bluuebunny/crossref_metadata_2025 huggingface dataset:
Prolific release of S-layer units and associated proteins by the methanotrophic bacteriumMethylomicrobium albumBG8
Authors: Hermary Mariah K. , Rodriguez Gallo Maria C. , Grigonyte Aurelija M. , Uhrig R. Glen , Sauvageau Dominic , Stein Lisa Y.
Published: January 2025

Some gammaproteobacterial methanotrophs are encapsulated by S-layers that overlay their outer membrane. In this study, TEM imaging revealed thatMethylomicrobium albumBG8 constitutively releases abundant cup-shaped S-layer units – a phenotype that was not observed in 7 other methanotroph strains, even inMethylotuvimicrobium buryatense5GB1 that produces a similar S-layer structure. Release of S-layer units occurred regardless of carbon (methane or methanol) or nitrogen (ammonium or nitrate) source, with 50X trace metal availability or under copper deprivation, and at all growth phases. The released S-layer units were isolated from the culture medium ofM. albumBG8 for proteome analysis. The proteome revealed an abundance of transporters related to calcium uptake including TolC and Repeats-in-Toxin (RTX) proteins, transporters for uptake for cobalamin and siderophores, proteins with Type I secretion system (T1SS) target domains, cell wall biogenesis proteins, and the S- layer protein units themselves. The gene encoding the S-layer protein is co-located in theM. albumBG8 genome with genes encoding the T1SS. Together, this information provides clues regardingM. albumBG8 S-layer biogenesis and function, including a role for the calcium and RTX protein domains, involvement of the T1SS in selecting associated proteins, and reasons behind prolific release of S-layer units. This S-layer release and involvement of the T1SS has biological implications and could be applied towards selective secretion of proteins byM. albumBG8 in bioindustrial applications.

Importance

The methanotrophic bacteriumM. albumBG8 produces and releases large quantities of its S-layer units into the culture medium regardless of carbon or nitrogen source, metal availability or phase of growth. Of the 8 methanotrophic bacteria screened, onlyM. albumBG8 possesses this phenotype. Proteomics analysis of purified S-layer units identified the S-layer protein itself along with associated proteins involved metal uptake and S-layer biogenesis, including involvement of the T1SS. Better understanding ofM. albumBG8 S-layer biogenesis and the release of its S-layer units into culture medium could be harnessed for exporting expressed proteins of bioindustrial interest for ease of collection and purification.
Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma
Authors: Joun George L. , Kempe Emma G. , Chen Brianna , Sterling Jayden R. , Abbassi Ramzi H. , Daniel du Preez W. , Recasens Ariadna , Clark Teleri , Du Tian Y. , Low Jason K.K. , Kim Hani , Yang Pengyi , Khor Jasmine , Hoque Monira , Indurthi Dinesh C. , Kuchibhotla Mani , Palanisamy Ranjith , Jorgensen William T. , Montgomery Andrew P. , Baker Jennifer R. , Higginbottom Sarah L. , Tomaskovic-Crook Eva , Crook Jeremy M. , Loo Lipin , Day Bryan W. , Neely G. Gregory , Guccione Ernesto , Johns Terrance G. , Kassiou Michael , Don Anthony S. , Munoz Lenka
Published: January 2025

Chemotherapy often kills a large fraction of cancer cells but leaves behind a small population of drug- tolerant persister cells. These persister cells survive drug treatments through reversible, non-genetic mechanisms and cause tumour recurrence upon cessation of therapy. Here, we report a drug tolerance mechanism regulated by the germ-cell-specific H3K4 methyltransferase PRDM9. Through histone proteomic, transcriptomic, lipidomic, and ChIP-sequencing studies combined with CRISPR knockout and phenotypic drug screen, we identified that chemotherapy-induced PRDM9 upregulation promotes metabolic rewiring in glioblastoma stem cells, leading to chemotherapy tolerance. Mechanistically, PRDM9-dependent H3K4me3 at cholesterol biosynthesis genes enhances cholesterol biosynthesis, which persister cells rely on to maintain homeostasis under chemotherapy- induced oxidative stress and lipid peroxidation. PRDM9 inhibition, combined with chemotherapy, resulted in strong anti-cancer efficacy in preclinical glioblastoma models, significantly enhancing the magnitude and duration of the antitumor response by eliminating persisters. These findings demonstrate a previously unknown role of PRDM9 in promoting metabolic reprogramming that enables the survival of drug-tolerant persister cells.
Proximity based proteomics reveals Git1 as a regulator of Smoothened signaling
Authors: Zhang Jingyi , Kaur Gurleen , Cai Eva , Gutierrez Oscar Torres , Liu Xiaoliang , Baboo Sabyasachi , Diedrich Jolene K , Zhu Ju-Fen , Myers Benjamin R. , Yates John R , Ge Xuecai
Published: January 2025

