bluuebunny/crossref_metadata_2025 huggingface dataset:
Rescue of hippocampal synaptic plasticity and memory performance by Fingolimod (FTY720) in APP/PS1 model of Alzheimer’s disease is accompanied by correction in metabolism of sphingolipids, polyamines, and phospholipid saturation composition
Authors: Kalecký Karel , Buitrago Luna , Alarcon Juan Marcos , Singh Abanish , Bottiglieri Teodoro , Kaddurah-Daouk Rima , Hernández Alejandro Iván ,   Alzheimer’s Disease Metabolomics Consortium
Published: January 2025

Previously, our metabolomic, transcriptomic, and genomic studies characterized the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer’s disease, and we demonstrated that FTY720, a sphingosine-1-phospahate receptor modulator approved for treatment of multiple sclerosis, recovers synaptic plasticity and memory in APP/PS1 mice. To further investigate how FTY720 rescues the pathology, we performed metabolomic analysis in brain, plasma, and liver of trained APP/PS1 and wild-type mice. APP/PS1 mice showed area-specific brain disturbances in polyamines, phospholipids, and sphingolipids. Most changes were completely or partially normalized in FTY720-treated subjects, indicating rebalancing the “sphingolipid rheostat”, reactivating phosphatidylethanolamine synthesis via mitochondrial phosphatidylserine decarboxylase pathway, and normalizing polyamine levels that support mitochondrial activity. Synaptic plasticity and memory were rescued, with spermidine synthesis in temporal cortex best corresponding to hippocampal CA3-CA1 plasticity normalization. FTY720 effects, also reflected in other pathways, are consistent with promotion of mitochondrial function, synaptic plasticity, and anti-inflammatory environment, while reducing pro-apoptotic and pro-inflammatory signals.
Deciphering Transcription inCryptosporidium parvum: Polycistronic Gene Expression and Chromatin Accessibility
Authors: Xiao Rui , Baptista Rodrigo P. , Agyabeng-Dadzie Fiifi , Li Yiran , Dong Yinxin , Schmitz Robert J. , Glenn Travis C. , Kissinger Jessica C.
Published: January 2025

Once considered rare in eukaryotes, polycistronic mRNA expression has been identified in kinetoplastids and, more recently, green algae, red algae, and certain fungi. This study provides comprehensive evidence supporting the existence of polycistronic mRNA expression in the apicomplexan parasiteCryptosporidium parvum. Leveraging long-read RNA-seq data from different parasite strains and using multiple long-read technologies, we demonstrate the existence of defined polycistronic transcripts containing 2-4 protein encoding genes, several validated with RT-PCR. Some polycistrons exhibit differential expression profiles, usually involving the generation of internal monocistronic transcripts at different times during development. ATAC-seq in sporozoites reveals that polycistronic transcripts usually have a single open chromatin peak at their 5-prime ends, which contains a single E2F binding site motif. Polycistronic genes do not appear enriched for either male or female exclusive genes. This study elucidates a potentially complex layer of gene regulation with distinct chromatin accessibility akin to monocistronic transcripts. This is the first report of polycistronic transcription in an apicomplexan and expands our understanding of gene expression strategies in this medically important organism.

Significance

Cryptosporidium parvumis a parasite that causes human gastrointestinal disease, profoundly impacting infants and immunocompromised individuals worldwide.C. parvumisolation, culturing, cloning, and its compact 9.2 Mb genome pose challenges for research. We have discovered that, unlike most eukaryotes, which express one gene per mRNA,C. parvumexhibits widespread polycistronic transcription, whereby 10% of its protein encoding genes are expressed as multiple genes per single mRNA molecule. Mining the publishedC. parvumsingle-cell atlas with proxy sequences for polycistronic expression, we observed patterns of polycistron expression that vary with developmental stages, suggesting a role in the parasite’s lifecycle. By illuminating this unique aspect ofC. parvumbiology, our findings provide novel insights intoCryptosporidiumgene expression.
Impact of meningioma and glioma on whole-brain dynamics
Authors: Juncá Albert , Escrichs Anira , Martín Ignacio , Deco Gustavo , Patow Gustavo
Published: January 2025

Brain tumors, particularly meningiomas and gliomas, can profoundly affect neural function, yet their impact on brain dynamics remains incompletely understood. This study investigates alterations in normal brain function among meningioma and glioma patients by assessing dynamical complexity through the Intrinsic Ignition Framework. We analyzed resting-state fMRI data from 34 participants to quantify brain dynamics using intrinsic ignition and metastability metrics. Our results revealed distinct patterns of disruption: glioma patients showed significant reductions in both metrics compared to controls, indicating widespread network disturbances. In contrast, meningioma patients exhibited significant changes predominantly in regions with substantial tumor involvement. Resting-state network analysis demonstrated strong metastability and metastability/ignition correlations between regions in controls, which were slightly weakened in meningioma patients and severely disrupted in glioma patients. These findings highlight the differential impacts of gliomas and meningiomas on brain function, offering insights into their distinct pathophysiological mechanisms. Furthermore, these results show that brain dynamics metrics can be effective biomarkers for identifying disruptions in brain information transmission caused by tumors.
Language models learn to represent antigenic properties of human influenza A(H3) virus
Authors: Durazzi Francesco , Koopmans Marion P. G. , Fouchier Ron A. M. , Remondini Daniel
Published: January 2025

