bluuebunny/crossref_metadata_2025 huggingface dataset:
High Dimensional Proteomic Multiplex Imaging of the Central Nervous System Using the COMET™ System
Authors: Najem Hinda , Pacheco Sebastian , Turunen Jillyn , Tripathi Shashwat , Steffens Alicia , McCortney Kathleen , Walshon Jordain , Chandler James , Stupp Roger , Lesniak Maciej S. , Horbinski Craig M. , Winkowski Dan , Kowal Joanna , Burks Jared K. , Heimberger Amy B.
Published: February 2025

Sequential multiplex methodologies such as Akoya CODEX, Miltenyi MACSima, Rarecyte Orion, and others require modification of the antibodies by conjugation to an oligo or a specific fluorophore which means the use of off-the-shelf reagents is not possible. Modifications of these antibodies are typically performed via reduction chemistry and thus require verification and validation post-modification. Fixed panels are therefore developed due to various limitations including spectral overlap that creates spectral unmixing issues, steric hindrance, harsh antibody removal, and tissue degradation throughout the labeling. As such, a complex interrogation evaluating multiple study hypotheses and/or endpoints requires the development of sequential panels, reconstruction, and realignment of the tissue that necessitate a z-stack strategy. Standardized antibody panels are typically fixed and require substantial validation efforts to modify a single target and thus do not evolve with the pace of research interests. To increase the throughput of profiling cells within the human central nervous system (CNS), we developed and validated a CNS-specific library with an associated analysis platform using the newly developed Lunaphore COMETTMplatform. The COMETTMis an automated staining/imaging instrument integrating a reagent deck for staining buffers and off-the-shelf label-free primary antibodies and fluorophore-labeled secondary antibodies, which feed into a circular plate holding up to 4 slides that are automatically imaged in microscope-operated control software. For this study, standard formalin fixed paraffin embedded histology slides are used. However, the COMET is capable of imaging fresh-frozen samples using specialized settings. Our methodologies address an unmet need in the neuroscience field while leveraging prior developmental efforts in the domain of immunology spatial profiling. Cataloging and validating a large series of antibodies on the COMET™ along with developing CNS autofluorescence management strategies while optimizing standard operating procedures have allowed for the visualization at the subcellular level. Forty analytes can be used to analyze one specimen which has clinical utility in cases in which the CNS can only be sampled by biopsy. CNS biopsies, depending on the anatomical location, can have limited available volume to a degree that requires prioritization and restriction to select analysis. In-depth bioinformatic imaging analysis can be done using standard bioinformatic tools and software such as Visiopharm®. These results establish a general framework for imaging and quantifying cell populations and networks within the CNS while providing the scientific community with standard operating procedures.
Polymer-assisted assembly of giant vesicles in physiological solutions
Authors: Cooper Alexis , Vijayananda Vignesha , Pazzi Joseph , Subramaniam Anand Bala
Published: February 2025

Obtaining high yields of giant unilamellar vesicles (GUVs) in solutions of physiological ionic strengths is one of the major challenges in the use of GUVs in cell-mimicking applications. This is because the free energy cost for forming GUVs increases in solutions of high ionic strengths due increased adhesion between membranes. Gel coated glass slides used in gel-assisted assembly shows promise in assembling GUVs in salty solutions. However, only limited types of gel forming polymers are known to be effective. Extensive localized micrometer-scale dewetting of the polymer film from the substrate upon hydration results in low yields of GUVs from commonly used polymers such as agarose and polyvinyl alcohol. Furthermore, for polymers that show limited dewetting, increased temperatures, required for assembling GUVs composed of lipids with high transition temperatures, results in significant dewetting which limits the temperature at which assembly can occur. Here, we show that nanocellulose paper provides a facile means of suppressing dewetting of water-soluble polymers in the gel-assisted hydration method. With dewetting is suppressed, only low amounts of polymers are necessary to obtain high yields of GUVs. We show the significant extension of the temperature range of GUV assembly using paper supported gel-assisted hydration by assembling GUVs at high yield with raft forming mixtures that require assembly at 45 °C. Moreover, we demonstrate that using nanocellulose paper as a substrate allows the assembly of GUVs from novel polymer classes such as biocompatible hyaluronic acid and dextran. We show the usage of scaled-down nanocellulose paper for the encapsulation of complex reactions in GUVs and the large scale assembly of GUVs for prototissue applications. Using nanocellulose paper as a substrate for polymer-assisted assembly of giant vesicles opens new avenues for using GUVs for biomedical and biophysical applications.
Proteome analysis of daily urine samples of pregnant rats unveils developmental processes of fetus as well as physiological changes of mother rats
Authors: Wang Haitong , Ge Linna , Chen Sijie , Sun Longqin , Sun Wei , Gao Youhe
Published: February 2025