The GPCR-like protein Smoothened (Smo) plays a pivotal role in the Hedgehog (Hh) pathway. To initiate Hh signaling, active Smo binds to and inhibits the catalytic subunit of PKA in the primary cilium, a process facilitated by G protein-coupled receptor kinase 2 (Grk2). However, the precise regulatory mechanisms underlying this process, as well as the events preceding and following Smo activation, remain poorly understood. To address this question, we leveraged the proximity labeling tool TurboID and conducted a time-resolved proteomic study of Smo-associated proteins over the course of Hh signaling activation. Our results not only confirmed previously reported Smo interactors but also uncovered new Smo-associated proteins. We characterized one of these new Smo interactors, Grk-interacting protein 1 (Git1), previously known to modulate GPCR signaling. We found that Git1 localizes to the base of the primary cilium, where it controls the cilium transport of Grk2, an early event in Hh signaling. Loss of Git1 impairs Smo phosphorylation by Grk2, a critical step for Smo-PKA interaction, leading to attenuated Hh signaling and reduced cell proliferation in granule neuron precursors. These results revealed a critical regulatory mechanism of Grk2 phosphorylation on Smo in the primary cilium. Our Smo-TurboID proteomic dataset provides a unique resource for investigating Smo regulations across different stages of Hh pathway activation.
Polymerase Eta Recruits FANCD2 to Common Fragile Sites to Maintain Genome Stability
Authors: Niljikar Mrunmai , Barreto-Galvez Angelica , Patel Saloni , Gagliardi Julia Elizabeth , Kumar Vasudha , Pradeep Archana , Juwarwala Aastha , Gerhardt Jeannine , Chang Yokechen , Montagna Cristina , Madireddy Advaitha
Published: January 2025

The replicative polymerase delta is inefficient copying repetitive DNA sequences. Error-prone translesion polymerases have been shown to switch with high-fidelity replicative polymerases to help navigate repetitive DNA. We and others have demonstrated the importance of one such translesion polymerase, polymerase Eta (pol eta), in facilitating replication at genomic regions called common fragile sites (CFS), which are difficult-to-replicate genomic regions that are hypersensitive to replication stress. However, the mechanistic basis for pol eta’s role in facilitating DNA replication at CFS and(or) at other genomic regions is currently unclear. Importantly, the functional importance of three non-catalytic domains of pol eta, the Ubiquitin-binding Zinc finger (UBZ), PCNA interacting protein (PIP) domain, and the F1 domain which mediates its switch with replicative DNA polymerases in mediating replication stress, especially at CFS loci is not clear. Here, we report that the PIP and UBZ domains of Pol Eta are both critical for its role in mediating cellular replication stress, especially at CFS. The absence of either domain induced elevated replication stress, replication stalling and DNA damage accumulation genome wide. This effect was even more pronounced at CFS loci leading to the accumulation of under replication DNA in G2/M. Importantly, while the inactivation of the UBZ domain resulted in a robust FANCD2 monoubiquitylation (a prominent marker of FANCD2 activation), FANCD2 recruitment genome wide was significantly impacted, especially at CFSs such as FRA16D. These S-phase phenotypes result in ssDNA gap formation and the persistence of under-replicated genomic regions upon transition to G2/M. While post-replicative gap filing/ repair by Mitotic DNA synthesis is activated in the mutants, it only effectively resolves UFBs in the F1* cells. The PIP*, UBZ* and pol eta−/−cells unfortunately manifest excessive toxic cytosolic DNA that instigates a strong innate immune response. These results collectively show that translesion polymerase Eta functions in a common pathway with FANCD2 to prevent replication perturbation and instability at CFS loci.
Structural insights into heterohexameric assembly of epilepsy-related ligand–receptor complex LGI1–ADAM22
Authors: Yamaguchi Takayuki , Okatsu Kei , Kubota Masato , Mitsumori Ayuka , Yamagata Atsushi , Fukata Yuko , Fukata Masaki , Shibata Mikihiro , Fukai Shuya
Published: January 2025

Leucine-rich glioma-inactivated 1 protein (LGI1) is a secreted neuronal protein consisting of the N-terminal leucine-rich repeat (LRR) and C-terminal epitempin repeat (EPTP) domains. LGI1 is linked to epilepsy, a neurological disorder caused by genetic mutations. ADAM22 is a membrane receptor that binds to LGI1 extracellularly and interacts with AMPA-type glutamate receptors via PSD-95 intracellularly to maintain normal synaptic signal transmission. Structural analysis of the LGI1–ADAM22 complex is important for understanding the molecular mechanism of epileptogenesis and developing new therapies against epilepsy. We previously reported the crystal structure of a 2:2 complex consisting of two molecules of LGI1 and two molecules of the ADAM22 ectodomain (ECD), which is suggested to bridge neurons across the synaptic cleft. On the other hand, multiangle light scattering, small-angle X-ray scattering, and cryo-EM analyses have suggested the existence of a 3:3 complex consisting of three molecules of LGI1 and three molecules of ADAM22. In the previous cryo-EM analysis, many observed particles were in a dissociated state, making it difficult to determine the three-dimensional (3D) structure of the 3:3 complex. In this study, we stabilized the 3:3 LGI1–ADAM22ECDcomplex using chemical crosslinking and determined the cryo-EM structures of the LGI1LRR–LGI1EPTP–ADAM22ECDand 3:3 LGI1–ADAM22ECDcomplexes at 2.78 Å and 3.79 Å resolutions, respectively. Furthermore, high-speed atomic force microscopy (HS-AFM) visualized the structural features and flexibility of the 3:3 LGI1–ADAM22ECDcomplex in solution. We discuss new insights into the interaction modes of the LGI1–ADAM22 higher-order complex and the structural properties of the 3:3 LGI1–ADAM22 complex.

