bluuebunny/crossref_metadata_2025 huggingface dataset:
A deep learning-based approach for unbiased kinematic analysis in CNS injury
Authors: Ascona Maureen , Tieu Ethan Kim , Gonzalez-Vega Erick , Liebl Daniel J , Brambilla Roberta
Published: April 2024

Traumatic spinal cord injury (SCI) is a devastating condition that impacts over 300,000 individuals in the US alone. Depending on the severity of the injury, SCI can lead to varying degrees of sensorimotor deficits and paralysis. Despite advances in our understanding of the underlying pathological mechanisms of SCI and the identification of promising molecular targets for repair and functional restoration, few therapies have made it into clinical use. To improve the success rate of clinical translation, more robust, sensitive, and reproducible means of functional assessment are required. The gold standards for the evaluation of locomotion in rodents with SCI are the Basso Beattie Bresnahan (BBB) and Basso Mouse Scale (BMS) tests.

To overcome the shortcomings of current methods, we developed two separate marker-less kinematic analysis paradigms in mice, MotorBox and MotoRater, based on deep-learning algorithms generated with the DeepLabCut open-source toolbox. The MotorBox system uses an originally designed, custom-made chamber, and the MotoRater system was implemented on a commercially available MotoRater device. We validated the MotorBox and MotoRater systems by comparing them with the traditional BMS test and extracted metrics of movement and gait that can provide an accurate and sensitive representation of mouse locomotor function post-injury, while eliminating investigator bias and variability. The integration of MotorBox and/or MotoRater assessments with BMS scoring will provide a much wider range of information on specific aspects of locomotion, ensuring the accuracy, rigor, and reproducibility of behavioral outcomes after SCI.

Highlights

MotorBox and MotoRater systems are two novel marker-less kinematic analysis paradigms in mice, based on deep-learning algorithms generated with DeepLabCut.

MotorBox and MotoRater systems are highly sensitive, accurate and unbiased in analyzing locomotor behavior in mice.

MotorBox and MotoRater systems allow for sensitive detection of SCI-induced changes in movement metrics, including range of motion, gait, coordination, and speed.

MotorBox and MotoRater systems allow for detection of movement metrics not measurable with the BMS.
Replicating a High-Impact Scientific Publication Using Systems of Large Language Models
Authors: Bersenev Dennis , Yachie-Kinoshita Ayako , Palaniappan Sucheendra K.
Published: April 2024

Publications focused on scientific discoveries derived from analyzing large biological datasets typically follow the cycle of hypothesis generation, experimentation, and data interpretation. The reproduction of findings from such papers is crucial for confirming the validity of the scientific, statistical, and computational methods employed in the study, and it also facilitates the foundation for new research. By employing a multi-agent system composed of Large Language Models (LLMs), including both text and code generation agents built on OpenAI’s platform, our study attempts to reproduce the methodology and findings of a high-impact publication that investigated the expression of viral-entry-associated genes using single-cell RNA sequencing (scRNA-seq). The LLM system was critically evaluated against the analysis results from the original study, highlighting the system’s ability to perform simple statistical analysis tasks and literature reviews to establish the purpose of the analyses. However, we also identified significant challenges in the system, such as nondeterminism in code generation, difficulties in data procurement, and the limitations presented by context length and bias from the model’s inherent training data. By addressing these challenges and expanding on the system’s capabilities, we intend to contribute to the goal of automating scientific research for efficiency, reproducibility, and transparency, and to drive the discussion on the role of AI in scientific discovery.
Monoclonal antibodies derived from B cells in subjects with cystic fibrosis reducePseudomonas aeruginosaburden in mice
Authors: Hale Malika , Takehara Kennidy K. , Thouvenel Christopher D. , Moustafa Dina A. , Repele Andrea , Fontana Mary F. , Netland Jason , McNamara Sharon , Gibson Ronald L. , Goldberg Joanna B. , Rawlings David J. , Pepper Marion
Published: April 2024

Pseudomonas aeruginosa(PA) is an opportunistic, frequently multidrug-resistant pathogen that can cause severe infections in hospitalized patients. Antibodies against the PA virulence factor, PcrV, protect from death and disease in a variety of animal models. However, clinical trials of PcrV-binding antibody-based products have thus far failed to demonstrate benefit. Prior candidates were derivations of antibodies identified using protein-immunized animal systems and required extensive engineering to optimize binding and/or reduce immunogenicity. Of note, PA infections are common in people with cystic fibrosis (pwCF), who are generally believed to mount normal adaptive immune responses. Here we utilized a tetramer reagent to detect and isolate PcrV-specific B cells in pwCF and, via single-cell sorting and paired-chain sequencing, identified the B cell receptor (BCR) variable region sequences that confer PcrV-specificity. We derived multiple high affinity anti-PcrV monoclonal antibodies (mAbs) from PcrV-specific B cells across 3 donors, including mAbs that exhibit potent anti-PA activity in a murine pneumonia model. This robust strategy for mAb discovery expands what is known about PA-specific B cells in pwCF and yields novel mAbs with potential for future clinical use.
Light exposure induces phenotypic plasticity of the upside-down jellyfishCassiopeaand its endosymbiotic dinoflagellates
Authors: Salas Rebecca , Anthony Colin J , Bentlage Bastian
Published: April 2024