Significant physiological changes occur in both fetus and mother during pregnancy. Urine proteins have been shown to reflect a wide range of physiological and pathological changes in the body. To comprehensively explore the daily changes in urine proteins during pregnancy, this study employed low-abundance protein-enriched magnetic nanobeads to conduct an in-depth analysis of the daily changes in urine proteins throughout the entire pregnancy of rats. Based on the 3,455 identified urine proteins, fetal and maternal dynamic changes were observed in the pregnancy group compared to the control group, including blastocyst formation and cell division in the early stage of pregnancy, embryonic development and organ morphogenesis in the intermediate and mid-to-late stages of pregnancy, and maternal-specific change such as lactation in the late stage of pregnancy. These results indicate that urine protein can reflect the fetal and maternal dynamic physiological alterations during pregnancy, which suggests the potential value of urine protein analysis in pregnancy health monitoring. It is emphasized that the analysis focuses on the daily variations in the urine proteins, as these daily changes are expected to reveal more dynamic and detailed information about the physiological processes during pregnancy.
The Current Landscape of Plasma Proteomics: Technical Advances, Biological Insights, and Biomarker Discovery
Authors: Kirsher Douglas Y. , Chand Shreya , Phong Aron , Nguyen Bich , Szoke Balazs G. , Ahadi Sara
Published: February 2025

Plasma is a rich source of biomolecules, including proteins, that reflect both health and disease. Due to their key roles in biological processes, proteins hold significant potential as biomarkers, fueling the rise of plasma proteome profiling in recent years. Despite widespread adoption, few studies have directly compared different plasma proteomics platforms, particularly those using mass spectrometry. Our study provides a comprehensive comparison of seven platforms across three leading technologies - SomaLogic, Olink, and Mass Spectrometry (MS) - including affinity-based approaches and various MS techniques, covering over 13,000 proteins. By applying these methods to the same cohort, we assess their performance, revealing key differences and complementary strengths. Our findings offer valuable insights for researchers, highlighting trade-offs in coverage and their implications for biomarker discovery and clinical applications. This study serves as an essential resource, offering both technical evaluation and biological insights to support the development of novel diagnostics and therapeutics through plasma proteomics.
Development of iPSC-Derived T Cells Targeting EGFR Neoantigens in Non-Small Cell Lung Cancer
Authors: Niizuma Kouta , Nishimura Toshinobu , Villanueva Jonathan , Amaya Laura , Fowler Jonas L. , Isobe Taichi , Nakauchi Yusuke , Saavedra Brandon , Xu Haojun , Nakanishi Mahito , Wilkinson Adam C. , Loh Kyle M. , Shrager Joseph B. , Nakauchi Hiromitsu
Published: February 2025

A long-sought goal of cancer immunotherapy is to mass-produce T cells that specifically target tumor neoantigens. One decisive challenge is the identification of neoantigens derived from cancer driver genes. Here, we identify T cells that recognize the NSCLC-associated EGFR C797S mutation, which confers resistance to current inhibitors and is linked to poor prognosis. To overcome limitations in T cell availability, we reprogrammed EGFR C797S-specific T cells into induced pluripotent stem cells (iPSCs) and re-differentiated them into CD8 T cells. These iPSC-derived T cells specifically recognized the EGFR C797S mutation and effectively killed cancer cells expressing this mutation. Our findings underscore the potential of targeting driver mutation-derived neoantigens for immunotherapy and demonstrate that iPSC-derived T cells can mediate antitumor effects. Collectively, this approach combining neoantigen identification with T cell reprogramming may offer a promising strategy for targeting drug-resistant tumors.
CellScope: High-Performance Cell Atlas Workflow with Tree-Structured Representation
Authors: Li Bingjie , Lin Runyu , Ni Tianhao , Yan Guanao , Burns Mannix , Li Jingyi Jessica , Yao Zhigang
Published: February 2025

Single-cell sequencing enables comprehensive profiling of individual cells, revealing cellular heterogeneity and function with unprecedented resolution. However, current analysis frameworks lack the ability to simultaneously explore and visualize cellular hierarchies at multiple biological levels. To address these limitations, we present CellScope, an innovative framework for constructing high-resolution cell atlases at multiple clustering levels. CellScope employs a two-step manifold fitting process for gene selection and noise reduction, followed by agglomerative clustering, and uniquely integrates UMAP visualization with hierarchical clustering to intuitively represent cellular relationships simultaneously at multiple levels—such as cell lineage, cell type, and cell subtype levels. Compared to established pipelines such as Seurat and Scanpy, CellScope comprehensively improves clustering performance, visualization clarity, computational efficiency, and algorithm interpretability, while reducing dependence on hyperparameters across a multitude of single-cell datasets. Most importantly, it can reveal new biological insights that other contemporary methods are unable to detect, thereby deepening our understanding of cellular heterogeneity and function, and potentially informing disease research.
Spatial and single-cell expression analyses reveal complex expression domains in early wheat spike development
Authors: Xu Xiaosa , Lin Huiqiong , Zhang Junli , Burguener German , Paraiso Francine , Tumelty Connor , Li Chengxia , Liu Yuchen , Dubcovsky Jorge
Published: February 2025

