bluuebunny/crossref_metadata_2025_split huggingface dataset:
PI(3)P signaling regulates endosomal flux underlying developmental synaptic remodeling via Rab4
Authors: Singh Kamaldeep , Das Semanti , Rai Dipti , Sutradhar Sabyasachi , Sarkar Asmita , Howard Jonathon , Ray Krishanu 
Published: February 2025

AbstractRab4 GTPase, essential for endosomal sorting and trafficking, is implicated in synaptic atrophy and dementia. To uncover the underlying mechanism, we studied the correlation between Rab4 vesicle transport in axons and episodic remodeling of synapses in the central nervous system (CNS) ofDrosophilalarvae. We found that synapse-bound traffic and presynaptic enrichment of Rab4 vesicles increase during the programmed, transient contraction of synapses in the ventral neuropil region at a specific larval stage. This coincides with the episodic activation of insulin and Vps34-mediated signaling, which elevates phosphatidylinositol-3-phosphate levels on Rab4 vesicles. The presence of this phospholipid on Rab4-associated vesicles recruit a PX-domain-containing motor protein, Klp98A, accelerating synapse-directed traffic. This, in turn, increases presynaptic enrichment of Rab4 during the developmentally programmed synapse contraction phase. Our findings elucidate the molecular mechanism that regulates developmental synaptic plasticity in the CNS via insulin signaling and directed axonal transport of endosomes.Author summaryHealthy brain function relies on the growth and remodeling of synaptic connections between nerve cells. This process involves carefully orchestrated movements of proteins and membranes inside the neurites. For instance, endosome movement in the nerve cell extensions helps guide neuronal growth, recycle parts of the synapse, and alter signal transmissions between neurons. Rab GTPases, a group of small G-proteins, are crucial for these processes. Here, we aimed to understand what triggers these processes and how the ’supply chain’ within nerve cell extensions is connected to changes at the synapse. In fruit fly larvae, we observed that the movement of Rab4 vesicles in the nerve cell extensions is inversely related to gross synapse content. A further examination revealed that onset of insulin signaling accelerates the Rab4 vesicles towards synapse through a lipid kinase called Vps34, which makes a signaling lipid called phospatidylinnositol-3-phosphate. Higher levels this lipid molecule on Rab4 vesicles attract a motor protein, Klp98A, speeding up their movement during the synaptic contraction phase. Our findings reveal a new mechanism that regulates Rab4 vesicle transport and its impact on synapse stability. The study further suggests potential targets for controlling age-related dementia likely to be caused by excessive insulin signaling in neurons.
CRISPR targeting of H3K4me3 activates gene expression and unlocks centromeric crossover recombination in Arabidopsis
Authors: Binenbaum Jenia , Adamkova Vanda , Fryer Hannah , Xu Linhao , Gorringe Nicola , Włodzimierz Piotr , Burns Robin , Papikian Ashot , Jacobsen Steven E. , Henderson Ian , Harris C. Jake 
Published: February 2025

AbstractH3K4me3 is a fundamental and highly conserved chromatin mark across eukaryotes, playing a central role in many genome-related processes, including transcription, maintenance of cell identity, DNA damage repair, and meiotic recombination. However, identifying the causal function of H3K4me3 in these diverse pathways remains a challenge, and we lack the tools to manipulate it for agricultural benefit. Here we use the CRISPR-based SunTag system to direct H3K4me3 methyltransferases in the model plant,Arabidopsis thaliana. Targeting of SunTag-SDG2 activates the expression of the endogenous reporter gene,FWA. We show that SunTag-SDG2 can be employed to increase pathogen resistance by targeting the H3K4me3-dependent disease resistance gene,SNC1. Meiotic crossover recombination rates impose a limit on the speed with which new traits can be transferred to elite crop varieties. We demonstrate that targeting of SunTag-SDG2 to low recombining centromeric regions can significantly stimulate crossover formation. Finally, we reveal that the effect is not specific to SDG2 and is likely dependent on the H3K4me3 mark itself, as the orthogonal mammalian-derived H3K4me3 methyltransferase, PRDM9, produces a similar effect on gene expression with reduced off-target potential. Overall, our study supports an instructive role for H3K4me3 in transcription and meiotic recombination and opens the door to precise modulation of important agricultural traits.
Seven blood biomarkers are associated with TGF-β and VHL-HIF signaling in patients with clear cell renal cell carcinoma
Authors: Mallikarjuna Pramod , Erdem Cemal , Hedman Harald , Sitaram Raviprakash T. , Beorlegui Ruben Ilundain , Aripaka Karthik , Larsson Anders , Ljungberg Börje , Kamali-Moghaddam Masood , Landström Maréne 
Published: February 2025

