bluuebunny/crossref_metadata_2025 huggingface dataset:
Antioxidant supplementation blunts the proteome response to three weeks of sprint interval training preferentially in human type 2 muscle fibres
Authors: Wyckelsma Victoria L , Murgia Marta , Kamandulis Sigitas , Gastaldello Stefano , Brazaitis Marius , Snieckus Audrius , Eimantas Nerijus , Pääsuke Mati , Edman Sebastian , Apro William , Andersson Daniel C , Westerblad Håkan , Venckunas Tomas
Published: January 2025

Sprint interval training (SIT) is a time-efficient type of endurance training that involves large type 2 muscle fibre recruitment. Effiective antioxidant supplementation may mitigate positive training adaptations by limiting the oxidant challenge. Our aim was to test whether SIT affiects type 2 more than type 1 muscle fibres, and whether the training response is mitigated by antioxidant treatment. Young men performed three SIT sessions (6 × 30 s all-out cycling) per week for three weeks while treated with antioxidants (vitamin C, 1 g/day; vitamin E, 235 mg/day) or placebo. Vastus lateralis biopsies were taken to measure (i) activation of genes for reactive oxygen/nitrogen species (ROS) sensors and inflammatory mediators with quantitative RT PCR and (ii) fibre type-specific proteome adaptations using mass spectrometry-based proteomics. Vitamin treatment decreased the upregulation of genes for ROS sensors and inflammatory regulators during the first SIT session. The three weeks of SIT caused generally larger proteome adaptations in type 2 than in type 1 fibres, and this included larger increases in abundance of proteins involved in mitochondrial energy production. Vitamin treatment blunted the SIT-induced proteome adaptations, whereas it did not affiect the training-induced improvement in maximal cycling performance. In conclusion, (i) the large type 2 fibre recruitment and resulting proteome adaptations are instrumental to the effiectiveness of SIT, and (ii) antioxidant supplementation counteracts positive muscular adaptations to SIT, which would blunt any improvement in submaximal endurance performance, whereas it does not affiect the improvement in maximal cycling performance, where O2 delivery to muscle would be limiting.
Synthetic FLS2 receptor oligomer boosts plant innate immunity
Authors: Ma Zhiming , Xie Yi , Chng Choon-Peng , Huang Changjin , Miao Yansong
Published: January 2025

Cell surface receptors’ gradual assembly and oligomerization are vital for controlling receptor activation and turnover. However, the spatiotemporal mechanisms of how surface receptor interactions achieve high efficiency and sustain plant immune signaling remain unclear. Here, we synthetically engineered theArabidopsispattern recognition receptor FLS2 to control its oligomerization precisely. We investigated the dynamic FLS2 nanoscale assemblies at the single-molecule level and their corresponding rewired immune signaling. Engineered FLS2 exhibits enhanced defense mechanisms in an oligomerization status-dependent manner. FLS2 dimerization significantly enhances immune responses, while the over-assembled tetrameric version impairs receptor endocytosis, disrupting its timely turnover and weakening sustained immune signaling. Our results reveal precise control of immune receptor assemblies for initial activation and long-lasting immune signaling, offering insights for engineering plant defense receptors.
Systematic Evaluation of Normalization Approaches in Tandem Mass Tag and Label-Free Protein Quantification Data Using PRONE
Authors: Arend Lis , Adamowicz Klaudia , Schmidt Johannes R. , Burankova Yuliya , Zolotareva Olga , Tsoy Olga , Pauling Josch K. , Kalkhof Stefan , Baumbach Jan , List Markus , Laske Tanja
Published: January 2025

Despite the significant progress in accuracy and reliability in mass spectrometry technology, as well as the development of strategies based on isotopic labeling or internal standards in recent decades, systematic biases originating from non-biological factors remain a significant challenge in data analysis. In addition, the wide range of available normalization methods renders the choice of a suitable normalization method challenging. We systematically evaluated 17 normalization and two batch effect correction methods, originally developed for pre-processing DNA microarray data but widely applied in proteomics, on six publicly available spike-in and three label-free and tandem mass tag datasets. Opposed to state-of-the-art normalization practice, we found that a reduction in intragroup variation is not directly related to the effectiveness of the normalization methods. Furthermore, our results demonstrated that the methods RobNorm and Normics, specifically developed for proteomics data, in line with LoessF performed consistently well across the spike-in datasets, while EigenMS exhibited a high false positive rate. Finally, based on experimental data, we show that normalization substantially impacts downstream analyses, and the impact is highly dataset-specific, emphasizing the importance of use-case-specific evaluations for novel proteomics datasets. For this, we developed the PROteomics Normalization Evaluator (PRONE), a unifying R package enabling comparative evaluation of normalization methods, including their impact on downstream analyses, while offering considerable flexibility, acknowledging the lack of universally accepted standards. PRONE is available on Bioconductor with a web application accessible athttps://exbio.wzw.tum.de/prone/.
Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach
Authors: Dvir Yoav , Snir Sagi
Published: January 2025

