bluuebunny/crossref_metadata_2025 huggingface dataset:
Coupling chromosome organization to genome segregation in Archaea
Authors: Kabli Azhar F. , Ng Irene W. , Read Nicholas , Pal Parul , Reimann Julia , Tran Ngat T. , Albers Sonja-Verena , Le Tung B. K. , Barillà Daniela
Published: February 2025

Chromosome segregation is a fundamental process in all life forms and requires coordination with genome organization, replication and cell division. The mechanism that mediates chromosome segregation in archaea remains enigmatic, despite the centre-stage role assumed by these organisms in the discourse about the origin of eukaryotes. Previously, we identified two proteins, SegA and SegB, which form a minimalist chromosome partition machine in Sulfolobales. Here we uncover patterns and mechanisms that the SegAB system employs to link chromosome organization to genome segregation. Deletion of the genes causes growth and chromosome partition defects. SegB binds to multiple sites scattered across the chromosome, but mainly localised close to thesegABlocus in most archaeal genera. The sites are predominantly intragenic and enriched in one of the two compartments into which the chromosome folds. We show that SegB coalesces into multiple foci through the nucleoid, exhibiting a biased localisation towards the cell periphery, which hints at potential tethers to the cell membrane. The short-range DNA compaction activity of SegB and long-range looping of distant sites point to a significant role for SegB in chromosome condensation that in turn enables genome segregation. Collectively, our data put forward SegAB as important players in bridging chromosome organization to genome segregation in archaea.
Benchmarking the impact of reference genome selection on taxonomic profiling accuracy
Authors: van Bemmelen Jasper , Nika Ioanna , Baaijens Jasmijn A.
Published: February 2025

Motivation

Over the past decades, genome databases have expanded exponentially, often incorporating highly similar genomes at the same taxonomic level. This redundancy can hinder taxonomic classification, leading to difficulties distinguishing between closely related sequences and increasing computational demands. While some novel taxonomic classification tools address this redundancy by filtering the input genome database, there is limited work exploring the impact of different sequence dereplication methods across taxonomic classification tools.

Results

We assess the effect of genome selection approaches on taxonomic classification using both bacterial and viral datasets. Our results demonstrate that careful selection of reference genomes can improve classification accuracy. We also show that using prior knowledge about a metagenomic sample, such as sampling location, can significantly improve classification accuracy. Finally, we find that using a redundancy-filtered genome database generally reduces the computational resources required, with minimal loss in classification accuracy.
miR-124acts duringDrosophiladevelopment to determine the phase of adult circadian behavior
Authors: Xia Yongliang , Chen Chenghao , Emery Patrick
Published: February 2025

Circadian behaviors need to be properly phased with the day/night cycle to be beneficial. We previously showed that the microRNAmiR-124regulates circadian behavior phase inDrosophila. Here, we report thatmiR-124expression during larval development is required for proper phasing of both morning and evening peaks of activity in adults. Loss ofmiR-124results in significant miswiring within the circadian neural network and severely alters neural activity rhythms in the ventral Lateral Neurons (s-LNvs) and the posterior Dorsal Neurons 1 (DN1ps), which control the timing of morning and evening activity. Silencing the s-LNvs inmiR-124mutant flies restores the phase of evening activity, while activating the DN1ps rescues the phases of both morning and evening activities. Our findings thus reveal the pivotal role ofmiR-124in sculpting the circadian neural network during development and its long-lasting impact on circuit activity and adult circadian behavior.
Versatile Modular Antibodies for Sensitive and Specific Detection of Poly-ADP-Ribose
Authors: Dauben Helen , Matić Ivan
Published: February 2025

ADP-ribosylation is a chemically versatile modification of proteins, RNA and DNA that regulates various important signaling pathways, many of which are implicated in human diseases. Despite being discovered 60 years ago in the form of poly-ADP-ribosylation - the most studied form of this modification - investigating ADP-ribosylation at the molecular level has historically been challenging. By applying serine ADP-ribosylation-based antibody engineering technology, we have developed the first site-specific, as well as sensitive, mono-ADP-ribosylation modular antibodies. Here, we extend the scope of this technology to poly-ADP-ribosylation. By combining serine poly-ADP-ribosylated peptides as antigens, PARP1 serine mono- and poly-ADP-ribosylation for validation, phage display and the SpyTag protein ligation systems, we developed modular antibodies that are highly specific for poly-ADP-ribosylation. SpyTag-based coupling of horseradish peroxidase at specific positions, distant from the antigen-binding region of the antibody, yields a format that simplifies immunoblotting while dramatically enhancing poly-ADP-ribosylation detection sensitivity. Additionally, the creation of synthetic immunoglobulin formats – mouse, rabbit and human – enables straightforward co-detection of mono- and poly-ADP-ribosylation in cells by immunofluorescence. Our new tools improve and simplify the detection of poly-ADP-ribosylation, particularly in immunoblotting, enabling specific investigations of this key cellular signal in the context of other distinct forms of ADP-ribosylation.
Cytokine mRNA Delivery and Local Immunomodulation in the Placenta using Lipid Nanoparticles
Authors: Hofbauer Samuel I. , Fink Luisa A. , Young Rachel E. , Vijayakumar Tara , Nelson Katherine M. , Bellopede Nia , Alameh Mohamad-Gabriel , Weissman Drew , Gleghorn Jason P. , Riley Rachel S.
Published: February 2025

