bluuebunny/crossref_metadata_2025 huggingface dataset:
Aggregation of HAPLN2, a component of the perinodal extracellular matrix, is a hallmark of physiological brain aging in mice
Authors: Watanabe Ayaka , Hirayama Shoshiro , Kominato Itsuki , Marchese Sybille , Esposito Pietro , Metodieva Vanya , Kameda Hiroshi , Sano Terunori , Takatori Sho , Takao Masaki , Koike Masato , Varela Juan Alberto , Tomita Taisuke , Murata Shigeo
Published: January 2025

Protein aggregation is a hallmark of neurodegenerative diseases and is also observed in the brains of elderly individuals without such conditions, suggesting that aging drives the accumulation of protein aggregates. However, the comprehensive understanding of age-dependent protein aggregates involved in brain aging remains unclear. Here, we investigated proteins that become sarkosyl-insoluble with age and identified hyaluronan and proteoglycan link protein 2 (HAPLN2), a hyaluronic acid-binding protein of the extracellular matrix at the nodes of Ranvier, as an age-dependent aggregating protein in mouse brains. Elevated hyaluronic acid levels and impaired microglial function reduced the clearance of HAPLN2, leading to its accumulation. HAPLN2 oligomers induced microglial inflammatory responses bothin vitroandin vivo. Furthermore, age-associated HAPLN2 aggregation was also observed in the human cerebellum. These findings suggest that HAPLN2 aggregation results from age-related decline in brain homeostasis and may exacerbate the brain environment by activating microglia. This study provides new insights into the mechanisms underlying cerebellar aging and highlights the role of HAPLN2 in age-associated changes in the brain.

Author Summary

To identify age-dependent protein aggregates unrelated to disease, we analyzed the sarkosyl-insoluble proteome of young and aged mouse brains. We discovered that hyaluronan and proteoglycan link protein 2 (HAPLN2), a hyaluronic acid-binding protein existing in the nodal extracellular matrix, accumulated with age. Age-dependently accumulated HAPLN2 formed large protein aggregates that cannot be solubilized by the anionic detergent sarkosyl or by hyaluronidase digestion. In addition, HAPLN2 formed irregularly shaped puncta that were mislocalized from the nodes of Ranvier in the cerebellar white matter of not only aged mice but also aged human brains. Oligomers of full-length HAPLN2 specifically induced microglial activationin vitroandin vivo. Our findings suggest that the accumulation of HAPLN2 aggregates is a new hallmark of brain aging and a possible factor contributing to brain inflammation.
Predictive acoustical processing in human cortical layers
Authors: Faes Lonike K. , Zulfiqar Isma , Vizioli Luca , Yu Zidan , Wu Yuan-Hao , Shin Jiyun , Cloos Martijn A. , Auksztulewicz Ryszard , Melloni Lucia , Uludag Kamil , Yacoub Essa , De Martino Federico
Published: January 2025

In our dynamic environments, predictive processing is vital for auditory perception and its associated behaviors. Predictive coding formalizes inferential processes by implementing them as information exchange across cortical layers and areas. With laminar-specific blood oxygenation level dependent we measured responses to a cascading oddball paradigm, to ground predictive auditory processes on the mesoscopic human cortical architecture. We show that the violation of predictions are potentially hierarchically organized and associated with responses in superficial layers of the planum polare and middle layers of the lateral temporal cortex. Moreover, we relate the updating of the brain’s internal model to changes in deep layers. Using a modeling approach, we derive putative changes in neural dynamics while accounting for draining effects. Our results support the role of temporal cortical architecture in the implementation of predictive coding and highlight the ability of laminar fMRI to investigate mesoscopic processes in a large extent of temporal areas.
Susceptibility of bovine respiratory and mammary epithelial cells to avian and mammalian derived clade 2.3.4.4b H5N1 highly pathogenic avian influenza viruses
Authors: Meliopoulos Victoria , Cherry Sean , Smith Maria , Sharp Bridgett , Brigleb Pamela H. , Roubidoux Ericka , Livingston Brandi , Morris Dorothea R. , Ripperger Tyler , Baker Pari , Gragg Sara , Dimitrov Kiril , Langel Stephanie , Schultz-Cherry Stacey
Published: January 2025