Wheat is an important crop for global food security and a better understanding of the molecular mechanisms driving spike and spikelet development can inform the engineering of more productive varieties. In this study, we integrated single-molecule fluorescencein situhybridization (smFISH) and single-cell RNA sequencing (scRNA-seq) to generate an atlas of cell types and expression domains during the early stages of wheat spike development. We characterized spatiotemporal expression of 99 genes by smFISH in 48,225 cells at the early transition (W1.5), late double ridge (W2.5) and lemma primordia (W3.25) stages. These cells were clustered into 21 different expression domains, including four beneath the developing spikelets and three different meristematic regions, which were consistent across spikelets and sections. We also identified genes differentially expressed during the transition of the inflorescence meristem into a terminal spikelet. The smFISH study was complemented by the scRNA-seq profiling of 26,009 cells from W2.5 and W3.25 that were clustered into 23 distinct cell types. We annotated the single-cell clusters as meristem, boundary domains, cortex, central spike, epidermis, and vasculature by using known markers, co-expression analysis of genes selected from the smFISH study, and correlation matrices of clusters identified in both studies. The scRNA-seq data uncovered genes associated with boundary genesTCP24andFZP, as well as the meristematic genesAGL6andULT1.The smFISH and scRNA-seq studies provided complementary tools for characterizing the gene networks that regulate spike development, supporting the functional characterization of key regulatory genes, and informing the engineering of more productive wheat spikes.
Towards population genetic assessments and species abundance from environmental DNA: A case study with zebrafish in controlled aquaria
Authors: Meenakshisundaram Abinaya , Jarman Simon , Power Haylea , Kennington Jason W. , Thomas Luke
Published: February 2025

Developing robust methods for amplifying and analysing highly-polymorphic nuclear genetic markers from environmental samples could assist in the reliable and scalable long-term monitoring of elusive, threatened or invasive species that are otherwise challenging to observe. In this study, we used zebrafish in controlled aquaria to apply forensic science approaches and demonstrate that microhaplotypes, which are short segments of nuclear DNA (100–300bp) containing two or more single nucleotide polymorphisms (SNPs), can be amplified from trace DNA in water samples to accurately estimate population genetic diversity and species abundance. We successfully amplified a panel of 17 microhaplotypes that comprised 69 SNPs which could reliably estimate population-level allele frequencies and genetic diversity estimates from water DNA. The panel of microhaplotypes amplified from water samples from replicate tanks strongly matched allele frequency estimates from corresponding tissue samples, and could also be used for estimating number of contributors from multi-individual samples. Our research demonstrates the effectiveness and potential of amplifying microhaplotype panels from eDNA as a non-invasive and scalable tool for population genetic studies of aquatic species.
Modulations of thalamo-cortical coupling during voluntary movement in patients with essential tremor
Authors: Steina Alexandra , Sure Sarah , Butz Markus , Vesper Jan , Schnitzler Alfons , Hirschmann Jan
Published: February 2025

The ventral intermediate nucleus of the thalamus (VIM) is the main thalamic hub for processing cerebellar inputs and the main deep brain stimulation target for the treatment of essential tremor (ET). As such, it presumably plays a critical role in motor control. So far, however, this structure has been rarely investigated in humans, and almost all of the existing studies focus on tremor. Here, we set out to study neural oscillations in the VIM and their coupling to cortical oscillations during voluntary movement.

We investigated thalamo-cortical coupling by means of simultaneous recordings of thalamic local field potentials and magnetoencephalography in 10 ET patients with externalized deep brain stimulation electrodes. Brain activity was measured while patients were pressing a button repeatedly in response to a visual cue. In a whole-brain analysis of coherence between VIM and cortex, we contrasted activity around a pre-movement baseline and button pressing.

Button pressing was associated with a bilateral decrease of thalamic power in the alpha (8– 12 Hz) and beta (13–21 Hz) band and a contralateral power increase in the gamma (35– 90 Hz) band. Moreover, changes in VIM-cortex coherence were observed. Alpha/low beta (8– 20 Hz) coherence decreased before and during movement, and the effect localized to the supplementary motor area and premotor cortex. A rebound of high beta (21–35 Hz) coherence occurred in the same region, but was more focal than the suppression. Pre-movement levels of thalamo-cortex low-beta coherence correlated with reaction time.

Our results demonstrate that voluntary movement is associated with modulations of behaviourally relevant thalamic coupling, primarily to premotor areas. We observed a clear distinction between low- and high-beta frequencies and our results suggest that the concept of “antikinetic” beta oscillations, originating from research on Parkinson’s disease, is transferable to ET.
Transcriptomic insights into the role of miR394 in the regulation of flowering time inArabidopsis thaliana
Authors: Belen Federico , Bernardi Yanel , Reutemann Andrea , Vegetti Abelardo , Dotto Marcela
Published: February 2025

The initiation of flowering is a highly coordinated process that requires synchronization of endogenous plant developmental program with environmental signals through a complex interplay of genetic regulatory networks. The developmental shift from vegetative to reproductive stage is controlled by multiple flowering pathways, which together with other signals participate in the orchestration of flowering time regulation. Collectively, the different pathways converge to modulate the expression of key floral integrator genes, which subsequently trigger the expression of genes related to the differentiation of the vegetative shoot apical meristem into a flower meristem with the subsequent development of floral organs. We had previously demonstrated a role for miR394 in the regulation of flowering time, sincemir394a mir394bdouble mutant plants harboring T-DNA insertions in the twoMIR394 Arabidopsisgenes exhibited an early flowering phenotype correlated with modified expression of flowering genes. In the present study we provide transcriptomic data and histological staining of reporter lines to give further insight into the role of miR394 in the regulation of flowering time inArabidopsis thalianaand present an initial bioinformatic characterization of a newly identified lncRNA, which is found partially overlapping theMIR394Blocus, and therefore we namedMIR394B-ASSOCIATEDTRANSCRIPT(MIRAST). We identified differential domains of expression during flower development, which together with the transcriptomic analysis allows us to propose a role for miR394 in the fine tuning ofArabidopsisflower development through the regulation of transcription factors and chromatin remodeling factors.