During pregnancy, the maternal immune system adapts to balance tolerance of the semi-allogenic fetus while protecting the fetus from pathogens. Dysregulated immune activity at the maternal-fetal interface contributes to pregnancy complications, such as recurrent pregnancy loss and preeclampsia. Compared to healthy placentas, preeclamptic placentas exhibit increased pro-inflammatory signaling, including a predominance of inflammatory macrophages, leading to impaired tissue remodeling and restricted blood flow. However, the precise mechanisms driving this immune imbalance remain poorly understood, in part due to the lack of tools to probe individual pathways. Here, we use lipid nanoparticles (LNPs) to deliver cytokine-encoded mRNA to placental cells, called trophoblasts, enabling local immunomodulation. LNP-mediated delivery of IL-4 and IL-13 mRNA induced cytokine secretion by trophoblasts, leading to polarization of primary human monocytes toward anti-inflammatory phenotypes. Notably, lowering the mRNA dose increased expression of alternatively-activated macrophage markers, revealing an inverse relationship between dose and polarization status. Intravenous injection of LNPs in pregnant mice achieved placental secretion of IL-4 and IL-13 with minimal changes to pro-inflammatory cytokines in the serum. These findings establish LNPs as a tool for local immunomodulation in the placenta, offering a strategy to study and treat immune dysfunction in pregnancy and in other inflammatory conditions.
Mouse-to-human modeling of microglia single-nuclei transcriptomics identifies immune signaling pathways and potential therapeutic candidates associated with Alzheimer’s disease
Authors: Bergendorf Alexander , Park Jee Hyun , Ball Brendan K. , Brubaker Douglas K.
Published: February 2025

Alzheimer’s disease (AD) is a progressive neurodegenerative disease characterized by memory loss and behavior change. Studies have found that dysregulation of microglial cells is pivotal to AD pathology. These mechanisms have been studied in mouse models to uncover potential therapeutic biomarkers. Despite these findings, there are limitations to the translatable biological information from mice to humans due to differences in physiology, timeline of disease, and the heterogeneity of humans. To address the inter-species discrepancies, we developed a novel implementation of the Translatable Components Regression (TransComp-R) framework, which integrated microglia single-nuclei mouse and human transcriptomics data to identify biological pathways in mice predictive of human AD. We compared model variations with sparse and traditional principal component analysis. We found that both dimensionality reduction techniques encoded similar AD disease biology on mouse principal components with limited differences in technical performance. Several mouse sparse principal components explained high amounts of variance in humans and significantly differentiated human AD from control microglial cells. Additionally, we identified FDA-approved medications that induced gene expression profiles correlated with projections of healthy human microglia on mouse principal components. Such medications included cabergoline, selumetinib, and palbociclib. This computational framework may support uncovering cross-species disease insights and candidate pharmacological solutions from single-cell datasets.
Allodiploid hybridization, loss-of-heterozygosity and aneuploidy in the green algaAuxenochlorella, an emerging model for discovery research and bioengineering
Authors: Craig Rory J. , Dueñas Marco A. , Camacho Dimitrios J. , Gallaher Sean D. , Blaby-Haas Crysten E. , Moseley Jeffrey L. , Merchant Sabeeha S.
Published: February 2025

Auxenochlorellaare diploid oleaginous green algae that are highly amenable to genetic transformation by homologous recombination, providing great potential for discovery research and bioengineering. Vegetatively diploid organisms experience specific evolutionary phenomena, including allodiploid hybridization, mitotic recombination, loss-of-heterozygosity and aneuploidy; however, studies of these forces have mostly focused on fungi. Here, we present a telomere-to-telomere phased diploid genome assembly ofAuxenochlorellaUTEX 250-A, revealing a streamlined nuclear genome architecture with a haploid length of 22 Mb. We demonstrate that UTEX 250-A is an allodiploid hybrid via sequencing ofAuxenochlorella protothecoidesandAuxenochlorella symbionticastrains, two close relatives differentiated by extensive chromosomal rearrangements. The UTEX 250-A haplotypes are a mosaic of each parental species following mitotic recombination, and two chromosomes are trisomic, which we confirm via allele-specific transformation of a trisomic chromosome. Loss-of-heterozygosity events are likely pervasive acrossAuxenochlorelladue to mitotic recombination and transient aneuploidy, and can evolve rapidly in laboratory culture. We present high-quality structural annotations, yielding ∼7,500 genes per haplotype.Auxenochlorellahave experienced extensive gene family loss and reduction, including core photosynthesis genes. Nevertheless, a minimal set of genes required for sexual reproduction is potentially present. We demonstrate periodic adenine and cytosine methylation around promoters and across gene bodies. Finally, ∼10% of genes, especially those involved in DNA repair and sex, overlap antisense long noncoding RNAs, potentially representing a regulatory mechanism. These results demonstrate the generality of several evolutionary forces associated with vegetative diploidy, and provide a genomic foundation for the use ofAuxenochlorellaas a reference organism.
Microbiome-oriented data mining of operational monitoring of anaerobic digestion reactor during steady operation period, failure, and restoration
Authors: Panou M. , Kavakiotis I. , Mitsopoulos Anastasios , Tsioni Vasiliki , Sfetsas Themistoklis
Published: February 2025