The upside-down jellyfish,Cassiopea, is an increasingly popular model organism gaining prominence for both its endosymbiotic dinoflagellates from the family Symbiodiniaceae and its behavioral changes of bell pulsations associated with environmental cues. Pulsation provides a unique window into the host’s response to environmental conditions, a typically difficult to access component of other symbiotic cnidarians. Pulsation has also been hypothesized to play a regulatory role on the endosymbiotic assemblage, but the magnitude of this regulatory effect is not well understood. Here, we used two light-acclimation experiments to help disentangle the complex phenotypic responses of the cnidarian host and its endosymbiotic dinoflagellates. The first experiment examined the phenotypic plasticity (size, behavior, color) ofCassiopeasp. in response to repeated ambient light acclimation trials to determine the rate and magnitude of phenotypic plasticity. The second experiment compared the acclimation response of jellyfish across three experimental groups to test whether a variable environment and resulting short acclimation times destabilized the host-endosymbiont relationship. Our goal was to identify covarying host-endosymbiont phenotypes to gain new insights into the dynamics of this relationship. We employed flow cytometric phenotypic profiling for high-throughput phenotypic characterization of endosymbiotic dinoflagellates in addition to pulse-amplitude modulated (PAM) fluorometry to characterize photosynthetic efficiency (Fv/Fm). Host phenotypes responded predictably to light-dark cycles, and stabilized after nine to twelve days of exposure to consistent light conditions. However, disruption of this acclimation period affected both the host’s circadian rhythm and the endosymbionts’ phenotypic profile. We also found evidence that phenotypic responses of the host and endosymbionts were generally decoupled, indicating a stronger regulatory response of light conditions on phenotypes than possible host-regulatory strategies on the endosymbiotic assemblage. This study provides unique insights into the acclimation strategies of upside-down jellyfish, an emerging model for the study of cnidarian-dinoflagellate symbiosis.

Highlights

Cassiopeabehavior and color respond predictably to changing light conditions

Inadequate acclimation time destabilizes the host’s circadian rhythm and causes unique phenotypic characteristics of the endosymbionts

Light may be a stronger influence on host and endosymbiont phenotypes than host-endosymbiont relationships
The causal arrows ̶ from genotype, environment and management to plant phenotype ̶ are double headed
Authors: Sadras Victor O , Hayman Peter T
Published: April 2024

Unidirectional, cause-and-effect arrows are drawn from genotype (G), environment (E), and agronomic management (M) to the plant phenotype in crop stands. Here we focus on the overlooked bidirectionality of these arrows. The phenotype-to-genotype arrow includes increased mutation rates in stressed phenotypes, relative to basal rates. From a developmental viewpoint, the phenotype modulates gene expression returning multiple cellular phenotypes with a common genome. From a computational viewpoint, the phenotype influences gene expression in a process of downward causation. The phenotype-to-environment arrow is captured in the process of niche construction, which spans from persistent and global (e.g., photosynthetic archaea and cyanobacteria that emerged ∼3.4 billion years agocreatedthe oxygen-rich atmosphere thatenabledthe evolution of aerobic organisms and eukaryotes) to transient and local (e.g., lucerne tap root constructs soil biopores that influence the root phenotype of the following wheat crop). Research on crop rotations illustrates but is divorced of niche construction theory. The phenotype-to-management arrow involves, for example, a diseased crop that triggers fungicide treatments. Making explicit the bidirectionality of the arrows in the G×E×M model allows to connect crop improvement and agronomy with other, theoretically rich scientific fields.

Highlight

In the G×E×M model, the plant phenotype is not only influenced by but also influences G, E and M.
MRAP2 modifies the signaling and oligomerization state of the melanocortin-4 receptor
Authors: Sohail Iqra , Laurin Suli-Anne , Kleinau Gunnar , Chunilal Vidicha , Morton Andrew , Kagiali Zeynep Cansu Uretmen , Tello Javier A. , Lohse Martin J. , Scheerer Patrick , Bouvier Michel , McCormick Peter , Annibale Paolo , Biebermann Heike
Published: April 2024

The melanocortin-4 receptor (MC4R) is a G protein-coupled receptor (GPCR) and a key regulator of appetite and metabolism. It can interact with the melanocortin-receptor accessory protein 2 (MRAP2), a single transmembrane helix protein known to interact with several different GPCRs. However, the consequences of this interaction are not completely understood. Here we report that co-expression of MRAP2 has multiple effects on the MC4R: it enhances G protein-mediated signaling and simultaneously impairs β-arrestin2 recruitment and, consequently, internalization. In addition, co-expression of MRAP2 leads to an increased number of monomers of MC4R by disrupting receptor oligomers. A structural homology model of the active state MC4R–MRAP2– Gs complex suggests interaction sites between MRAP2 and MC4R that are relevant for receptor activation. Taken together, our data indicate that MRAP2 is an accessory protein that interacts with and influences MC4R structure, biasing its signaling towards G protein-mediated effects.
Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions
Authors: Schmid Ernst W. , Walter Johannes C.
Published: April 2024