Given that influenza vaccine effectiveness depends on a good antigenic match between the vaccine and circulating viruses, it is important to assess the antigenic properties of newly emerging variants continuously. With the increasing application of real-time pathogen genomic surveillance, a key question is if antigenic properties can reliably be predicted from influenza virus genomic information. Based on validated linked datasets of influenza virus genomic and wet lab experimental results,in silicomodels may be of use to learn to predict immune escape of variants of interest starting from the protein sequence only. In this study, we compared several machine-learning methods to reconstruct antigenic map coordinates for HA1 protein sequences of influenza A(H3N2) virus, to rank substitutions responsible for major antigenic changes, and to recognize variants with novel antigenic properties that may warrant future vaccine updates. Methods based on deep learning language models (BiLSTM and ProtBERT) were shown to outperform more classical approaches that involved predictions based solely on genetic distances and physicochemical properties of amino acid sequences, particularly for fine-grained features like single amino acid-driven antigenic change andin silicodeep mutational scanning experiments to rank the substitutions with the largest impact on antigenic properties. Given that the best performing model that produces protein embeddings is agnostic to the specific pathogen, the presented approach may be applicable to other pathogens.
VitisC: Visualizing interested target via integrated scaffold of cytoophidium
Authors: Yin Boqi , Hu Huan-Huan , Zhong Jiale , Liu Ji-Long
Published: January 2025

Cryo-electron microscopy (cryo-EM) single-particle analysis has become a widely used technique for high-resolution structural determination of biological macromolecules and complexes. However, the determination of the structure of small molecule proteins remains a limitation of this technology. To address this issue, here we develop a novel approach termed Visualizing interested target via integrated scaffold of cytoophidium (VitisC). We use a filamentous structure formed byEscherichia coliCTP synthase (CTPS) as the scaffold, termed the scaffold of cytoophidium. Through artificial design and modification, small proteins can be attached to this symmetrical scaffold, which is very suitable for cryo-EM imaging. The formation conditions for stable filament structures of the fusion protein are optimized in vitro, and the three-dimensional structure of the fusion protein is reconstructed using cryo-EM single-particle analysis, achieving an overall resolution of 3.39 Å. Therefore, cryo-EM is successfully applied to visualize small proteins. VitisC not only demonstrates the feasibility of employing cytoophidia as scaffolds, but also provides an approach for high-resolution structural analysis of small proteins using Cryo-EM.
REV7 associates with ATRIP and inhibits ATR kinase activity
Authors: Biller Megan , Kabir Sara , Nipper Sarah , Allen Sydney , Kayali Yara , Kuncik Skyler , Sasanuma Hiroyuki , Zhou Pei , Vaziri Cyrus , Tomida Junya
Published: January 2025

Integration of DNA replication with DNA repair, cell cycle progression, and other biological processes is crucial for preserving genome stability and fundamentally important for all life. Ataxia-telangiectasia mutated and RAD3-related (ATR) and its partner ATR-interacting protein (ATRIP) function as a critical proximal sensor and transducer of the DNA Damage Response (DDR). Several ATR substrates, including p53 and CHK1, are crucial for coordination of cell cycle phase transitions, transcription, and DNA repair when cells sustain DNA damage. While much is known about ATR activation mechanisms, it is less clear how ATR signaling is negatively regulated in cells. Here, we identify the DNA repair protein REV7 as a novel direct binding partner of ATRIP. We define a REV7-interaction motif in ATRIP, which when mutated abrogates the REV7-ATRIP interactionin vitroand in intact cells. Usingin vitrokinase assays, we show that REV7 inhibits ATR-mediated phosphorylation of its substrates, including p53. Disruption of the REV7-ATRIP interaction also enhances phosphorylation of CHK1 at Ser317 (a known ATR target site) in intact cells. Taken together our results establish REV7 as a critical negative regulator of ATR signaling. REV7 has pleiotropic roles in multiple DDR pathways including Trans-Lesion Synthesis, DNA Double-Strand Break resection, and p53 stability and may play a central role in the integration of multiple genome maintenance pathways.
Native nucleosome-positioning elements for the investigation of nucleosome repositioning
Authors: Chen Ruo-Wen , Stoeber Shane D. , Nodelman Ilana M. , Chen Hengye , Yang Lloyd , Bowman Gregory D. , Bai Lu , Poirier Michael G.
Published: January 2025

