bluuebunny/crossref_metadata_2025 huggingface dataset:
Human adipose-derived mesenchymal stromal cells improved wound healing in enterocutaneous fistulizing disease mouse model
Authors: Marsiano Noga , Levi Yeshurun , Schneider Peleg , Schouten Iftach , Nisim-Eliraz Einat , Yagel Simcha , Kong Kok-Fai , Lombardo Eleuterio , Shpigel Nahum Y
Published: November 2024

A significant complication of Crohn disease is the formation of perianal fistulas. While local application of human adipose tissue-derived mesenchymal stromal cells (AT-MSC INN Darvadstrocel, Takeda) is an approved therapy for this condition, challenges in studying human clinical tissue and the absence of a robust experimental model have hindered deeper understanding of the preclinical efficacy and mechanisms behind the therapy. We have developed a model that closely mimics the clinical scenario, using human gut tissue transplanted subcutaneously into SCID mice. In this model, enterocutaneous fistulas are reliably induced by combining imiquimod-induced psoriatic dermatitis above the transplant with systemic lipopolysaccharide (LPS), a major component of the bacterial cell wall. Similar to clinical observations, local application of AT-MSC significantly improved fistula wound healing and re-epithelialization. This model system enabled comprehensive tissue harvesting for histopathological analysis, spatial transcriptomics, and protein profiling. Our findings demonstrate that AT-MSC applied around the fistula wound survive for up to three weeks, migrating into the fistula tract and further into the inflamed human gut tissue. Within the fistula tract, AT-MSCs acquired immune-active properties, with increased expression of SOD2 and CCL2, and were associated with a substantial population of M2 macrophages. In contrast, AT-MSC located in healthy tissue near the fistula remained stationary, adopting a fibroblast-like phenotype within a collagen-rich extracellular matrix. These preclinical results support the safety and efficacy of AT-MSC for treating fistulizing gut disease. Furthermore, our data suggest that the inflamed fistula tract acts as a scaffold promoting AT-MSC activity and migration. Enhancing SOD2 and CCL2 expression through pre-activation or genetic modification may further improve the therapeutic potential of these cells.
Understanding How Biopolymers Found in Marine Ecosystems Impact the Efficacy of Bacteriophages against Bacteria
Authors: Rupareliya Rhea , Kwack Joyce , Quan Dylan , Kim Tay
Published: November 2024

Bacteriophages are abundant in Earth’s ecosystem and serve as valuable mediators in marine environments, regulating bacterial populations in oceans, hot springs, and salterns, among others. However, bacteriophages have high-specificity to their host, thus making it difficult to study bacteria-phage relationships. In this study, we observe whether naturally occurring biopolymers (coral mucin (from Stylophora pistillata), chitin, and sodium alginate) increase bacteriophage affinity to bacteria by recording the plaques formed throughout 15-minute time intervals. We use an isolatedE. colistrain and its corresponding T7 phage, as well as isolated bacteria and phage strains from a coral sample (labeled Stylophora pistillata or “Coral 1”). The research conducted plaque assays using minimal media solution to quantify phage-forming units (PFUs) using 2 bacterial forms, Coral 1 and E. coli and Mucin, Sodium Alginate, and Chitin as biopolymers. Our research found that the biopolymers had an effective impact on the generation of PFUs in our bacterial cultures for all samples. While we were unable to conduct future plaque assays, the information we have now is important to discovering ways to increase phage efficiency in marine environments to help maintain nutrient resource levels in such ecosystems.
Elucidating the Mechanism Underlying UBA7•UBE2L6 Disulfide Complex Formation
Authors: Chen Pei-Tzu , Yeh Jia-Yin , Weng Jui-Hsia , Wu Kuen-Phon
Published: November 2024

We elucidate cryo-EM structure and formation of the ubiquitin-associated bovine UBA7•UBE2L6 disulfide complex, shedding light on a highly specific and evolutionarily conserved mechanism governing ISG15 conjugation, a pivotal process in the immune response. UBA7 displays a unique capacity to recognize UBE2L6, distinct from this latter’s homolog UBE2L3, highlighting the intricacies of cellular regulation. Inter-species interactions of the resulting complex further underscore its significance. We characterize three crucial factors that influence UBA7•UBE2L6 disulfide complex formation: (1) strong binding affinity and specificity; (2) conformational differences in the catalytic cysteine capping loop (CCL); and (3) increased thiolate/thiol ratios at catalytic cysteines. Modification of any of these factors profoundly impacts complex activation and the ISG15 transfer cascade. This redox-sensitive complex implies a link between oxidative stress and regulation of the immune response, highlighting a potential therapeutic target for modulating immune reactions arising from infections and inflammatory conditions.
Stalling of the endometrial decidual reaction determines the recurrence risk of miscarriage
Authors: Muter Joanne , Kong Chow-Seng , Nebot Mireia Taus , Tryfonos Maria , Vrljicak Pavle , Brighton Paul J. , Dimakou Danai B. , Vickers Megan , Yoshihara Hiroyuki , Ott Sascha , Tan Bee K. , Bennett Phillip R. , Quenby Siobhan , Richter Alex , Van de Velde Hilde , Lucas Emma S. , Rawlings Thomas M. , Brosens Jan J.
Published: November 2024