Anaerobic digestion (AD) is an essential biotechnology for sustainable waste management and bioenergy production, driven by a complex microbial ecosystem. However, the stability and efficiency of AD reactors are frequently challenged by microbial shifts resulting from operational disturbances. This study employs microbiome-oriented data mining and bioinformatics approaches to analyze microbial community dynamics in an anaerobic digestion reactor under steady-state operation, failure, and restoration phases. Data were extracted from a biogas plant and used to evaluate a system failure, providing crucial insights into microbial shifts associated with operational instability. A custom-built microbiome-oriented database, μ2Gas, was developed to integrate sequencing data with physicochemical monitoring results, enabling structured data storage, retrieval, and correlation analysis. This database was instrumental in identifying key microbial taxa responsible for reactor destabilization and in predicting failure events based on microbial and physicochemical trends. Through high-throughput 16S rRNA gene sequencing and advanced bioinformatics analysis, microbial shifts were correlated with key operational parameters such as pH, volatile fatty acids (VFAs), and ammonia concentrations. Results indicate that methanogenic archaea, particularly Methanosarcina, experienced a sharp decline during reactor failure, followed by a gradual recovery, demonstrating their sensitivity to environmental stressors. Additionally, the balance between Firmicutes and Actinobacteria was identified as a crucial determinant of reactor stability, with Firmicutes recovering in tandem with system restoration. Feedstock composition was found to play a significant role in microbial shifts, with seasonal variability influencing community composition and reactor performance. Machine learning models applied to the database suggested the potential for predictive analytics in anticipating system failures. By leveraging microbial abundance patterns, these models were able to identify early warning signs of instability. Restoration efforts, including feedstock adjustments and operational parameter optimization, successfully reinstated core microbial communities essential for biogas production. This study underscores the critical role of microbiome monitoring in anaerobic digestion and highlights the potential of bioinformatics tools for enhancing reactor resilience. Future research should focus on real-time microbiome tracking, machine learning-driven predictive maintenance, and adaptive operational strategies to further improve AD efficiency and biogas yield.
Functional Connectivity Shapes Spine Stability in the Hippocampus
Authors: Rais Cynthia , Wiegert J. Simon
Published: February 2025

Synaptic connections between neurons determine the flow of information in the brain. Changes in synaptic weight, along with synapse formation and pruning, reshape the functional connectivity of neural circuits—key mechanisms underlying learning and memory. However, the relationship between functional strength and the structural dynamics of individual glutamatergic synapses in the living mammalian brain remains poorly understood. Specifically, how spine morphology and stability relate to functional adaptations is unclear. Here, we repeatedly recorded excitatory postsynaptic calcium transients in single postsynaptic spines of CA1 neurons in response to optogenetic stimulation of presynaptic CA3 cells in awake, head-fixed mice for over 2 weeks. We found that functional connectivity predicted both the structural stability and clustering of synaptic inputs. Spines with large responses exhibited larger volume and higher stability compared to non-responding spines. Over time, responses were highly variable at individual synapses, but stable at the dendritic level, suggesting that dendritic branches receive stable input despite large fluctuations at individual synapses.
CryoEM structure of ALK2:BMP6 reveals distinct mechanisms that allow ALK2 to interact with both BMP and Activin ligands
Authors: Goebel Erich J. , Aykul Senem , Saotome Kei , Economides Aris N. , Franklin Matthew C. , Idone Vincent J.
Published: February 2025

Ligands in the TGFβ family (activins, BMPs and TGFβs), signal by bringing together two type I and two type II receptors. ALK2 is the only type I receptor among the seven TGFβ type I receptors that interacts with both activin and BMP ligands. With BMPs, ALK2 acts as a signaling receptor to activate SMAD1/5/8 signaling. Alternatively, with activins, such as Activin A (ActA), ALK2 forms nonsignaling complexes that negatively regulate ALK2 and ActA signaling. To gain insight into how ALK2 interacts with two distinct classes of ligands, we resolved the cryoelectron microscopy structure of ALK2 in complex with the type II receptor, ActRIIB, and the ligand, BMP6, in parallel with the corresponding structure with ALK3 for direct comparison. These structures demonstrate that ALK2 and ALK3 utilize different mechanisms to interact with BMP6 at the wrist interface, with ALK2 relying on BMP6 glycosylation and ALK3 relying on a salt bridge. Modeling of ALK2:ActA reveals that binding relies on ActA’s fingertip region, mirroring the interaction of ActA with its other receptor, ALK4. Our results demonstrate that ALK2 is a ‘hybrid’ receptor that incorporates features of BMP type I receptors such as ALK3 at the wrist interface, and an activin type I receptor such as ALK4 at the fingertip.

Significance

ALK2 interacts with two different classes of TGFβ ligands: the BMPs and the activins. With BMP ligands, ALK2 signals to play roles in bone modeling, while with activins, ALK2 negatively regulates signaling by forming nonsignaling complexes. We demonstrate that ALK2 binds to favored ligand, BMP6, by utilizing the ligand wrist-helix stabilized by a glycosylation, rather than a charged interaction observed with similar receptor, ALK3. We also show that ALK2 interaction with activin ligand, ActA, is reliant on a single interaction at the other side of the receptor – the fingertip interface. Thus, this study elucidates first structure of ALK2 in complex with a ligand and provides the molecular insight into how ALK2 is able to bind to BMP and activin ligands.
Genomic Characterization of Novel Endophyte Strains from Tall Fescue Shows Genome Fragmentation Post-Hybridization
Authors: Lee Kendall , Bentz Philip , Vaughn Justin , Missaoui Ali
Published: February 2025