Significance

The neuronal secretory protein Leucine-rich glioma-inactivated 1 (LGI1) and its receptor protein ADAM22 play a critical role in maintaining normal synaptic signal transmission. Genetic mutations in LGI1 are linked to epilepsy. Structural analysis of the LGI1–ADAM22 complex is crucial for understanding the molecular mechanisms of epileptogenesis and for developing targeted treatments. In this study, we determined the cryo-EM structure of the heterohexameric LGI1–ADAM22 complex and visualized the dynamics of this complex by high-speed atomic force microscopy.
MLC1alteration in iPSCs give rise to disease-like cellular vacuolation phenotype in the astrocyte lineage
Authors: Sharma Saumya , Bharti Vishal , Das Prosad Kumar , Rahman Abdul , Sharma Harshita , Rauthan Riya , RC Madhumita , Gupta Neerja , Shukla Rashmi , Mohanty Sujata , Kabra Madhulika , Francis Kevin R , Chakraborty Debojyoti
Published: January 2025

Background

Megalencephalic leukoencephalopathy with subcortical cysts (MLC), a rare and progressive neurodegenerative disorder involving the white matter, is not adequately recapitulated by current disease models. Somatic cell reprogramming, along with advancements in genome engineering, may allow the establishment ofin-vitrohuman models of MLC for disease modeling and drug screening. In this study, we utilized cellular reprogramming and gene-editing techniques to develop induced pluripotent stem cell (iPSC) models of MLC to recapitulate the cellular context of the classical MLC-impacted nervous system.

Methods

Somatic cell reprogramming of peripheral patient-derived blood mononuclear cells (PBMCs) was used to develop iPSC models of MLC. CRISPR-Cas9 system-based genome engineering was also utilized to create theMLC1knockout model of the disease. Directed differentiation of iPSCs to neural stem cells (NSCs) and astrocytes was performed in a 2D cell culture format, followed by various cellular and molecular biology approaches, to characterize the disease model.

Results

MLC iPSCs established by somatic cell reprogramming and genome engineering were well characterized for pluripotency. iPSCs were subsequently differentiated to disease-relevant cell types: neural stem cells (NSCs) and astrocytes. RNA sequencing profiling of MLC NSCs revealed a set of differentially expressed genes related to neurological disorders and epilepsy, a common clinical finding within MLC disease. This gene set can serve as a target for drug screening for the development of a potential therapeutic for this disease. Upon differentiation to the more disease relevant cell type-astrocytes, MLC-characteristic vacuoles were clearly observed, which were distinctly absent from controls. This emergence recapitulated a distinguishing phenotypic marker of the disease.

Conclusion

Through the creation and analyses of iPSC models of MLC, our work addresses a critical need for relevant cellular models of MLC for use in both disease modeling and drug screening assays. Further investigation can utilize MLC iPSC models, as well as generated transcriptomic data sets and analyses, to identify potential therapeutic interventions for this debilitating disease.
Diverse ssRNA viruses associated withKarenia brevisharmful algal blooms in Southwest Florida
Authors: Lim Shen Jean , Rogers Alexandra , Rosario Karyna , Kerr Makenzie , Garrett Matt , Koester Julie , Hubbard Katherine , Breitbart Mya
Published: January 2025

Harmful algal blooms (HABs) caused by the dinoflagellateKarenia brevisfrequently occur in the eastern Gulf of Mexico, where they negatively impact the environment, human health, and economy. Very little is known about viruses associated withK. brevisblooms, although viral infection of other HAB-forming phytoplankton species can play an important role in bloom dynamics. We used viral metagenomics to identify viruses in 11 pooled seawater samples collected from Southwest Florida, USA in 2021 during a severe, spatiotemporally dynamicK. brevisbloom. Assembled viral genomes were similar to published genomes from the orderPicornavirales, familyMarnaviridae, and generaSogarnavirus,Bacillarnavirus, andMarnarnavirus. Viruses from these groups infect bloom-forming diatoms (Chaetocerossp. andRhizosolenia setigera) and the raphidophyteHeterosigma akashiwo. We also recovered unclassifiedRiboviriagenomes related to aSymbiodiniumpositive-sense ssRNA virus sequenced from coral dinoflagellate symbionts. Reverse-transcriptase PCR assays were performed to monitor the occurrence of seven representative virus genomes in these 2021 samples and 43 seawater samples collected during a subsequent, typical bloom between November 2022 and May 2023. Over half of the samples contained multiple viruses, and at least one viral genome was detected in 44 of 54 samples, collected across seasons and years, highlighting the ubiquity of these viruses in this region. Alpha diversity was highest in the summer months and positively correlated withK. breviscell counts. Multiple regression revealed month and the presence of unclassifiedRiboviriasequences most similar to dinoflagellate viruses as significant predictors ofK. breviscellular abundance.