Protein-protein interactions (PPIs) are ubiquitous in biology, yet a comprehensive structural characterization of the PPIs underlying biochemical processes is lacking. Although AlphaFold-Multimer (AF-M) has the potential to fill this knowledge gap, standard AF-M confidence metrics do not reliably separate relevant PPIs from an abundance of false positive predictions. To address this limitation, we used machine learning on well curated datasets to train aStructurePrediction andOmics informedClassifier called SPOC that shows excellent performance in separating true and false PPIs, including in proteome-wide screens. We applied SPOC to an all-by-all matrix of nearly 300 human genome maintenance proteins, generating ∼40,000 predictions that can be viewed at predictomes.org, where users can also score their own predictions with SPOC. High confidence PPIs discovered using our approach suggest novel hypotheses in genome maintenance. Our results provide a framework for interpreting large scale AF-M screens and help lay the foundation for a proteome-wide structural interactome.
Non-negative matrix factorization and deconvolution as dual simplex problem
Authors: Kleverov Denis , Aladyeva Ekaterina , Serdyukov Alexey , Artyomov Maxim N.
Published: April 2024

Non-negative matrix factorization (NMF) is one of the most powerful linear algebra tools, which has found application in various areas of data analysis, including computational biology. Despite numerous optimization methods devised for NMF, our comprehension of the inherent topological structure within factorizable matrices remains limited. In this work, we reveal the topological properties of the linear mixture data, which allow for a remarkable reduction in the dimensionality of the NMF problem and reformulation of the NMF problem as an optimization problem with onlyK(K−1)variables, with K representing the number of pure components, irrespective of the initial data matrix dimensionality. This is achieved by uncovering the dual simplex structure of the data, with complementary simplex structures existing in both the features’ and samples’ spaces and leveraging the Sinkhorn transformation to uncover the relationship between these simplexes. We validate this approach in the context of an unconstrained general mixed images scenario and achieve a significant improvement in decomposition accuracy. Furthermore, we successfully apply the proposed approach in the biological context of bulk RNA-seq gene expression data unmixing and single-cell RNA-seq data clustering.
A narrow ratio of nucleic acid to SARS-CoV-2 N-protein enables phase separation
Authors: Laughlin Patrick M. , Young Kimberly , Gonzalez-Gutierrez Giovanni , Wang Joseph C.Y. , Zlotnick Adam
Published: April 2024

SARS-CoV-2 Nucleocapsid protein (N) is a viral structural protein that packages the 30kb genomic RNA inside virions and forms condensates within infected cells through liquid-liquid phase separation (LLPS). N, in both soluble and condensed forms, has accessory roles in the viral life cycle including genome replication and immunosuppression. The ability to perform these tasks depends on phase separation and its reversibility. The conditions that stabilize and destabilize N condensates and the role of N-N interactions are poorly understood. We have investigated LLPS formation and dissolution in a minimalist system comprised of N protein and an ssDNA oligomer just long enough to support assembly. The short oligo allows us to focus on the role of N-N interaction. We have developed a sensitive FRET assay to interrogate LLPS assembly reactions from the perspective of the oligonucleotide. We find that N alone can form oligomers but that oligonucleotide enables their assembly into a three-dimensional phase. At a ∼1:1 ratio of N to oligonucleotide LLPS formation is maximal. We find that a modest excess of N or of nucleic acid causes the LLPS to break down catastrophically. Under the conditions examined here assembly has a critical concentration of about 1 µM. The responsiveness of N condensates to their environment may have biological consequences. A better understanding of how nucleic acid modulates N-N association will shed light on condensate activity and could inform antiviral strategies targeting LLPS.
Muscle-Specific Pyruvate Kinase Isoforms, Pkm1 and Pkm2, Regulate Mammalian SWI/SNF Proteins and Histone 3 Phosphorylation During Myoblast Differentiation
Authors: Olea-Flores Monserrat , Sharma Tapan , Verdejo-Torres Odette , DiBartolomeo Imaru , Thompson Paul R. , Padilla-Benavides Teresita , Imbalzano Anthony N.
Published: April 2024

Pyruvate kinase is a glycolytic enzyme that converts phosphoenolpyruvate and ADP into pyruvate and ATP. There are two genes that encode pyruvate kinase in vertebrates;PkmandPklencode muscle- and liver/erythrocyte-specific forms, respectively. Each gene encodes two isoenzymes due to alternative splicing. Both muscle-specific enzymes, Pkm1 and Pkm2, function in glycolysis, but Pkm2 also has been implicated in gene regulation due to its ability to phosphorylate histone 3 threonine 11 (H3T11) in cancer cells. Here, we examined the roles of Pkm1 and Pkm2 during myoblast differentiation. RNA-seq analysis revealed that Pkm2 promotes the expression ofDpf2/Baf45dandBaf250a/Arid1A. Dpf2 and Baf250a are subunits that identify a specific sub-family of the mammalian SWI/SNF (mSWI/SNF) of chromatin remodeling enzymes that is required for activation of myogenic gene expression during differentiation. Pkm2 also mediated the incorporation of Dpf2 and Baf250a into the regulatory sequences controlling myogenic gene expression. Pkm1 did not affect expression but was required for nuclear localization of Dpf2. Additionally, Pkm2 was required not only for the incorporation of phosphorylated H3T11 in myogenic promoters, but also for the incorporation of phosphorylated H3T6 and H3T45 at myogenic promoters via regulation of AKT and protein kinase C isoforms that phosphorylate those amino acids. Our results identify multiple unique roles for Pkm2 and a novel function for Pkm1 in gene expression and chromatin regulation during myoblast differentiation.
Anin silicoframework for the rational design of vaginal probiotic therapy
Authors: Lee Christina Y. , Bonakdar Sina , Arnold Kelly B.
Published: April 2024