Interspecific hybridization in fungi has gained attention for its role in fungal evolution and potential commercial applications. Successful hybridization can enhance fitness and facilitate adaptation to new ecological niches. However, the genomic consequences of hybridization in fungi remain poorly understood.Epichloëis a genus of fungi that includes both non-hybrid and hybrid species, with the hybrids forming through parasexual hybridization and reproducing asexually. SomeEpichloëhybrids are of commercial significance, as they colonizeLolium arundinaceum(Schreb.) Darbysh., a crucial forage and turf grass species. In this study, we sought to generate high-quality genome assemblies for two previously uncharacterizedEpichloëhybrid strains, both of which are similar toEpichloësp. FaTG-3. We aimed to characterize their genomes and examine the effects of parasexual interspecific hybridization on fungal genome structure. Our results reveal that the genomes of both strains are rich in AT-rich blocks and repetitive elements. Upon comparison with putative progenitor genomes, we observed significant fragmentation and rearrangement. Despite the genomic instability, more than 85% of gene homologs from each progenitor species were retained. This study demonstrates that while parasexual hybridization dramatically alters genome structure, it does not significantly affect gene content.
Top-DTI: Integrating Topological Deep Learning and Large Language Models for Drug Target Interaction Prediction
Authors: Talo Muhammed , Bozdag Serdar
Published: February 2025

Motivation

The accurate prediction of drug–target interactions (DTI) is a crucial step in drug discovery, providing a foundation for identifying novel therapeutics. Traditional drug development is both costly and time-consuming, often spanning over a decade. Computational approaches help narrow the pool of compound candidates, offering significant starting points for experimental validation. In this study, we propose Top-DTI framework for predicting DTI by integrating topological data analysis (TDA) with large language models (LLMs). Top-DTI leverages persistent homology to extract topological features from protein contact maps and drug molecular images. Simultaneously, protein and drug LLMs generate semantically rich embeddings that capture sequential and contextual information from protein sequences and drug SMILES strings. By combining these complementary features, Top-DTI enhances predictive performance and robustness.

Results

Experimental results on the public BioSNAP and Human DTI benchmark datasets demonstrate that the proposed Top-DTI model outperforms state-of-the-art approaches across multiple evaluation metrics, including AUROC, AUPRC, sensitivity, and specificity. Furthermore, the Top-DTI model achieves superior performance in the challenging cold-split scenario, where the test and validation sets contain drugs or targets absent from the training set. This setting simulates real-world scenarios and highlights the robustness of the model. Notably, incorporating topological features alongside LLM embeddings significantly improves predictive performance, underscoring the value of integrating structural and sequence-based representations.

Availability

The data and source code of Top-DTI is available athttps://github.com/bozdaglab/Top_DTIunder Creative Commons Attribution Non Commercial 4.0 International Public License.
Differences Among Fungal Microbiomes Associated with Tar Spot of Corn in Ecuador, Guatemala, and Indiana, USA
Authors: Sic-Hernandez Wily R. , Gribskov Michael , Acosta Alex G. , Cruz Andres , Zambrano Jose L. , Racancoj Coyoy Astrid J. , Cruz C. D. , Goodwin Stephen B.
Published: February 2025

Tar spot of corn, caused by the obligate fungal pathogenPhyllachora maydis, was previously found to be associated withMonographella maydis(syn.Microdochium maydis) andConiothyrium phyllachoraein Mexico. WhileM. maydiswas once believed to cause fisheye lesions andC. phyllachoraewas described as a mycoparasite ofP. maydis, their presence and roles in tar spot remain uncertain. This study hypothesizes that the tar spot-associated fungal microbiome varies geographically and includes fungal species with inconsistent associations with the disease. To test this, tar spot-infected leaves were collected in Guatemala, Ecuador, and the USA. This study shows that the distribution and abundance of these fungi exhibit a geographical pattern and are not consistently associated with tar spot lesions in all locations. We confirmed the presence ofMicrodochiumin some parts of Ecuador and Guatemala but not in the USA. The role ofMicrodochiumremains unclear and whether it can be a primary pathogen needs to be tested by additional research, as its occurrence and abundance depend more on geographical locations rather than the presence of fisheye lesions.Coniothyriumwas detected at low abundance in samples from Ecuador and Guatemala but was absent in the USA. Additionally, we identified the likely mycoparasiteParaphaeosphaeriaas highly prevalent across samples from all three countries. Microbiome diversity analysis grouped tar spot samples into four distinct clusters: two dominated byP. maydis, one primarily associated withMicrodochium, and a fourth characterized by a combination ofP. maydisandParaphaeosphaeria.
The effect of feeding on microbiome and biogas composition in anaerobic CSTR
Authors: Samiotis Georgios , Panou Manthos , Tsioni Vassiliki , Sfetsas Themistoklis
Published: February 2025

his study investigates the performance of two Continuous Stirred Tank Reactors (CSTRs) with a focus on biogas yield, physicochemical parameters, and microbial dynamics. By integrating experimental observations with insights from recent literature, the research aims to elucidate the intricate relationships between reactor conditions, microbiome composition, and biogas production efficiency. Two substrates were used: a control substrate (SB1) and a protein-rich test substrate (SB2). The study monitored key parameters such as pH, Total Alkalinity of Carbonates (TAC), and volatile fatty acids (FOS), and analyzed the microbial communities using high-throughput sequencing. Results indicated significant temporal variations in pH, TAC, and nitrogen levels, with a declining FOS/TAC ratio. The introduction of SB2 led to increased biogas production and methane content, particularly at higher Hydraulic Retention Times (HRT). The study also high-lighted the role of specific microbial taxa in enhancing biogas quality. These findings contribute to the development of optimized strategies for sustainable biogas production and process control.
Optogenetic restoration of neuron subtype-specific cortical activity ameliorates motor deficits in Huntington’s Disease mice
Authors: Blumenstock Sonja , Arakelyan David , del Grosso Nicholas , Schneider Sonja , Shao Yufeng , Gjoni Enida , Klein Rüdiger , Dudanova Irina , Komiyama Takaki
Published: February 2025