The advent of the genomic era has produced an incredible wealth and resolution of molecular data, posing an unprecedented challenge for molecular systematics, necessitating novel techniques and paradigms. Consequently, whole genome approaches were developed to extract the evolutionary signal by taking advantage of a larger amount of data. In parallel and in light of the understanding that in prokaryotes, genome dynamics (GD) events, primarily gene gain and loss, provide a significantly richer signal than point mutations in ubiquitous housekeeping genes, GD-based approaches were suggested. However, proper modeling of these data and the processes generating them has lagged in their pace of accumulation, both because of a lack of deep understanding and because of technical difficulties. Among the central hurdles of accurate modeling of real data is the relaxation of rate constancy, particularly the untying of gain and loss rates. This relaxation violates key assumptions such as constant genome sizes, gene set, and model reversibility and has vast implications for implementation. This work presents a generic stochastic model, the two-ratio process (TRP), which encompasses and deals with these complications. As a special case, it contains the Poissonian process with different gene gain and loss rates as a form of the Birth-Death process with varying population sizes. The lack of reversibility invalidates traditional phylogenetic approaches, yielding a novel two-stage phylogenetic approach in which accurate, bidirectional parameters are first inferred for triplets and later combined by a special cherry-picking method to a complete tree. We show by algebraic techniques that this method is theoretically statistically consistent. The method implemented by the software TDDR (Triplets Directed Distances Reconstruction) was applied to synthetic data, showing an advantage over other approaches handling similar data but without the same model assumption. We also applied it to the Alignable Tight Genomic Clusters (ATGC) Database, which showed a high adequacy to the observed data. The TDDR code is available on GitHub:https://github.com/YoavDvir/TDDR.
Biocompatible sulfonium-based covalent probes for endogenous tubulin fluorescence nanoscopy in live and fixed cells
Authors: Auvray Marie , Koenen Tanja , Dybkov Olexandr , Urlaub Henning , Lukinavičius Gražvydas
Published: January 2025

Fluorescent probes enable the visualization of dynamic cellular processes with high precision, particularly when coupled with super-resolution imaging techniques that surpass the diffraction limit. Traditional methods include fluorescent protein fusion (e.g., GFP) or organic fluorophores linked to ligands targeting the protein of interest. However, these approaches often introduce functional disruptions or ligand-associated biological effects. Herein, we address these challenges by developing covalent fluorescent probes for endogenous tubulin, a critical cytoskeletal protein involved in processes such as cell movement, division, and biomolecule trafficking. Using well-known tubulin binder cabazitaxel and cell permeable fluorophore silicon-rhodamine—as a basis, we introduce a novel biocompatible cleavable linker containing a sulfonium center. This allowed the construction of the optimized probe, 6-SiR-o-C9-CTX, demonstrating excellent cell permeability, fluorogenic properties, and the ability to covalently label tubulin across various human cell lines. Importantly, the targeting moiety could be washed out while preserving tubulin staining, ensuring minimal disruption of tubulin function. This labeling technique is compatible with STED nanoscopy in both live and fixed cells, offering a powerful high-resolution imaging tool.
Passive symplastic phloem loading in the duckweedSpirodela polyrhiza
Authors: Li Jiazhou , Liesche Johannes
Published: January 2025

The lemnoidae, commonly called duckweeds, are a group of small, rapidly growing aquatic plants that play an important role in pond ecosystems and are used in biotechnological and remediation applications. While small, duckweeds feature phloem tissue in fronds and roots. To gain insight on duckweed phloem function, we investigated how sugar is loaded into the phloem sieve elements in the giant duckweedSpirodela polyrhiza. Genomes ofS. polyrhizaand three other duckweeds do not feature genes for the sucrose transporters typically associated with active apoplastic phloem loading. Neither did a sucrose transporter inhibitor affect sucrose concentration in phloem exudate. Active symplastic phloem loading was excluded based on the conventional plasmodesmata configuration and absence of oligosaccharides inS. polyrhizaphloem. Instead, uniform plasmodesmata density along the phloem loading pathway indicated a passive symplastic phloem loading type. When plasmodesmata permeability was artificially reduced by hormone treatment, the sucrose concentration in the phloem exudate was reduced, highlighting the potential role of plasmodesmata regulation in setting carbon export rates in species with passive phloem loading. Our results identifyS. polyrhizaas the first monocot species with passive phloem loading. Moreover, they indicate opportunities for optimization of duckweed growth.
Neur-Ally: A deep learning model for regulatory variant prediction based on genomic and epigenomic features in brain and its validation in certain neurological disorders
Authors: Prakash Anil , Banerjee Moinak
Published: January 2025

Large scale quantitative studies have identified significant genetic associations for various neurological disorders. Expression quantitative trait loci [eQTL] studies have shown the effect of single nucleotide polymorphisms [SNPs] on the differential expression of genes in brain tissues. However, a large majority of the associations are contributed by SNPs in the noncoding regions which can have significant regulatory function but are often ignored. Besides mutations that are in high linkage disequilibrium [LD] with actual regulatory SNPs will also show significant associations. Therefore, it is important to differentiate a regulatory non-coding SNPs with a non-regulatory one. To resolve this, we developed a deep-learning model named Neur-Ally, which was trained on epigenomic datasets from nervous tissue and cell line samples. The model predicts differential occurrence of regulatory features like chromatin accessibility, histone modifications and transcription-factor [TF] binding on genomic regions using DNA sequence as input. The model was used to predict the regulatory effect of neurological condition specific non-coding SNPs using in-silico mutagenesis. The effect of associated SNPs reported in Genome-wide association studies [GWAS] of neurological condition, Brain eQTLs, Autism Spectrum Disorder [ASD] and reported probable regulatory SNPs in neurological conditions were predicted by Neur-Ally.
Legacy effects of European colonialism on hotspots of biocultural diversity threat
Authors: Lenzner Bernd , Baumann Andreas , Norder Sietze , Essl Franz , Fellner Hannes A.
Published: January 2025