Zoonotic transmission of avian influenza viruses into mammals is relatively rare due to anatomical differences in the respiratory tract between species. Recently, clade 2.3.4.4b highly pathogenic H5N1 avian influenza viruses were detected circulating in North American cattle. Sporadic transmission between cattle, humans, and other animals proximal to cattle or after consuming products from infected cattle has occurred, but thus far there is no evidence of human-to-human transmission. However, the virus has the potential to adapt to the mammalian respiratory tract with every transmission event that occurs, making it crucial to understand cellular and species tropism of the H5N1 2.3.4.4b viruses. We compared viral kinetics of clade 2.3.4.4b viruses isolated from birds and mammals in respiratory epithelial cells derived from cattle, human, swine, and ferret. We found that avian derived viruses could replicate in swine cells only, yet mammalian derived strains could replicate efficiently in all tracheal and nasal epithelial cells tested. Interestingly, only bovine mammary epithelial cells (MEC) and swine respiratory epithelial cells were permissive to both avian and mammalian derived strains, possibly due to increased sialic acid expression on bovine MEC compared to bovine tracheal epithelial cells (TEC). However, sialic acid expression differed between dairy and beef cows: TEC derived from a dairy cow had increased expression of α2,3 sialic acid receptors compared to TEC from a beef-dairy cow cross. This study highlights the ability of clade 2.3.4.4b H5N1 viruses derived from mammals but not wild birds to infect the respiratory epithelium of other mammalian hosts.
CpgD is a phosphoglycerate cytidylyltransferase required for ceramide diphosphoglycerate synthesis
Authors: Dhakephalkar Tanisha , Guan Ziqiang , Klein Eric A.
Published: January 2025

Lipopolysaccharide (LPS) is essential in most Gram-negative bacteria, but mutants of several species have been isolated that can survive in its absence.Caulobacter crescentusviability in the absence of LPS is partially dependent on the anionic sphingolipid ceramide diphosphoglycerate (CPG2). Genetic analyses showed thatccna_01210, which encodes a nucleotidyltransferase, is required for CPG2 production. Using purified recombinant protein, we determined that CCNA_01210 (CpgD) is a phosphoglycerate cytidylyltransferase which uses CTP and 3-phosphoglycerate to produce CDP-glycerate, which we hypothesize is the phosphoglycerate donor for CPG2 synthesis. CpgD had optimum activity at pH 7.5-8 in the presence of magnesium. CpgD exhibited Michaelis-Menten kinetics with respect to 3-phosphoglycerate (Km,app = 10.9 ± 0.7 mM; Vmax,app = 0.72 ± 0.02 µmol/min/mg enzyme) and CTP (Km,app = 4.8 ± 0.9 mM; Vmax,app = 0.44 ± 0.03 µmol/min/mg enzyme). The characterization of this enzyme uncovers another piece of the pathway towards CPG2 synthesis.
Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism
Authors: Matsumura Emi , Kato Hiromi , Hara Shintaro , Ohbayashi Tsubasa , Ito Koji , Shingubara Ryo , Kawakami Tomoya , Mitsunobu Satoshi , Saeki Tatsuya , Tsuda Soichiro , Minamisawa Kiwamu , Wagai Rota
Published: January 2025

Soil particles in plant rooting zone are largely clustered to form complex porous structural unit called aggregates where highly diverse microbes coexist and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microbes exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. Yet, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus adequate cell extraction method from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) isolated from a topsoil of cultivated Acrisol. Using the same six individual aggregates, we performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion methods improved the extractability of bacterial cells compared to previous studies, the latter yielded higher number and more diverse microbes compared to the former. The analyses of nitrogen-cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to greater recovery of microbes strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microbes having the genes (i.e., potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. In addition, all six aggregates studied showed overall similarity in pore characteristics, phylum-level composition, and the microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggest that conventional methods employed for the extraction of cell and DNA may not be optimal. The current findings underscore the necessity to advance extraction methodologies, thereby facilitating a more comprehensive understanding of the microbial diversity and functioning within soil environments.
Neural plate pre-patterning enables specification of intermediate neural progenitors in the spinal cord
Authors: Nandagopal Sandy , Cha Anna , Jia Bill Z. , Liao Hongyu , Comenho Caroline , Lahav Galit , Wagner Daniel E. , Tsai Tony Y-C , Megason Sean G.
Published: January 2025

Dorsal-ventral patterning of neural progenitors in the posterior neural tube, which gives rise to the spinal cord, has served as a model system to understand how extracellular signals organize developing tissues. While previous work has shown that signaling gradients diversify progenitor fates at the dorsal and ventral ends of the tissue, the basis of fate specification in intermediate regions has remained unclear. Here we use zebrafish to investigate the neural plate, which precedes neural tube formation, and show that its pre-patterning by a distinct signaling environment enables intermediate fate specification. Systematic spatial analysis of transcription factor (TF) expression and signaling activity using a reference-based mapping approach shows that the neural plate is partitioned into a striking complexity of TF co-expression states that, in part, correspond to the activity of gastrulation signals such as FGF and Wnt that persist through axis extension. Usingin totoanalysis of cellular movement combined with fate mapping, we find thatdbx1b-expressing intermediate progenitors (p0) originate from a neural-plate specific state characterized by transient co-expression of the TFspax3a,olig4andher3. Finally, we show that this state is defined by Wnt signaling in the posterior neural plate and that ectopic Wnt activation withinpax3a/olig4+ cells is sufficient to promotedbx1bexpression. Our data broadly support a model in which neural progenitor specification occurs through the sequential use of multiple signals to progressively diversify the neural tissue as it develops. This has implications forin vitrodifferentiation of spinal cord cell types and for understanding signal-based patterning in other developmental contexts.
Chd4 remodels chromatin to control retinal cell type specification and lineage termination
Authors: Shah Sujay , Lourenço Fernandes José Alex , Medisetti Suma , Mattar Pierre
Published: January 2025