Huntington’s disease (HD) is a devastating movement disorder without a current cure. Although the monogenic basis of HD is well-defined, the complex downstream effects that underlie behavioral symptoms are poorly understood. These effects include cortical dysfunctions, yet the role of specific cortical neuronal subtypes in HD symptoms remain largely unexplored. Here, we used longitudinalin vivotwo-photon calcium imaging to examine the activity of two cortical inhibitory neuron (IN) subtypes and excitatory corticostriatal projection neurons (CSPNs) in the motor cortex of R6/2 HD mouse model throughout disease progression. We found that motor deficits in R6/2 mice were accompanied by neuron type-specific abnormalities in movement-related activity, including hypoactivity of vasoactive intestinal peptide (VIP)-INs and CSPNs. Optogenetic activation of VIP-INs in R6/2 mice restored healthy levels of activity in VIP-INs and their downstream CSPNs and ameliorated motor deficits in R6/2 mice. Our findings highlight cortical INs as a potential therapeutic target for HD and possibly other neurological diseases.
Next-Generation Protein Sequencing and individual ion mass spectrometry enable complementary analysis of interleukin-6
Authors: Skinner Kenneth A. , Fisher Troy D. , Lee Andrew , Su Taojunfeng , Forte Eleonora , Sanchez Aniel , Caldwell Michael A. , Kelleher Neil L.
Published: February 2025

The vast complexity of the proteome currently overwhelms any single analytical technology in capturing the full spectrum of proteoform diversity. In this study, we evaluated the complementarity of two cutting-edge proteomic technologies—single-molecule protein sequencing and individual ion mass spectrometry—for analyzing recombinant human IL-6 (rhIL-6) at the amino acid, peptide, and intact proteoform levels. For single-molecule protein sequencing, we employ the recently released Platinum®instrument. Next-Generation Protein Sequencing™(NGPS™) on Platinum utilizes cycles of N-terminal amino acid recognizer binding and aminopeptidase cleavage to enable parallelized sequencing of single peptide molecules. We found that NGPS produces single amino acid coverage of multiple key regions of IL-6, including two peptides within helices A and C which harbor residues that reportedly impact IL-6 function. For top-down proteoform evaluation, we use individual ion mass spectrometry (I2MS), a highly parallelized orbitrap-based charge detection MS platform. Single ion detection of gas-phase fragmentation products (I2MS2) gives significant sequence coverage in key regions in IL-6, including two regions within helices B and D that are involved in IL-6 signaling. Together, these complementary technologies deliver a combined 52% sequence coverage, offering a more complete view of IL-6 structural and functional diversity than either technology alone. This study highlights the synergy of complementary protein detection methods to more comprehensively cover protein segments relevant to biological interactions.

Abstract Figure
Early life infection withCryptosporidium parvuminduces inflammatory responses to dietary antigens
Authors: Saraav Iti , Huang Wanyi , Jung Jisun , Xu Rui , Fu Yong , McDonald Keely , Schriefer Lawrence A. , Rodgers Rachel , Baldridge Megan T. , Newberry Rodney D , Hsieh Chyi , Sibley L. David
Published: February 2025

To examine the effect of early-life infection withCryptosporidium parvumon the development of oral tolerance, we developed a low-dose infection model in neonatal mice.C. parvuminfection in neonatal mice results in immunopathology in the colon. IL-1β released duringC. parvuminfection blocked the formation of colonic goblet cell associated antigen passages, which normally serve as a conduit for antigen uptake and development of peripheral regulatory T cells (pTregs), responsible for long-term oral tolerance. Following infection withC. parvum, adoptively transferred OT-II cells, which respond to ovalbumin (ova), developed reduced frequency of Foxp3+Rorγt+cells in mesenteric lymph nodes with an expansion of TH1-like Tregs in the colon. The altered pTreg profile was accompanied by a strong TH1 immune response and robust IgG2c antibody responses to orally administered ova. Our findings suggest that intestinal inflammation and altered pTreg development leads to loss of oral tolerance during early life infection withC. parvum.
Enabling the Study of Gene Function in Gymnosperms: VIGS inEphedra tweedieana
Authors: Garcia Anthony , Bùi Jo Trang , Michael Todd P. , Ickert-Bond Stefanie M. , Di Stilio Verónica S.
Published: February 2025

Premise

As the sister clade to angiosperms, gymnosperms are key to enabling the reconstruction of ancestral gene regulatory networks for seed plants. However, tools to rapidly and efficiently investigate gene function in gymnosperms remain limited due to the challenges of long life cycles and large genome sizes. Species within the xerophytic genusEphedra(Gnetales) have comparatively smaller genomes and shrubby growth habits with shorter life spans, making them better suited for greenhouse cultivation and laboratory experiments.