Importance

Harmful algal blooms caused by the dinoflagellateKarenia brevisnegatively impact the tourism, fisheries, and public health sectors. Anticipated impacts of climate change, nutrient pollution, and ocean acidification may sustain and/or exacerbateK. brevisblooms in the future, underscoring the need for proactive monitoring, communication, and mitigation strategies. This study represents a pioneering effort in monitoring viruses associated withK. brevisblooms. The findings lay the groundwork for studying the effects of environmental drivers onK. brevisblooms and their associated viruses, as well as for exploring the roles of viruses in bloom dynamics and potential applications of viruses as biocontrol agents forK. brevisblooms. Furthermore, the comparison of viral dynamics relative to local and regional bloom dynamics in this study helps inform future monitoring and modeling needs.
Fine-tuning molecular mechanics force fields to experimental free energy measurements
Authors: Rufa Dominic , Fass Joshua , Chodera John D.
Published: January 2025

Alchemical free energy methods using molecular mechanics (MM) force fields are essential tools for predicting thermodynamic properties of small molecules, especially via free energy calculations that can estimate quantities relevant for drug discovery such as affinities, selectivities, the impact of target mutations, and ADMET properties. While traditional MM forcefields rely on hand-crafted, discrete atom types and parameters, modern approaches based on graph neural networks (GNNs) learn continuous embedding vectors that represent chemical environments from which MM parameters can be generated. Excitingly, GNN parameterization approaches provide a fully end-to-end differentiable model that offers the possibility of systematically improving these models using experimental data. In this study, we treat a pretrained GNN force field—here, espaloma-0.3.2—as afoundation simulation modelandfine-tuneits charge model using limited quantities of experimental hydration free energy data, with the goal of assessing the degree to which this can systematically improve the prediction of other related free energies. We demonstrate that a highly efficient “one-shot fine-tuning” method using an exponential (Zwanzig) reweighting free energy estimator can improve prediction accuracy without the need to resimulate molecular configurations. To achieve this “one-shot” improvement, we demonstrate the importance of using effective sample size (ESS) regularization strategies to retain good overlap between initial and fine-tuned force fields. Moreover, we show that leveraging low-rank projections of embedding vectors can achieve comparable accuracy improvements as higher-dimensional approaches in a variety of data-size regimes. Our results demonstrate that linearly-perturbative fine-tuning of foundation model electrostatic parameters to limited experimental data offers a cost-effective strategy that achieves state-of-the-art performance in predicting hydration free energies on the FreeSolv dataset.
Cleavage cascade of the sigma regulator FecR orchestrates TonB-dependent signal transduction
Authors: Yokoyama Tatsuhiko , Miyazaki Ryoji , Suzuki Takehiro , Dohmae Naoshi , Nagai Hiroki , Tsukazaki Tomoya , Kubori Tomoko , Akiyama Yoshinori
Published: January 2025

TonB-dependent signal transduction is a versatile mechanism observed in gram-negative bacteria, integrating energy-dependent substrate transport with signal relay. InEscherichia coli, the TonB-ExbBD motor complex energizes the TonB-dependent transporter FecA, facilitating ferric citrate import. FecA also functions as a sensor, transmitting signals to the cytoplasmic membrane protein FecR. We previously demonstrated that FecR undergoes a three-step cleavage process, culminating in the activation of the cytoplasmic sigma factor FecI, which drivesfecgene transcription. Here, we describe the complete mechanism of FecR cleavage-mediated ferric citrate signaling involving FecA and TonB. The cleavage cascade begins with FecR autoproteolysis prior to membrane integration. The soluble C-terminal domain (CTD) fragment of FecR is co-translocated with the N-terminal domain (NTD) fragment through a Tat system-mediated process. In the periplasm, the interaction between the CTD and NTD fragments prevents further cleavage. This inhibition is lifted by TonB-mediated motor function, which releases the CTD, allowing the cleavage cascade to proceed. This process is essential for ferric citrate signal-induced activation offecgene expression. Our findings reveal that the regulation of FecR cleavage, relying on the TonB-FecA axis, plays a central role in bacterial response to ferric citrate signals.

Significance Statement

Scarcity of iron, an essential element for life, has driven bacteria to evolve intricate acquisition systems, yet the molecular basis of their signal transduction mechanisms remains elusive. Unlike conventional pathways, iron transport systems employ outer membrane receptors that mediate signal transduction across both the outer and cytoplasmic membranes, powered by TonB. Using theEscherichia coliFec system, we uncovered the mechanism by which FecR’s cleavage cascade orchestrates ferric citrate signaling through TonB-mediated energy transfer. These findings shed light on similar mechanisms in gram-negative bacteria and have significant implications for understanding bacterial adaptation and pathogenesis.
DNA data (genome skims and metabarcodes) paired with chemical data demonstrate utility for retrospective analysis of forage linked to fatal poisoning of cattle
Authors: Cook Daniel , Kocurek Brandon , Stonecipher Clint , Welch Kevin D. , Gardner Dale R. , Mammel Mark , Reed Elizabeth , Ramachandran Padmini , Erickson David , Commichaux Seth , Ottesen Andrea
Published: January 2025

Prepared and stored feeds, fodder, silage, and hay may be contaminated by toxic plants resulting in the loss of livestock. Several poisonous plants have played significant roles in livestock deaths from forage consumption in recent years in the Western United States includingSalvia reflexa. Metagenomic data, genome skims and metabarcodes, have been used for identification and characterization of plants in complex matrices including diet composition of animals, mixed forages, and herbal products. Here, chemistry, genome skims, and metabarcoding were used to retrospectively describe the composition of contaminated alfalfa hay from a case ofSalvia reflexapoisoning that killed 165 cattle. Genome skims and metabarcoding provided similar estimates of the relative abundance of theSalviain the hay samples when compared to chemical methods. Additionally, genome skims and metabarcoding provided similar estimates of species composition in the contaminated hay and rumen contents of poisoned animals. The data demonstrate that genome skims and DNA metabarcoding may provide useful tools for plant poisoning investigations.
Machine learning differentiation of Parkinson’s disease and normal pressure hydrocephalus using wearable sensors capturing gait impairments
Authors: Magni Stefano , Bremm Rene Peter , Verros Konstantinos , He Xin , Lecossois Sylvie , Jelke Finn , Husch Andreas , Gonçalves Jorge , Hertel Frank
Published: January 2025