AbstractClear cell renal cell carcinoma (ccRCC) is an aggressive kidney cancer subtype frequently associated with poor prognosis. Most ccRCC cases are asymptomatic in early stages and symptomatic mostly in advanced stages. Furthermore, the heterogeneity of ccRCC presents a challenge to design new treatments. In this study, using proximity extension assay (PEA), we analyzed blood samples from 134 patients with ccRCC and from 111 age- and gender-matched healthy donors. We identified a panel of seven proteins (ANXA1, ESM1, FGFBP1, MDK, METAP2, SDC1, and TFPI2) that are associated with clinicopathological parameters and patient survival. These biomarkers can differentiate patients with ccRCC from the control individuals with high diagnostic sensitivity and specificity. Moreover, by studying protein expression in solid tumors from the same ccRCC patients, we revealed associations between the panel biomarkers and proteins in the TGF-β and VHL-HIF signaling pathways. We found that most tumor promoting biomarkers were positively associated with TGF-β signaling and HIF-2α, and negatively associated with pVHL and HIF-1α. We also found that most tumor suppressing biomarkers were positively associated with pVHL and HIF-1α and negatively associated with TGF-β signaling and HIF-2α. For ccRCC patients, the blood protein biomarkers that were connected to poor prognosis and TGF-β/HIF-2α signaling, as identified in this study, are potentially important assets in personalized medicine.
De-novo DNA Methylation of Bivalent Promoters Induces Gene Activation through PRC2 Displacement
Authors: O’Geen Henriette , Mihalovits Alina , Brophy Benjamin D. , Yang He , Miller Maxwell W. , Lee Chelsey J. , Segal David J. , Tomkova Marketa 
Published: February 2025

AbstractPromoter DNA methylation is a key epigenetic mark, commonly associated with gene silencing. However, we noticed that a positive association between promoter DNA methylation and expression is surprisingly common in cancer. Here, we use hit-and-run CRISPR/dCas9 epigenome editing to evaluate how deposition of DNA methylation can regulate gene expression dependent on pre-existing chromatin environment. While the predominant effect of DNA methylation in non-bivalent promoters is gene repression, we show that in bivalent promoters this often leads to gene activation. We demonstrate that gain of DNA methylation leads to reduced MTF2 binding and eviction of H3K27me3, a repressive mark that guards bivalent genes against activation. Our cancer patient data analyses reveal that in cancer, this mechanism likely leads to activation of a large group of transcription factors regulating pluripotency, apoptosis, and senescence signalling. In conclusion, our study uncovers an activating role of DNA methylation in bivalent promoters, with broad implications for cancer and development.
Endothelial cell Pannexin1 overexpression impairs ischemic stroke outcome in a sex-dependent manner
Authors: Tomàs-Gracia Maria , Mauro Amanda K , Duffy Colleen K , Dai Eric Y , Shahab Guleer , Medina Christopher B , Ravichandran Kodi S , Isakson Brant E , Good Miranda E 
Published: February 2025

AbstractIschemic stroke is a leading cause of morbidity and mortality. We have previously shown that deletion of endothelial cell (EC) Panx1 reduces ischemic stroke infarct volume and reduces cerebral arterial myogenic reactivity, which regulates cerebral blood flow. We hypothesized that EC Panx1 content dictates ischemic stroke outcome and thus increased EC Panx1 expression will worsen ischemic stroke outcomes due to exacerbated myogenic tone development and impaired cerebral blood flow recovery. To test this, we generated the Cdh5-CreERT2+ROSA26-hPanx1Tgmouse model that conditionally overexpresses the human isoform of Panx1 specifically in EC. We have found that cerebral myogenic reactivity is significantly increased with overexpression of EC Panx1 only in female mice, without alterations in peripheral vascular reactivity or blood pressure regulation. Similarly, we found that infarct size was increased and recovery of cerebral blood flow was reduced in female but not male EC Panx1 overexpressing mice. Our findings indicate a role for EC Panx1 as a mediator of ischemic stroke recovery. Furthermore, these data suggest a potential sex-dependent effect for EC Panx1, where females are more sensitive to increased EC Panx1 in cerebral vascular function and may provide a potential therapeutic target for the treatment of ischemic stroke in women.
Magnetic activation of electrically active cells
Authors: Duret Guillaume , Coffler Samantha , Avant Ben , Kim Wonjune , Peterchev Angel V. , Robinson Jacob 
Published: February 2025