Bacterial vaginosis is a common condition characterized by a shift in vaginal microbiome composition that is linked to negative reproductive outcomes and increased susceptibility to sexually transmitted infections. Despite the commonality of BV, standard-of-care antibiotics provide limited control of recurrent BV episodes and development of new biotherapies is limited by the lack of controlled models needed to evaluate new dosing and treatment regimens. Here, we develop anin silicoframework to evaluate selection criteria for potential probiotic strains, test adjunctive therapy with antibiotics, and alternative dosing strategies. This framework highlighted the importance of resident microbial species on the efficacy of probiotic strains, identifying specific interaction parameters between resident non-optimal anaerobic bacteria (nAB) andLactobacillusspp. with candidate probiotic strains as a necessary selection criteria. Model predictions were able to replicate results from a recent phase 2b clinical trial for the live biotherapeutic product, Lactin-V, demonstrating the relevance of thein silicoplatform. Results from the model support that the probiotic strain in Lactin-V requires adjunctive antibiotic therapy to be effective, and that increasing the dosing frequency of the probiotic could have a moderate impact on BV recurrence at 12 and 24 weeks. Altogether, this framework could provide evidence for the rational selection of probiotic strains and help optimize dosing frequency or adjunctive therapies.
The NS1 protein of contemporary West African Zika virus is efficient to increase cellular permissiveness to virus replication
Authors: Dana Machmouchi , Marie-Pierre Courageot , Eva Ogire , Alain Kohl , Desprès Philippe , Marjolaine Roche
Published: April 2024

Mosquito-borne Zika virus (ZIKV; orthoflavivirus,Flaviviridae) has become a global health problem due to expansion of the geographic distribution of Asian Lineage virus. Contemporary ZIKV strains of African lineage have recently gained increased attention due to their epidemic potential and their capacity to be highly teratogenic in humans. The ZIKV non-structural NS1 protein from recent West African strains Africa was been studied where with view of its importance in the pathogenicity. NS1 protein from contemporary West African ZIKV (NS1CWA) and historical African ZIKV strain MR766 (NS1MR766) differ by seven amino-acid substitutions. Expression of recombinant NS1 proteins showed differences in the subcellular distribution between NS1CWAand NS1MR766in HEK-293T cells. There was an increased secretion efficiency of soluble NS1CWAcompared to NS1MR766. The replication of a chimeric MR766/NS1CWAvirus was studied in Vero and A549 cells. Insertion of NS1CWAinto MR766 enhances virus replication in both cell lines leading to more pronounced cell death. This correlated with lower up-regulation ofIFN-βand interferon-stimulated gene mRNA in A549 cells infected by MR766/NS1CWAvirus. Our data raise the question on the importance of NS1 protein in the pathogenicity of contemporary ZIKV from West Africa, and point to differences within viral strains belonging to the same African lineage.

AUTHOR SUMMARY

Mosquito-borne Zika virus (ZIKV) of African lineage has the potential to cause epidemic along with a high risk of fetal pathogenicity. Too little is still known on the features of contemporary ZIKV from West Africa. We find there is a remarkable conservation of NS1 amino-acid residues between ZIKV strains recently isolated in Senegal and Guinea. Analysis of recombinant ZIKV NS1 protein revealed efficient secretion of contemporary African NS1 protein from human cells. Using infectious molecular clone of African ZIKV, we showed that contemporary West Africa NS1 protein influences virus replication and innate immune activation. The NS1 protein has been proposed as playing a major role in the pathogenicity of contemporary ZIKV from West Africa.
Coatomer complex I is required for the transport of SARS-CoV-2 progeny virions from the endoplasmic reticulum-Golgi intermediate compartment
Authors: Hirabayashi Ai , Muramoto Yukiko , Takenaga Toru , Tsunoda Yugo , Wakazaki Mayumi , Sato Mayuko , Fujita-Fujiharu Yoko , Nomura Norimichi , Yamauchi Koji , Onishi Chiho , Nakano Masahiro , Toyooka Kiminori , Noda Takeshi
Published: April 2024

SARS-CoV-2 undergoes budding within the lumen of the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) and delivers progeny virions to the cell surface by employing vesicular transport. However, the molecular mechanisms remain poorly understood. Using three-dimensional electron microscopic analysis, such as array tomography and electron tomography, we found that virion-transporting vesicles possessed a coated protein on their membrane and demonstrated that the coated protein was coatomer complex I (COPI). During the later stages of SARS-CoV-2 infection, we observed a notable alteration in the distribution of COPI and ERGIC throughout the cytoplasm. Depletion of COPB2, a key component of COPI, led to the confinement of SARS-CoV-2 structural proteins in the perinuclear region, where progeny virions were accumulated within the ERGIC. While the expression levels of viral proteins within cells were comparable, this depletion significantly reduced the efficiency of virion release, leading to the significant inhibition of viral replication. Hence, our findings suggest COPI as a critical player in facilitating the transport of SARS-CoV-2 progeny virions from the ERGIC. Thus, COPI could be a promising target for the development of antivirals against SARS-CoV-2.
Single-cell imaging of the lytic phage life cycle in bacteria
Authors: Wedd Charlie , Yunusov Temur , Smith Aaron , Li Ruizhe , Hardo Georgeos , Hunter Michael , Majed Racha , Fusco Diana , Bakshi Somenath
Published: April 2024