Gait impairments in patients with Parkinson’s Disease (PD) and Normal Pressure Hydrocephalus (NPH) are diagnosed with visual clinical assessments. Despite standardized gait tests and clinicians’ expertise, such approaches can be subjective and challenging due to similar symptoms between the two diseases. Wearable sensors and machine learning (ML) can assist clinicians by offering objective and quantitative assessments of gait impairments that can help distinguishing between PD and NPH. This study consists of a cohort of 12 PD and 11 NPH patients that performed standardized gait tests. Gait was measured by wearable sensors embedded in patients’ shoes: a three-axis gyroscope, a three-axis accelerometer and eight pressure sensors in each insole. Sensors and computational pipeline to extract gait cycle features were validated and calibrated on 21 healthy subjects. ML approaches were employed to identify changes in gait cycle features between the PD and NPH patients groups. Twenty-seven ML classifiers were compared, leading to select linear support vector machines, resulting in a classification accuracy of 0.70 ± 0.28 and an area under the ROC curve of 0.74 ± 0.39. Combining wearable sensors with ML algorithms trained on gait cycle features from those sensors showed the potential for objective differentiation of gait patterns between PD and NPH patients.
Genome-wide analysis of screen behaviors among adolescents identifies novel loci and overlap with educational attainment and mental disorders
Authors: Frei Evgeniia , Filiz Tahir Tekin , Frei Oleksandr , Loughnan Robert , Jaholkowski Piotr , Bakken Nora R. , Birkenæs Viktoria , Shadrin Alexey A. , Ask Helga , Andreassen Ole A. , Smeland Olav B.
Published: January 2025

Technological devices play a central role in adolescents’ life. Despite concerns about negative effects of excessive screen time on mental health and development, there is little knowledge of fundamental features of screen behaviours and underlying genetic architecture. Using self-reports from adolescents (14-16 years old) in the Norwegian Mother, Father, and Child Cohort Study (MoBa,n= 18 490), we performed genome-wide association analysis for four screen behaviors: time spent 1) watching movies/series/TV; 2) gaming; 3) sitting/lying down with PC, mobile or tablet; and 4) communicating with friends on social media. The resulting summary statistics were analysed using the conditional false discovery rate (condFDR) approach to increase genetic discovery. We also estimated SNP-based heritabilities of the screen behaviours and the genetic correlations with six major psychiatric disorders (schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorder, attention-deficit hyperactivity disorder, alcohol use disorder), and educational attainment. The screen-based phenotypes displayed significant SNP-based heritabilities (0.048–0.12). We also observed significant genetic correlations between screen behaviours and psychiatric disorders (rgrange: 0.21–0.42). Educational attainment demonstrated significant negative genetic correlation with screen behaviours, most strongly with social media use (rg= −0.69). CondFDR analysis identified three novel loci associated with social media use. Thus, we show that screen behaviors are heritable, polygenic traits that partly share genetic signal with mental disorders and educational attainment. Future studies and larger samples are required to clarify causal relationships between these traits and disorders, and to validate the identified genetic loci associated with social media use.
Higher Brain Grey Matter Density in Mild to Moderate Chronic Low Back Pain Patients
Authors: Sean Monica , Cote Samantha , Alexia-Coulombe-Lévêque  , Huck Julia , Martel Marylie , Léonard Guillaume , Whittingstall Kevin , Tétreault Pascal
Published: January 2025

Chronic low back pain (CLBP) is the leading cause of disability worldwide. Structural abnormalities in the lumbar region rarely account for the pain symptoms observed. In contrast, the brain plays a central role in chronic pain, with several studies suggesting that chronic pain may result from the persistence of pain memories and/or the inability to extinguish these memories following an initial inciting injury. Previous research has reported a reduction in grey matter density (GMD) in CLBP patients, as measured by magnetic resonance imaging (MRI). Notably, lower GMD has been observed in patients with moderate to severe CLBP who are undergoing prescribed pharmacological treatments. However, it remains unclear whether these differences in GMD could be associated with a less severe condition.

This study aimed to investigate whether GMD is altered in a cohort with mild to moderate CLBP symptoms, and who have not been prescribed pharmacological treatments. To achieve this, we acquired T1-weighted MRI scans from 25 healthy controls (HC) and 27 untreated individuals with mild to moderate CLBP. Scans were taken at baseline, 2 months, and 4 months after baseline. GMD analysis was carried out using the FMRIB Software.