Methods and Results

Here, we implement Virus-Induced Gene Silencing (VIGS) to manipulate gene expression inEphedra tweedieana. Agrobacterium-mediated vacuum infiltration of Tobacco Rattle Virus (TRV2 and TRV1) in seedlings resulted in highly efficient silencing of theE. tweedieana PHYTOENE DESATURASEorthologEtwPDS. The expected photobleaching phenotype was observed as early as two weeks. It lasted at least three months, in stems, shoot tips, leaves, axillary meristems, and lateral branches of treated plants.

Conclusions

This first report of transient transformation and targeted gene silencing in a gymnosperm will further enable functional studies of the genetic mechanisms underpinning adaptations in this important and underrepresented lineage of seed plants.
Construction of a low-temperature degrading synthetic bacterial community of corn straw
Authors: Fang Yi , Li Jiaqi , Zhang Wanyi , Ye xuhong , Zhu Xiaolin Zhu , Xie Yang , Feng Youzhi , Yu Yongjie , Yu Susu , Zhang Li , Zou Hongtao
Published: February 2025

The stability of the cellulose structure in straw creates a challenge for short-term degradation in the natural environment, especially in the cold regions of north China. Therefore, to secure strains that can degrade straw at low temperatures, we selected soil samples from straw-returning land and used cellulose as the only carbon source. After conducting preliminary screening and further re-screening, we ultimately selected three strains that exhibited efficient degradation of corn straw at a temperature of 4 ℃. Subsequently, the synthetic bacterial community C was constructed using these strains:Stenotrophomonas maltophilia,Flavobacterium johnsoniaeandPantoea rodasii.

We conducted a 45-day solid-state and liquid-state fermentation experiment at low-temperature (12 ℃). The activity of lignocellulase was determined, and the enzyme production conditions were optimized. The results show that the liquid fermentation degradation rate of straw increased by 40 % compared with the control group in the natural state (without adding C). Similarly, the solid-state fermentation degradation rate of straw increased by 30 %, which was significantly faster than that of the control group. Finally, the enzyme production conditions of strain C were optimized as follows: culture time 96 h, inoculation amount 4 %, temperature 12 ℃, pH 6.0, and Alkaline Carboxymethyl Cellulase (CMCase) activity 24.34 U/mL. The microbial system C efficiently degrades straw at low temperature, which is valuable for improving the comprehensive utilization rate of straw and has a broad application prospect in improving soil fertility.
DMT-induced shifts in criticality correlate with ego-dissolution
Authors: Irrmischer Mona , Aqil Marco , Luan Lisa , Wang Tongyu , Engelbregt Hessel , Carhart-Harris Robin , Linkenkaer-Hansen Klaus , Timmermann Christopher
Published: February 2025

Psychedelics profoundly alter subjective experience and brain dynamics. Brain oscillations express signatures of near-critical dynamics, relevant for healthy function. Alterations in the proximity to criticality have been suggested to underlie the experiential and neurological effects of psychedelics. Here, we investigate the effects of a psychedelic substance (DMT) on the criticality of brain oscillations, and in relation to subjective experience. We find that DMT shifts the dynamics of brain oscillations away from criticality in alpha and adjacent frequency bands. In this context, entropy is increased while complexity is reduced. We find that the criticality shifts observed in alpha and theta bands correlate with the intensity ratings of ego-dissolution, a hallmark of psychedelic experience. Finally, using a recently developed metric, the functional excitatory-inhibitory ratio, we find that the DMT-induced criticality shift in brain oscillations is towards subcritical regimes. These findings have major implications for the understanding of psychedelic mechanisms of action in the human brain and for the neurological basis of altered states of consciousness.
Bridge protein-mediated viral targeting of cells expressing endogenous μ-opioid G protein-coupled receptors in the mouse and monkey brain
Authors: Kamaguchi Riki , Amemori Satoko , Amemori Ken-ichi , Osakada Fumitaka
Published: February 2025

Targeting specific cell types is essential for understanding their functional roles in the brain. Although genetic approaches enable cell-type-specific targeting in animals, their application to higher mammalian species, such as nonhuman primates, remains challenging. Here, we developed a nontransgenic method using bridge proteins to direct viral vectors to cells endogenously expressing μ-opioid receptors (MORs), a G protein-coupled receptor. The bridge protein comprises the avian viral receptor TVB, the MOR ligand β-endorphin (βed), and an interdomain linker. EnvB-enveloped viruses bind to the TVB component, followed by the interaction of βed with MORs, triggering viral infection in MOR-expressing cells. We optimized the secretion signals, domain configurations, and interdomain linkers of the bridge proteins to maximize viral targeting efficiency and specificity. Alternative configurations incorporating different ligands and viral receptors also induced viral infection in MOR-expressing cells. The optimized βed-f2-TVB bridge protein with EnvB-pseudotyped lentiviruses induced infection in MOR-expressing cells in the striatum of mice and monkeys. An intersectional approach combining βed-f2-TVB with a neuron-specific promoter refined cell-type specificity. This study establishes the foundation for the rational bridge protein design and the feasibility of targeting G protein-coupled receptors beyond tyrosine kinase receptors, thereby expanding targetable cell types in the brain and throughout the body.