When a lytic bacteriophage infects a bacterial cell, it commandeers the cell’s resources to replicate, ultimately causing cell lysis and the release of new virions. As phages function as obligate parasites, each stage of the infection process depends on the physiological parameters of the host cell. Given the inherent variability of bacterial physiology, we ask how the phage infection dynamic reflects such heterogeneity.

Here, we introduce an imaging assay for investigating the kinetics of individual infection steps by a single T7 phage on a single bacterium. The high-throughput, time-resolved nature of the assay allows us to monitor the infection progression simultaneously in multiple cells, revealing substantial heterogeneity in each step and correlations between the dynamics of infection steps and physiological properties of the infected cell. Simulations of competing phage populations with distinct lysis time distributions indicate that this heterogeneity can have considerable impact on phage fitness, recognising variability in infection kinetics as a potential evolutionary driver of phage-bacteria interactions.
Archaeal type six secretion system mediates contact-dependent antagonism
Authors: Zachs Tobias , Malit Jessie James L. , Xu Jingwei , Schürch Alexandra , Sivabalasarma Shamphavi , Nußbaum Phillip , Albers Sonja-Verena , Pilhofer Martin
Published: April 2024

Microbial communities are shaped by cell-cell interactions. Even though archaea are often found in associations with other microorganisms, the mechanisms structuring these communities are poorly understood. Here we report the structure and function of haloarchaeal contractile injection systems (CISs). Using a combination of functional assays and time lapse imaging, we show that Halogeometricum borinquense exhibits antagonism towards Haloferax volcanii by inducing cell lysis and inhibiting proliferation. This antagonism is contact-dependent and requires a functional CIS, which is encoded by a gene cluster that is associated with toxin-immunity pairs. Cryo-focused ion beam milling and imaging by cryo-electron tomography revealed CISs bound to the cytoplasmic membrane, resembling bacterial type six secretion systems (T6SSs). We show that related T6SS gene clusters are conserved and expressed in other haloarchaeal strains with antagonistic behavior. Our data provides a mechanistic framework for understanding how archaea may shape microbial communities and impact the food webs they inhabit.

Teaser

T6SSs are widespread in the archaeal domain and used to kill other archaea.
Impact of redox fluctuations on the spatial distribution of the microbial community in a forest soil: A lysimeter experiment
Authors: Wang Simiao , Miele Filippo , Benettin Paolo , Asadollahi Mitra , Pasqualini Jacopo , Frutschi Manon , Rossi Pierre , Jacquemin Nicolas , Rinaldo Andrea , Bernier-Latmani Rizlan
Published: April 2024

The soil microbial community is structured by several factors including environmental conditions such as varying water content, dissolved oxygen, and redox potential. Here, we experimentally investigate the impact of the redox regimes, i.e., oxic, fluctuating, or anoxic conditions, on the microbial community composition and probe the widespread hypothesis that the diversity of the redox fluctuating layer is greater than that of the zones with static redox conditions. A 50-cm homogenized soil column was subjected to realistic intermittent artificial precipitation for 3 months and the hydrological and geochemical parameters (redox potential, pH, dissolved oxygen, soil moisture, matric potential, chemical speciation) measured as a function of time and depth. The change in microbial community over the 3-month experiment was distinct in the three redox zones. The oxic zone exhibited increased biomass and the highest diversity, the redox fluctuation zone exhibited less growth and diversity, and the anoxic zone was characterized by little change in biomass and minimal change in diversity. Interestingly, the redox fluctuation zone and anoxic zone microbiomes most resembled that of the initial soil. Rather than the redox potential alone, the vertical DOC gradients were found to dominate the compositional trajectory of the microbiome. Additionally, this work validated a recently developed spatially explicit biogeochemical model with both geochemical and microbial data and revealed the horizontal and vertical characteristics of microbial community diversity under varying hydrological regimes.
Reconstitution of human DNA licensing and the structural and functional analysis of key intermediates
Authors: Wells Jennifer N. , Leber Vera , Edwardes Lucy V , Allyjaun Shenaz , Peach Matthew , Tomkins Joshua , Kefala-Stavridi Antonia , Faull Sarah V , Aramayo Ricardo , Pestana Carolina M. , Ranjha Lepakshi , Speck Christian
Published: April 2024