Patterns of biological diversity have been shaped by cultural practices in the past, while in turn, cultures and languages have evolved in close interaction with local species and ecosystems. However, in the Anthropocene, humans are putting increasingly more and diverse pressures on ecosystems and cultures resulting in accelerating threat levels on both. Understanding where biological and linguistic diversity (a common measure of cultural diversity) is threatened globally, and which drivers shape their distribution is crucial for pinpointing hotspots and prioritizing efforts to counter these threats. We find that the spatial patterns of the erosion of biological and cultural diversity are weakly congruent on a global scale and that they are driven by differential sets of mechanisms. However, our results also indicate that particularly large-scale historic socio-political events like the European colonial expansion have left long-lasting imprints on both biological and cultural diversity. The duration of European colonialism (i.e., the time a specific region was occupied by Europeans powers) significantly increases contemporary observed threat levels of biological and linguistic diversity.

Significance Statement

Biological and cultural diversity are closely intertwined. However, in an increasingly changing world where anthropogenic drivers put increasing pressures on ecosystems and cultures, both are threatened. Understanding how these threats to both, biological and linguistic diversity, are organized in space and where their individual and combined threat hotspots are is crucial for prioritization efforts to safeguard both. We also show what drivers affect their threat level globally and pinpoint that particularly large-scale socio-political events like the European colonial expansion have left long-lasting imprints on both biological and cultural diversity.
Molecular Basis of PAC1R Allosteric Modulation with Lipids in Membranes
Authors: Hamilton Nicholas B , Yang Bo , Xiang Chijian , Li Tongtong , Schneebeli Severin T. , Li Jianing
Published: January 2025

The pituitary adenylate cyclase-activating polypeptide receptor I (PAC1R) represents a highly sought-after therapeutic target for chronic pain, migraine, and post-traumatic stress. As a class B G protein-coupled receptor (GPCR), the PAC1R is highly expressed throughout the neuronal and central nervous system membranes, with the receptor subject to hormone activation and subsequent signal transduction. Despite its desirable indication, small molecule agonists for PAC1R have been notoriously difficult to develop due to competition with PACAP. For this reason, allosteric activation of the receptor has emerged as a promising pathway. To probe potential allosteric sites, herein, we present a study of the receptor in biomimetic concentrations of lipid membranes. Our results reveal that cholesterol recognizes two canonical and two non-canonical binding sites at PAC1R, which may influence critical residues in the transmembrane domain and PAC1R activation. Also, our simulations suggest the glycolipid GM3 interacts with PAC1R in both the extracellular and transmembrane domains. These lipid binding hotspots may hold high potential for advancing our understanding of class B GPCR signaling and the discovery of new molecules targeting PAC1R.

Statement of Significance

The PAC1R is a highly sought after therapeutic target in the GPCR family. Understanding its natural process signaling is highly interesting in identifying new modes of control and is currently not well established. This work uses coarse-grained molecular dynamics simulations to examine diverse PAC1R models’ interactions with their endogenous lipid bilayer in compositions that match the regions in the brain where the receptor is expressed. Two lipids, cholesterol and GM3, have been previously identified in similar receptors as allosteric modulators and were specifically examined in this study. This work also showcases multiple new lipid binding sites at transmembrane and extracellular sites highly implicated in PAC1R signaling.
Arousal State Control of Physiological Human Brain Pulsations
Authors: Järvelä Matti , Kananen Janne , Helakari Heta , Korhonen Vesa , Huotari Niko , Raitamaa Lauri , Tuunanen Johanna , Kallio Mika , Piispala Johanna , Ansakorpi Hanna , Kiviniemi Vesa
Published: January 2025

Sleep promotes cerebrospinal fluid (CSF) to interstitial fluid (ISF) exchange in brain facilitated by brain pulsations. Especially brain vasomotion and arterial pulsations modulated by noradrenaline drive the intracranial fluid dynamics. Narcolepsy type 1 (NT1) entails lessened hypocretinergic output to wake-promoting systems including the noradrenergic locus coeruleus. As arousal state and noradrenergic signaling affect CSF-ISF clearance, we chose patients with NT1 as a human hypocretin-targeted model of sleep-related pathology bridging the gap between healthy awake and sleep with respect to CSF flow pulsations. We also investigated the sensitivity of MREG to detect flow with a phantom model and sought to replicate earlier pulsation findings in sleep.

In this case-control study, we used fast fMRI to map brain pulsations in groups of healthy sleeping controls (n=13), healthy awake controls (n=79) and awake NT1 (n=21) patients. We measured the very low frequency (0.008-0.1) and cardiorespiratory frequencies and calculated in each frequency band the coefficient of variation, spectral power, and full band spectral entropy to obtain brain pulsation maps.