Nucleosome repositioning is essential for establishing nucleosome-depleted regions (NDRs) to initiate transcription. This process has been extensively studied using structural, biochemical, and single-molecule approaches, which require homogenously positioned nucleosomes. This is often achieved using the Widom 601 sequence, a highly efficient nucleosome positioning element (NPE) selected for its unusually strong binding to the H3-H4 histone tetramer. Due to the artificial nature of 601, native NPEs are needed to explore the role of DNA sequence in nucleosome repositioning. Here, we characterize the position distributions and nucleosome formation free energy for a set of yeast native nucleosomes (YNNs) fromSaccharomyces cerevisiae. We show these native NPEs can be used in biochemical studies of nucleosome repositioning by transcription factors (TFs) and the chromatin remodeler Chd1. TFs could directly reposition a fraction of nucleosomes containing native NPEs, but not 601-containing nucleosomes. In contrast, partial unwrapping was similar for 601 and native NPE sequences, and the rate of ATP-dependent remodeling by Chd1 was within the range of the fast and slow directions of the 601 nucleosomes. This set of native NPEs provides an alternative to the 601 NPE that can be used for probing the repositioning of nucleosomes that contain native DNA sequences.
Conformational Dynamics and Membrane Insertion Mechanism of B4GALNT1 in Ganglioside Synthesis
Authors: Welland Jack W. J. , Barrow Henry G. , Stansfeld Phillip J. , Deane Janet E.
Published: January 2025

Glycosphingolipids (GSLs) are crucial membrane components involved in essential cellular pathways. Complex GSLs, known as gangliosides, are synthesised in the ER/Golgi by a series of glycosyltransferase enzymes. Imbalances in GSL metabolism can lead to severe diseases, often affecting the nervous system. B4GALNT1 is a key enzyme in the ganglioside synthetic pathway, synthesising complex gangliosides including GM2 and GD2 from GM3 and GD3. These products are precursors to the major brain gangliosides. Loss of B4GALNT1 function causes hereditary spastic paraplegia 26 (HSP26), while its overexpression is linked to cancers including childhood neuroblastoma. Here, we present crystal structures of the homodimeric B4GALNT1 enzyme demonstrating conformational changes upon binding of donor substrate ligands and product. These structures support a catalytic mechanism that involves dynamic remodelling of the substrate binding site during catalysis. We also demonstrate that processing of lipid substrates by B4GALNT1 is severely compromised when surface loops flanking the active site are mutated from hydrophobic residues to polar. Molecular dynamics simulations support that these loops can insert into the lipid bilayer explaining how B4GALNT1 accesses and processes lipid substrates. By combining structure prediction and molecular simulations we propose that this mechanism of dynamic membrane insertion is exploited by other, structurally distinct GSL synthesising enzymes.
Efficacy of functional connectome fingerprinting using tangent-space brain networks
Authors: Curic Davor , Kalasapura Venugopal Krishna Sudhanva , Davidsen Jörn
Published: January 2025

Functional connectomes (FCs) are estimations of brain region interaction derived from brain activity, often obtained from functional Magnetic Resonance Imaging recordings. Quantifying the distance between FCs is important for understanding the relation between behaviour, disorders, disease, and changes in connectivity. Recently, tangent space projections, which account for the curvature of the mathematical space of FCs, have been proposed for calculating FC distances. We compare the efficacy of this approach relative to the traditional method in the context of subject identification using the Midnight Scan Club dataset, in order to study resting-state and task-based subject discriminability. The tangent space method is found to universally out-perform the traditional method. We also focus on the subject identification efficacy of subnetworks. Certain subnetworks are found to outperform others, a dichotomy which largely follows the ‘control’ and ‘processing’ categorization of resting state networks, and relates subnetwork flexibility with subject discriminability. Identification efficacy is also modulated by tasks, though certain subnetworks appear task independent. The uniquely long recordings of the dataset also allow for explorations of resource requirements for effective subject identification. The tangent space method is found to universally require less data, making it well suited when only short recordings are available.

AUTHOR SUMMARY

Functional connectomes, which describe the similarity between the recorded activity of different brain regions, are ubiquitous for researcher trying to understand brain dynamics on short and long time scales in the presence and absence of neurophysiological diseases. This work applies a Tangent Space approach, a novel method to calculate the distance between functional connectomes, to a unique high-quality dataset (the Midnight Scan Club) in order to better understand the variability and uniqueness of connectomes across subjects, and how subject identification (also called fingerprinting) compares across tasks. We also show that not only does the tangent space method offer greater sensitivity to changes, it does so with significantly fewer resources, and in some scenarios reveals qualitatively different interpretations than the traditional method.
Lecanemab binds to transgenic mouse model-derived amyloid-β fibril structures resembling Alzheimer’s disease type-I, type-II and Arctic folds
Authors: Peralta Reyes Fernanda S. , Willbold Dieter , Schröder Gunnar F. , Gremer Lothar
Published: January 2025

Lecanemab, an Alzheimer’s disease US Food and Drug Administration approved monoclonal antibody was previously reported to have a high affinity against intermediately sized amyloid-β aggregates. Subsequently, it was observed by immunogold labelling that lecanemab can also bind to human type-I amyloid-β fibrils. Therefore, to determine whether lecanemab binds to amyloid-β fibril structures other than type-I, we performed immunogold labelling on extracted amyloid-β fibril preparations from six different Alzheimer’s disease mouse models whose structures were previously solved by cryo-EM. Our results show that lecanemab exhibits high binding affinity to amyloid-β fibril structures that have a flexible N-terminus in common, as it is the case for type-I, type-II and murine type-III amyloid-β fibril polymorphs which resemble or are identical to human structures observed in sporadic and familial cases of Alzheimer’s disease, including a case with the Arctic (E22G) mutation. In contrast, only weak, if any, lecanemab binding was observed for amyloid-β fibril folds with a fixed and ordered N-terminus.