In each menstrual cycle, progesterone acting on estrogen-primed endometrium elicits an inflammatory decidual reaction, rendering it poised for embryo implantation and transformation into the decidua of pregnancy. Here, we show that the sequential functions of the decidual reaction - implantation and decidualization - pivot on the time-sensitive loss of progesterone-resistant stromal cells that form a transient implantation niche and reciprocal expansion of progesterone-responsive pre-decidual cells. In parallel, proliferation and differentiation increase the abundance of immunotolerant uterine natural killer (uNK) cells. Examination of pre-pregnancy endometrial biopsies from 924 women revealed that the frequency of cycles culminating in a blunted or stalled decidual reaction closely aligns with the age-independent recurrence risk of miscarriage. Further, analysis of 632 biopsies obtained in different cycles from 316 women indicated that prior miscarriages disrupt intercycle endometrial homeostasis, an observation supported by modelling the impacts of prolonged decidual inflammation in three-dimensional endometrial assembloids. Although stalling of the decidual reaction is often accompanied by a poor expansion of immunotolerant uNK cells, miscarriages do not impact intercycle uNK cell dynamics. Our findings indicate that intrinsic uterine mechanisms hardwire the recurrence risk of miscarriage, underscoring the need for pre-pregnancy diagnostics and therapeutics.

One Sentence Summary

The frequency of menstrual cycles culminating in a suboptimal decidual reaction determines the recurrence risk of miscarriage.
SARS-CoV-2 infection enhancement by Amphotericin B: Implications for disease management
Authors: Nguyen Dung , Laidlaw Stephen M. , Dong Xiaofeng , Wand Matthew , Horton Amanda , Sutton Mark , Tree Julia , Milligan Rachel , Erdmann Maximilian , Matthews David , Davidson Andrew D. , Rahman Khondaker Miraz , Hiscox Julian A. , Carroll Miles
Published: November 2024

Severe coronavirus disease 2019 (COVID-19) patients who require hospitalisation are at high risk of invasive pulmonary mucormycosis. Amphotericin B (AmB), which is the first line therapy for invasive pulmonary mucormycosis, has been shown to promote or inhibit replication of a spectrum of viruses. In this study, we first predicted that AmB and Nystatin had strong interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins using in silico screening, indicative of drugs with potential therapeutic activity against this virus. Subsequently, we investigated the impact of AmB, Nystatin, Natamycin, Fluconazole and Caspofungin on SARS-CoV-2 infection and replicationin vitro. Results showed that AmB and Nystatin actually increased SARS-CoV-2 replication in Vero E6, Calu-3 and Huh7 cells. At optimal concentrations, AmB and Nystatin increase SARS-CoV-2 replication by up to 100-and 10-fold in Vero E6 and Calu-3 cells, respectively. The other antifungals tested had no impact on SARS-CoV-2 infectionin vitro. Drug kinetic studies indicate that AmB enhances SARS-CoV-2 infection by promoting viral entry into cells. Additionally, knockdown of genes encoding for interferon-induced transmembrane (IFITM) proteins 1, 2, and 3 suggests AmB enhances SARS-CoV-2 cell entry by overcoming the antiviral effect of the IFITM3 protein. This study further elucidates the role of IFITM3 in viral entry and highlights the potential dangers of treating COVID-19 patients, with invasive pulmonary mucormycosis, using AmB.

Importance

AmB and Nystatin are common treatments for fungal infections but were predicted to strongly interact with SARS-CoV-2 proteins, indicating their potential modulation or inhibition against the virus. However, our tests revealed that these antifungals, in fact, enhance SARS-CoV-2 infection by facilitating viral entry into cells. The magnitude of enhancement could be up to 10-or 100-fold depending on cell lines used. These findings indicate that AmB and Nystatin have the potential to enhance disease when given to patients infected with SARS-CoV-2 and therefore should not be used for treatment of fungal infections in active COVID-19 cases.
Axenisation of oleaginous microalgal cultures via anoxic photosensitisation.
Authors: Iyer Ajay , Monissen Matthias , Ma Qinge , Osborne Matthieu , Schaedig Eric , Modin Oskar , Halim Ronald
Published: November 2024

Growing interest in sustainable biofuel research has necessitated high quality axenic oleaginous microalgal strains. Unfortunately, most strains available in culture banks contain commensal microbes such as bacteria and the default decontamination method involves antibiotic treatment which has begun to exacerbate the emergence of antibiotic resistance. To overcome this problem, anoxic photosensitisation was investigated as an alternate approach. Four oleaginous microalgal species (Tetradesmus obliquus,Desmodesmus armatus,Chlorella vulgarisandNannochloropsis limnetica) were incubated in varying concentrations of Rose Bengal (0 μM, 1 μM, 3 μM and 9 μM) either in normal (oxic) or anoxic conditions, for 72 h under light (8.85 ± 0.40 W m-2 ) in a specially designed heterotrophic growth complex (HGC) medium, followed by 72 h in standard Bolds Basal Medium (BBM). Commonly used antibiotics-based protocol was used as the control method. Post treatment, cell numbers and percentage populations were counted with Flow cytometry, and viability was tested using standard plating methods using BBM and LB. Additionally, the contaminating microbes in the cultures were profiled using 16s rRNA sequencing. Anoxic conditions were able to significantly decrease bacterial content, albeit with an equally detrimental effect on the microalgal population. Although the responses differed between the microalgae, anoxic incubation along with Rose Bengal at 3 μM was able to completely decontaminateN. limneticaandC. vulgaris, whileD. armatusandT. obliquuscould be decontaminated with an additional streak-plating step. None of the cultures could be decontaminated using antibiotics treatment owing to the presence of gram-negative, multi-drug resistant bacteria such asS. maltophilia,M. foliorumandS. chilensis. These results suggest that decontamination of xenic microalgal cultures was largely due to anoxy, that was synergistically enhanced by Rose Bengal at a concentration of ≥3 μM.
Integrative cell bin segmentation on spatial transcriptomics by Voronoi
Authors: Lin Ming
Published: November 2024

