc
Published: March 2024

The bacterial flagellum is an organelle utilized by many Gram-negative bacteria to facilitate motility. The flagellum is composed of a several µm long, extracellular filament that is connected to a cytoplasmic rotor-stator complex via a periplasmic rod. Composed of ∼20 structural proteins, ranging from a few subunits to several thousand building blocks, the flagellum is a paradigm of a complex macromolecular structure that utilizes a highly regulated assembly process. This process is governed by multiple checkpoints that ensure an ordered gene expression pattern coupled to the assembly of the various flagellar building blocks in order to produce a functional flagellum. Using epifluorescence, super-resolution STED and transmission electron microscopy, we discovered that inSalmonella, the absence of one periplasmic protein, FlhE, prevents proper flagellar morphogenesis and results in the formation of periplasmic flagella. The periplasmic flagella disrupt cell wall synthesis, leading to a loss of the standard cell morphology resulting in cell lysis. We propose a model where FlhE functions as a periplasmic chaperone to control assembly of the periplasmic rod to prevent formation of periplasmic flagella. Our results highlight that bacteria evolved sophisticated regulatory mechanisms to control proper flagellar assembly and minor deviations from this highly regulated process can cause dramatic physiological consequences.
Monkeys have rhythm
Authors: Rajendran Vani G. , Marquez Juan Pablo , Prado Luis , Merchant Hugo
Published: March 2024

Synchronizing movements to music is one of the hallmarks of human culture whose evolutionary and neurobiological origins remain unknown. The ability to synchronize movements requires 1) detecting a steady rhythmic pulse, or beat, out of a stream of complex sounds, 2) projecting this rhythmic pattern forward in time to predict future input, and 3) timing motor commands in anticipation of predicted future beats. Here, we demonstrate that the macaque is capable of synchronizing taps to a subjective beat in real music, and even spontaneously chooses to do so over alternative strategies. This contradicts the influential “vocal learning hypothesis” that musical beat synchronization is only possible in species with complex vocalizations such as humans and some songbirds. We propose an alternative view of musical beat perception and synchronization ability as a continuum onto which a wider range of species can be mapped depending on their ability to perform and coordinate the general abilities listed above through association with reward.
Modulation of GABAAreceptor trafficking by WWC2 reveals class-specific mechanisms of synapse regulation by WWC family proteins
Authors: Dunham Thomas L. , Wilkerson Julia R. , Johnson Richard C. , Huganir Richard L. , Volk Lenora J.
Published: March 2024

WWC2 (WW and C2 domain-containing protein) is implicated in several neurological disorders, however its function in the brain has yet to be determined. Here, we demonstrate that WWC2 interacts with inhibitory but not excitatory postsynaptic scaffolds, consistent with prior proteomic identification of WWC2 as a putative component of the inhibitory postsynaptic density. Using mice lacking WWC2 expression in excitatory forebrain neurons, we show that WWC2 suppresses GABAAR incorporation into the plasma membrane and regulates HAP1 and GRIP1, which form a complex promoting GABAAR recycling to the membrane. Inhibitory synaptic transmission is dysregulated in CA1 pyramidal cells lacking WWC2. Furthermore, unlike the WWC2 homolog KIBRA (WWC1), a key regulator of AMPA receptor trafficking at excitatory synapses, deletion of WWC2 does not affect synaptic AMPAR expression. In contrast, loss of KIBRA does not affect GABAAR membrane expression. These data reveal unique, synapse class-selective functions for WWC proteins as regulators of ionotropic neurotransmitter receptors and provide insight into mechanisms regulating GABAAR membrane expression.
Microtubule poleward flux as a target for modifying chromosome segregation errors
Authors: Risteski Patrik , Martinčić Jelena , Tintor Erna , Jagrić Mihaela , Tolić Iva M.
Published: March 2024