Key points

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Lecanemab binds to Aβ fibrils from several Alzheimer’s disease tg-mice whose structures resemble the type-I, type-II and Arctic folds found in Alzheimer’s patients, all of which share a flexible, unstructured N-terminus.

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Lecanemab is therefore expected to be active against all common familial and sporadic Alzheimer’s cases containing these folds.

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Lecanemab binding ability is unaffected by and tolerates the Arctic E22G mutation, at least in type-I or Arctic folds.

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Weak, if any, lecanemab binding was observed to Aβ fibrils derived from tg-SwDI mice, whose structures DI1, DI2 and DI3 all share structured and fixed N-termini.

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Since the fixed N-termini of tg-SwDI DI1 fibrils and human meningeal Aβ40 fibrils derived from CAA-affected brain are identical, most likely preventing lecanemab binding, treatment with lecanemab may be less or ineffective against CAA, but may explain the reported beneficial low ARIA-E frequency with this antibody.

Table of Contents Graphic (TOC)
Competition for light color between marineSynechococcusstrains with fixed and variable pigmentation
Authors: Dufour Louison , Garczarek Laurence , Mattei Francesco , Gouriou Bastian , Clairet Julia , Ratin Morgane , Kehoe David M. , Huisman Jef , Verspagen Jolanda M. H. , Partensky Frédéric
Published: January 2025

Competition between phytoplankton species for light has triggered an extensive diversification of photosynthetic pigments. InSynechococcuscyanobacteria, three major pigment types occur in the ocean: blue light (BL) specialists that have a high ratio of the BL-absorbing chromophore phycourobilin (PUB) to the green light (GL)-absorbing chromophore phycoerythrobilin (PEB), GL specialists that have a low PUB:PEB ratio, and cells that modify their PUB:PEB ratio to match the ambient color, a process called ‘Type IV chromatic acclimation’ (CA4). The abundance of CA4-capable cells in marine ecosystems suggests that CA4 confers a fitness advantage in certain light conditions compared to cells with fixed pigmentation. This hypothesis was tested by performing mono- and co-cultures of a BL specialist, a GL specialist and a CA4-capable strain in chemostats under different light conditions. Monocultures enabled us to parameterize a resource competition model that was used to predict competition between the three pigment types in co-cultures. In line with the model predictions, the BL specialist won in low blue light and the GL specialist won in low and high green light. Interestingly, we found that while the CA4-capable strain was at a disadvantage at low light, it was able to outcompete specialists in high blue light.

IMPORTANCE

Synechococcuscyanobacteria are ubiquitous and abundant in the lit layer of most marine ecosystems. This ubiquity relies in part on the wide pigment diversity of their light-harvesting complexes, with three main pigment types thriving in open ocean waters: green light specialists, blue light specialists and chromatic acclimaters, the latter being capable of matching their pigment content to the ambient spectral field. Here, we simulated the competition for light color that occurs between these pigment types in the field by co-culturing them in various light color and intensity conditions, and compared the resulting data to that of a competition model. This study provides new insights on how this key group of phytoplankton colonized the various spectral niches of the marine environment.
Matching Heterogeneous Cohorts by Projected Principal Components Reveals Two Novel Alzheimer’s Disease-Associated Genes in the Hispanic Population
Authors: Willett Julian Daniel Sunday , Mullin Kristina , Tanzi Rudolph E. , Prokopenko Dmitry
Published: January 2025

Alzheimer’s disease (AD) is the most common form of dementia in elderly, affecting 6.9 million individuals in the United States. Some studies have suggested the prevalence of AD is greater in individuals who self-identify as Hispanic. Focused results are relevant for personalized and equitable clinical interventions. Ethnicity as a stratifying tool in genetic studies is often accompanied by genomic inflation due to heterogeneity. In this study, we report GWAS and meta-analyses conducted among NIAGADS subjects who self-identified as Hispanic and All of Us (AoU) sub-cohorts matched to that cohort, using projected genetically-derived principal components, with and without age and sex. In Hispanic NIAGADS subjects, we identified a common variant inPIEZO2that was protective for AD with a p-value just beyond genome-wide significance (p = 5.4 * 10-8). Meta-analyses with genetically-matched AoU participants yielded three (two novel) genome-wide significant AD-associated loci based on rare lead variants: rs374043832 (RGS6/PSEN1), rs192423465 (ASPSCR1), and rs935208076 (GDAP2), which were also nominally significant in AoU sub-cohorts. We also show how genomic inflation can be mitigated in heterogeneous populations while increasing sample size and result generalizability.
PD-1 prelimits both the cytotoxic and exhaustion potential in thymic CD8+ T cells and impacts the maintenance of peripheral tumor immunity
Authors: Mao Zhiming , Hirdler Jacob B. , Gicobi Joanina K. , Maynes Mark , Hsu Michelle A. , Dellacecca Emilia R. , Zhang Wenjing , Teske Jacob J. , Li Ying , Zhao Geoffrey , Lucien-Matteoni Fabrice , Borges da Silva Henrique , Billadeau Daniel D. , Dong Haidong
Published: January 2025