Key message

Differential domains of activity ofMIR394AandMIR394Bgene promoters together with transcriptomic analysis of mutant plants, indicate that miR394 participates in the fine tuning ofArabidopsisflower development through regulation of transcription factors and chromatin remodeling factors.
Clade-specific multiplex digital PCR assay for monkeypox virus detection in wastewater
Authors: Pitton Melissa , Gan Charles , Schmidhalter Patrick , Ort Christoph , Julian Timothy R.
Published: February 2025

Monkeypox virus (MPXV) is a zoonotic pathogen that has recently caused outbreaks in non-endemic areas. Wastewater-based surveillance (WBS) offers substantial potential for monitoring MPVX clades, and it can inform population-level disease dynamics. Here, we report a four-plex digital PCR assay to detect and quantify different clades and subclades of MPXV. The assay demonstrated specificity in distinguishing and quantifying MPXV by clade, which is advantageous for application in both clinical and wastewater settings.
Depression and Anxiety Symptom Networks Across the Lifespan
Authors: Harlev Daniel , Vituri Aya , Shahar Moni , Wolpe Noham
Published: February 2025

Background

The relationship between anxiety and depressive symptoms is complex and may vary across the lifespan. Symptom network analyses offer a powerful tool to examine these interactions, but few studies have directly compared symptom networks in younger and older adults.

Methods

We analysed data from the Cambridge Centre for Ageing and Neuroscience (Cam-CAN) study, including 786 participants aged 18 to 88, who reported at least subclinical levels of symptoms on the Hospital Anxiety and Depression Scale (HADS). Network analysis was employed to examine symptom communities, within- and between-community connectivity, and centrality measures across age groups.

Results

The overall network structure, largely separating anxiety and depressive symptoms into two communities, remained stable across age groups. However, in older adults, there was a reduction in connectivity within the depression community, and a reduction in between-community connectivity for both the depression and anxiety communities. Moreover, while “panic” emerged as a consistently central symptom across both age groups, “rumination” and “restlessness” were the key bridge symptoms in young and older adults, respectively.

Discussion

Our findings reveal both stable and dynamic aspects of depression and anxiety symptoms across the lifespan. Reduced within-community connectivity for depressive symptoms suggests greater heterogeneity in how depression manifests in older populations. The shift in bridging symptoms, from cognitive (rumination) in young adults to somatic (restlessness) in older adults, suggests subtle yet clinically important differences in how depression and anxiety are linked across the lifespan. Our results underscore the need for tailored, age-dependent treatment in depression and anxiety.
Reporting of pre-analytical Processes in Biobanked Biomaterials: A Missed Opportunity to Address the Replicability Crisis in Clinical Biomarker Research
Authors: Jansen Jannes A.W. , van den Brand Mariël A. , de Vegt Femmie , Swinkels Dorine W.
Published: February 2025

Biobanks are crucial for clinical biomarker research, but pre-analytical processing can impact sample suitability. Insufficient reporting of pre-analytical methods can lead to invalid conclusions. This study evaluated the pre-analytical reporting quality in 294 clinical biomarker studies using biobank plasma and serum samples published from 2018 to 2023, based on the SPREC and BRISQ guidelines. The analysis revealed frequent incomplete reporting. Key underreported elements included fasting time (reported in 31% of articles), freeze-thaw cycles (22.8%), internal transport (8.5%), and centrifugation settings (20-35%). Demographic data (96.9%), storage temperatures (81%), and blood tube additives (82.7%) were more consistently reported. No significant correlation was found between reporting quality and journal impact factor. This highlights the need for standardized pre-analytical reporting to improve research replicability and biomarker study quality.
Effect of obesity on the acute response to SARS-CoV-2 infection and development of post-acute sequelae of COVID-19 (PASC) in nonhuman primates
Authors: Sauter Kristin A. , Webb Gabriela M. , Bader Lindsay , Kreklywich Craig N. , Takahashi Diana L. , Zaro Cicely , McGuire Casey M. , Lewis Anne D. , Colgin Lois M. A. , Kirigiti Melissa A. , Blomenkamp Hannah , Pessoa Cleiton , Humkey Matthew , Hulahan Jesse , Sleeman Madeleine , Zweig Robert C. , Thomas Sarah , Thomas Archana , Gao Lina , Hirsch Alec. J. , Levy Mayaan , Cherry Sara R. , Kahn Steven E. , Slifka Mark K. , Streblow Daniel N. , Sacha Jonah B. , Kievit Paul , Roberts Charles T.
Published: February 2025