We uncovered a brain pulsation profile from healthy waking to sleep to a sleep-related pathology NT1 prominently affected in the vascular-related vasomotor and brain arterial pulsations. Our results established how drivers of brain hydrodynamics are affected by a specific loss of key neurotransmitter governing arousal compared to healthy sleep. We also showed with a phantom model that MREG is sensitive to flow-related signal changes and solidified evidence of brain pulsations in the healthy states of sleep and wakefulness.

Significance statement

This study establishes how a specific depletion of arousal state controlling neurotransmitter hypocretin-1 affects brain fluid dynamics by comparing patients with narcolepsy type 1 (NT1) to healthy wake and sleeping controls. We used fast fMRI to reveal that reduced hypocretinergic activity and following postulated inconsistent noradrenergic signaling in NT1 leads to high vasomotor and low brain arterial pulsations compared to healthy wakefulness while healthy sleep produces brain arterial and respiratory pulsations that dominate over those observed in NT1. The water flow biometrics we verified in this study with a phantom model indicate that deficient hypocretin-noradrenaline axis in humans leads to opposing changes in vasomotor and arterial induced brain pulsation that may propagate to altered glymphatic solute transportation.
Immunity can impose a reproduction-survival tradeoff on human malaria parasites
Authors: Patterson Denis D. , Childs Lauren M. , Stopard Isaac J. , Chitnis Nakul , Serrato-Arroyo Sergio , Greischar Megan
Published: January 2025

Many pathogenic organisms produce specialized life stages for within-host multiplication versus on-ward transmission, including malaria parasites. Traits that enable faster multiplication—including limited investment into transmission stage production—should put host health at greater risk (all else equal). Yet it is not clear why parasites do not evolve ever faster multiplication rates, since malaria parasites do not appear to adhere to tradeoffs between the rate and duration of transmission that are classically predicted to constrain parasite evolution. To address this puzzle, we introduce an age-of-infection structured within-host mathematical model incorporating dynamic immune clearance to investigate potential tradeoffs and understand how parasites optimize their transmission investment. When investment is constant across all ages of infection, increased transmission investment reduces infection duration and parasite fitness, with optimal investment occurring at a relatively low value (around 5%), far lower than the optimum recovered from models that lack dynamic feedbacks between parasite investment and immune clearance. For age-varying strategies, our model shows that malaria parasites can enhance their fitness by delaying transmission investment to allow for faster within-host multiplication initially. Our results indicate that adaptive immunity can impose a survival-reproduction tradeoff that explains why malaria parasites cannot evolve ever faster within-host multiplication. Our theoretical framework provides a basis for understanding how transmission investment strategies alter the timing of infectiousness over the lifespan of malaria infections, with implications for parasite evolution in response to control efforts.
Generalizable prediction of liquid-liquid phase separation from protein sequence
Authors: MohammadHosseini Amir M. , Teimouri Hossein , Gureghian Vincent , Najjar Rayan , Lindner Ariel B. , Pandi Amir
Published: January 2025

Liquid-liquid phase separation (LLPS) is a physicochemical process through which a homogeneous liquid solution spontaneously separates into distinct liquid phases with different compositions and properties. Driven by weak multivalent interactions, LLPS in living systems allows the dynamic compartmentalization of biomolecules to regulate and enhance various cellular processes. Despite recent advances, predicting phase-separating proteins and their key LLPS-driving regions remains limited by the versatility of models. Here, we developed Phaseek, a generalizable LLPS predicting model that combines contextual sequence encoding with statistical protein graph representations. Phaseek accurately predicts diverse LLPS-prone proteins, as well as key regions and effects of point mutations within them. Proteome-wide analysis across eighteen species suggests that LLPS is evolutionary conserved and involved in multiple biological processes. Additionally, predictions by Phaseek highlight the key physicochemical and structural properties associated with LLPS. Provided as an open-access model with a user-friendly implementation, Phaseek serves as a versatile LLPS predictor for advancing fundamental and applied research in related fields.
From temperate to polar waters: Transition to non-cyanobacterial diazotrophy upon entering the Atlantic gateway of the Arctic Ocean
Authors: von Friesen Lisa W. , Laber Christien P. , Kristensen Bjarke H. , Nysted Emma , Sundbom Marcus , Bertilsson Stefan , Snoeijs-Leijonmalm Pauline , Farnelid Hanna , Riemann Lasse
Published: January 2025