Durable T cell immunity against cancer depends on the continual replenishment of effector CD8+ T cells. Thymic output has been correlated with favorable prognosis in cancer patients across a range of ages, suggesting that the thymus is an important source for replenishing T cells capable of controlling cancer progression. However, the effector potential of thymic mature CD8+ T cells and their regulation have not been clearly defined. In this study, we identified the ability of thymic single positive CD8+ T cells to gain effector potential after thymic selection, but they are subject to the regulation of PD-1. We found a previously undisclosed role of PD-1 in limiting both the cytotoxic and exhaustion potential of thymic and peripheral CD8+ T cells. Our results show that although PD-1 inhibition facilitates the expansion of effector CD8+ T cells, effector CD8+ cells gradually lose their antitumor activity within tumor tissues due to advanced exhaustion in the absence of PD-1. Thus, although the preset effector potential in thymic mature CD8+ T cells allows them to rapidly respond to malignant cells in the periphery, PD-1, as a checkpoint, is embedded in the thymic mature CD8+ T cells after positive selection to balance their effector function from exaggeration and exhaustion. Therefore, we propose that a strategy capable of upholding the cytotoxic capacity and avoiding exhaustion of CD8+ T cells during the early stages of PD-1 inhibition therapy is needed to achieve durable antitumor immunity.
Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk
Authors: Khouri-Farah Nagham , Winchester Emma Wentworth , Schilder Brian M. , Robinson Kelsey , Curtis Sarah W. , Skene Nathan G. , Leslie-Clarkson Elizabeth J. , Cotney Justin
Published: January 2025

Craniofacial development gives rise to the complex structures of the face and involves the interplay of diverse cell types. Despite its importance, our understanding of human-specific craniofacial developmental mechanisms and their genetic underpinnings remains limited. Here, we present a comprehensive single-nucleus RNA sequencing (snRNA-seq) atlas of human craniofacial development from craniofacial tissues of 24 embryos that span six key time points during the embryonic period (4–8 post-conception weeks). This resource resolves the transcriptional dynamics of seven major cell types and uncovers distinct major cell types, including muscle progenitors and cranial neural crest cells (CNCCs), as well as dozens of subtypes of ectoderm and mesenchyme. Comparative analyses reveal substantial conservation of major cell types, alongside human biased differences in gene expression programs. CNCCs, which play a crucial role in craniofacial morphogenesis, exhibit the lowest marker gene conservation, underscoring their evolutionary plasticity. Spatial transcriptomics further localizes cell populations, providing a detailed view of their developmental roles and anatomical context. We also link these developmental processes to genetic variation, identifying cell type-specific enrichments for common variants associated with facial morphology and rare variants linked to orofacial clefts. Intriguingly, Neanderthal-introgressed sequences are enriched near genes with biased expression in cartilage and specialized ectodermal subtypes, suggesting their contribution to modern human craniofacial features. This atlas offers unprecedented insights into the cellular and genetic mechanisms shaping the human face, highlighting conserved and distinctly human aspects of craniofacial biology. Our findings illuminate the developmental origins of craniofacial disorders, the genetic basis of facial variation, and the evolutionary legacy of ancient hominins. This work provides a foundational resource for exploring craniofacial biology, with implications for developmental genetics, evolutionary biology, and clinical research into congenital anomalies.
Persistent interferon signaling that causes sensory neuron plasticity and pain in arthritis
Authors: Su Jie , Zhang Ming-Dong , Kupari Jussi , Kwak Dongoh , Picton Laurence , Xu Bingze , Hu Yizhou , Alvarez Alejandro Gonzalez , Usoskin Dmitry , Xu Zhongwei , Manira Abdeljabbar El , Holmdahl Rikard , Ernfors Patrik
Published: January 2025

While the inflammatory processes in rheumatoid arthritis have been described, mechanisms driving pain are poorly defined. Here, we used a multitude of approaches to uncover the neural basis, mediators, intracellular signaling pathway and the mechanism of inflammatory pain. In cartilage autoantibody-induced arthritis mice, an early immune-activation and a cytokine storm were mainly driven by vascular cells and monocyte/macrophages in the dorsal root ganglion. However, persistently elevated interferons and receptor-activation of the MNK1/2-eIF4E signaling pathway at all disease phases caused sensory-motor dysfunction and pain by inducing hyperexcitability and sensitization ofGfra3+ sensory neurons. Like mice, human sensory neurons expressed interferon receptors and interferons were elevated only in individuals with painful rheumatoid arthritis. Signaling pathway inhibitionin vivoreversed pain and restored limb function. The finding that joint pain before and during arthritis is caused by a defined cytokine and signaling pathway holds promise for targeted therapies for pain relief in arthritis.
Thermal cycling transcription boosts RNA production
Authors: Liu Yuxuan , Shi Lu , Brosius Juergen , Mo Dingding
Published: January 2025

Efficient RNA production is essential for therapeutic applications. Currently, mRNA is generated byin vitrotranscription with RNA polymerases at a constant temperature. The success of these transcriptions depends on various factors including sequence composition and size. Sometimes, especially for long RNAs, achieving efficient transcript yields are challenging.