AbstractMagnetic control of cell activity has applications ranging from non-invasive neurostimulation to remote activation of cell-based therapies. Unlike other methods of regulating cell activity like heat and light, which are based on known receptors or proteins, no magnetically gated channel has been identified to date. As a result, effective approaches for magnetic control of cell activity are based on strong alternating magnetic fields able to induce electric fields or materials that convert magnetic energy into electrical, thermal, or mechanical energy to stimulate cells. In our investigations of magnetic cell responses, we found that a spiking HEK cell line with no other co-factors responds to a magnetic field that reaches a maximum of 500 mT within 200 ms using a permanent magnet. The response is rare, approximately 1 in 50 cells, but is fast and reproducible, generating an action potential within 200 ms of magnetic field stimulation. The magnetic field stimulation is over 10,000 times slower than the magnetic fields used in transcranial magnetic stimulation (TMS) and the induced electric field is more than an order of magnitude lower than necessary for neuromodulation, suggesting that induced electric currents do not drive the cell response. Instead, our calculation suggests that this response depends on mechanoreception pathways activated by the magnetic torque of TRP-associated lipid rafts. Despite the relatively rare response to magnetic stimulation, when cells form gap junctions, the magnetic stimulation can propagate to nearby cells, causing tissue-level responses. As an example, we co-cultured spiking HEK cells with beta-pancreatic MIN6 cells and found that this co-culture responds to magnetic fields by increasing insulin production. Together, these results point toward a method for the magnetic control of biological activity without the need for a material co-factor such as synthetic nanoparticles. By better understanding this mechanism and enriching for magneto-sensitivity it may be possible to adapt this approach to the rapidly expanding tool kit for wireless cell activity regulation.
Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality
Authors: Navarrete Méndez Maria José , Amini Sina S. , Santos Juan Carlos , Saal Jacob , Wake Marvalee H. , Ron Santiago R. , Tarvin Rebecca D. 
Published: February 2025

ABSTRACTVisual systems are tuned to animals’ ecologies, evolving in response to specific light environments and visual needs. Ecological transitions to fossorial lifestyles impose strong selective pressures favoring morphological adaptations for underground life, such as increased skull ossification and reduced eye protrusion. Fossoriality may simultaneously relax constraints on other aspects of vision leading to diminished visual capabilities. Caecilians (Gymnophiona)— specialized, fossorial amphibians—possess reduced eyes covered by skin or bone. For years, these traits, along with the presence of a single photoreceptor expressing one functional opsin gene, have been interpreted as evidence of limited visual capabilities, including an inability to focus or perceive color. Our results challenge these assumptions: we identified the long-wavelength-sensitive (LWS) opsin gene in 11 species of caecilians spanning 8 of 10 recognized families. Molecular evidence indicates thatLWSis intact and transcribed in the eye of at least one species (Caecilia orientalis). Anatomical observations from five caecilian families indicate highly organized retinae even in families with vestigial eyes. While the presence of cone cells in our study species remains uncertain, a putatively functionalLWSgene suggests that the visual capabilities of caecilians and the role of light perception in their ecology may be underestimated.
Use of massive DNA barcoding to monitor biodiversity: a test on forest soil fauna
Authors: Jabot Franck , Auger Gwenaëlle , Bonnal Pauline , Pizaine Mathilde , Roncoroni Marilyn , Revaillot Sandrine , Pottier Julien 
Published: February 2025