Nitrogen fixation, the microbial reduction of dinitrogen to ammonia, is increasingly recognized to occur in the Arctic Ocean. However, knowledge about the composition, biogeography, abundance, and ecology of nitrogen-fixing organisms (diazotrophs) is poor. This ultimately hinders prediction of ecosystem productivity fueled by nitrogen fixation in this rapidly changing and predominantly nitrogen-limited ocean. We assessed the composition and abundance of total and active diazotrophs in sub-surface water (8 m; amplicon sequencing and quantification of the marker genenifH) over ∼3,400 km from the mouth of the brackish Baltic Sea to the sea ice edge in the Arctic Ocean. Upon entering nutrient-rich waters in the Atlantic gateway to the Arctic, we discovered an abrupt transition from autotrophic to heterotrophic diazotrophic activity. Our findings suggest that diazotrophy is functionally distinct in the Arctic Ocean compared to adjacent temperate-boreal waters – a difference likely driven by inorganic nutrients, salinity, and temperature. We identify three key non-cyanobacterial diazotroph groups in the Arctic Ocean with Arctic-specific (Rhodocyclales and Oceanospirillales) or more widespread (unknown Gammaproteobacterium) distribution patterns and report theirnifHgene transcription levels (up to 103nifHtranscripts L−1). In contrast, actively transcribing diazotrophs in the warmer and more nutrient-poor Norwegian Sea with coastal-influenced water were dominated by sublineages of CandidatusAtelocyanobacterium thalassa(UCYN-A1, UCYN-A2, UCYN-A4; up to 104nifHtranscripts L-1). With ongoing atlantification of the Arctic pushing oceanic provinces and biogeographical ranges poleward, we predict a future displacement of the transition from autotrophic to heterotrophic diazotrophic activity with likely significant changes in nitrogen fixation.
A Grapevine MYC2-MYB24 Regulatory Module Activates Terpenoid Biosynthesis Upon Methyl Jasmonate Elicitation
Authors: Zhang Chen , Echeverria Jone , Foresti Chiara , Santiago Antonio , El Idrissi Moubtassim Hafsa , Amato Alessandra , Sonego Paolo , Pindo Massimo , Zenoni Sara , Moretto Marco , Matus José Tomás
Published: January 2025

Terpenes contribute to the characteristic flavor and aroma of grapes and their derived products while serving protective roles in plants against radiation, oxidative stress, and biotic challenges. The phytohormone methyl jasmonate (MeJA) mediates many of these processes and enhances terpene content in grape berries, but its underlying regulatory mechanism remains unclear. To address this, we treatedVitis viniferacv. ‘Gamay Fréaux’ berry cell suspensions with MeJA (100 μM) and cyclodextrins (50 mM), generating transcriptomic data. Upregulated genes (URGs) were enriched in jasmonic acid biosynthesis and signaling pathways, and transcription factors (TF) that represent novel candidates modulating MeJA responses. Inspection of these TFs in terms of their co-expressed genes allowed us to focus onMYC2, the sole bHLH IIIe subgroup member in grapevine. Using DAP-seq, we identified MYC2-bound genes and integrated them with MeJA-URGs andMYC2co-expressed genes (CEGs) to produce a high-confidence target list. These targets were bound via a conserved G-box motif and included jasmonate-related genes (e.g.,LOXandJAZ) and TFs such as MYB24, previously found to interact with MYC2 to activate terpenoid biosynthesis genes. Consistently, MeJA treatment induced 15 terpene synthase genes (TPS), eleven of which were bound by MYB24, MYC2, or both. Terpenoid compounds associated with these inducedTPSsaccumulated both intra- and extracellularly following treatment with MeJA and cyclodextrins, but not with abscisic acid (ABA). Our findings suggest that MYC2 regulates the jasmonate pathway and cooperates with MYB24 to mediate MeJA-induced terpene biosynthesis, shedding light on mechanisms that may extend to flower and fruit development, where this MYB-bHLH complex is also expressed.
High conformational flexibility of phosphomannomutase 2: Implications for functioning mechanisms, stability and pharmacological chaperone design
Authors: del Caño-Ochoa Francisco , Vilar Marçal , Vilas Alicia , Company Rebeca , Pérez Belén , Ramón-Maiques Santiago
Published: January 2025

Phosphomannomutase 2 (PMM2) is a critical enzyme in the N-glycosylation pathway, and its defect is the cause of the most common congenital disorder of glycosylation. Despite its biological relevance, the understanding of PMM2 is limited, as the catalytic mechanism and required conformational dynamics remain unknown. In this study, we investigated murine PMM2 (Pmm2) to elucidate its structural flexibility and functional insights. High-resolution crystal structures of Pmm2 in both apo and activator-bound forms provided a more detailed model of the protein, underscoring the role of three ionic cofactors that are essential for dimerization, catalysis, and stability. The Pmm2 structures also provided eight distinct conformations of the protein subunit, highlighting its dynamic nature. Structural comparisons among Pmm2, human PMM2 and other phosphomannomutases helped define the architecture of the enzyme as a dimer assembled by the rigid association of the cap domains, which provide a flat platform from which the core domains of each subunit protrude in a flexible manner. Molecular dynamics (MD) simulations of the human and murine PMM2s further emphasized the enzyme’s substantial conformational flexibility, revealing extensive core domain movements and suggesting potential inter-subunit communication within the dimer. This study refines the model of PMM2 function, demonstrating its dynamic role in substrate binding, intermediate reorientation, and product release. The observed flexibility provides new opportunities to target specific enzyme states, enabling the development of pharmacological chaperones.
Nemo-like kinase disrupts nuclear import and drives TDP43 mislocalization in ALS
Authors: Bekier Michael E. , Pinarbasi Emile , Mesojedec Jack J. , Ghaffari Layla , de Majo Martina , Ullian Erik , Koontz Mark , Coleman Sarah , Li Xingli , Tank Elizabeth M. H. , Waksmacki Jacob , Barmada Sami
Published: January 2025