Spatial transcriptomics is undergoing rapid advancements and iterations. It is a beneficial tool to significantly enhance our understanding of tissue organization and relationships between cells. Recent technological advancements have achieved subcellular resolution, providing much denser spot placement for downstream analysis. A key challenge for this following analysis is accurate cell segmentation and the assignment of spots to individual cells. The primary objective of this study was to evaluate the effectiveness of a new cell segmentation approach based on subcellular level spatial transcriptomic data by confirming nuclei positions and using Voronoi diagrams, compared to direct clustering with cellbin data. Our findings demonstrate that the Voronoi method not only outperforms traditional methods in providing clearer boundaries and better separation of cell types but also excels in preserving the most transcripts, addressing the issue of low capture efficiency. This integrative methodology presents a substantial advancement in spatial transcriptomics, offering improved cell type classification and spatial pattern recognition. All codes in the paper are available at the GitHub repository: https://github.com/Charlottttttte/Cell_Segmentation_Voronoi
Dystrophininteracts withMsp300to Regulate Myonuclear Positioning and Microtubule Organization
Authors: Padilla Jorel R. , Qiu Yunshu , Aleck Grace , Ferreria Lillie , Wu Sharon , Gibbons William , Mandigo Torrey , Folker Eric S.
Published: November 2024

DuringDrosophilamyognesis, myonuclei are actively moved during embryogenesis, and their spacing is maintained through an anchoring mechanism in the fully differentiated myofiber. While we have identified microtubule associated proteins, motors, and nuclear envelope proteins that regulate myonuclear spacing, the developmental time during which each gene functions has not been tested. Here we have identified aDystrophinas required only for the maintenance of myonuclear spacing. Furthermore, we demonstrate thatDystrophingenetically interacts with the KASH-domain proteinMsp300to maintain myonuclear spacing. Mechanistically, bothDystrophinandMsp300regulate microtubule organization. Specifically, in animals with disrupted expression of bothDystrophinandMsp300, microtubule colocalization with sarcomeres is reduced. Taken altogether, these data indicate that the peripheral membrane protein Dystrophin, and the outer nuclear membrane protein Msp300, together regulate the organization of the microtubule network which then acts as an anchor to restrict myonuclear movement in contractile myofibers. These data are consistent with growing evidence that myonuclear movement and myonuclear spacing are critical to muscle development, muscle function, and muscle repair and provide a mechanism to connect disparate muscle diseases.

Summary Statement

Here we show thatDystrophinis required to maintain the spacing of nuclei in differentiated myofibers. Furthermore,Dystrophinachieves this function via a genetic interaction withMsp300which regulates microtubule organization.
From aerial drone to QTL: Leveraging next-generation phenotyping to reveal the genetics of color and height in field-grownLactuca sativa
Authors: Dijkhuizen Rens , van Eijnatten Abraham L. , Mehrem Sarah L. , van den Bergh Esther , van Lieshout Jelmer , Spaninks Kiki , Kaandorp Steven , Offringa Remko , Proveniers Marcel , van den Ackerveken Guido , Snoek Basten L.
Published: November 2024

In recent years, the automation of genotyping has significantly enhanced the efficiency of genome-wide association studies. As a result, phenotyping rather than genotyping is now the rate-limiting step, especially in field experiments. For this reason, there is a strong need to further automate in-field phenotyping. Here we present a GWAS study on 194 field-grown accessions of lettuce (Lactuca sativa). These accessions were non-destructively phenotyped at two time points 15 days apart using an unmanned aerial vehicle. Our high throughput phenotyping approach integrates an RGB camera, a multispectral camera to measure the reflectance at 5 wavelengths (blue, green, red, red edge, near-infrared), and precise height estimation. We used the mean and other descriptives such as median, quantiles, minimum and maximum to quantify different aspects of color and height variation in lettuce from the drone images. Using this approach, we confirm several previously described QTLs, now in populations grown under field conditions, and identify several new QTLs for plant-height and color.
Alterations and Imbalance of Dorsal and Ventral Mossy Cells in a Mouse Model of Epilepsy
Authors: Huang Christine S. , Houser Carolyn R.
Published: November 2024