Human DNA licensing initiates the process of replication fork assembly. Specifically, this reaction leads to the loading of hMCM2-7 on DNA, which represents the core of the replicative helicase that unwinds DNA during S-phase. Here, we report the biochemical reconstitution of human DNA licensing using purified proteins, the structural and functional analysis of the process and reveal the impact of cancer-associated mutations on DNA licensing. We showed that thein vitroreaction is specific and results in the assembly of high-salt resistant hMCM2-7 double-hexamers, the final product of DNA licensing. We used ATPγS to block complex assembly at the hOrc1-5-Cdc6-Cdt1-MCM2-7 step. We observed that the assembly of this intermediate is independent of hOrc6, although hOrc6 enhances the loading of the second hMCM2-7 hexamer. The structural and mutational analysis of the hOrc1-5-Cdc6-Cdt1-MCM2-7 complex provides insights into hORC-Cdc6 dependent recruitment of hMCM2-7 via five hMcm winged-helix domains. The structure highlights how hOrc1 activates the hCdc6 ATPase, while the analysis of hOrc1 and hCdc6 ATPase mutants uncovered an unexpected role for hCdc6 ATPase in complex disassembly. The structure highlights that Cdc6 binding to Orc1-5 stabilises Orc2-DNA interactions and supports Mcm3-dependent recruitment of MCM2-7. Finally, the structure allowed us to locate cancer-associated mutations at the hCdc6-Mcm3 interface, which showed specific helicase loading defects.
Medium Composition Affects Microbial Corrosion Rates
Authors: Wang Di , Ueki Toshiyuki , Ma Peiyu , Xu Dake , Lovley Derek R.
Published: April 2024

Desulfovibrio vulgarisandDesulfovibrio ferrophiluswere previously proposed to have distinct iron corrosion mechanisms becauseD. ferrophiluscorroded faster. However, the chloride concentration in theD. ferrophilus‘marine’ medium was much higher than in theD. vulgaris‘freshwater’ medium.D. vulgariscorrosion rates accelerated with increasing chloride and were faster thanD. ferrophilusin the same marine medium. Differences inD. ferrophiluscorrosion rates in two different media with the same chloride concentration suggested that minor differences in other medium constituents also impact on microbial corrosion. These results demonstrate the importance of considering medium composition in microbial corrosion studies.
Ancestral versus Modern Substrate Scope in Family-1 Glycosidases
Authors: Gutierrez-Rus Luis I. , Petrovic Dusan , Schneider Pascal , Zorn Katja , Gamiz-Arco Gloria , De Maria Leonardo , Falcioni Francesco , Risso Valeria A. , Hayes Martin A. , Sanchez-Ruiz Jose M.
Published: April 2024

Promiscuity, the capability of catalyzing a diversity of chemical reactions, is a desirable feature in many enzymes intended for biotechnological applications. Promiscuous activities, however, are typically depressed in specialized modern enzymes. On the other hand, several ancestral reconstruction studies have reported enzymes with enhanced promiscuity. Glycosidases catalyze the hydrolysis of glycosidic bonds in all living cells but find practical applications in the synthesis of glycoconjugates as catalysts of the reverse reaction. Here, we use a library of about 500 possible substrates to compare the catalytic scope of the modern family-1 glycosidase from Halothermothrix orenii with that of a putative ancestral family-1 glycosidase derived from sequence reconstruction at a bacterial-eukaryotic common ancestor. The modern enzyme is the better catalyst for the hydrolysis of small substrates typically used to assess the activity of family-1 glycosidases. We identify, however, a trend for the modern enzyme to become less catalytically efficient with increasing substrate size. Such trend is not apparent in the conformationally-flexible ancestral glycosidase, which is in fact the better catalyst for the hydrolysis of flavonoid glycosides. Our results support that ancestral sequence reconstruction may provide a basis for enzyme engineering for the synthesis of glycoconjugates with large glycosyl acceptors.
Mechanical stress through growth on stiffer substrates impacts animal health and longevity inC. elegans
Authors: Oorloff Maria , Hruby Adam , Averbukh Maxim , Alcala Athena , Dutta Naibedya , Torres Toni Castro , Moaddeli Darius , Vega Matthew , Kim Juri , Bong Andrew , Coakley Aeowynn J. , Hicks Daniel , Wang Jing , Wang Tiffany , Hoang Sally , Tharp Kevin M. , Garcia Gilberto , Higuchi-Sanabria Ryo
Published: April 2024

Mechanical stress is a measure of internal resistance exhibited by a body or material when external forces, such as compression, tension, bending, etc. are applied. The study of mechanical stress on health and aging is a continuously growing field, as major changes to the extracellular matrix and cell-to-cell adhesions can result in dramatic changes to tissue stiffness during aging and diseased conditions. For example, during normal aging, many tissues including the ovaries, skin, blood vessels, and heart exhibit increased stiffness, which can result in a significant reduction in function of that organ. As such, numerous model systems have recently emerged to study the impact of mechanical and physical stress on cell and tissue health, including cell-culture conditions with matrigels and other surfaces that alter substrate stiffness and ex vivo tissue models that can apply stress directly to organs like muscle or tendons. Here, we sought to develop a novel method in an in vivo, model organism setting to study the impact of mechanical stress on aging, by increasing substrate stiffness in solid agar medium ofC. elegans. To our surprise, we found shockingly limited impact of growth ofC. eleganson stiffer substrates, including limited effects on cellular health, gene expression, organismal health, stress resilience, and longevity. Overall, our studies reveal that altering substrate stiffness of growth medium forC. eleganshave only mild impact on animal health and longevity; however, these impacts were not nominal and open up important considerations forC. elegansbiologists in standardizing agar medium choice for experimental assays.
Multiplexed in vivo imaging with fluorescence lifetime modulating tags
Authors: Hajji Lina El , Lam France , Avtodeeva Maria , Benaissa Hela , Rampon Christine , Volovitch Michel , Vriz Sophie , Gautier Arnaud
Published: April 2024