Long-term adverse consequences of SARS-CoV-2 infection, termed “long COVID” or post-acute sequelae of COVID (PASC), are a major component of overall COVID-19 disease burden. Prior obesity and metabolic disease increase the severity of acute disease, but SARS-CoV-2 infection also contributes to the development of new-onset metabolic disease. Since the COVID pandemic occurred in the context of the global obesity epidemic, an important question is the extent to which pre-existing obesity modifies long-term responses to SARS-CoV-2 infection. We utilized a nonhuman primate model to compare the effects of infection with the SARS-CoV-2 delta variant in lean and obese/insulin-resistant adult male rhesus macaques over a 6-month time course. While some longitudinal responses to SARS-CoV-2 infection, including overall viral dynamics, SARS-CoV-2-specific IgG induction, cytokine profiles, and tissue persistence of viral RNA, did not appreciably differ between lean and obese animals, other responses, including neutralizing Ab dynamics, lung pathology, body weight, degree of insulin sensitivity, adipocytokine profiles, body temperature, and nighttime activity levels were significantly different in lean versus obese animals. Furthermore, several parameters in lean animals were altered following SARS-CoV-2 infection to resemble those in obese animals. Notably, persistent changes in multiple parameters were present in most animals, suggesting that PASC may be more prevalent than estimated from self-reported symptoms in human studies.
Galleria mellonellamodel for studying Gram-positive bacterial implant biofilms
Authors: Mirza Kamran A. , Nietzsche Sandor , Tchatchiashvili Tinatini , Makarewicz Oliwia , Pletz Mathias W. , Thieme Lara
Published: February 2025

Implant-associated biofilm infections, particularly those caused byStaphylococcus aureusandEnterococcus faecalis, present significant challenges in clinical settings, often necessitating surgical removal. This study investigates the potential of the invertebrate modelGalleria mellonellafor evaluating biofilm formation ofS. aureusandE. faecalisclinical isolates, the leading causes of implant-associated infections. Utilizing expanded polytetrafluoroethylene (ePTFE) sutures as a surrogate for cardiac implants, we employed two biofilm formation methodologies reflecting the two main routes of implant infections:in vivobiofilm development within larvae mimicking hematogenous spread and pre-formed biofilm transplantation mimicking contamination during surgery. Scanning electron microscopy revealed complex biofilm structures for the biofilm formed inside of the larvae on implant, closely mimicking clinical conditions. Antibiotic treatments with vancomycin and rifampicin demonstrated significant reductions in bacterial biofilms, proving highly effective. The study highlights theG. mellonellamodel’s potential for preclinical biofilm research, offering a cost-effective and ethical alternative to vertebrate models while providing valuable insights into biofilm-related infections and their treatment.
Membrane vesicles ofShewanella oneidensisMR-1 enhance denitrification growth in a species-specific manner
Authors: Takahashi Kohei , Takeda Riku , Savage Thomas Kouyou , Kataoka Masahito , Yamamoto Tatsuya , Okabe Satoshi , Nomura Nobuhiko , Oshiki Mamoru , Toyofuku Masanori , Tokunou Yoshihide
Published: February 2025

Denitrification, a fundamental bacterial respiratory process that occurs in anoxic environments, plays a pivotal role in energy synthesis and the global nitrogen cycle. Although the significance of this process is well-recognized, its regulation within polymicrobial communities remains poorly understood, particularly concerning interspecies interactions. In this study, we investigated the role that bacterial membrane vesicles (MV) play in modulating denitrification across bacterial species. MV is known to carry specific biomolecules such as secondary metabolites, proteins, and nucleic acids, therefore considered to be a secretion pathway. We found that MV produced byShewanella oneidensisenhanced denitrification in a species-specific manner. Bacteria with highly hydrophobic surfaces tended to respond to denitrification enhancement, suggesting that the MV–bacteria attachment process is the key to generating species specificity. Transcriptome analysis and isotopic metabolite tracking indicated that the MV influenced denitrifying activities, rather than the transcription of denitrification-related genes. We further demonstrated thatc-type cytochromes in MV act as key components that enhance denitrification. These insights expand our understanding of bacterial ecology, highlighting the role of membrane vesicles in facilitating respiratory competition and cooperation in polymicrobial communities.
Cholesterol efflux protein, ABCA1, supports anti-cancer functions of myeloid immune cells
Authors: Bendre Shruti V. , Wang Yu , Hajyousif Basel , Rajendra K C , Bhogale Shounak G. , Pradeep Dhanya , Krawczynska Natalia , Schane Claire P. , Weisser Erin , Singh Avni , Han Simon , Kim Hannah , Kockaya Lara , Das Gupta Anasuya , Nelczyk Adam T. , Gamage Hashni Epa Vidana , Fei Yifan , Guo Xingyu , Deaton Ryan J. , Sverdlov Maria , Gann Peter H. , Sinha Saurabh , Wang Kun , Bortle Kevin Van , Tajkorshid Emad , Woodward Wendy A. , Cho Wonhwa , Nelson Erik R.
Published: February 2025