Mossy cells (MCs) in the hilus of the dentate gyrus (DG) are important for regulating activity of dentate granule cells and are particularly vulnerable to excitotoxic damage in epilepsy. Recent studies have demonstrated that MCs in the dorsal and ventral DG differ in the patterns of their axonal projections and neurochemical identities. Such differences raised questions about the vulnerability and plasticity of dorsal and ventral MCs in epilepsy and led to this study using a mouse pilocarpine model of epilepsy. Dorsal MCs were labeled by transfection of Cre-dependent eYFP in the dorsal DG ofCalcrl-Cremice that express Cre selectively in MCs. Ventral MCs were labeled with calretinin (CR), which labels ventral but not dorsal MCs. At 6-8 weeks after pilocarpine treatment, MC loss and axonal projections of remaining MCs were studied in control and pilocarpine-treated mice with confocal microscopy. Dorsal MCs were severely depleted, but many ventral MCs remained, and quantitative analysis of GluA2-labeled hilar neurons demonstrated a proportionally greater loss of dorsal MCs (77.6% loss) than ventral MCs (21.5% loss). Loss of dorsal MCs led to a marked reduction in the dorsal commissural pathway, while the remaining ventral MCs maintained a prominent, though reduced, ventral to dorsal association pathway. In pilocarpine-treated animals, a plexus of CR-labeled fibers extended into the middle molecular layer, suggesting axonal sprouting of remaining ventral MCs, with some of these fibers in contact with parvalbumin-labeled dendrites. These findings suggest that dorsal and ventral MCs differ in their vulnerability to seizure-induced damage in this animal model, creating an imbalance between the dorsal and ventral MC pathways that could alter the excitatory/inhibitory balance within the dentate gyrus.
Organ structure and bacterial microbiogeography in a reproductive organ of the Hawaiian bobtail squid reveal dimensions of a defensive symbiosis
Authors: Kamp Derrick L. , Kerwin Allison H. , McAnulty Sarah J. , Nyholm Spencer V.
Published: November 2024

Many plants and animals house symbiotic microorganisms in specialized tissues or organs. Here, we used multidimensionalin-situimaging techniques to illuminate how host organ structure and bacterial microbiogeography contribute to the symbiotic function of an organ in the Hawaiian bobtail squid,Euprymna scolopes. Along with the well-studied light organ, femaleE. scolopesharbor a community of bacteria in the accessory nidamental gland (ANG). The ANG is a dense network of epithelium-lined tubules, some of which are dominated by a single bacterial taxon. These bacteria are deposited into squid eggs, where they defend the developing embryos from harmful biofouling. This study used a combination of imaging techniques to visualize different dimensions of the ANG and its bacterial communities. Imaging entire organs with light sheet microscopy revealed that the ANG is a composite tissue of individual, non-intersecting tubules that each harbor their own bacterial population. The organ is bisected, with tubules converging towards two points in the organ. At these points, tubules empty in a space where bacteria can mix with squid jelly to be deposited onto eggs. Observations of bacterial populations correlated bacterial taxa with cell morphology and show that tubule populations varied: some contained populations of mixed phyla while some tubules contained only one genus of bacteria. Together, these data shed light on how bacterial populations interact within the ANG and how the host uses physical structure to maintain and employ a symbiotic bacterial population in a defensive context.

IMPORTANCE

Sequence-based microbiome studies have revealed much about how hosts interact with communities of symbiotic microbiota, but often lack a spatial understanding of how microbes relate with each other and the host in which they reside. This study used a combination of microscopy techniques to reveal how the structure of a symbiotic organ in the female bobtail squid,Euprymna scolopeshouses diverse, beneficial bacterial populations and deploys them for egg defense. These findings suggest that spatial partitioning may be key to harboring a diverse population of antimicrobial-producing bacteria and establish a foundation for further understanding how host structures mediate symbiotic interactions.
Development of the Left Arcuate Fasciculus is Linked to Learning Gains in Reading, but not Math
Authors: Roy Ethan , Harriott Emily M. , Nguyen Tin Q. , Richie-Halford Adam , Rokem Ariel , Cutting Laurie E. , Yeatman Jason D.
Published: November 2024

Past studies leveraging cross-sectional data have raised questions surrounding the relationship between diffusion properties of the white matter and academic skills. Some studies have suggested that white matter properties serve as static predictors of academic skills, whereas other studies have observed no such relationship. On the other hand, longitudinal studies have suggested that within-individual changes in the white matter are linked to learning gains over time. In the present study, we look to replicate and extend the previous longitudinal results linking longitudinal changes in the white matter properties of the left arcuate fasciculus to individual differences in reading development. To do so, we analyzed diffusion MRI data, along with reading and mathematics scores in a longitudinal sample of 340 students as they progressed from 1st grade into 4th grade. Longitudinal growth models revealed that year-to-year within-individual changes in reading scores, but not math, were related to the development of the left arcuate fasciculus. These findings provide further evidence linking the dynamics of white matter development and learning in a unique sample and highlight the importance of longitudinal designs.
Systematic review and meta-analysis of bulk RNAseq studies in human Alzheimer’s disease brain tissue
Authors: Heberle Bernardo Aguzzoli , Fox Kristin L. , Libermann Lucas Lobraico , Xavier Sophia Ronchetti Martins , Dallarosa Guilherme Tarnowski , Santos Rhaná Carolina , Fardo David W. , Viola Thiago Wendt , Ebbert Mark T. W.
Published: November 2024

Objective

To systematically review and meta-analyze bulk RNA sequencing studies comparing Alzheimer’s disease (AD) patients with controls in human brain tissue, assessing study quality and identifying key genes and pathways.

Methods

We searched PubMed, Web of Science, and Scopus on September 23, 2023, for studies using bulk RNAseq on primary human brain tissue from AD patients and controls. Excluded were non-primary tissue, re-analyses without new data, limited RNA types and gene panels. Quality was assessed with a 10-category tool. Meta-analysis used high-quality datasets.