Cancer cells often display errors in chromosome segregation, some of which result from improper chromosome alignment at the spindle midplane. Chromosome alignment is facilitated by different rates of microtubule poleward flux between sister kinetochore fibers. However, the role of the poleward flux in supporting mitotic fidelity remains unknown. Here, we introduce the hypothesis that the finely tuned poleward flux safeguards against lagging chromosomes and micronuclei at mitotic exit by promoting chromosome alignment in metaphase. We used human untransformed RPE-1 cells depleted of KIF18A/kinesin-8 as a system with reduced mitotic fidelity, which we rescued by three mechanistically independent treatments, comprising low-dose taxol or co-depletion of the spindle proteins HAUS8 or NuMA. The rescue of mitotic errors was due to shortening of the excessively long overlaps of antiparallel microtubules, serving as a platform for motor proteins that drive the flux, which in turn slowed down the overly fast flux and improved chromosome alignment. In contrast to the prevailing view, the rescue was not accompanied by reduction of overall microtubules growth rates. Speckle microscopy revealed that the improved chromosome alignment in the rescue treatments was associated with slower growth and flux of kinetochore microtubules. In a similar manner, a low-dose taxol treatment rescued mitotic errors in a high-grade serous ovarian carcinoma cell line OVKATE. Collectively, our results highlight the potential of targeting microtubule poleward flux to modify chromosome instability and provide insight into the mechanism through which low doses of taxol rescue mitotic errors in cancer cells.
Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain
Authors: Yang Hanjing , Pacheco Josue , Kim Kyumin , Ebrahimi Diako , Ito Fumiaki , Chen Xiaojiang S.
Published: March 2024

APOBEC3G (A3G) belongs to the AID/APOBEC cytidine deaminase family and is essential for antiviral immunity. It contains two zinc-coordinated cytidine-deaminase (CD) domains. The N-terminal CD1 domain is non-catalytic but has a strong affinity for nucleic acids, whereas the C-terminal CD2 domain catalyzes C-to-U editing in single-stranded DNA. The interplay between the two domains in DNA binding and editing is not fully understood. Here, our studies on rhesus macaque A3G (rA3G) show that the DNA editing function in linear and hairpin loop DNA is greatly enhanced by AA or GA dinucleotide motifs present downstream (in the 3’-direction) but not upstream (in the 5’-direction) of the target-C editing sites. The effective distance between AA/GA and the target-C sites depends on the local DNA secondary structure. We present two co-crystal structures of rA3G bound to ssDNA containing AA and GA, revealing the contribution of the non-catalytic CD1 domain in capturing AA/GA DNA and explaining our biochemical observations. Our structural and biochemical findings elucidate the molecular mechanism underlying the cooperative function between the non-catalytic and the catalytic domains of A3G, which is critical for its antiviral role and its contribution to genome mutations in cancer.
Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells
Authors: Raza Saad , Sarkar Daipayan , Chan Leanne Jade G. , Mae Joshua , Sutter Markus , Petzold Christopher J. , Kerfeld Cheryl A. , Ralston Corie Y. , Gupta Sayan , Vermaas Josh V.
Published: March 2024

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semi-permeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant formin vivo, the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We use molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells foundin vivo. Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from theHaliangium ochraceummodel BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.
Global RNA Virome in Wastewater Treatment Plants Reveals Ecological Insights and Human Health Implications
Authors: Yuan Ling , Chen Lin-xing , Yu Hanqing , Zhou Jizhong , Sun Ren , Ju Feng
Published: March 2024