Although immune therapy has seen significant advances, the majority of breast and other solid tumors do not respond or quickly developde novoresistance. One factor driving resistance is highly immune suppressive myeloid cells (MCs) such as macrophages. Previous work has established clinical links between cholesterol and cancer outcome, and that MC function can be regulated through disruption in cholesterol metabolism. Thus, we screened for proteins that were expressed in MCs, involved in cholesterol homeostasis and whose expression was associated with survival; we identify the cholesterol efflux protein ABCA1. Preclinical studies revealed that ABCA1 activity resulted in increased anti-cancer functions of macrophages: enhanced tumor infiltration, decreased angiogenic potential, reduced efferocytosis, and improved support of CD8+ T cell activity. Mechanistically, different AKT isoforms are involved, through both PI3K dependent and independent mechanisms. Assessment of human blood and breast tumors revealed correlations between ABCA1 in macrophages and angiogenic potential,VEGFA, and CD8 T cell abundance and activity, highlighting the clinical relevance of our findings. The culmination of the effects of ABCA1 on MC function were demonstrated through increased tumor growth and metastasis in mice with MC specific knockout of ABCA1. Therefore, modulating ABCA1 activity within MCs may represent a novel approach to immune therapy.
Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation
Authors: Oksanen Marika , Mastropasqua Francesca , Mazan-Mamczarz Krystyna , Martindale Jennifer L. , Ye Xuan , Arora Abishek , Banskota Nirad , Gorospe Myriam , Tammimies Kristiina
Published: February 2025

HNRNPU is an RNA-binding protein with diverse roles in regulating gene expression. Pathogenic genetic variants of HNRNPU cause a severe neurodevelopmental disorder (NDD), but the underlying molecular mechanisms are unclear. Here, we investigated the protein-protein interaction (PPI) network and RNA targets of HNRNPU in neuroepithelial stem cells (NES) and differentiating neural cells derived from human induced pluripotent stem cells. Using high-throughput approaches, we found HNRNPU interacting with the mammalian SWI/SNF complex and highlight its putative role in multiple stages of mRNA regulation. Notably, both PPI partners and interacting mRNAs implicated HNRNPU in translation, a role that had not been recognized before. Also, we found that HNRNPU associated with mRNAs encoding proteins important for neuronal development. Based on our findings, we propose a regulatory model in which HNRNPU, in coordination with SWI/SNF, modulates the levels and accessibility of DNA methylation factors, leading to global methylation differences in HNRNPU deficiency states, as we validated in our cell model. This mechanism provides a molecular link to the distinct methylation signature seen in individuals with HNRNPU-related NDDs as well as to crucial epigenetic regulation during early brain development.
DdiA, an XRE family transcriptional regulator, regulates a LexA-independent DNA damage response inMyxococcus xanthus
Authors: Jung Jana , Glatter Timo , Herfurth Marco , Søgaard-Andersen Lotte
Published: February 2025

Repair of DNA damage is essential for genome integrity. DNA damage elicits a DNA damage response (DDR) that includes error-free and error-prone, i.e. mutagenic, repair. The SOS response is a widely conserved system in bacteria that regulates the DDR and depends on the recombinase RecA and the transcriptional repressor LexA. However, RecA/LexA-independent DDRs have been identified in several bacterial species. Here, using a whole-cell, label-free quantitative proteomics approach, we map the proteomic response inMyxococcus xanthusto mitomycin C treatment and the lack of LexA. In doing so, we confirm a LexA-independent DDR inM. xanthus. Using a candidate approach, we identify DdiA, a transcriptional regulator of the XRE family, and demonstrate that it regulates a subset of the LexA-independent DDR genes.ddiAis expressed heterogeneously in a subpopulation of cells in the absence of exogenous genotoxic stress and reversibly induced population-wide in response to such stress. DdiA, indirectly or directly, activates the expression ofdnaE2, which encodes the DnaE2 error-prone DNA polymerase, and inhibits the expression ofrecX, which encodes RecX, a negative regulator of RecA. Accordingly, the ΔddiAmutant has a lower mutation frequency than the wild-type but also a fitness defect, suggesting that DdiA mediates a trade-off between fitness and mutagenesis. We speculate that the DdiA-dependent response is tailored to counter replication stress, thereby preventing the induction of the complete RecA/LexA-dependent DDR in the absence of exogenous genotoxic stress.

Importance

DNA damage repair is essential for genome integrity and depends on the DNA damage response (DDR). While the RecA/LexA-dependent SOS response is widely conserved in bacteria, there are also RecA/LexA-independent DDRs. Here, we identify the DNA damage-induced transcriptional regulator DdiA inMyxococcus xanthusand demonstrate that it regulates part of the RecA/LexA-independent DDR. DdiA activates the expression ofdnaE2, which encodes the DnaE2 error-prone DNA polymerase, and inhibits the expression ofrecX, which encodes RecX, a negative regulator of RecA. Because the ΔddiAmutant has a lower mutation frequency than the wild-type but also a fitness defect, we suggest that DdiA mediates a trade-off between fitness and mutagenesis and that the DdiA-dependent DDR is specifically tailored to counter replication stress.
Design, development, and evaluation of gene therapeutics specific to KSHV-associated diseases
Authors: Inagaki Tomoki , Espera Jonna , Wang Kang-Hsin , Komaki Somayeh , Nair Sonali , Davis Ryan R. , Kumar Ashish , Nakajima Ken-ichi , Izumiya Yoshihiro
Published: February 2025

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s sarcoma (KS) and two human lymphoproliferative diseases: primary effusion lymphoma and AIDS-related multicentric Castleman’s disease. KSHV-encoded latency-associated nuclear antigen (LANA) is expressed in KSHV-infected cancer cells and is responsible for maintaining viral genomes in infected cells. Thus, LANA is an attractive target for therapeutic intervention for KSHV-associated diseases.