Fluorescence lifetime imaging opens new dimensions for highly multiplexed imaging in live cells and organisms using differences in fluorescence lifetime to distinguish spectrally identical fluorescent probes. Here, we describe a set of fluorescence-activating and absorption-shifting tags (FASTs) capable of modulating the fluorescence lifetime of embedded fluorogenic 4-hydroxybenzylidene rhodanine (HBR) derivatives. We show that changes in the FAST protein sequence can vary the local environment of the chromophore and lead to significant changes in fluorescence lifetime. These fluorescence lifetime modulating tags enabled multiplexed imaging of up to three targets in one spectral channel using a single HBR derivative in live cells and live zebrafish embryo. The combination of fluorescence lifetime multiplexing with spectral multiplexing allowed us to successfully image six targets in live cells, opening great prospects for multicolor fluorescence lifetime multiplexing.
Coupled spin-lattice dynamics from the tight-binding electronic structure
Authors: Cardias Ramon , Streib Simon , Lu Zhiwei , Pereiro Manuel , Bergman Anders , Sjöqvist Erik , Barreteau Cyrille , Delin Anna , Eriksson Olle , Thonig Danny
Published: April 2024

We developed a method which performs the coupled adiabatic spin and lattice dynamics based on the tight-binding electronic structure model, where the intrinsic magnetic field and ionic forces are calculated from the converged self-consistent electronic structure at every time step. By doing so, this method allows us to explore limits where the physics described by a parameterized spin-lattice Hamiltonian is no longer accurate. We demonstrate how the lattice dynamics is strongly influenced by the underlying magnetic configuration, where disorder is able to induce significant lattice distortions. The presented method requires significantly less computational resources than methods, such as time-dependent density functional theory (TD-DFT). Compared to parameterized Hamiltonian-based methods, it also describes more accurately the dynamics of the coupled spin and lattice degrees of freedom, which becomes important outside of the regime of small lattice and spin fluctuations.

Published by the American Physical Society
2024
Anisotropy of magnetized quark matter
Authors: Goswami Kangkan , Sahu Dushmanta , Dey Jayanta , Sahoo Raghunath , Stock Reinhard
Published: April 2024

Strong transient magnetic fields are generated in noncentral relativistic heavy-ion collisions. These fields induce anisotropy within the strongly interacting medium that, in principle, can affect the thermodynamic properties of the medium. We use the Polyakov loop extended Nambu Jona-Lasinio model to study the quark matter subjected to an external magnetic field at vanishing baryon chemical potential (μB). We have estimated the degree of anisotropy in the speed of sound and isothermal compressibility within the magnetized quark matter as a function of temperature (T) and magnetic field (). This study helps us to understand the extent of directionality generated in the initial stages of noncentral collisions while giving us useful information about the system.

Published by the American Physical Society
2024
Test of the vector portal with dark fermions in the charge-exchange reactions in the NA64 experiment at CERN SPS
Authors: Gninenko Sergei N. , Kirpichnikov Dmitry V. , Kuleshov Sergey , Lyubovitskij Valery E. , Zhevlakov Alexey S.
Published: April 2024

We consider an experiment to search for dark sector particles in invisible (or semi-invisible) decays of neutral mesons M0=π0, η, η′, ω, f2(1270), which produced the charge-exchange reactions π−+(A,Z)→M0+(A,Z−1);M0→ of high-energy pions (or kaons) on a nuclei target in the NA64 experiment at the CERN SPS. This reaction chain would lead to a striking signature of the signal event—the complete disappearance of the beam energy in the setup []. Using data obtained from the measurements at IHEP (Protvino) and Fermilab (Batavia) we show that the integral cross sections σ for the production of the M0  s slightly deviate from the phenomenological formula σ∼Z2/3, where Z is the nuclei charge. In particular, we present the formulas for the differential and integral cross sections that explicitly depend on the Mandelstam and Z variables. Derived formulas are used to predict the M0 yield as a function of beam energy for several target nuclei, and to estimate the projection sensitivity for the proposed search in the dark vector portal model. Sensitivity to different decay modes of M0s is explored.

Published by the American Physical Society
2024
Relevance of one-loop SMEFT matching in the 2HDM
Authors: Das Bakshi Supratim , Dawson Sally , Fontes Duarte , Homiller Samuel
Published: April 2024

The two-Higgs doublet model (2HDM) is a well understood alternative to the Standard Model of particle physics. If the new particles included in the 2HDM are at an energy scale much greater than the weak scale, the theory can be matched to the Standard Model effective field theory (SMEFT). We compute for the first time the complete one-loop matching at dimension-6. We compare its numerical impact with that of tree-level matching at dimension-8 by performing a global fit to single Higgs and precision electroweak measurements, and we emphasize the importance of comparing one-loop SMEFT results with corresponding one-loop results in the full 2HDM model. In the SMEFT, we consider the relative importance of both one-loop matching and the inclusion of renormalization group evolution. Our results demonstrate the necessity of studying the impact of various expansions to quantify the uncertainties of the SMEFT matching.