RNA viruses are widely recognized for their roles in causing human diseases and shaping Earth’s biodiversity. Wastewater treatment plants (WWTPs) are eco-friendly biotechnological systems where the roles of RNA viruses in process engineering and sanitation remain unclear. This study analyzed RNA sequencing dataset (> 3.8 Tb) from global WWTPs to examine the diversity, host associations, and auxiliary metabolic functions of RNA viruses. We identified 11,414 RNA virus operational taxonomic units (vOTUs), expanding the known diversity of RNA viruses in WWTPs by 67%. The RNA viral community in WWTPs was dominated by prokaryotic viruses, including both established RNA phage lineages and novel clades with broad ecological distributions, highlighting their underestimated diversity and broad niche breadths. Notably, a vOTU from the base-Howeltoviricetesphage clade was associated with the pathogenic bacteriumAliarcobacter cryaerophilus, suggesting potential applications in RNA phage therapy. Furthermore, the examined distribution and fate of human RNA viruses emphasized the utility of quantitative metatranscriptomics-based wastewater surveillance for public health monitoring. The discovery of auxiliary metabolic genes encoded by RNA viruses further revealed their involvement in critical host metabolic pathways such as translation and cellular respiration. These findings underscore the multifaceted roles of RNA viruses in the critical engineered systems.
Requirement of Nek2a and cyclin A2 for Wapl-dependent removal of cohesin from prophase chromatin
Authors: Hellmuth Susanne , Stemmann Olaf
Published: March 2024

Sister chromatid cohesion is mediated by the cohesin complex. In mitotic prophase cohesin is removed from chromosome arms in a Wapl- and phosphorylation-dependent manner. Sgo1-PP2A protects pericentromeric cohesion by dephosphorylation of cohesin and its associated Wapl antagonist sororin. However, Sgo1-PP2A relocates to inner kinetochores well before sister chromatids are separated by separase, leaving pericentromeric regions unprotected. Why deprotected cohesin is not removed by Wapl remains enigmatic. By reconstituting Wapl-dependent cohesin removal from chromatin in vitro, we discovered a requirement for Nek2a and Cdk1/2-cyclin A2. These kinases phosphorylate cohesin-bound Pds5b, thereby converting it from a sororin- to a Wapl-interactor. Replacement of endogenous Pds5b by a phosphorylation mimetic variant causes premature sister chromatid separation (PCS). Conversely, phosphorylation-resistant Pds5b impairs chromosome arm separation in prometaphase-arrested cells and suppresses PCS in the absence of Sgo1. Early mitotic degradation of Nek2a and cyclin A2 may therefore explain why only separase, but not Wapl, can trigger anaphase.
Hybrid Exb/Mot stators require substitutions distant from the chimeric pore to power flagellar rotation
Authors: Ridone Pietro , Baker Matthew AB
Published: March 2024

Powered by ion transport across the cell membrane, conserved ion-powered rotary motors (IRMs) drive bacterial motility by generating torque on the rotor of the bacterial flagellar motor. Homologous heteroheptameric IRMs have been structurally characterized in ion channels such as Tol/Ton/Exb/Gld, and most recently in phage defense systems such as Zor. Functional stator complexes synthesized from chimeras of PomB/MotB (PotB) have been used to study flagellar rotation at low ion-motive force achieved via reduced external sodium concentration. The function of such chimeras is highly sensitive to the location of the fusion site, and these hybrid proteins have thus far been arbitrarily designed. To date, no chimeras have been constructed using interchange of components from Tol/Ton/Exb/Gld and other ion powered motors with more distant homology. Here we synthesised chimeras of MotAB, PomAPotB and ExbBD to assess their capacity for cross-compatibility. We generated motile strains powered by stator complexes with B-subunit chimeras. This motility was further optimised by directed evolution. Whole genome sequencing of these strains revealed that motility-enhancing residue changes occurred in the A-subunit and at the peptidoglycan binding domain of the B-unit, which could improve motility. Overall, our work highlights the complexity of stator architecture and identifies the challenges associated with rational design of chimeric IRMs.
Structural insights into physiological activation and antagonism of melanin-concentrating hormone receptor MCHR1
Authors: Ye Xiaofan , Liu Guibing , Li Xiu , He Binbin , Tao Yuyong , Liu Haiping , Gong Weimin
Published: March 2024