Cytoplasmic TDP43 mislocalization and aggregation are pathological hallmarks of amyotrophic lateral sclerosis (ALS). However, the initial cellular insults that lead to TDP43 mislocalization remain unclear. In this study, we demonstrate that Nemo-like kinase (NLK)—a proline-directed serine/threonine kinase—promotes the mislocalization of TDP43 and other RNA-binding proteins by disrupting nuclear import. NLK levels are selectively elevated in neurons exhibiting TDP43 mislocalization in ALS patient tissues, while genetic reduction ofNLKreduces toxicity in human neuron models of ALS. Our findings suggest that NLK is a promising therapeutic target for neurodegenerative diseases.
Cigarette smoke and biological age induce degenerative heterogeneity in retinal pigment epithelium
Authors: Singh Krishna , Jin Yang , Hu Ming-Wen , Palazzo Isabella , Cano Marisol , Hoang Thanh , Bhutto Imran , Wang Shusheng , Sinha Debasish , Blackshaw Seth , Qian Jiang , Handa James T.
Published: January 2025

Environmental exposure such as cigarette smoke induces epigenetic changes that can induce degenerative heterogeneity and accelerate aging. In early age-related macular degeneration (AMD), the leading worldwide cause of blindness among the elderly, retinal pigment epithelial (RPE) cell heterogeneity is a key change. Since smoking is the strongest environmental risk factor for AMD, we hypothesized that cigarette smoke induces degenerative RPE heterogeneity through epigenetic changes that are distinct from aging, and that with aging, the RPE becomes vulnerable to cigarette smoke insult. We administered cigarette smoke condensate (CSC) intravitreally to young and aged mice and performed snRNA-seq and snATAC-seq on the RPE/choroid. This analysis identified separate cell clusters corresponding to healthy and abnormal, dedifferentiated RPE in both aged vehicle-treated and young CSC-treated mice. The dedifferentiated RPE were characterized by a global decrease in chromatin accessibility and decreased expression of genes in functional categories that were linked to hallmarks of aging. Notably, young, dedifferentiated RPE also exhibited a compensatory upregulation of hallmarks of aging-related genes, specifically those related to mitochondrial function and proteostasis. In contrast, aged dedifferentiated RPE did not express these compensatory changes, and did not survive CSC treatment, as experimentally verified with TUNEL labeling. These changes are relevant to early AMD because we identified through scRNA-seq, similar dedifferentiated and healthy macular RPE clusters in a donor who smoked and another with early AMD, but not from a nonsmoker. Degenerative cellular heterogeneity can include an abnormal cluster that jeopardizes cell survival and may represent an additional hallmark of ocular aging.
A fresh perspective on carp feeding behavior in an aquaculture pond and its consequences for individual growth
Authors: Říha Milan , Rabaneda-Bueno Rubén , Prchalová Marie , Kajgrová Lenka , Vrba Jaroslav , Meador Trevis B. , Kuklina Irina , Bláha Martin , Draštík Vladislav , Kočvara Luboš , Veselý Lukáš
Published: January 2025

The common carp (Cyprinus carpio) is an important species in global aquaculture. To optimize its production, it is necessary to understand its behaviour in relation to environmental and management factors. This study investigated the spatial and temporal dynamics of carp behaviour in a semi-intensive aquaculture pond under controlled feeding regimes over two growing seasons (2022–2023). Using telemetry and stable isotope analysis, we investigated activity, depth utilisation and feeding behaviour in relation to growth and aquaculture practices.

The activity of carp and their spatial use changed over time, influenced by temperature, food availability and stocking density. Activity peaked in spring and early summer and was highest at night and twilight. In the warmer months, shallow areas (<0.5 m) were favoured, probably due to thermoregulation, oxygen levels or access to prey. Individual variability in foraging site use and food composition correlated with growth, highlighting the importance of behavioural traits in resource acquisition. A flood-induced rise in stocking density in 2022 increased competition for food, resulting in higher activity and lower growth compared to 2023. Stable isotope analysis showed that benthic invertebrates were the main food source, supplemented by cereals, emphasising the importance of a balanced natural and artificial diet.

Our results emphasise the value of telemetry and isotope analysis for improving aquaculture practises. Recommendations include adapting feeding to seasonal and individual behaviour, mitigating density effects and promoting sustainable practises to optimise carp production.
Efficient Techniques for Comprehensive Tissue Sampling in Adult Xenopus
Authors: Jonas-Closs Rachael A , Anderson Cora E , Peshkin Leonid
Published: January 2025

Xenopushas long been a pivotal model organism for investigating vertebrate development and disease, offering deep insights into cellular processes and gene function. Despite the wealth of information on embryonicXenopu,sthere remains a significant gap in standardized methods for adult tissue sampling, especially for modern approaches like quantitative proteomics. This study introduces a comprehensive protocol for rapid, precise, and efficient sampling of multiple tissues in adultXenopu.sThe protocol addresses challenges associated with the subtle anatomical differences compared to other anurans, ensuring reproducibility even for those with limited experience in frog dissection. This protocol is optimized for high- quality biochemical analyses by prioritizing sample freshness. We are facilitating the rapid collection of up to 18 tissues within an hour. Additionally, the methods apply to perfused and unperfused conditions, providing flexibility for a range of experimental needs. This work not only fills a critical methodological gap forXenopus laevisandtropicalisbut also serves as a valuable resource for researchers adapting techniques to similar amphibian models, thereby enhancing the scope and reliability of comparative biological and evolutionary studies.