We developed a novel approach by incorporating a high-temperature denaturation step. Our protocol includes the following two steps of thermal cycling RNA transcription: the initial enzyme-driven RNA transcription step is done at RNA polymerase active temperature (37 °C); then the nucleic acids melting step is carried out at elevated temperatures (55–70°C); after the reaction is cooled to the temperature of optimal polymerase activity, the first step is repeated.

Denaturation enables the generation of optimized, more stable mRNAs, which alleviates the mRNA instability that often occurs during RNA-based therapeutic development. For example, this new thermal cycling RNA transcription approach can employ high GC content, thus increasing RNA stability.

For long and difficult templates, the combination of sequence optimization by LinearDesign algorithm in conjunction with transcription via thermal cycling significantly improved mRNA production. Thermal cycling transcription dramatically increased the efficiency of most RNA products while reducing costs, facilitating RNA-based therapeutic development.
Integrative Gene Co-expression Network Analysis Reveals Protein-Coding and lncRNA Genes Associated with Alzheimer’s Disease Pathology
Authors: Zebardast Fatemeh , Sascha Riethmüller Michael Peter , Nowick Katja
Published: January 2025

Introduction

Alzheimer’s disease (AD) is a complex neurodegenerative disorder involving widespread molecular disruptions, many of which remain poorly understood. While AD pathology progresses through distinct brain regions, it is unclear whether these regions are similarly affected. Long non-coding RNAs (lncRNAs) have emerged as key regulators in cellular processes, but their roles in AD remain largely unexplored. A comprehensive analysis of the complex molecular interactions underlying AD, particularly the roles of lncRNAs in their interactions with protein-coding genes and the comparison of networks across brain regions, could offer valuable insights into the disease’s progression and underlying mechanisms.

Method

To address this, we applied consensus weighted gene co-expression network analysis using a meta-analytic approach to 396 postmortem brain RNA-seq samples to explore AD pathophysiology mechanisms.

Results

Our study revealed significant network rewiring in AD, with pronounced alterations in the temporal cortex compared to the frontal cortex. While the temporal cortex showed adaptive changes in gene interactions, the frontal cortex exhibited a loss of healthy correlations, potentially reflecting different levels of disease progression. We identified key players in the temporal cortex AD network, including 46 protein-coding genes and 27 lncRNAs. Using the established functions of protein-coding genes as anchors, we provided functional annotations for over 100 lncRNAs across two brain regions, identifying potential lncRNAs involved in AD pathology and highlighting their roles in both healthy and diseased states.

Conclusion

We provided novel insights into the molecular interactions underlying AD and introduced new candidate protein-coding and lncRNA genes for further experimental validation and therapeutic exploration.
7-ketocholesterol contributes to microglia-driven increases in astrocyte reactive oxygen species in Alzheimer’s disease
Authors: Radhakrishnan Kayalvizhi , Zhang Yiyu , Mustapha Oluwaseun , Weigel Thaddeus K. , Upchurch Clint M. , Tian Xiaodong , Herbert Franklin , Huang Wenyuan , Leitinger Norbert , Eyo Ukpong B. , Ai Huiwang , Ferris Heather A.
Published: January 2025

Oxidative stress is a prominent feature of Alzheimer’s disease. Within this context, cholesterol undergoes oxidation, producing the pro-inflammatory product 7-ketocholesterol (7-KC). In this study, we observe elevated levels of 7-KC in the brains of the 3xTg mouse model of AD. To further understand the contribution of 7-KC on the oxidative environment, we developed a method to express a genetically encoded fluorescent hydrogen peroxide (H2O2) sensor in astrocytes, the primary source of cholesterol in the brain. With this sensor, we discovered that 7-KC increases H2O2levels in astrocytes in vivo, but not when directly applied to astrocytes in vitro. Interestingly, when 7-KC was applied to a microglia cell line alone or mixed astrocyte and microglia cultures, it resulted in microglia activation and increased oxidative stress in astrocytes. Depletion of microglia from 3xTg mice resulted in reduced 7-KC in the brains of these mice. Taken together, these findings suggest that 7-KC, acting through microglia, contributes to increased astrocyte oxidative stress in AD. This study sheds light on the complex interplay between cholesterol oxidation, microglia activation, and astrocyte oxidative stress in the pathogenesis of AD.
C-terminal tagging, transmembrane domain hydrophobicity, and an ER retention motif influence the secretory trafficking of the inner nuclear membrane protein emerin
Authors: Mella Jessica , Volk Regan , Zaro Balyn , Buchwalter Abigail
Published: January 2025