Melanin-concentrating hormone (MCH) is a 19-amino-acid neuropeptide playing crucial roles in energy homeostasis, sleep, and various physiological processes. It acts through two G protein-coupled receptors, MCHR1 and MCHR2, with MCHR1 being universally present in mammals and a potential target for treating metabolic and mental health conditions. However, drug development efforts have been impeded by the lack of structural information. Here, we present the cryo-EM structures of MCHR1 in its active state complexed with MCH and Gi1, as well as in its inactive state bound to a selective antagonist SNAP-94847. Structural and mutagenesis analyses disclosed the recognition mechanisms for both MCH and SNAP-94847, the activation mechanism and antagonism of MCHR1, and the determinants of ligand specificity. These findings are expected to accelerate the development of better drugs targeting the MCH system.
Metabolism of FAD, FMN and riboflavin (vitamin B2) in the human parasitic blood flukeSchistosoma mansoni
Authors: Da’dara Akram A. , Nation Catherine S. , Skelly Patrick J.
Published: March 2024

Schistosomiasis is a parasitic disease caused by trematode worms of the genusSchistosoma.The intravascular worms acquire the nutrients necessary for their survival from host blood. Since all animals are auxotrophic for riboflavin (vitamin B2), schistosomes too must import it to survive. Riboflavin is an essential component of the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD); these support key functions of dozens of flavoenzymes. In this work we focus on the biochemistry of riboflavin and its metabolites inSchistosoma mansoni. We show that when schistosomes are incubated in murine plasma, levels of FAD decrease over time while the levels of FMN increase. We show that live schistosomes can cleave exogenous FAD to generate FMN and this ability is significantly blocked when expression of the surface ectoenzyme SmNPP5 is suppressed using RNAi. Recombinant SmNPP5 cleaves FAD with a Km of 178 ± 5.9 µM. The FAD-dependent enzyme IL-4I1 drives the oxidative deamination of phenylalanine to produce phenylpyruvate and H2O2in the extracellular environment. Since schistosomes can be damaged by H2O2, we determined if SmNPP5 could impede H2O2production by blocking IL-4I1 actionin vitro. We found that this was not the case, suggesting that covalently bound FAD on IL-4I1 is inaccessible to SmNPP5. We also report here that live schistosomes can cleave exogenous FMN to generate riboflavin and this ability is significantly impeded when expression of a second surface ectoenzyme (alkaline phosphatase, SmAP) is suppressed. Recombinant SmAP cleaves FMN with a Km of 3.82 ± 0.58 mM. Thus, the sequential hydrolysis of FAD by tegumental ecto-enzymes SmNPP5 and SmAP can generate free vitamin B2 around the worms from where it can be conveniently imported by, we hypothesize, the recently described schistosome riboflavin transporter SmaRT. In this work we also identifiedin silicoschistosome homologs of enzymes that are involved in intracellular vitamin B2 metabolism. These are riboflavin kinase (SmRFK) as well as FAD synthase (SmFADS); cDNAs encoding these two enzymes were cloned and sequenced. SmRFK is predicted to convert riboflavin to FMN while SmFADS could further act on FMN to regenerate FAD in order to facilitate robust vitamin B2-dependent metabolism in schistosomes.
Electron-beam-based Compton scattering x-ray source for probing high-energy-density physics
Authors: Rinderknecht Hans G. , Bruhaug G. , Muşat V. , Gregori G. , Poole H. , Bishel D. , Chin D. A. , Rygg J. R. , Collins G. W.
Published: March 2024

The physics basis for an electron-beam-based Compton scattering x-ray source is investigated for single-shot experiments at the major high-energy-density facilities, such as the Omega Laser Facility, National Ignition Facility, and Z pulsed power facility. A source of monoenergetic (δε/ε<5%) 10- to 50-keV x rays can be produced by scattering of a short-pulse optical laser by a 23- to 53-MeV electron beam and collimating the scattered photons. The number and spectrum of scattered photons are calculated as a function of electron packet charge, electron and laser pulse duration, laser intensity, and collision geometry. A source delivering greater than 1010 photons in a 1-mm-radius spot and 100-ps time resolution is plausible with the available electron gun and laser technology. Applications of this source for x-ray diffraction, x-ray imaging, x-ray absorption fine structure, and x-ray absorption spectroscopy in high-energy-density physics experiments are described, demonstrating significant advancements compared to the present state of the art.