Here, we devised a cancer gene therapy vector using the adeno-associated virus (AAV), which capitalizes the LANA’s function to maintain terminal repeat (TR) containing circular genome in latently infected cells and the TR’s enhancer function for KSHV inducible gene promoters. By including two TR copies with a lytic inducible gene promoter (TR2-OriP), we prepared an AAV vector, which expresses an engineered thymidine kinase (TK) selectively in KSHV-infected cells. Ganciclovir (GCV), an anti-herpesvirus drug, effectively eradicated multiple KSHV-infected cells that include iPSC-derived epithelial colony-forming cells, but not non-KSHV-infected counterparts in the presence of AAV8-TR2-OriP-TK. In addition, AAV8-TR2-OriP-TK prevents KSHV virion production from reactivated cells, spreading KSHV infections from reactivated cells. Anti-cancer drugs, known to reactivate KSHV, stimulated TK expression from the vector and, therefore, synergized with AAV8 TR2-OriP-TK to induce KSHV-infected cancer cell death. Finally, the AAV8-TR2-OriP-TK with GCV completely diminished KSHV-infected cancer cells in the xenograft tumor model. The new cancer gene therapeutics should augment the current clinical protocol for KS.
Development of a Transcriptional Biosensor for Hydrogen Sulfide that Functions under Aerobic and Anaerobic Conditions
Authors: Fernez Matthew T. , Hegde Shanthi , Hayes Justin A. , Hoyt Kathryn O. , Carrier Rebecca L. , Woolston Benjamin M.
Published: February 2025

Hydrogen sulfide (H2S) is a gaseous gut metabolite with disputed effects on gastrointestinal health. Monitoring H2S concentration in the gut would provide insight into its role in disease, but is complicated by sulfide’s reactivity and volatility. Here we develop a transcriptional sulfide biosensor inE. coli. The sensor relies on enzymatic oxidation of sulfide catalyzed by a sulfide:quinone reductase (Sqr) to polysulfides, which bind to the repressor SqrR, triggering unbinding from the promoter and transcription of the reporter. Through promoter engineering and improving soluble SqrR expression, we optimized the system to provide an operational range of 50 µM - 750 µM and dynamic range of 18 aerobically. To enable sensing in anaerobic environments, we identified an Sqr fromWolinella succinogenesthat uses menaquinone, facilitating reoxidation through the anaerobic electron transport chain by fumarate or nitrate. Use of this homolog resulted in an anaerobic H2S response up to 750 µM. This sensor could ultimately enable spatially and temporally resolved measurements of H2S in the gastrointestinal tract to elucidate the role of this metabolite in disease, and potentially as a non-invasive diagnostic.
Resummation of Threshold Double Logarithms in Hadroproduction of Heavy Quarkonium
Authors: Chung Hee Sok , Kim U-Rae , Lee Jungil
Published: February 2025

We resum threshold double logarithms that appear in inclusive production of heavy quarkonium. This resolves the catastrophic failure of fixed-order perturbation theory where quarkonium cross sections at large transverse momentum can turn negative due to large radiative corrections. We find that resummation is imperative for describing measured prompt production rates of J/ψ at large transverse momentum.

Published by the American Physical Society
2025
Slice'N'Dice: maximizing the value of predicted models for structural biologists
Authors: Simpkin Adam J. , Elliot Luc G. , Joseph Agnel Praveen , Burnley Tom , Stevenson Kyle , Sánchez Rodríguez Filomeno , Fando Maria , Krissinel Eugene , McNicholas Stuart , Rigden Daniel J. , Keegan Ronan M.
Published: February 2025

With the advent of next-generation modelling methods, such as AlphaFold2, structural biologists are increasingly using predicted structures to obtain structure solutions via molecular replacement (MR) or model fitting in single-particle cryogenic sample electron microscopy (cryoEM). Differences between the domain–domain orientations represented in a predicted model and a crystal structure are often a key limitation when using predicted models. Slice'N'Dice is a software package designed to address this issue by first slicing models into distinct structural units and then automatically placing the slices using either Phaser, MOLREP or PowerFit. The slicing step can use the AlphaFold predicted aligned error (PAE) or can operate via a variety of Cα-atom-based clustering algorithms, extending the applicability to structures of any origin. The number of splits can either be selected by the user or determined automatically. Slice'N'Dice is available for both MR and automated map fitting in the CCP4 and CCP-EM software suites.
Role of social media dependency and online reputation in instituting stress among social media users
Authors: Karunarathne E.A.C.P. , Wijesundara W.M.T.H. , Athukorala A.S.T. , Chithrananda K.P.S.P.
Published: February 2025

Purpose

Despite the growing use of social media platforms, it’s important to acknowledge and understand the potential negative aspects associated with its usage. This paper aims to explore the impacts of social media stress development and understand the roles of self-esteem, social media dependency and online reputation.

Design/methodology/approach

A survey-based quantitative approach was followed for this study, targeting social media users over 18 years of age, and the data were gathered through an online questionnaire. Exploratory factor analysis (EFA) and structural equation modeling (SEM) were employed to evaluate the study model.

Findings

Study findings indicate that higher self-esteem reduces reliance on social media. Also, social media users’ concern about the digital image is caused by increasing social media dependency, which may lead to stress as individuals struggle to maintain a positive digital image on these platforms.