The inner nuclear membrane (INM), a subdomain of the endoplasmic reticulum (ER), sequesters hundreds of transmembrane proteins within the nucleus. We previously found that one INM protein, emerin, can evade the INM by secretory transport to the lysosome, where it is degraded. In this work, we used targeted mutagenesis to identify intrinsic sequences that promote or inhibit emerin’s secretory trafficking. By manipulating these sequences across several tag and expression level combinations, we now find that emerin’s localization is sensitive to C-terminal GFP tagging. While emerin’s long, hydrophobic C-terminal transmembrane domain facilitates trafficking to the lysosome, extending its lumenal terminus with a GFP tag biases the protein toward this pathway. In contrast, we identify a conserved ER retention sequence that stabilizes N- and C-terminally tagged emerin by limiting its lysosomal flux. These findings underscore long-standing concerns about tagging artifacts and reveal novel determinants of tail-anchored INM protein targeting.
Through a child’s eyes: eye tracking to study children’s consumer behavior
Authors: Huddleston Patricia , McAlister Anna R. , Alade Fashina
Published: January 2025

Purpose

This conceptual paper provides an overview of eye-tracking technology (ETT) as a process-tracing method to study children’s consumer behavior. This paper aims to provide a literature review of the child as consumer-focused eye-tracking research, identifying theoretical and research gaps. This paper discusses the benefits, drawbacks and ethical implications of ETT and highlights opportunities and best practices for future research.

Design/methodology/approach

This paper details eye movement and how ETT captures it. This paper delivers a typology of different approaches to eye-tracking research and presents information about ETT equipment and metrics. This paper also summarizes previous studies using eye tracking to study children. This paper concludes with research questions and topics for future research where ETT can be used to study child consumers in contexts such as playing advergames, using social media and shopping (in-person and online).

Findings

ETT is commonly used to assess children’s behavior in a variety of contexts but has scarcely been used to study children’s consumer behavior. ETT has great potential to be used to better understand children as consumers.

Originality/value

To the best of the authors’ knowledge, this is the first paper to review using ETT to study children’s consumer behavior.
Psychological ownership of health promotes self and other-oriented health behaviors
Authors: Rao Mahendra Singh , Leonhardt James M.
Published: January 2025

Purpose

This research introduces and validates psychological ownership of health as a novel theoretical construct characterized by individuals’ perceived possessiveness, attachment and responsibility toward their health. This study aims to examine the construct’s ability to predict and explain consumers’ health-related decision-making for themselves and others.

Design/methodology/approach

Two online surveys with US participants (N = 680) were conducted. The psychological ownership of health scale was first validated through confirmatory factor analysis. Next, the influence of psychological ownership of health on positive health behaviors and blood donation intentions was assessed using multiple regression analyses and conditional process modeling.

Findings

Psychological ownership of health demonstrated significant positive associations with health-promoting behaviors (dietary choices, physical activity, sleep hygiene) mediated by health self-efficacy. In addition, psychological ownership of health predicted increased blood donation intentions, and this relationship is amplified among individuals high in cultural collectivism.

Practical implications

The findings suggest that interventions fostering psychological ownership of health may simultaneously promote personal health maintenance and prosocial health behaviors. These dual implications offer promising applications for individualized and public health initiatives.

Originality/value

This research advances psychological ownership theory by establishing and validating a health-specific dimension that predicts critical health behaviors at individual and societal levels. By identifying cultural collectivism as a moderator, this research also integrates psychological ownership theory with cultural dimensions theory, revealing cultural variability in health ownership’s influence on prosocial health outcomes.
Variation in risk and protective factors among boy and girl gang involved youth: a direct comparison
Authors: Palau Citlaly , Scott Daniel
Published: January 2025

Purpose

This study aims to directly compare risk and protective factors of male and female gang-involved youth.

Design/methodology/approach

This study uses the 2022 Arizona Youth Survey data. Gang-involved boys and girls are compared through multivariate logistic regression analyses to examine the relationship between risk and protective factors and youth gang membership.

Findings

Multivariate analyses reveal significant differences in risk and protective factors between gang-involved boys and girls in connection with family conflict.

Practical implications

There is a need for semi-specialized prevention and intervention programming for male and female gang youth. Gang programs should emphasize addressing issues with family and home life more for girls than for boys. School-based gang programs need to similarly emphasize educational commitment and positive peer influence for both gang-involved boys and girls. Improving positive neighborhood attachment through community programming will be beneficial for reducing the likelihood of gang involvement for both girls and boys.

Originality/value

There is a need to improve comprehension of the similarities and differences among male and female gang youth. Few studies directly compare the two groups, and by focusing on risk/protective factors, the results can help to provide direct applications to existing intervention and prevention programming.
Entrepreneurship through acquisition in the digital age: exploring website ownership patterns and motivations for selling
Authors: Hoffmann Alexander , Kanbach Dominik K. , Kraus Sascha
Published: January 2025

Purpose

This study aims to explore the potential of entrepreneurship through acquisition (ETA) in the underexplored sector of small and medium-sized web-based businesses, addressing the succession crisis in industrialized nations and offering insights into the digital ETA landscape.