This is part one of a comprehensiveXenopussampling protocol. The tissues sampled are the heart ventricle, arterial trunk, left liver lobe, gallbladder, lung, pancreas, spleen, larynx, esophagus, stomach, intestines, testes, fat bodies, oviduct, paired kidneys, sciatic plexus, skin, thymus, and whole eye.
Imbalanced mitochondrial dynamics in human and mouse PD brains
Authors: Brown Harry J. , Fan Rebecca Z. , Bell Riley , Salehe Said S. , Martínez Carlos Martínez , Lai Yanhao , Tieu Kim
Published: January 2025

Mitochondrial dysfunction is a major pathogenic mechanism in Parkinson’s disease (PD). Emerging studies have shown that dysregulation in mitochondrial dynamics (fission/fusion/movement) has a major negative impact on mitochondria - both morphologically and functionally. Partial genetic deletion and pharmacological inhibition of the mitochondrial fission dynamin-related protein 1 (Drp1) have been demonstrated to be beneficial in experimental models of PD. However, the expression of DRP1 (and other fission and fusion genes/proteins) has not been investigated in the brains of Parkinson’s patients. Without these data, the question remains whether targeting DRP1 is a valid therapeutic target for PD. To address this gap of knowledge, first, we used post-mortem substantia nigra specimens of Parkinson’s patients and controls. Significant increases in the levels of bothDNM1L, which encodes DRP1, as well as the DRP1 protein were detected in Parkinson’s patients. Immunostaining revealed increased DRP1 expression in dopamine (DA) neurons, astrocytes, and microglia. In addition to DRP1, the levels of other fission and fusion genes/proteins were also altered in Parkinson’s patients. To complement these human studies and given the significant role of α-synuclein in PD pathogenesis, we performed time-course studies (3-, 6- and 12-month) using transgenic mice overexpressing human wild-typeSNCAunder the mouseThy-1promoter. As early as 6 months old, we detected an upregulation ofDnm1land Drp1 in the nigral DA neurons of theSNCAmice as compared to their WT littermates. Furthermore, these mutant animals exhibited more Drp1 phosphorylation at serine 616, which promotes its translocation to mitochondria to induce fragmentation. Together, this study shows an upregulation of DRP1/Drp1 and alterations in other fission/fusion proteins in both human and mouse PD brains, leading to a pro-fission phenotype, providing additional evidence that blocking mitochondrial fission or promoting fusion is a potential therapeutic strategy for PD.
Exploring sex-specific alterations in early Alzheimer’s disease using network MRI analyses
Authors: Ben Abdallah Ines , Sourty Marion , Rame Marion , Degiorgis Laetitia , Isik Amine , Mathis Chantal , Harsan Laura-Adela
Published: January 2025

Alzheimer’s disease (AD) is characterized by the accumulation of amyloid-β plaques and tau neurofibrillary tangles, leading to progressive cognitive decline. Subtle cognitive and neural adaptations mark the preclinical stage of AD, occurring years before mild cognitive impairment and AD diagnosis. Throughout the continuum of AD, women (∼60% of AD cases) demonstrate faster rates of cognitive decline, greater hippocampal atrophy, and more extensive tau pathology compared to men. This is particularly evident in early AD phases. Therefore, investigating early sex-specific changes is crucial for identifying biomarkers and developing targeted interventions.

In the present study, we conducted a longitudinal investigation on theAppNL-F/MAPTdouble knock-in (dKI) mouse model, to identify sex-specific resting-state functional connectivity (FC) patterns associated with early cognitive deficits. Male and female wild-type and dKI mice were tested for associative and long-term memory deficits, followed by resting-state functional magnetic resonance imaging to examine the default mode network (DMN) connectivity at 2 and 4 months of age. Female dKI mice exhibited earlier and more pronounced memory impairments, with deficits apparent at 2 months, while male deficits emerged at 4 months. FC analyses revealed distinct sex-specific alterations within DMN and between DMN hubs and memory processing nodes. Notably, female dKI mice showed hypersynchrony between the retrosplenial cortex (RSP) and key memory-related regions such as the entorhinal cortex (ENT) and hippocampus (HIP), but also towards subcortical regions overlapping thalamic nuclei, amygdala, and substantia nigra. Meanwhile, male dKI mice exhibited hypoconnectivity along RSP-HIP axis, RSP-reuniens nucleus, and RSP-sensorimotor cortex. Our data particularly highlight sexually dimorphic RSP-ENT and RSP-HIP connectivity.