Results

From 3,266 records, 24 studies met criteria. Meta-analysis found 571 differentially expressed genes (DEGs) in temporal lobe and 189 in frontal lobe; overlapping pathways included "Tube morphogenesis" and "Neuroactive ligand-receptor interaction."

Limitations

Study heterogeneity and limited data tables constrained the review.

Conclusions

Rigorous methods are vital in AD transcriptomic studies. Findings enhance understanding of transcriptomic changes, aiding biomarker and therapeutic development.

Registration

PROSPERO (CRD42023466522).
Trial-by-trial learning of successor representations in human behavior
Authors: Kahn Ari E. , Bassett Dani S. , Daw Nathaniel D.
Published: November 2024

Decisions in humans and other organisms depend, in part, on learning and using models that capture the statistical structure of the world, including the long-run expected outcomes of our actions. One prominent approach to forecasting such long-run outcomes is the successor representation (SR), which predicts future states aggregated over multiple timesteps. Although much behavioral and neural evidence suggests that people and animals use such a representation, it remains unknown how they acquire it. It has frequently been assumed to be learned by temporal difference bootstrapping (SR-TD(0)), but this assumption has largely not been empirically tested or compared to alternatives including eligibility traces (SR-TD(λ> 0)). Here we address this gap by leveraging trial-by-trial reaction times in graph sequence learning tasks, which are favorable for studying learning dynamics because the long horizons in these studies differentiate the transient update dynamics of different learning rules. We examined the behavior of SR-TD(λ) on a probabilistic graph learning task alongside a number of alternatives, and found that behavior was best explained by a hybrid model which learned via SR-TD(λ) alongside an additional zeroth-order predictive model. The relatively largeλwe estimate indicates a predominant role of eligibility trace mechanisms over the bootstrap-based chaining typically assumed. Our results provide insight into how humans learn predictive representations, and demonstrate that people simultaneously learn the SR alongside lower-order predictions.
From Quantitative Trait Loci towards Mechanisms: Linkage Integration Hypothesis Testing (LIgHT) Sheds Light on the Mechanisms of Genetically Modulated Stress Tolerance
Authors: Hoh Donghee , Osei-Bonsu Isaac , Kanazawa Atsuko , Fisher Nicholas , Cruz Jeffrey , Roberts Philip A. , Huynh Bao-Lam , Kramer David M.
Published: November 2024

The goal of this work is to assess the mechanistic bases of natural genetic variations in plant responses of photosynthesis to stress. To achieve this goal, we devised the Linkage Integration Hypothesis Testing (LIgHT) approach, comparing chromosomal locations of quantitative trait loci (QTL) for multiple phenotypes to distinguish between hypothetical mechanisms. As a use case, we explored genetic variations in photosynthesis-related processes under chilling stress in recombinant inbred lines of cowpea (Vigna unguiculataL. Walp.). We focused on photosynthesis-related parameters measurable in high throughput and indicative of proposed chilling responses, including the states of photosystems I (PSI) and II (PSII), photoprotective nonphotochemical quenching, PSII photodamage, and nyctinastic leaf movements (NLM). The patterns of QTL linkages indicated chilling stress tolerance is genetically controlled by avoiding PSII photodamage rather than PSI damage or NLM. This model was validated in a separate experiment measuring the rates of PSII photodamage and repair. Additional linkages suggest that chilling-induced damage to PSII is controlled by the thylakoid proton motive force and redox state of PSII. This regulation is modulated by thylakoid fatty acid composition, as suggested in Hoh et al., 2022. We propose the LIgHT approach can be broadly applied to test mechanisms underlying genetic variations.

Highlight

This work Introduces the Linkage Integration Hypothesis Testing(LIgHT) approach for mechanistic studies of natural variations, identifying photosynthetic regulatory mechanisms underlying natural variations to abiotic stresses by applying this approach.
OsMORF protein selectively promotes the dual-localized RNA editing factor OsPGL1 binding to its target RNA
Authors: Xiao Haijun , Wang Qiuren , Lin Yingru , Zhong Yang , Ma Chilin , Lin Honghui
Published: November 2024

Post-transcriptional RNA editing plays a key regulatory role and serves as a genetic information proofreading mechanism. In flowering plants, RNA editing typically involves the removal of amino groups from cytidine to produce uridine in both plastids and mitochondria. In our previous work, we identified OsPGL1 as a rare organelle editing factor that regulates both mitochondrial and chloroplast RNA in rice. This protein mediates RNA editing and is associated with several OsMORFs. We speculated that they may form editing complex to regulate editing events, but we are still unclear about the detailed mechanism between OsMORF proteins and OsPGL1, as well as their roles in target RNA recognition and binding. In this study, we found that three OsMORFs can significantly promote the binding of OsPGL1 to target RNA in vitro. Notably, OsMORF8 can promote OsPGL1 to form a homologous dimer, thereby enhancing RNA binding to a greater extent. The E and DYW motifs do not affect the role of MORF proteins in RNA editing events, ruling out the potential influence of these two special motifs. In addition, we predicted a series of supercomplex structures of OsPGL1, the OsPGL1-RNA ligand complex, the OsPGL1-OsMORF2-OsMORF8-OsMORF9 complex, and the OsPGL1-OsMORF2-OsMORF8-OsMORF9-RNA complex. We determined that the conformational changes and newly added positively charged surface caused by OsMORF on OsPGL1 are the main reasons for MORF to promote the binding of OsPGL1 to RNA. Based on some new discoveries, we have expanded the RNA editing complex model, which greatly enhances our understanding of plant RNA editing complexes.