Published by the American Physical Society
2024
Selective observation of enantiomeric chiral phonons in
α
-quartz
Authors: Oishi Eiichi , Fujii Yasuhiro , Koreeda Akitoshi
Published: March 2024

We report anomalous circularly polarized Raman spectra of phonons in right- and left-handed quartzes. The phonon branches splitting from the E-mode at a finite wave number were found to be chiral with mutually opposite angular momenta. Our analysis reveals the Raman selection rules for chiral phonons. We also find that the conservation of angular momentum should be satisfied between two photons and one chiral phonon in the Raman process. Furthermore, we experimentally proved that the helicity of phonons with a certain frequency and wave vector should be opposite in the other enantiomer.

Published by the American Physical Society
2024
Energy dependence of
J/ψ
production in
pp
collisions from the PACIAE model
Authors: Ye Kai-Fan , Wang Qiang , Shi Jia-Hao , Qin Zhi-Ying , Zhang Wen-Chao , Lei An-Ke , She Zhi-Lei , Yan Yu-Liang , Sa Ben-Hao
Published: March 2024

In this work we investigate the J/ψ production in proton-proton collisions at the center-of-mass energy (s) equal to 2.76, 5.02, 7, 8, and 13 TeV with the parton and hadron cascade model PACIAE 2.2a. It is based on PYTHIA but extended considering the partonic and hadronic rescatterings before and after hadronization, respectively. In the PYTHIA sector the J/ψ production quantum chromodynamics processes are selected specially and a bias factor is proposed correspondingly. The calculated total cross sections, the transverse momentum differential, and the rapidity differential cross sections of J/ψ in the forward rapidity region reproduce the corresponding experimental measurements reasonably well. In the mid-rapidity region, the double-differential cross sections at s=5.02, 7, and 13 TeV are also in a good agreement with the experimental data. Moreover, we interpolate the double-differential cross section as well as the total cross section of J/ψ in the mid-rapidity region at s=8 TeV, which could be validated if the experimental data are available.

Published by the American Physical Society
2024
Spin-flavor oscillations of relic neutrinos in primordial magnetic field
Authors: Alok Ashutosh Kumar , Chall Trambak Jyoti , Chundawat Neetu Raj Singh , Mandal Arindam
Published: March 2024

The neutrino magnetic moment operator clasps a tiny but nonzero value within the standard model (SM) of particle physics and rather enhanced values in various new physics models. This generation of the magnetic moment (μν) is through quantum loop corrections which can exhibit spin-flavor oscillations in the presence of an external magnetic field. Also, several studies predict the existence of a primordial magnetic field (PMF) in the early Universe, extending back to the era of Big Bang nucleosynthesis (BBN) and before. The recent North American Nanohertz Observatory for Gravitational Waves measurement can be considered as a strong indication of the presence of these PMFs. In this work, we consider the effect of the PMF on the flux of relic neutrinos. For Dirac neutrinos, we show that half of the active relic neutrinos can become sterile due to spin-flavor oscillations well before becoming nonrelativistic owing to the expansion of the Universe and also before the timeline of the formation of galaxies and hence intergalactic fields, subject to the constraints on the combined value of μν and the cosmic magnetic field at the time of neutrino decoupling. For the upper limit of PMF allowed by the BBN, this can be true even if the experimental bounds on μν approach a few times its SM value.