Graphical abstract
Pancreatic cancer-intrinsic HuR regulates the pro-tumorigenic properties of extracellular vesicles
Authors: Finan Jennifer M. , Guo Yifei , Bartlett Alexandra Q. , Reyer Matthew , Hawthorne Kevin , Haerr Margaret , Halamish Hen , Lamikanra Olayinka , Calvert Valerie , Chen Canping , Xia Zheng , Petricoin Emanuel F. , Sears Rosalie C. , Byrne Katelyn T. , Brody Jonathan R.
Published: February 2025

Pancreatic ductal adenocarcinoma (PDAC) tumors contain chaotic vasculature that limits immune surveillance and promotes early events in the metastatic cascade. However, current antiangiogenic therapies have failed in PDAC, and thus, it remains important to uncover mechanisms by which cancer cells signal to endothelial cells to increase angiogenesis. Our lab has shown that the tumor-intrinsic RNA-binding protein HuR (ELAVL1) plays an important role re-shaping the tumor microenvironment (TME) by regulating the stability and translation of cytokine encoding transcripts. Herein, we demonstrate that PDAC-intrinsic HuR influences endothelial cell function in the TME via extracellular vesicle (EV) signaling, an underexplored signaling axis in tumor progression. We found that HuR knockout (KO) tumors have impaired growth in an immunocompetent mouse model, and that administering purified wildtype (WT) EVs can increase tumor growth. Further, we observed that PDAC EVs contain HuR-dependent mRNA and protein cargoes relating to endothelial cell function and angiogenesis. Treatment of endothelial cells with HuR WT EVs strongly increased the expression of genes involved in barrier function and endothelial cell development, and directly increased their migratory and tube forming functions. In an immunocompetent orthotopic mouse model of PDAC, we showed that HuR increases endothelial cell presence and sprouting, while decreasing ICAM-1 expression. Importantly, we found utilizing a genetic EV reporter, that decreased ICAM-1 within WT tumors occurs in endothelial cells that have imported PDAC EVs, suggesting that this signaling axis is directly modulating endothelial cell behaviorin vivo. Collectively, our data reveal a new role of HuR in EV signaling to endothelial cells, promoting angiogenesis while restricting endothelial cell leukocyte trafficking behavior.
Cortical astrocyte activation triggers meningeal nociception and migraine-like pain
Authors: Bree Dara , Zhao Jun , Stratton Jennifer , Levy Dan
Published: February 2025

Migraine attacks are believed to originate in the brain, but the exact mechanisms by which the brain generates peripheral nociceptive signals that drive migraine pain remain unclear. Sensory cortex hyperexcitability has been observed consistently across different migraine subtypes. Astrocytes detect aberrant increases in cortical activity via their Gq-coupled receptors and respond by releasing gliotransmitters and other factors with proinflammatory and nociceptive properties. In the present study, we used a rat model to investigate whether heightened cortical astrocyte Gq-coupled signaling is sufficient to drive peripheral trigeminal meningeal nociceptive responses linked to the generation of migraine headaches. We used an AAV-based chemogenetic approach that allows selective activation of cortical astrocyte Gq-GPCR signaling. We targeted astrocytes in the visual cortex as hyperexcitability in this region has been implicated in migraine. Furthermore, the meninges overlying the visual cortex are densely innervated by nociceptive fibers. We combined this chemogenetic approach with in vivo single-unit recording of meningeal nociceptors to assess changes in their ongoing activity and mechanosensitivity, along with testing of migraine-like behaviors. We further targeted calcitonin gene-related peptide (CGRP), using a monoclonal antibody (anti-CGRP mAb), to assess the relevance of cortical astrocyte activation to migraine. We discovered that heightened activation of Gq-coupled signaling in visual cortex astrocytes drives persistent discharge and increased mechanosensitivity of meningeal nociceptors. Cortical astrocytic activation also generated cephalic mechanical pain hypersensitivity, reduced exploratory behavior, and anxiety-like behaviors linked to migraine headaches. Blocking calcitonin gene-related peptide signaling suppressed astrocyte-mediated increases in meningeal nociceptor discharge and alleviated associated migraine-related behaviors. Our findings reveal a previously unappreciated role for augmented visual cortex astrocyte signaling as a triggering factor sufficient to generate meningeal nociception and migraine pain and greatly expand our understanding of migraine pathophysiology.
Alternatively Folded State of IgG4: Acid-Induced Compaction is Common between IgG1 and IgG4
Authors: Imamura Hiroshi , Honda Shinya
Published: February 2025

Immunoglobulin G1 (IgG1) antibodies undergo denaturation in acidic conditions, resulting in an alternatively folded state (AFS). The AFS structure is more compact than the native state. However, the prevalence of AFS in other subclasses remains largely unexplored. This study provides evidence that humanized IgG4 can also adopt AFS structure, as demonstrated through size-exclusion chromatography coupled with small-angle X-ray scattering (SEC-SAXS) analysis. These findings suggest that the anomalous compaction of immunoglobulins G (IgGs) is resilient to variations in sequence and structure among subclasses.
Impact of Soil Salinity on Microbial Community Composition in Coastal Agricultural lands of Bangladesh: A Metagenomic Approach
Authors: Das Sumit , Nayem Maksudur Rahman , Hira Kamrun Nahar , Shermin Romana , Hosen Md. Razib , Hossain Md. Amzad , Tariquzzaman Md. , biswas Razib , Rahman Farazi Abinash , Saha Mithun Kumar , Rabbi Mohammad Fazle Alam
Published: February 2025