Short summary

PPRs and MORFs are two kinds of RNA editing factors, both can mediate organelle RNA editing, the difference between them is that PPR can directly bind target RNA, MORF does not directly bind RNA, but can independently or assist PPR in performing RNA editing. Function of MORF protein in post-transcriptional processing is not clear, our study verifies the function of MORFs in the process of PPR binding RNA through molecular biology. We also analyzed the interaction network between PPR-MORF-RNA from the perspective of structural biology.
MdAGG apple lectins in Fire Blight resistance: CRISPR/Cas9 validation and their potential for intragenesis approaches.
Authors: Bodelot Antoine , Dousset Nicolas , Ravon Elisa , Heintz Christelle , Brisset Marie-Noelle , Degrave Alexandre , VERGNE Emilie
Published: November 2024

Fire blight, caused by the bacterium Erwinia amylovora, represents a significant threat to apple (Malus domestica) production. Currently, only a limited number of effective sources of resistance to E. amylovora have been identified. To diversify these sources, we focused on a multigene family encoding amaranthin-like lectins, which are highly upregulated following chemical elicitation by acibenzolar-S-methyl (ASM). These lectins are believed to contribute to downstream defense by promoting bacterial aggregation, which led to their designation as M. domestica agglutinins (MdAGG). When loss-of-function editions were introduced into MdAGG genes, the plant's ability to mount a fully effective defense response against fire blight upon ASM treatment was compromised, confirming the role of MdAGGs in fire blight resistance. Next, we coupled the pPPO16 promoter, endogenous to apple and known to be rapidly induced during E. amylovora infection, with the coding sequence of MdAGG10 to create apple lines with fire blight-inducible MdAGG10 expression. Early MdAGG10 expression in these lines significantly improved resistance to fire blight, and an additional ASM treatment further enhanced this resistance. In summary, we conclude that MdAGGs act as defense genes whose timely expression can provide effective resistance against E. amylovora.
Investigating the Impact of Habitual Sleep Quality on Episodic Memory Performance: An EEG-Based Representational Similarity Analysis
Authors: Seraji Masoud , Mirjalili Soroush , Duarte Audrey , Calhoun Vince D
Published: November 2024

Sleep is crucial for episodic memory consolidation, yet the impact of habitual sleep quality on memory performance remains underexplored. This study investigates the relationship between sleep quality and episodic memory retrieval using EEG-based representational similarity analysis (RSA). Thirty-six participants wore wrist accelerometers for one week to capture habitual sleep patterns, including total sleep time and restlessness. Memory performance was assessed through a paired associate learning task, with EEG data recorded during encoding and retrieval phases. RSA was applied to EEG oscillatory power across time-frequency windows to examine the neural similarity between encoding and retrieval. The results showed both positive and negative correlations between sleep metric and memory performance, with sleep restlessness being linked to both increases and decreases in neural similarity across specific clusters. These findings emphasize the important role of sleep quality in shaping the neural processes underlying episodic memory retrieval, indicating a strong connection between sleep patterns and memory function.
Parametrically controlled microwave-photonic interface for the fluxonium
Authors: Nie Ke , Bista Aayam , Chow Kaicheung , Pfaff Wolfgang , Kou Angela
Published: November 2024

Converting quantum information from stationary qubits to traveling photons enables both fast qubit initialization and efficient generation of flying qubits for redistribution of quantum information. This conversion can be performed using cavity-sideband transitions. In the fluxonium, however, direct cavity-sideband transitions are forbidden due to parity symmetry. Here we circumvent this parity selection rule by using a three-wave mixing element to couple the fluxonium to a resonator. We experimentally demonstrate a scheme for interfacing the fluxonium with traveling photons through microwave-induced parametric conversion. We perform fast reset on the fluxonium qubit, initializing it with >95% ground-state population. We then implement controlled release and temporal shaping of a flying photon, useful for quantum state transfer and remote entanglement. The simplicity and flexibility of our demonstrated scheme enables fluxonium-based remote entanglement architectures.

Published by the American Physical Society
2024
Quantitative loss analysis of opaque perovskite solar cells using transient and steady-state characterization
Authors: Cudo Katarzyna , Ollearo Riccardo , Gelinck Gerwin H. , Galagan Yulia , Glowienka Damian
Published: November 2024

Perovskite solar cells have emerged as a promising technology in the field of photovoltaics, owing to their notable advancements in power-conversion efficiency. Recent investigations have revealed a crucial dependency of efficiency on the source of bromide within the perovskite absorption layer. To elucidate the underlying nature of traps within these solar cells, a comprehensive series of measurements was conducted under varying light intensities. Subsequently, employing an electrodynamic theoretical model, the intrinsic processes inherent to caesium and lead-based perovskite solar cells with different bromide sources were analyzed. The study reveals significant differences in transient photocurrent measurements and photocurrent-voltage characteristics among perovskites originating from different bromide sources, measured under different light intensities. Leveraging theoretical analyses on the picosecond scale, the recombination mechanism of crystal defects was meticulously described revealing the pronounced influence of capture rates on electron-hole recombination dynamics. Furthermore, the investigation substantiated the presence of a band-bending phenomenon at the interface between the hole transport layer (HTL) and perovskite, elucidating the observed transient photocurrent phenomena. The findings significantly advance the understanding of the mechanisms underlying perovskite solar cells, offering valuable insights into their performance and paving the way for enhanced efficiency and stability in future device design and optimization.