AbstractBiodiversity monitoring primarily focuses on particular taxonomic groups for which identification expertise is widely available, such as vascular plants or birds. As a result, the response of many taxonomic groups to forest management is much less documented. With the advent of low-cost next generation barcoding approaches, it is now possible to envisage monitoring strategies based on molecular approaches, beyond metabarcoding/eDNA strategies that do not give access to species abundances and integrate species presence over largely unknown spatio-temporal scales. In this contribution, we demonstrate the use of massive DNA barcoding – also referred as megabarcoding – as a promising solution to overcome identification difficulties in demanding taxonomic groups. We performed a proof of concept study in a mountainous beech forest in the Massif Central, France. We sampled soil macrofauna at 25 sampling sites and managed to visually identify at the species level 130 out of the 1413 sampled individuals. Using megabarcoding on the 1283 remaining non-identified individuals, we managed to assign 1124 additional individuals to an operational taxonomic species at a competitive cost. We present the summary statistics of barcoding success in the different taxonomic groups encountered and in larvae versus adult individuals. We demonstrate that larvae individuals, which can hardly be visually identified at the species level, make a substantial contribution to overall macrofauna diversity. We finally showcase how this megabarcoding approach provides a concrete avenue for forest biodiversity monitoring, by assessing the cost and labour intensity of this approach.
Mycobacterial infection uncovers plasticity of Kupffer cells
Authors: Neuber Jana , Lohrmann Florens , Wald Samuel , Göçer Merve , Lösslein Anne Kathrin , Obwegs David , Gres Vitka , Goldmann Torsten , Rogg Manuel , Schell Christoph , Preißl Sebastian , Sagar  , Henneke Philipp 
Published: February 2025

AbstractBona fideKupffer cells (KCs) are prenatally seeded and show unique functional and immunophenotypic features among tissue macrophages. They are considered as terminally differentiated, and adaptability in disease is attributed to recruited, monocyte-derived KCs. Here, we investigated the extent of KC plasticity and the impact of origin in mycobacterial infections that target macrophages and can persist for months. Fate-mapping combined with high-resolution imaging revealed the emergence of a unique, infection specific KC subset which downregulated the signature markers CLEC4F and VSIG4 (“KClow”). KClowwere derived frombona fideKCs and located exclusively to granuloma cores. In contrast, monocyte-derived macrophages were contained at the granuloma borders and contributed to this tissue reaction. ATAC and single-cell RNA sequencing identified a specific signature of KClowwith high antimycobacterial activity and specialization to a hypoxic microenvironment. Despite their fundamental deviation from the classical KC phenotype, KClowshowed remarkable adaptability, and were capable to return to a homeostatic-like KC state. Accordingly, mycobacterial infections unmask KCs as highly plastic cells, capable of responding to extreme environmental changes.
Ångström-resolution imaging of cell-surface glycans
Authors: Masullo Luciano A. , Almahayni Karim , Pachmayr Isabelle , Honsa Monique , Heinze Larissa , Fritsche Sarah , Grabmayr Heinrich , Jungmann Ralf , Möckl Leonhard 
Published: February 2025

AbstractGlycobiology is rooted in the study of monosaccharides, Ångström-sized molecules that are the building blocks of intricate glycosylation patterns. Glycosylated biomolecules form the glycocalyx, a dense coat encasing every human cell with central relevance – among others – in immunology, oncology, and virology. In order to understand glycosylation function, visualizing its molecular structure is fundamental. However, the ability to visualize the molecular architecture of the glycocalyx has remained elusive. Techniques like mass spectrometry, electron microscopy, and fluorescence microscopy lack the necessary cellular context, specificity, and resolution. Here, we address these limitations by combining metabolic labeling with Ångström-resolution fluorescence microscopy, enabling the first-ever visualization of individual sugars within glycans on the cell surface. Our work provides unprecedented insights into the molecular architecture of the glycocalyx and constitutes the foundation for future explorations of its function in health and disease.
Mechanical comparison ofEscherichia colibiofilms with altered matrix composition: a study combining shear-rheology and microindentation
Authors: Siri Macarena , Sarlet Adrien , Ziege Ricardo , Zorzetto Laura , Sotelo Guzman Carolina , Amini Shahrouz , Hengge Regine , Blank Kerstin G. , Bidan Cécile M. 
Published: February 2025