These results underscore the critical role of sex in shaping neural network reorganization and cognitive decline during preclinical AD. These findings position neural network connectivity as a sensitive biomarker of early memory dysfunction and highlight the need for sex-specific investigations and potentially tailored therapeutic strategies in AD.
Synergistic olfactory nerve input and cholinergic neuromodulation can activate ERK in rat olfactory bulb vasopressin cells
Authors: Reichardt Nicolas , Kindler Lisa , Pino Esteban , Lukas Michael , Egger Veronica , Suyama Hajime
Published: January 2025

Social discrimination in rats relies on vasopressin cells (VPCs) intrinsic to the olfactory bulb (OB). We had observed that VPCs responded to electrical stimulation of the olfactory nerve in acute OB slices with inhibitory postsynaptic potentials, and that the neuromodulator acetylcholine could revert these responses to excitation, resulting in action potentials (AP). Moreover, in behaving rats that were exposed to conspecifics, more VPCs were immunopositive to the neural activity marker pERK (pERK+VPC) than in control rats. However, it is unclear whether these two observations, the increased ERK activationin vivo, and the generation of APs in the presence of AChin vitro, can be actually mapped onto each other. Here we investigated ERK activation in acute OB slices from transgenic VP-eGFP rats upon either chemical stimulation or tetanic olfactory nerve stimulation. Both KCl and NMDA stimulation resulted in substantial pERK induction across bulbar layers and caused VPC spiking in whole-cell recordings, but only NMDA slightly increased pERK+VPC percentage. Tetanic olfactory nerve stimulation yielded localized, column-like ERK activation of neurons across bulbar layers. The presence of ACh during tetanic stimulation substantially and specifically increased percentages of pERK+VPCs within columns, indicating that columnar pERK+VPCs were preferentially activated by coincident cholinergic neuromodulation and synaptic input.

Our results validate pERK induction as a tool to monitor synaptic VPC excitation in the OB, and imply that depolarization of VPCs alone is insufficient to activate ERK. We propose that synaptically evoked APs are a prerequisite for pERK induction in VPCs.
Continuous feedback protocols for cooling and trapping a quantum harmonic oscillator
Authors: De Sousa Guilherme , Bakhshinezhad Pharnam , Annby-Andersson Björn , Samuelsson Peter , Potts Patrick P. , Jarzynski Christopher
Published: January 2025

Quantum technologies and experiments often require preparing systems in low-temperature states. Here we investigate cooling schemes using feedback protocols modeled with a quantum Fokker-Planck master equation (QFPME) recently derived by Annby-Andersson []. This equation describes systems under continuous weak measurements, with feedback based on the outcome of these measurements. We apply this formalism to study the cooling and trapping of a harmonic oscillator for several protocols based on position and/or momentum measurements. We find that the protocols can cool the oscillator down to, or close to, the ground state for suitable choices of parameters. Our analysis provides an analytically solvable case study of quantum measurement and feedback and illustrates the application of the QFPME to continuous quantum systems.

Published by the American Physical Society
2025
Synthesis and crystal structure analysis of 1-ethyl-1,3-dihydro-2H-benzo[d]imidazole-2-thione
Authors: Gurbanov Atash V. , Guseinov Firudin I. , Samigullina Aida I. , Hökelek Tuncer , Hasanov Khudayar I. , Javadzade Tahir A. , Belay Alebel N.
Published: January 2025

The asymmetric unit of the title compound, C9H10N2S, contains two crystallographically independent, almost planar, molecules. In the crystal, intermolecular N—H...S hydrogen bonds link the molecules into pseudocentrosymmetric dimers, enclosing R
2
2(8) ring motifs. There are mutual π–π interactions between the five- and six-membered rings of each independent molecule in the chosen asymmetric unit, with ring centroid-to-centroid distances of 3.6685 (12) and 3.7062 (12) Å. A weak C—H...π(ring) interaction is also observed. The N—H...S hydrogen bonds, the π–π interactions and the weak C—H...π(ring) interaction are effective in the stabilization of the crystal structure. The structure was refined as an inversion twin with a component occupancy ratio of 0.546 (15):0.454 (16).
Beyond the minimum: designing for neurodiversity in museums and galleries
Authors: Granland Madeleine Ella , Sadia Toar , Cooper Elizabeth
Published: January 2025

Purpose

This study explored the relationship between architectural excellence and designing for neurodiversity in museums and galleries. It examined the conflicts and overlaps in design preferences between neurodivergent groups in relation to the materials and spatial layout of museums and galleries. It also compares these design preferences to existing theories of architectural excellence.

Design/methodology/approach

A mixed-methods approach was used including an online survey directed at neurodivergent populations that generated 281 survey responses (from 23 countries). Survey results were analysed alongside seven interviews with neurodivergent people that were conducted in three case study museums: The Metropolitan Museum of Art, British Museum, and Mathematics: The Winton Gallery, Science Museum. In both the survey and interviews, a diverse range of neurodivergent conditions were recorded.

Findings

Results showed that almost half of neurodivergent participants are avoiding museums and galleries due to sensory overload or underload. Participants indicated that sensory mapping in 3D/isometric formats would assist with managing their experience when visiting these sites. The findings suggested that preferences for architectural features (such as layouts and materials) were associated more strongly with individual preference than neurodivergent condition.

Originality/value

The study found that applying elements of prospect, refuge and context theory were successful predictors of design preferences for neurodivergent populations. Therefore, the application of these themes is expected to lead to improved visitor experiences in museums and galleries. Future research should expand on the use of prospect, refuge and context theories when designing for neurodiversity.