Published by the American Physical Society
2024
Uncertainty quantification of time-average quantities of chaotic systems using sensitivity-enhanced polynomial chaos expansion
Authors: Kantarakias Kyriakos D. , Papadakis George
Published: April 2024

We consider the effect of multiple stochastic parameters on the time-average quantities of chaotic systems. We employ the recently proposed sensitivity-enhanced generalized polynomial chaos expansion, se-gPC, to quantify efficiently this effect. se-gPC is an extension of gPC expansion, enriched with the sensitivity of the time-averaged quantities with respect to the stochastic variables. To compute these sensitivities, the adjoint of the shadowing operator is derived in the frequency domain. Coupling the adjoint operator with gPC provides an efficient uncertainty quantification algorithm, which, in its simplest form, has computational cost that is independent of the number of random variables. The method is applied to the Kuramoto-Sivashinsky equation and is found to produce results that match very well with Monte Carlo simulations. The efficiency of the proposed method significantly outperforms sparse-grid approaches, such as Smolyak quadrature. These properties make the method suitable for application to other dynamical systems with many stochastic parameters.

Published by the American Physical Society
2024
Amplitudes at Strong Coupling as Hyper-Kähler Scalars
Authors: Frost Hadleigh , Gürdoğan Ömer , Mason Lionel
Published: April 2024

Alday and Maldacena conjectured an equivalence between string amplitudes in AdS5×S5 and null polygonal Wilson loops in planar N=4 super-Yang-Mills (SYM) theory. At strong coupling this identifies SYM amplitudes with areas of minimal surfaces in anti–de Sitter space. For minimal surfaces in AdS3, we find that the nontrivial part of these amplitudes, the , satisfies an integrable system of nonlinear differential equations, and we give its Lax form. The result follows from a new perspective on “Y systems,” which defines a new psuedo-hyper-Kähler structure on the space of kinematic data, via a natural twistor space defined by the Y-system equations. The remainder function is the (pseudo-)Kähler scalar for this geometry. This connection to pseudo-hyper-Kähler geometry and its twistor theory provides a new ingredient for extending recent conjectures for nonperturbative amplitudes using structures arising at strong coupling.

Published by the American Physical Society
2024
Pedagogical relationships in short-term study abroad programmes: exploring the role of consumer identity in collaborative learning among Chinese students in the UK
Authors: Liu Yaqiao , Liang Yifei , Guo Yilan
Published: April 2024

Purpose

The marketisation of higher education fosters the notion of students as consumers, highlighting the shifting dynamics of student–teacher relationships. This paper aims to contribute to ongoing discussions about students as consumers and their involvement in pedagogical practices. We explore students’ experiences in short-term study abroad (SA) programmes that involve collaborative learning, examining how a consumerism-oriented approach affects students’ perceptions of their pedagogical identities and student–teacher pedagogical relationships.

Design/methodology/approach

A qualitative exploratory study was conducted to capture students’ rich and subjective perceptions and experiences. The data were gathered through semi-structured interviews with 15 Chinese undergraduate students who participated in a short-term SA programme at a UK university. Following data translation and transcription, a thematic analysis approach facilitated our exploration.

Findings

Chinese students engage in SA programmes as a strategic investment in personal growth and transformation, with their consumer-oriented identity fostering a mutually beneficial relationship with educators and group members. This consumer mindset appears to enhance active student engagement and, to some extent, create reciprocal student–teacher interactions through power sharing and collaborative involvement.

Originality/value

This study presents empirical data exploring the impact of consumer identity on the dynamics of student–teacher relationships in the SA context. It provides recommendations for implementing pedagogical approaches designed to mediate the influence of consumerism on student engagement, particularly in shaping collaborative student–teacher relationships. This study offers insights for future research on the effects of consumerism in higher education within cross-cultural contexts.
How travel live streaming servicescape affects users' travel intention: evidence from structural equation model and fuzzy-set qualitative comparative analysis
Authors: Ji Siyu , Pu Bo , Sang Wenyuan
Published: April 2024

Purpose

It is unclear what constitutes the tourism live streaming (TLS) servicescape and how it affects users' travel intention (TI). The study aims to explore the composition of the TLS servicescape, the influence mechanism of the TLS servicescape on users' TI and the formation of users' TI.

Design/methodology/approach

Based on stimulus organism response theory (SOR), we develop a mediation model to explore the influence of TLS servicescape on users' TI. This study collected data from 432 Chinese TLS users through an online questionnaire, and we used the structural equation model and the SPSS PROCESS macro to test the proposed model. In addition, we tested the variable relationships using fuzzy-set qualitative comparative analysis (fsQCA).

Findings

TLS servicescape is a second-order variable that can be categorized into physical element (PE), social element (SOE), symbolic element (SYE) and natural element (NE). TLS servicescape influences TI by affecting social presence (SP) and customer engagement (CE). The fsQCA reveals seven combinations of PE, SOE, SYE, NE, SP and CE that form a high TI for TLS users.

Originality/value

Using multiple data analysis methods, the study emphasizes the significance of the TLS servicescape for TLS. It explores how to evoke users' TI in TLS and provides a reference for TLS marketing.