Our results consistently showed higher GMD in the CLBP group compared to HC. These findings suggest that the observed alterations in GMD may be related to the condition itself, and can occur even in patients with milder symptoms and better physical function, without the influence of opioids, anticonvulsants, or antidepressants. Given that our participants differ from those typically studied in the literature, our results imply that they may be in a distinct brain state relative to the condition. Further research is needed to elucidate the underlying biological mechanisms and confirm whether these brain alterations are indeed a characteristic feature of CLBP.
Flow-induced bending of flagella controls bacterial surface behavior
Authors: Palalay Jessica-Jae S. , Sanfilippo Joseph E.
Published: January 2025

Bacteria engage in surface-specific behaviors that are assumed to be driven by biological signaling. However, surface behaviors could be controlled by mechanical reorientation of bacterial appendages. Here, we use microfluidics and flagellar labeling to discover how shear force bends flagella to control surface behavior of the human pathogenPseudomonas aeruginosa. By imaging flagellar rotation and using mutants with paralyzed flagella, we establish that flagellar rotation promotes surface departure in host-relevant shear regimes. Our single-cell experiments reveal two distinct subpopulations in flow: cells with their flagellum positioned upstream and cells with their flagellum positioned downstream. Shear force bends upstream flagella around the cell and blocks rotation. In contrast, downstream flagella can continue to rotate after surface arrival. Cells with downstream flagella depart the surface more frequently than cells with upstream flagella, indicating how flow direction can determine bacterial cell fate on surfaces. Together, our results demonstrate how the geometric relationship between flow and cell appendages can generate subpopulations and control surface behaviors.
Mitoxantrone inhibits and downregulates ERαthrough binding at the DBD-LBD interface
Authors: Wang Han , Luo Yuxuan , Artham Sandeep , Wang Qianqian , Peng Yi , Yun Zixi , Li Xinyue , Wu Chen , Liu Zhenghao , Weber-Bonk Kristen L. , Pai Chun-Peng , Cao Yuan , Yue Jiangan , Park Sunghee , Keri Ruth A. , Geng Lisheng , McDonnell Donald P. , Kao Hung-Ying , Yang Sichun
Published: January 2025

Targeting the estrogen receptor (ER or ERα) through competitive antagonists, receptor downregulators, or estrogen synthesis inhibition remains the primary therapeutic strategy for luminal breast cancer. We have identified a novel mechanism of ER inhibition by targeting the critical interface between its DNA-binding domain (DBD) and ligand-binding domain (LBD). We demonstrate that mitoxantrone (MTO), a topoisomerase II inhibitor, binds at this previously unexplored DBD-LBD interface. Using comprehensive computational, biophysical, biochemical, and cellular analyses, we show that independent of its DNA damage response activity, MTO binding induces distinct conformational changes in ER, leading to its cytoplasmic redistribution and subsequent proteasomal degradation. Notably, MTO effectively inhibits clinically relevant ER mutations (Y537S and D538G) that confer resistance to current endocrine therapies, outperforming fulvestrant in bothin vitroandin vivoassays. Our findings establish domain-domain interaction targeting as a viable therapeutic strategy for ER, with translational implications for other nuclear receptors.
Human cortical dynamics reflect graded contributions of local geometry and network topography
Authors: Royer Jessica , Paquola Casey , Rodriguez-Cruces Raul , Auer Hans , Ngo Alexander , Sahlas Ella , Arafat Thaera , Abdallah Chifaou , Mansilla de Latorre Daniel , Pana Raluca , Hall Jeffrey A. , Leech Robert , Smallwood Jonathan , Frauscher Birgit , Bernhardt Boris
Published: January 2025

The brain is a physically embedded and heavily interconnected system that expresses neural rhythms across multiple time scales. While these dynamics result from the complex interplay of local and inter-regional factors, the relative contribution of such mechanisms across the cortex remains unclear. Our study explored geometric, microstructural, and connectome-level constraints on cortex-wide neural activity. We leveraged intracranial electroencephalography recordings to derive an intrinsic coordinate system of human cortical dynamics. Using multimodal neuroimaging, we could then demonstrate that these patterns were largely explainable by geometric properties indexed by inter-regional distance. However, dynamics in transmodal association regions were additionally explainable by incorporation of inter-regional microstructural similarity and connectivity information. Our findings were consistent when cross-referencing electroencephalography and imaging data from large-scale atlases and when using data obtained in the same individuals, suggesting subject-specificity and population-level generalizability. Together, our results support gradual shifts in the balance of local and macroscale constraints on cortical dynamics and highlight a key role of transmodal networks in inter-regional cortical coordination.
Nondestructive Detection and Quantification of Dysprosium in Plant Tissues
Authors: Hernández-Pagán Edmaritz , Laosuntisuk Kanjana , Harris Alex T. , Haynes Allison N. , Buitrago David , Rajabu Cyprian , Kudenov Michael W. , Doherty Colleen J.
Published: January 2025

Background

The growing demand for rare-earth elements (REEs), particularly dysprosium (Dy), in part driven by clean energy technologies, underscores the need for sustainable extraction methods. Recovery of Dy, particularly from geographically distributed waste sources is challenging. This gap positions phytomining—a technique using plants to accumulate metals— as a promising alternative. However, plant species differ in their ability to accumulate metals in high concentrations, necessitating efficient screening methods. In this study, we developed a high-throughput fluorescence-based assay to detect and quantify Dy uptake in plant tissues.

Results

Our Dy detection method exploits Dy’s unique spectroscopic properties for sensitive and efficient analysis, enabling detection of concentrations as low as 0.3 µM. By incorporating sodium tungstate (Na WO) as a fluorescence enhancer, we achieved robust emissions at 480 and 580 nm, facilitating Dy quantification in complex plant matrices. Additionally, time-resolved fluorescence techniques reduced background autofluorescence from plant tissues, enhancing signal specificity. Validation against Inductively Coupled Plasma Mass Spectrometry (ICP-MS) demonstrated strong correlation. Greenhouse trials confirmed the method’s utility for screening Dy accumulation in living plants and highlight the potential for rapid standoff detection.