Published by the American Physical Society
2024
Complementary LHC searches for UV resonances of the
0νββ
decay operators
Authors: Li Gang , Yu Jiang-Hao , Zhao Xiang
Published: March 2024

We investigate the quark-level effective operators related to the neutrinoless double beta (0νββ) decay process and their ultraviolet completions relevant to chiral enhancement effects at the hadronic level. We have classified several kinds of leptoquark models, matching to different standard model effective operators. Assuming weakly coupled new physics, we find the ongoing 0νββ decay experiments are sensitive to new physics scale at around 2–4 TeV, which is in the reach of LHC searches. We discuss the discovery potential of such resonances in the same-sign dilepton channels at the LHC. Therefore, the direct LHC searches and indirect 0νββ decay searches are complementary to each other in testing the UV completions of the effective operators for 0νββ decay.

Published by the American Physical Society
2024
Full phase space resonant anomaly detection
Authors: Buhmann Erik , Ewen Cedric , Kasieczka Gregor , Mikuni Vinicius , Nachman Benjamin , Shih David
Published: March 2024

Physics beyond the Standard Model that is resonant in one or more dimensions has been a longstanding focus of countless searches at colliders and beyond. Recently, many new strategies for have been developed, where sideband information can be used in conjunction with modern machine learning, in order to generate synthetic datasets representing the Standard Model background. Until now, this approach was only able to accommodate a relatively small number of dimensions, limiting the breadth of the search sensitivity. Using recent innovations in point cloud generative models, we show that this strategy can also be applied to the full phase space, using all relevant particles for the anomaly detection. As a proof of principle, we show that the signal from the R&D dataset from the LHC Olympics is findable with this method, opening up the door to future studies that explore the interplay between depth and breadth in the representation of the data for anomaly detection.

Published by the American Physical Society
2024
Detecting defect dynamics in relativistic field theories far from equilibrium using topological data analysis
Authors: Noel Viktoria , Spitz Daniel
Published: March 2024

We study nonequilibrium dynamics of relativistic N-component scalar field theories in Minkowski space-time in a classical statistical regime, where typical occupation numbers of modes are much larger than unity. In this strongly correlated system far from equilibrium, the role of different phenomena such as nonlinear wave propagation and defect dynamics remains to be clarified. We employ persistent homology to infer topological features of the nonequilibrium many-body system for different numbers of field components N via a hierarchy of cubical complexes. Specifically, we show that the persistent homology of local energy density fluctuations can give rise to signatures of self-similar scaling associated with topological defects, distinct from the scaling behavior of nonlinear wave modes. This contributes to the systematic understanding of the role of topological defects for far-from-equilibrium time evolutions of nonlinear many-body systems.

Published by the American Physical Society
2024
Inhomogeneous condensation in the Gross-Neveu model in noninteger spatial dimensions
1≤d<3
. II. Nonzero temperature and chemical potential
Authors: Koenigstein Adrian , Pannullo Laurin
Published: March 2024

We continue previous investigations of the (inhomogeneous) phase structure of the Gross-Neveu model in a noninteger number of spatial dimensions (1≤d<3) in the limit of an infinite number of fermion species (N→∞) at (non)zero chemical potential μ [L. Pannullo, Inhomogeneous condensation in the Gross-Neveu model in noninteger spatial dimensions 1≤d<3, ]. In this work, we extend the analysis from zero to nonzero temperature T. The phase diagram of the Gross-Neveu model in 1≤d<3 spatial dimensions is well-known under the assumption of spatially homogeneous condensation with both a symmetry broken and a symmetric phase present for all spatial dimensions. In d=1 one additionally finds an inhomogeneous phase, where the order parameter, the condensate, is varying in space. Similarly, phases of spatially varying condensates are also found in the Gross-Neveu model in

d

=

2

and d=3, as long as the theory is not fully renormalized, i.e., in the presence of a regulator. For d=2, one observes that the inhomogeneous phase vanishes, when the regulator is properly removed (which is not possible for d=3 without introducing additional parameters). In the present work, we use the stability analysis of the symmetric phase to study the presence (for 1≤d<2) and absence (for 2≤d<3) of these inhomogeneous phases and the related moat regimes in the fully renormalized Gross-Neveu model in the μ, T-plane. We also discuss the relation between “the number of spatial dimensions” and “studying the model with a finite regulator” as well as the possible consequences for the limit d→3.