AbstractThe mechanical properties of bacterial biofilms depend on the composition and micro-structure of their extracellular matrix (ECM), which constitutes a network of extracellular proteins and polysaccharide fibers. In particular,E. colimacrocolony biofilms were suggested to present tissue-like elasticity due to a dense fiber network consisting of amyloid curli and phosphoethanolamine-modified cellulose (pEtN-cellulose). To understand the contribution of these two main ECM components to the emergent mechanical properties ofE. colibiofilms, we performed shear-rheology and microindentation experiments on biofilms grown fromE. colistrains that produce different ECM. We measured that biofilms containing curli fibers are stiffer in compression than curli-deficient biofilms. We further quantitatively demonstrate the crucial contribution of pEtN-cellulose, and especially of the pEtN modification, to the stiffness and structural stability of biofilms when associated with curli fibers. To compare the differences observed between the two methods, we also investigated how the structure and mechanical properties of biofilms with different ECM compositions are affected by the sample preparation method used for shear-rheology. We found that biofilm homogenization, used prior to shear-rheology, destroys the macroscale structure of the biofilm while the microscopic ECM architecture may remain intact. The resulting changes in biofilm mechanical properties highlight the respective advantages and limitations of the two complementary mechanical characterization techniques in the context of biofilm research. As such, our work does not only describe the role of the ECM on the mechanical properties ofE. colibiofilms. It also informs the biofilm community on considering sample preparation when interpreting mechanical data of biofilm-based materials.
Steering the chain-elongating microbiome to specific medium-chain carboxylates with ethanol and lactate as co-electron donors: maximizing C8 or C6
Authors: Wang Han , Jeon Byoung Seung , Ortiz-Ardila Andres E. , Angenent Largus T. 
Published: February 2025

ABSTRACTMicrobial chain elongation is a sustainable process to convert organic residues into valuable biochemicalsviaanaerobic fermentation. The operating conditions for the bioreactor and the ecological interactions among functional populations are crucial in controlling this process, but they have not been completely ascertained. Here, we unraveled two operating conditions (i.e., environmental factors):(1)the substrate ratio of ethanol and lactate as co-electron donors, and(2)the temperature, which affected both the product specificity (i.e., function) and microbial dynamics of chain-elongating microbiomes in a continuously fed bioreactor with product extraction. Specifically, we found that the increase in the substrate ratio of ethanol to lactate shifted the microbiomes towardn-caprylate (C8) production, while the slightly higher operating temperatures of 37°C or 42°C were advantageous ton-caproate (C6) production. We detected a core microbiome that was similar for all environmental conditions and the two bioreactors, consisting of populations fromSphaerochaetaspp.,Caproiciproducensspp., and Oscillospiraceae. Besides the core microbiome, we observed positive correlations between Erysipelaclostridiaceae UCG-004,Bacteroidesspp., Oscillospiraceae NK4A214, Rikenellaceae RC9, andPseudoclavibacterspp. withn-caprylate production. Similar populations compared to the core microbiome were positively correlated withn-caproate production. We showed that we can steer microbiomes toward a high specificity of certain medium-chain carboxylates.Abstract GraphicsSYNOPSISGenerating medium-chain carboxylates is a promising open-culture biotechnology production platform for converting organic waste streams into biofuels and chemicals.
An ensemble learning method for joint kernel association testing and principal component analysis on multiple kernels
Authors: Koh Hyunwook 
Published: February 2025

AbstractIn high-dimensional omics studies, researchers often conduct kernel association testing to power-fully detect the relationship of the genetic or microbial composition with human health or disease. Especially, in human microbiome studies, its dimension reduction analysis follows to visually represent complex microbiome data in a simple two- or three-dimensional coordinate space. However, various kernels exist, and they produce all different outcomes; hence, it is hard to interpret them all consistently. Then, omnibus testing has recently been a subject of intense investigation for a unified and powerful statistical inference. However, current omnibus tests are purely a test for significance producing only aP-value as their outcome with no related dimension reduction and visualization approach; hence, their utility is still limited. In this paper, I introduce an ensemble learning method, named as enKern, for joint kernel associating testing and principal component analysis on multiple kernels. enKern is based on a weight learning scheme that leverages complementary contributions from multiple kernels for powerful performance for various association patterns. I show that applying the weights to individual test statistics or individual kernels is equivalent, which in turn enables a visualization in a reduced dimensional coordinate space based on the weighted kernel to be matched with its original significance testing scheme. I demonstrate its use for human microbiomeβ-diversity analysis. I also demonstrate its outperformance in validity and power through simulation experiments. enKern is freely available in R computing environment athttps://github.com/hk1785/enkern.