Originality/value

This study provides valuable insights into the negative aspects of social media use, emphasizing the need for strategies to mitigate the risks associated with excessive social media use and encourage the use of healthier digital habits to ensure user’s psychological well-being.
Integration of knowledge and technology in the co-production of AI-based solutions for the healthcare sector
Authors: Leszczyński Grzegorz , Zieliński Marek , Gaczek Piotr , Kociński Jędrzej
Published: February 2025

Purpose

This article aims to explain how organizations create and integrate medical knowledge to develop AI-based medical solutions. The study resulted from a discussion on value co-production with digital technologies and the capabilities needed for it.

Design/methodology/approach

The study explores the case of value co-production with the digitalization of traditional medical stethoscopes. It considers integrated resources to create AI-based medical solutions, actors engaged in co-production and activities related mainly to knowledge embodiment.

Findings

This article presents operand and operant resources integration when AI is implemented in innovative medical solutions. Furthermore, it shows which activities are undertaken for value co-production and what roles actors from various fields play in resource integration.

Originality/value

Our article discusses the integration of knowledge and the role of knowledge embodiment among resource integration in value co-production when working on AI.
The late mover advantage: unveiling Bajaj Auto’s potential to lead in the two-wheeler EV space
Authors: Das Arindam , Ghosal Debraj
Published: February 2025

Learning outcomes

On completion of the analysis of this case, students would be able to: analyze how external environmental factors impact the product market matrix; evaluate growth choices open to an incumbent business and how they create and capture value; and develop corporate strategies of a multi-business firm to respond to external dynamics.

Case overview/synopsis

The case presents an opportunity to examine the timing of entry of an incumbent firm in a new market segment. Bajaj Auto, a well-established Indian two-wheeler and three-wheeler manufacturer and exporter, chose to enter the electric vehicle space much later than technology start-ups and other incumbents. After three years, the company’s business in this segment might appear successful, but it is not in a position to dislodge the market leader, Ola Electric. The case focuses on the dilemma of market entry timing, positioning of a new product, managing an interlinked product portfolio, the need to develop a robust ecosystem of partners and dealing with unpredictable export markets.

Complexity academic level

The case can be discussed in a session of graduate-level business strategy/corporate strategy/international business course that deals with the growth strategies of an incumbent.

Supplementary material

Teaching notes are available for educators only.

Subject code

CSS 11: Strategy.
Making sustainable voices heard at the workplace
Authors: Nazeer Shakira , Naveed Shabana , Sair Shrafat Ali , Khan Kamran
Published: February 2025

Purpose

This study aims to investigate employee motivation, enabling environmental factors and barriers to exercising green voice behavior (GVB) in Oil and Gas companies in Pakistan using the theoretical lens of the theory of planned behavior (TPB) and value–belief–norm (VBN) theory.

Design/methodology/approach

Thirty-five in-depth, semistructured interviews were conducted with middle-level employees of the three Oil and Gas exploration companies to explore the antecedents behind GVB of professionals.

Findings

Qualitative data show various antecedents of GVB (i.e. biospheric values, ecological worldview, awareness of adverse environmental consequences of irresponsible behavior, previous negative experiences with the environment, ascribed responsibility, personal norms, proenvironmental attitude, leaders’ related subjective norms, colleagues-related subjective norms, organizational-related subjective norms and perceived behavioral controls) and several contextual factors (employee’s previous eroded relationship with the management, inaction of management on green voice, organizational limited green capacity in terms of technical, financial or intellectual resources) as significant determinants to influence the exercise of GVB in the workplace. Out of the interviewees’ responses, a two-phase decision-making model has been developed showing the individual’s decision to engage in a proenvironmental voice.

Originality/value

This research integrates TPB and VBN theory to explain the GVB of industry professionals in Pakistan’s Oil and Gas sector. The study uniquely highlights how personal, organizational and environmental factors influence proenvironmental behavior.
Kyoto's Clean Development Mechanism for Emissions Reduction in Developing Economies
Authors: Fernando Lakmini , McWhinnie Stephanie
Published: February 2025

This paper investigates the effectiveness of Kyoto's Clean Development Mechanism (CDM) on emissions reduction in developing countries. Whilst global responses are needed for global problems, global environmental policies are likely to have heterogeneous impacts. Understanding this heterogeneity allows for more nuanced policy evaluation and design. We use a quantile difference‐in‐differences approach to uncover where a significant early global mechanism for implementing climate policy, the CDM, does and does not have an impact. Evaluating a panel of 104 developing countries over the period 1996–2016, we find that the CDM had a strong impact only at lower quantiles of the distribution of greenhouse gas (GHG) emissions. In particular, countries in the 10th and 25th quantiles show a 9% reduction in emissions, whereas countries in the 90th quantile exhibit a 21% increase over the post‐policy period. Emissions intensity and emissions per capita also experience mixed results with strong reductions in the bottom half of the distribution but increases at the very top. Decomposition across GHG emissions types indicates mixed results across the distribution for each; with carbon dioxide results acting similarly to aggregate emissions but fluorinated gases reducing across the distribution. Heterogeneity of the policy effect is observed across regions, the CDM is associated with: reduced emissions in the Latin America and Caribbean region; weaker reductions in Asia–Pacific; and mixed results in Africa. Identification of heterogeneity across subgroups of countries can assist with effective policy design and implementation of future global environmental policies.