Published by the American Physical Society
2024
Endowing black holes with beyond-Horndeski primary hair: An exact solution framework for scalarizing in every dimension
Authors: Baake Olaf , Cisterna Adolfo , Hassaine Mokhtar , Hernandez-Vera Ulises
Published: March 2024

This work outlines a straightforward mechanism for endorsing primary hair into Schwarzschild black holes, resulting in a unique modification within the framework of a special scalar-tensor theory, the so-called beyond-Horndeski gravity. The derived solutions are exact, showcase primary hair with a regular scalar field profile everywhere, and continuously connect with the vacuum geometry. Initially devised to introduce primary hair in spherically symmetric solutions within general relativity in any dimension, our investigation explores the conditions under which spherically symmetric black holes in alternative gravitational theories become amenable to the endowment of primary hair through a similar pattern. As a preliminary exploration, we embark on the process of endowing primary hair to the Reissner-Nordström black hole. Subsequently, we extend our analysis to encompass spherically symmetric solutions within Lovelock and cubic quasitopological gravity theories.

Published by the American Physical Society
2024
Rényi entanglement asymmetry in (
1+1
)-dimensional conformal field theories
Authors: Chen Miao , Chen Hui-Huang
Published: March 2024

In this paper, we consider the Rényi entanglement asymmetry of excited states in the (1+1) dimensional free compact boson conformal field theory (CFT) at equilibrium. We obtain a universal CFT expression written by correlation functions for the charged moments via the replica trick. We provide detailed analytic computations of the second Rényi entanglement asymmetry in the free compact boson CFT for excited states Ψ=Vβ+V−β and Φ=Vβ+J with Vβ and J=i∂ϕ being the vertex operator and current operator, respectively. We make numerical tests of the universal CFT computations using the XX spin chain model. Taking the non-Hermite fake reduced density matrices into consideration, we propose an effective way to test them numerically, which can be applied to other excited states. The CFT predictions are in perfect agreement with the exact numerical calculations.

Published by the American Physical Society
2024
Topological phases in the dynamics of the simple exclusion process
Authors: Garrahan Juan P. , Pollmann Frank
Published: March 2024

We study the dynamical large deviations of the classical stochastic symmetric simple exclusion process (SSEP) by means of numerical matrix product states. We show that for half filling, long-time trajectories with a large enough imbalance between the number hops in even and odd bonds of the lattice belong to distinct symmetry-protected topological (SPT) phases. Using tensor network techniques, we obtain the large deviation (LD) phase diagram in terms of counting fields conjugate to the dynamical activity and the total hop imbalance. We show the existence of high activity trivial and nontrivial SPT phases (classified according to string order parameters) separated by either a critical phase or a critical point. Using the leading eigenstate of the tilted generator, obtained from infinite-system density-matrix renormalization group simulations, we construct a near-optimal dynamics for sampling the LDs, and show that the SPT phases manifest at the level of rare stochastic trajectories. We also show how to extend these results to other filling fractions, and discuss generalizations to asymmetric SEPs.

Published by the American Physical Society
2024
Electrostatic Trapping of
N2
Molecules in High Rydberg States
Authors: Rayment M. H. , Hogan S. D.
Published: March 2024

N2 molecules traveling in pulsed supersonic beams have been excited from their X Σg+1 ground electronic state to long-lived Rydberg states with principal quantum numbers between 39 and 48 using a resonance-enhanced two-color three-photon excitation scheme. The Rydberg states populated had static electric dipole moments exceeding 5000 D which allowed deceleration of the molecules to rest in the laboratory-fixed frame of reference and three-dimensional trapping using inhomogeneous electric fields. The trapped molecules were confined for up to 10 ms, with effective trap decay time constants increasing with principal quantum number, and ranging from 450 to 700  μs. These observations, and comparison with the results of similar measurements with He atoms, indicate that the decay dynamics of the trapped Rydberg N2 molecules are dominated by spontaneous emission and do not exhibit significant contributions from effects of intramolecular interactions that lead to non-radiative decay.