A significant obstacle to agricultural productivity is soil salinity, especially in coastal areas where the problem is made worse by climate change and rising sea levels. This study investigates the impact of salinity on microbial community structure and function in agricultural soils from Kuakata, Bangladesh, using 16S rRNA metagenomic sequencing technique. Both saline (EC > 4 dS/m) and non-saline (EC < 1.5 dS/m) areas had soil samples taken; saline soils showed symptoms of crop stress, such as yellowing and blackish discoloration. In comparison to their non-saline counterparts, our investigation showed that saline soils had much reduced microbial diversity and different community compositions. Both soil types were dominated by Proteobacteria and Chloroflexi, while saline soils displayed an enrichment of anaerobic texa (e.g., Desulfobacterota, Pseudomonas) and sulfate-reducing bacteria (e.g., Desulfobacterota, Deferrisomatota). Interestingly, saline soils had a much larger percentage of anaerobic microorganisms (36.4%) than non-saline soils (29.3%) which might results in enhanced denitrification, sulphate reduction, and hydrogen sulphide buildup. These processes disrupt nutrient cycling, lower organic matter decomposition and create toxic conditions for plant growth, ultimately contributing to crop failure. This study provides an insight into the distinct microbial composition in saline and non-saline samples, which can assist in understanding the role of microbial populations in agriculture in saline environments.
Flavoaffinins, elusive cellulose-binding natural products from an anaerobic bacterium
Authors: Kountz Duncan J. , Yu Ruocheng , Lee Jessie H. , Maloney Katherine N. , Balskus Emily P.
Published: February 2025

Cellulose is the most abundant polymer on earth and plays a key role in the carbon cycle, agriculture, and human health. Many anaerobic cellulose-degrading bacteria produce uncharacterized yellow-orange, cellulose-binding pigments known as yellow affinity substances (here referred to as flavoaffinins) that are associated with efficient cellulose degradation. Here, we isolate and structurally characterize the flavoaffinins fromClostridium(Hungateiclostridium)thermocellum, a key workhorse for the industrial conversion of cellulosic feedstocks to ethanol. Flavoaffinins represent an unprecedented structural juxtaposition of an aryl polyene chain with a hydroxy-diene γ-lactone. We also shed light on their biosynthetic origins using stable-isotope feeding experiments. This effort lays the groundwork for understanding the biological function(s) of the flavoaffinins and expands the limited number of natural products isolated from obligately anaerobic microbes.

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Towards a tracking of bird migratory behaviour through geological time: an isotopic and histological approach
Authors: Duhamel Anaïs , Canoville Aurore , Vinçon-Laugier Arnaud , Joseph Julien , Fourel François , Lécuyer Christophe , Amiot Romain , Louchart Antoine
Published: February 2025

Bird seasonal migration is a remarkable biogeographic phenomenon, yet its deep-time origin(s) and evolutionary history remain poorly understood, with the bird fossil record largely overlooked. This study explores the predictability of bird migratory behaviour from the oxygen isotope composition of their bone apatite phosphate (δ18Op), a promising approach in this regard because: (i) sedentary and migratory birds tend to occupy distinct climatic niches year-round; (ii) their δ18Opvalues primarily reflect the climate-driven isotopic composition of their drinking water; and (iii) this isotopic signature can persist through fossilisation.

Bone tissues were categorised based on their potential to yield spatio-temporally distinct climatic records: “early bone tissues” (EBT), deposited before somatic maturity, and “late bone tissues” (LBT), resulting from bone remodelling events over the lifespan. The predictability of migratory behaviour was theoretically assessed by modelling tissue-specific δ18Opvalues for thousands of birds across 77 migratory and sedentary species, based on their tracking or observational data, using a revised phosphate-water fractionation equation. These theoretical results were confronted with data from 11 extant bird species obtained using a new experimental framework that combines histological and isotopic analyses.

We emphasised that, under specific sampling protocols, a significantly positive correlation between the δ18Opvalue and the proportion of LBT of bone samples is characteristic of long-distance migratory birds. Additionally, migratory birds that perished outside their natal sites can be identified when their δ18Op,EBTvalue falls outside the range observed in local juvenile and sedentary birds.

We conclude that the migratory behaviour of birds can be inferred from the δ18Opvalues of their skeletal remains, with relatively low sensitivity (not all migratory behaviours are detected), but with high specificity (sedentary birds are rarely misclassified as migratory). We argue that the same method can be used to infer past bird migratory behaviours from well-preserved fossil bones, provided the palaeoclimatic context is carefully considered. More broadly, this study establishes a framework for inferring the migratory behaviour of any vertebrate from non-fully remodelled biomineralised remains.
Wildlife trade drives animal-to-human pathogen transmission over 40 years
Authors: Gippet Jerome M. W. , Carlson Colin J , Klaftenberger Tristan , Schweizer Matteo , Bertelsmeier Cleo
Published: February 2025

Wildlife trade affects a quarter of terrestrial vertebrates(1) and creates novel opportunities for cross-species pathogen transmission(2-4). Yet, its precise role in shaping human-wildlife pathogen exchanges remains unclear. Analysing 40 years of global wildlife trade data, we show that traded mammals are twice as likely to share pathogens with humans than non-traded species. Moreover, time spent in trade strongly predicts the number of zoonotic pathogens that wildlife species host: on average, a species shares an additional pathogen with humans for every 9 years of presence in trade. This work highlights the importance of the wildlife trade in driving animal-to-human pathogen transmission, offering key insights into pathogen biogeography in the Anthropocene and the prevention of future pandemics.