Conclusions

This fluorescence-based approach offers a scalable, efficient tool for identifying Dy-accumulating plants, advancing phytomining as a sustainable strategy for REE recovery.
Distinct Control of histone H1 expression within the Histone Locus body by CRAMP1
Authors: Bodner Justin , Vadlamani Pranathi , Helmin Kathryn A. , Liu Qianli , Mendillo Marc L. , Singer Benjamin D. , Srivastava Shashank , Foltz Daniel R.
Published: January 2025

Proper histone gene expression is critical to cell viability and maintaining genomic integrity. Multiple histone genes organized into three genomic loci encode for replication coupled core and linker histones. Histone gene expression and transcript processing is orchestrated in the histone locus body (HLB) within the nucleus. We identified human CRAMP1 as a selective regulator of linker histone H1 expression. CRAMP1 is recruited to the HLB in RPE1hTERTcells. Affinity purification shows that CRAMP1 physically associates the HLB component GON4L (a.k.a. YARP). We show that the PAH domains of GON4L interact with CRAMP1. CRAMP1 disruption results in a loss of histone H1 expression and a reduction in H1 protein. CRAMP1 occupies the unmethylated promoters of the replication coupled linker histone genes that reside within the histone locus body, and the replication independent histone H1 loci, which reside in a region of the genome without other histone genes. Together these data identify CRAMP1 as a novel and selective regulator of histone H1 gene expression.
A Single-Graph Visualization to Reveal Hidden Explainability Patterns of SHAP Feature Interactions in Machine Learning for Biomedical Issues
Authors: Furger Félix , Aligon Julien , Thomas Miguel , Doumard Emmanuel , Delpierre Cyrille , Casteilla Louis , Monsarrat Paul
Published: January 2025

Background

In the last decades, the utility of Machine Learning (ML) in the biomedical domain has been demonstrated repeatedly. Their inherent opacity need augmenting ML with explainability techniques. A common practice in model explainability however, is to focus solely on the explanatory values themselves without accounting for both the main and interaction effects. While this approach simplifies interpretation, it potentially overlooks critical medical information since the nature of the interactions may provide clues to the underlying biological mechanisms.

Results

This article introduces a novel method for analyzing explanatory values of machine learning (ML) models, in the form of a comprehensive graphical visualization. The method not only emphasises the individual contributions of the features but also gives insights about the interactions they share with one another. Designed for local additive explanation methods, the proposed tool effectively translates the complex and multidimensional nature of these values into an intuitive single-graph format. It offers a clear window into how feature interactions contribute to the overall prediction of the ML model while aiding in the identification of various interaction types, such as mutual attenuation, positive/negative synergies or dominance of one feature over another.

Conclusions

This approach provides insights for generating hypotheses, improving the transparency of ML models, particularly in the context of biology and medicine since living organisms are characterised by a multitude of parameters in complex interactions, a complexity that ensures the “stability” and robustness of structures and functions.
Using artificial intelligence-based software for an unbiased discrimination of immune cell subtypes in the fracture hematoma and bone marrow of non-osteoporotic and osteoporotic mice
Authors: Fischer Verena , Ignatius Anita , Schmidt-Bleek Katharina , Duda Georg , Haffner-Luntzer Melanie
Published: January 2025

It is well established that the early inflammatory response following fracture is essential for initiating subsequent bone regeneration. An imbalance in inflammation, whether within the innate or adaptive immune response, can result in impaired fracture healing. In our previous studies, we demonstrated that, for example, mice with ovariectomy-induced osteoporosis exhibit altered immune cell populations in the early fracture hematoma and bone marrow, leading to delayed healing. These analyses were conducted using conventional FACS/flow cytometry software, where surface marker expression was assessed using a single threshold based on isotype controls—a binary “yes or no” decision. Recent advances have highlighted that immune cell populations are often more heterogeneous, with distinct phenotypic subgroups depending on their polarization status. This has been particularly well documented for macrophage subpopulations (M1, M2, and intermediate polarization states). In light of this, we employed a commercially available artificial intelligence-based clustering software (Cytolution) to more accurately and objectively identify immune cell subpopulations. We re-analyzed flow cytometry raw data from fracture hematoma and bone marrow of non-osteoporotic and osteoporotic mice at day 1 after fracture. Our findings revealed distinct subclusters for granulocytes (27 subclusters), macrophages (7 subclusters), B cells (4 subclusters), and T cells (6 subclusters) within the fracture hematoma and bone marrow. Comparing osteoporotic and non-osteoporotic mice, we observed an increased abundance of a specific B cell subpopulation in osteoporotic mice, alongside a significant reduction of a particular granulocyte subpopulation in the early fracture hematoma. Several subclusters of granulocytes, T cells, and macrophages were also altered in the bone marrow. The specific role of these immune cell subclusters remains to be investigated in the future. These results suggest that AI-based clustering may provide a powerful tool for identifying immune cell phenotypes during bone regeneration, offering a more nuanced understanding of flow cytometry data.
Pluripotent stem cell-derived NK progenitor cell therapy prevents tumour occurrence and eradicates minimal residual disease
Authors: Wang Zhiqian , Lin Yunqing , Huang Dehao , Zhang Leqiang , Xia Chengxiang , Weng Qitong , Liu Yanhong , Wang Tongjie , Zhang Mengyun , Wu Jiaxin , Qi Hanmeng , Liu Lijuan , Shen Yiyuan , Chen Yi , Zhu Yanping , Hu Fangxiao , Wang Jinyong
Published: January 2025