Published by the American Physical Society
2024
Observation of Subdiffusive Dynamic Scaling in a Driven and Disordered Bose Gas
Authors: Martirosyan Gevorg , Ho Christopher J. , Etrych Jiří , Zhang Yansheng , Cao Alec , Hadzibabic Zoran , Eigen Christoph
Published: March 2024

We explore the dynamics of a tuneable box-trapped Bose gas under strong periodic forcing in the presence of weak disorder. In absence of interparticle interactions, the interplay of the drive and disorder results in an isotropic nonthermal momentum distribution that shows subdiffusive dynamic scaling, with sublinear energy growth and the universal scaling function captured well by a compressed exponential. We explain that this subdiffusion in momentum space can naturally be understood as a random walk in energy space. We also experimentally show that for increasing interaction strength, the gas behavior smoothly crosses over to wave turbulence characterized by a power-law momentum distribution, which opens new possibilities for systematic studies of the interplay of disorder and interactions in driven quantum systems.

Published by the American Physical Society
2024
Role of mentorship, career conceptualization, and leadership in developing women’s physics identity and belonging
Authors: Rosenberg Jessica L. , Holincheck Nancy , Fernández Kathryn , Dreyfus Benjamin W. , Wardere Fardousa , Stehle Stephanie , Butler Tiffany N.
Published: March 2024

The percentage of women receiving bachelor’s degrees in physics (25%) in the U.S. lags well behind that of men, and women leave the major at higher rates. Achieving equity in physics will mean that women stay in physics at the same rates as men, but this will require changes in the culture and support structures. A strong sense of belonging can lead to higher retention rates so interventions meant to increase dimensions of physics identity (interest, recognition, performance, and competence) may increase persistence overall and increase women’s retention differentially. We describe our model in which mentorship, an understanding of career options (career conceptualization), and leadership are inputs into the development of these dimensions of physics identity. This paper includes preliminary results from a qualitative study that aims to better understand how career conceptualization, leadership, and mentorship contribute to the development of physics identity and belonging. We report results from a survey of 15 undergraduate physics students which was followed up by interviews with 5 of those students. The students were from 2 institutions: a small private liberal arts college in the midwest region of the U.S. and a large public university in the southeast region of the U.S. classified as a Hispanic-serving institution (HSI). With respect to mentorship, consistent with the existing literature, we found that it could provide critical support for students’ engagement in the physics community. Leadership experiences have not previously been positioned as an important input into identity, yet we found that they helped women in physics feel more confident, contributing to their recognition of themselves as physics people. While the data on how career conceptualization contributed to the building of identity is limited, there are some connections to recognition and competence, and it will be an interesting avenue of future exploration.

Published by the American Physical Society
2024
Does culture moderate the innovation input–output relationship? A two-stage configurational analysis
Authors: Duarte Marcelo Pereira , Carvalho Fernando Manuel P.O.
Published: March 2024

Purpose

This study analyses configurations of national culture as boundary conditions of countries’ national systems of innovation (NSI). Drawing from the NSI approach, we argue that culture’s role is that of a contingency factor shaping the relationship between investments in innovation and national innovation outputs.

Design/methodology/approach

We assessed the moderation effect of national culture through a systematic, two-stage approach using fuzzy-set Qualitative Comparative Analysis (fsQCA), which allows the analysis of changes induced by the moderator variables. Analyses were conducted with a diverse sample of 61 countries over a period spanning 12 years, from 2011 to 2022.

Findings

Findings reveal that investments in innovation, but not individual cultural dimensions, is a necessary condition for high innovation outputs. Furthermore, several configurations of cultural dimensions were identified as moderators of the relationship between investments in innovation and innovation outputs.

Originality/value

This study provides insights into cross-national innovation research by exposing the role of cultural configurations, rather than just individual cultural dimensions, as boundary conditions involved in the achievement of high levels of innovation.