Design/methodology/approach

The research uses a qualitative approach, conducting in-depth interviews with 19 established website owners from diverse backgrounds and industries. The study investigates their business models, selling motivations and characteristics to provide insights for potential buyers in the digital ETA space.

Findings

Web-based small and medium-sized enterprises (SMEs) present unique opportunities for ETA, characterized by lower initial investment, higher scalability and diverse revenue streams. Key considerations for buyers include understanding seller motivations, evaluating niche focus and assessing the impact of emerging technologies such as artificial intelligence on content creation and search engine optimization. The findings also highlight the importance of authenticity and user engagement in maintaining website value.

Practical implications

The findings offer valuable insights for entrepreneurs considering ETA in the digital space, highlighting critical factors for success, potential risks and mitigation strategies in acquiring web-based businesses.

Originality/value

This paper bridges a significant gap in ETA literature by focusing on web-based SMEs, which have previously been overlooked despite their growing importance in the digital economy. It provides a comprehensive analysis of relevant factors when evaluating web-based businesses in the context of ETA, particularly in light of technological advancements and changing online landscapes.
Prediction of efficiency of the filled-trench in layered soil through artificial neural network
Authors: Naghizadeh Mehran
Published: January 2025

Purpose

Vibrations are transmitted through the ground surface to building foundations, causing distress to structures and their occupants. Installing a wave barrier between the vibration source and buildings is a suitable method to mitigate ground vibration. However, the complexity arises in selecting the right trench design due to various influencing parameters. This paper aims to present a novel method to predict the efficiency of a geofoam-filled trench in mitigating ground vibrations within layered soil using an artificial neural network (ANN).

Design/methodology/approach

This study extends a parametric investigation conducted by Naghizadeh (Naghizadehrokni, 2022), where they identified key parameters influencing the trench’s efficiency. A multilayered feedforward neural network using the back-propagation training method was developed for the prediction task. The ANN model comprises input variables, including location, depth, width of the trench, thickness and shear wave velocity of the first layer as well as geofoam type. With a total of 18,750 data points from the parametric study, the network was trained and validated.

Findings

The accuracy of the trained model was evaluated using separate training, validation and testing data sets. Different neural network configurations were evaluated by comparing the coefficient of determination (

R2) and mean square error. The optimal architecture was used to predict previous results, revealing the accuracy and effectiveness of the ANN approach. Furthermore, the ANN’s predictive performance was compared with finite element model results. The results indicate a high level of accuracy, with a regression R-value of 0.98 for the regression analysis of the entire data set.

Originality/value

After studying previous research, the author identified a need for a prediction model to evaluate the efficiency of geofoam-filled trenches. To meet this requirement, an ANN model was developed using data collected from Naghizadeh (Naghizadehrokni, 2022) to precisely predict the performance of these trenches.
Adoption of environmentally friendly urban freight logistics practices: the role of communication and governance
Authors: Namagembe Sheila , Nantumbwe Shamim
Published: January 2025

Purpose

Environmental emissions are increasing in the urban areas. Much of the emissions arise from public procurement activities given that public sector firms are major customers to many supplying firms. Given the tremendous contribution, this study aims to examine the adoption of environmentally friendly urban freight logistics practices among public sector firms through assessing the impact of urban environmental governance, government environmental communication and organizational environmental governance.

Design/methodology/approach

Data for the study were collected in a single time period from central procuring and disposing entities (public sector firms) in the urban areas. A sample of 105 public sector firms in were used. One procurement officer and one member of the contracts committee were the key informants in the study. AMOS SPSS version 26 was used to obtain the results for the structural model and measurement model, respectively.

Findings

The findings indicate that the adoption of environmentally friendly urban freight logistics practices among public sector firms is significantly influenced by government environmental communication, organizational environmental governance and urban environmental governance. Urban environmental governance significantly influences organizational environmental governance. Urban environmental governance fully mediates the relationship between government environmental communication and public sector firms’ adoption of environmentally friendly urban freight logistics practices. Also, urban environmental governance and organizational environmental governance mediate the relationship between government environmental communication and adoption of environmentally friendly urban freight logistics practices.

Research limitations/implications

This study examined the adoption of environmentally friendly urban freight logistics practices among public sector firms. However, the study was conducted in a public procurement setting rather than a private sector procurement setting. Also, the study examined the impact of government environmental communication on public sector firms’ adoption of environmentally friendly urban freight logistics practices ignoring the impact of internal communications made within the public sector firms on environmental issues.

Originality/value

This study examined the adoption of environmentally friendly urban freight logistics practices among public sector firms. Freight logistics in public sector procurement has not been given significant attention in earlier research. Emphasis is placed on sustainable public sector procurement ignoring other aspects that would help curb environmental emissions that may arise during and after the delivery of public procurement requirements.