The lack of persistence and short-term efficacy presents a major challenge for CAR-NK cell therapy. Here, we addressed this issue by developing pluripotent stem cell-derived NK lineage-committed progenitor (iNKP) cell therapy. For the first time, we generated abundant iNKP cells via an organoid culture system. The iNKP cells, engineered to express CXCR4 and chimeric antigen receptors (CAR), efficiently migrated to the bone marrow and generated CAR-iNK cells persisting in peripheral blood (PB) for over 80 days. Notably, CAR-iNKP cell therapy durably protected animals from tumour occurrence. Furthermore, a single low-dose infusion of CAR-iNKP cells following conventional chemotherapy eradicated minimal residual disease (MRD), leading to long-term complete remission. Our findings present a novel strategy to overcome the limitations of traditional CAR-NK cell therapy and offer dural breakthroughs for the prevention of tumour occurrence and relapse.
Enterococcus faeciumMBBL3 Exhibits Promising Probiotic Potential and Antimicrobial Efficacy Against Bovine Mastitis-AssociatedEscherichia coli and Klebsiella pneumoniae
Authors: Siddique Naim , Rahman Md. Morshedur , Hasnat Soharth , Rahman ANM Aminoor , Talukder Anup Kumar , Karim Md. Robiul , Das Ziban Chandra , Islam Tofazzal , Hoque M. Nazmul
Published: January 2025

Enterococcus faecium, a promising probiotic, combats pathogens, supports gut health, strengthens immunity, and provides a natural approach to address the escalating global challenge of antimicrobial resistance. This study aimed to investigate the genome ofE. faeciumMBBL3, isolated from healthy cow milk, to assess its probiotic potential and antimicrobial activity against pathogens causing bovine mastitis. The strain was analyzed through whole genome sequencing, along within-vitroandin-silicoassessments were conducted to determine its antimicrobial efficacy against bovine mastitis pathogens,Klebsiella pneumoniaeMBBL2 (KpMBBL2) andEscherichia coliMBBL4 (EcMBBL4). The genome assembly and functional annotations uncovered many important probiotic traits in MBBL3, where genome comparison revealed its high genetic similarity with otherEnterococcusstrains. MBBL3 demonstrated the ability to ferment a wide range of carbohydrates and possessed 76 carbohydrate-active enzyme-related genes, including five key CAZy families namely GH73, GH18, CBM50, CE4, and AA10. It also possessed importance genes for bile salt and acid tolerance, stress resistance, and surface adhesion. Additionally, MBBL3 contained metabolite regions involved in the biosynthesis of antimicrobial compounds such as 2,4-DAPG, aborycin, enterocin NKR-5-3B, and sodorifen, and bacteriocin gene clusters forsactipeptides,Enterolysin_A, andUviB. Safety assessments indicated low pathogenic potential, whilein-vitroassays demonstrated antibiotic susceptibility and suppressed the growth ofKpMBBL2 andEcMBBL4, respectively. Its bacteriocin compound Enterolysin_A exhibited strong molecular interactions with virulence proteins of these mastitis pathogens. Therefore, the promising probiotic potential and antimicrobial efficacy ofE. faeciumMBBL3, especially against mastitis pathogens combined with its safety, position it as a valuable candidate for therapeutic applications.

Key points

E. faeciumMBBL3 genosme showed high similarity with other species of this genera.

Genetic makeup of MBBL3 revealed its ability to survival and adaptation in different niches including host’s gut.

In-vitroandin-silicostudy results, along with several genes linked to antimicrobials demonstrated its ability to combat against mastitis pathogens.
CellPhePy: a Python implementation of the CellPhe toolkit for automated cell phenotyping from microscopy time-lapse videos
Authors: Wiggins Laura , Lacy Stuart , Park Graeme , Marrison Joanne , Powell Ben , Cimini Beth , O’Toole Peter , Wilson Julie , Brackenbury William J.
Published: January 2025

We previously developed the CellPhe toolkit1, an open-source R package for automated cell phenotyping from ptychography time-lapse videos. To align with the growing adoption of python-based image analysis tools and to enhance interoperability with widely used software for cell segmentation and tracking, we developed a python implementation of CellPhe, named CellPhePy. CellPhePy preserves all of the core functionality of the original toolkit, including single-cell phenotypic feature extraction, time-series analysis, feature selection and cell type classification. In addition, CellPhePy introduces significant enhancements, such as an improved method for identifying features that differentiate cell populations and extended support for multiclass classification, broadening its analytical capabilities. Notably, the CellPhePy package supports CellPose segmentation and TrackMate tracking, meaning that a set of microscopy images are the only required input with segmentation, tracking and feature extraction fully automated for downstream analysis, without reliance on external applications. The workflow’s increased flexibility and modularity make it adaptable to different imaging modalities and fully customisable to address specific research questions. CellPhePy can be installed via PyPi or GitHub, and we also provide a CellPhePy GUI to aid user accessibility.