Published by the American Physical Society
2024
Hard-scattering approach to strongly hindered electric dipole transitions between heavy quarkonia
Authors: Jia Cai-Ping , Jia Yu , Lu Junliang , Mo Zhewen , Zhang Jia-Yue
Published: November 2024

The conventional wisdom in dealing with electromagnetic transition between heavy quarkonia is the multipole expansion, when the emitted photon has a typical energy of order quarkonium binding energy. Nevertheless, in the case when the energy carried by the photon is of order typical heavy quark momentum, the multipole expansion doctrine is expected to break down. In this work, we apply the “hard-scattering” approach originally developed to tackle the strongly hindered magnetic dipole (M1) transition [Y. Jia , ] to the strongly hindered electric dipole (E1) transition between heavy quarkonia. We derive the factorization formula for the strongly hindered E1 transition rates at the lowest order in velocity and αs in the context of the nonrelativistic QCD, and conduct a detailed numerical comparison with the standard predictions for various bottomonia and charmonia E1 transition processes.

Published by the American Physical Society
2024
Timelike meson form factors beyond the elastic region from lattice QCD
Authors: Ortega-Gama Felipe G. , Dudek Jozef J. , Edwards Robert G. ,   for the Hadron Spectrum Collaboration
Published: November 2024

We present a calculation of the vector-isovector timelike form factors of the pion and the kaon using lattice quantum chromodynamics. We calculate two-point correlation functions with mπ∼280  MeV, extracting both the finite-volume spectrum and matrix elements for these states created from the vacuum by a vector current. After determining the coupled-channel ππ,KK¯ scattering amplitudes, we perform the necessary correction for the significant finite-volume effects present in the current matrix elements, leading to the timelike form factors. We find these to be dominated by the presence of the ρ resonance, and we extract its decay constant by an analytic continuation of the amplitudes to the resonance pole. In addition, the spacelike pion form factor is determined on the same lattice configurations, and a dispersive parametrization is used to simultaneously describe the spacelike and elastic timelike regions.

Published by the American Physical Society
2024
Electrical conductivity of hot relativistic plasma in a strong magnetic field
Authors: Ghosh Ritesh , Shovkovy Igor A.
Published: November 2024

We employ first-principles quantum field theoretical methods to investigate the longitudinal and transverse electrical conductivities of a strongly magnetized hot quantum electrodynamics (QED) plasma at the leading order in coupling. The analysis employs the fermion damping rate in the Landau-level representation, calculated with full kinematics and exact amplitudes of one-to-two and two-to-one QED processes. In the relativistic regime, both conductivities exhibit an approximate scaling behavior described by σ∥,⊥=Tσ˜∥,⊥, where σ˜∥,⊥ are functions of the dimensionless ratio |eB|/T2 (with

T

denoting temperature and B magnetic field strength). We argue that the mechanisms for the transverse and longitudinal conductivities differ significantly, leading to a strong suppression of the former in comparison to the latter.

Published by the American Physical Society
2024
Strategies for Enhancing Spin-Shuttling Fidelities in
Si
/
Si
Ge
Quantum Wells with Random-Alloy Disorder
Authors: Losert Merritt P. , Oberländer Max , Teske Julian D. , Volmer Mats , Schreiber Lars R. , Bluhm Hendrik , Coppersmith S.N. , Friesen Mark
Published: November 2024

Coherent coupling between distant qubits is needed for many scalable quantum computing schemes. In quantum dot systems, one proposal for long-distance coupling is to coherently transfer electron spins across a chip in a moving dot potential. Here, we use simulations to study challenges for spin shuttling in Si/SiGe heterostructures caused by the valley degree of freedom. We show that for devices with valley splitting dominated by alloy disorder, one can expect to encounter pockets of low valley splitting, given a long-enough shuttling path. At such locations, intervalley tunneling leads to dephasing of the spin wave function, substantially reducing the shuttling fidelity. We show how to mitigate this problem by modifying the heterostructure composition, or by varying the vertical electric field, the shuttling velocity, the shape and size of the dot, or the shuttling path. We further show that combinations of these strategies can reduce the shuttling infidelity by several orders of magnitude, putting shuttling fidelities sufficient for error correction within reach.

Published by the American Physical Society
2024
Exploiting Friedel pairs to interpret scanning 3DXRD data from complex geological materials
Authors: Jacob Jean-Baptiste , Wright Jonathan , Cordonnier Benoît , Renard François
Published: November 2024

The present study introduces a processing strategy for synchrotron scanning 3D X-ray diffraction (s3DXRD) data, aimed at addressing the challenges posed by large, highly deformed, polyphase materials such as crystalline rocks. Leveraging symmetric Bragg reflections known as Friedel pairs, our method enables diffraction events to be precisely located within the sample volume. This method allows for fitting the phase, crystal structure and unit-cell parameters at the intra-grain scale on a voxel grid. The processing workflow incorporates several new modules, designed to (i) efficiently match Friedel pairs in large s3DXRD datasets containing up to 108 diffraction peaks; (ii) assign phases to each pixel or voxel, resolving potential ambiguities arising from overlap in scattering angles between different crystallographic phases; and (iii) fit the crystal orientation and unit cell locally on a point-by-point basis. We demonstrate the effectiveness of our technique on fractured granite samples, highlighting the ability of the method to characterize complex geological materials and show their internal structure and mineral composition. Additionally, we include the characterization of a metal gasket made of a commercial aluminium alloy, which surrounded the granite sample during experiments. The results show the effectiveness of the technique in recovering information about the internal texture and residual strain of materials that have undergone high levels of plastic deformation.
Crystal structure of AlPCl8
Authors: Seo Hyeonjin , Shin Seungyong , Hong Seung-Tae
Published: November 2024

The crystal structure of aluminium phosphorus chloride (systematic name: phosphorus tetrachloride tetrachloridoaluminate), (PCl4)[AlCl4] or AlPCl8, was determined and refined using single-crystal X-ray diffraction data. The compound crystallizes in the orthorhombic space group Pbcm. The asymmetric unit comprises one Al atom, one P atom, and five Cl atoms. The structure is characterized by isolated AlCl4 and PCl4 tetrahedra, isostructural with FePCl8 and GaPCl8.
Fear more or fear no more: examining the emotional and behavioral consequences of FOMO and JOMO
Authors: Tan Poh Ling , Tjiptono Fandy , Tan Ser Zian
Published: November 2024

Purpose

Fear of Missing Out (FOMO) is characterized by anxiety over potentially missed experiences, while Joy of Missing Out (JOMO) embraces contentment in opting out of social engagements. Drawing on cognitive appraisal theory, this study aims to investigate how FOMO and JOMO appeals influence pride, gratitude and purchase intention while considering the impacts of age and social comparison orientation.

Design/methodology/approach

Three experiments examined the impact of FOMO (Study 1), JOMO (Study 2), and comparison between FOMO and JOMO (Study 3) on pride, gratitude and purchase intention. Moderated-moderated mediation models were also tested to assess the roles of age and social comparison orientation (SCO).

Findings

FOMO appeals tend to boost feelings of pride, while JOMO appeals promote gratitude, both of which result in a higher likelihood of making a purchase. The effect of FOMO appeal on purchase intention via pride is stronger among younger consumers with high SCO. In contrast, the impact of JOMO appeal on purchase intention via gratitude is higher among older consumers with low SCO.

Practical implications

Understanding the nuances of different advertising appeals and their effect on consumer emotions (e.g. pride and gratitude) and purchase intention can inform marketers and advertising agencies in crafting more targeted and effective advertising campaigns that resonate with diverse consumer segments.

Originality/value

This study adds to the consumer emotion literature and generational research by emphasizing the role of emotions and age in shaping consumer responses to advertisements.
The shape of careers in the future workplace: extreme scenarios and their prospect impact
Authors: Rabenu Edna , Baruch Yehuda
Published: November 2024

Purpose

The purpose of this study is to discuss the way future workplaces may operate and how careers will be developed under possible extreme scenarios.

Design/methodology/approach

We propose a thought-provoking conceptual discussion of the challenges for people’s careers under such scenarios.

Findings

We identified four such possible extreme scenarios and elaborated on the theoretical knowledge regarding the essence of each scenario. We discussed their impact on future workplaces in general and on careers in particular. These are (1) highly developed artificial intelligence and other cyber entities; (2) massive immigration due to wars, refugees and other forces; (3) widescale de-globalization; and (4) major global recession.

Originality/value

Employing the career ecosystem and sustainability theories, we identify possible outcomes and implications for theory as well as practice of managing careers under these extreme scenarios. This offers a novel perspective for individuals, organizations and policymakers at national and global levels.
Performance of repair pre-damaged RC columns using steel straps tensioning techniques (SSTT) confinement: experimental data and modelling
Authors: Mohd Apandi Nazirah , Ahmad Zailani Warid Wazien , Chin Chee-Loong , Ma Chau-Khun
Published: November 2024

Purpose

A model that extends study parameters to predict repaired column behaviour is efficient. Three-dimensional nonlinear finite element models were created in ABAQUS to simulate steel strap confinement with inclusion of pre-damaged levels.

Design/methodology/approach

Experimental and analytical studies demonstrate that restored reinforced concrete (RC) columns usually crush at mid-height under axial compressions. Numerical models verified RC column load-deformation. Although some specimens have considerable column stiffness differences, a numerical model based on statistical analysis matches experimental test results.

Findings

It shows that, finite element model exhibited a tendency to overestimate the stiffness of the columns, with an average absolute error (AAE) of 23.1%. The validation results indicate that the AAE values for strength and ductility were 15.1% and 12.3%. It has been demonstrated that the combination of strength and ductility is capable of yielding predictions with an error rate of approximately 20%. A parametric study focused on finite element model-predicted load bearing capacity reduction.

Originality/value

A numerical analysis employing finite element modelling has been formulated to investigate the behaviour of confined columns. The model underwent validation through comparison with the experimental results. The validated model is utilised to perform additional parametric investigations on the confined column.