During development, neural progenitor cells modify their output over time to produce different types of neurons and glia in chronological sequences. Previous studies have shown that epigenetic processes play a crucial role in regulating neural progenitor potential, but the underlying mechanisms are not well understood. Here, we hypothesized that nucleosome remodelling would regulate the competence transitions of retinal progenitors. We generated retina-specific conditional knockouts (cKOs) in the key nucleosome remodelling enzymeChd4.Chd4cKOs overproduced early-born retinal ganglion and amacrine cells. Postnatally, later-born rod photoreceptors were drastically underproduced. Concomitantly, progenitors failed to be exhausted at late phases of development and ultimately overproduced Müller glia. To determine how Chd4 regulates the genome, we used cut&run-seq to reveal Chd4 genome occupancy, and ATAC-seq experiments to visualize nucleosome remodelling. These data revealed that genome accessibility was significantly increased at ∼10,000 regulatory elements and ∼4,000 genes in theChd4cKO. Together, these results suggest that Chd4 restricts the genome to repress progenitor identity and promote rod photoreceptor production. Accordingly, multiplexed single-cell transcriptomics demonstrated that deletion ofChd4led to markedly divergent gene expression profiles. However, despite overproduction of early fates and underproduction of later-born rods, the perinatal transition between early and late progenitor competence was not altered as determined by birthdating experiments and transcriptomic signatures. Taken together, our data suggest that Chd4-dependent chromatin remodelling regulates cell fate specification, and is also required to terminate retinal neurogenesis, but that it does not regulate the progenitor competence windows that restrict early- vs. late-cell-type production.

Key findings

1)

Chd4cKOs exhibit a strong shift in neurogenesis, with early-born neurons overproduced and late-born neurons underproduced.

2)

We present an epigenetic atlas that combines the occupancy of NuRD proteins such as Chd4 and Mbd3, with nucleosome remodelling data and transcriptomic correlates.

3)

We show that NuRD regulates the competence transition that terminates the retinal lineage but not earlier competence transitions, showing for the first time that the epigenetic mechanisms governing retinal competence transitions may vary.
Epithelial to Mesenchymal Transition in the Endometrium Mediated by HOXA10 drives Embryo Implantation
Authors: Ashary Nancy , Suresh Sanjana , Bhide Anshul , Shyamal Sharmishtha , Pranya N , Mishra Anuradha , Anuradha A , Hansda Shruti , Harshavardhan B V , Jolly Mohit Kumar , Modi Deepak
Published: January 2025

Embryo implantation requires the breaching of the endometrial luminal epithelium (LE) to facilitate invasion. In this study, we report that during implantation, endometrial LE cells undergo partial epithelial-to-mesenchymal transition (pEMT) specifically at the implantation sites. This pEMT in the LE is critical, as thein vivoknockdown of the EMT transcription factorTwist2 inhibits embryo implantation. Furthermore, we observed a reduction in the expression of the transcription factor HOXA10 in LE cells at the implantation sites. Interestingly, LE cells of HOXA10-hypomorphic mice and human endometrial epithelial cells (RL95-2) withHOXA10knockdown (HOXA10KD) also undergo pEMT and acquire a migratory phenotypein vitro, suggesting that the loss of HOXA10 drives pEMT in the endometrial epithelium. TheHOXA10KD cells have a higher pEMT score and differential expression of genes associated with cell migration and TGF-β signaling pathways. We also determined the genome-wide occupancy sites of HOXA10 in human endometrial epithelial cells and identified 1,246 direct targets that had significant roles in EMT. Collectively, our findings suggest that HOXA10 is required to maintain an epithelial state and its loss activates mesenchymal genes resulting in a pEMT phenotype. This adds HOXA10 as a member of the MET inducer team that engage in mutually inhibitory feedback loops directly or indirectly with EMT inducer team. In summary, our study establishes that pEMT in the LE as a critical step for embryo implantation and reveals that HOXA10 regulates this process.
The Q226L mutation can convert a highly pathogenic H5 2.3.4.4e virus to bind human-type receptors
Authors: Carrasco María Ríos , Lin Ting-Hui , Zhu Xueyong , García Alba Gabarroca , Uslu Elif , Liang Ruonan , Spruit Cindy M. , Richard Mathilde , Boons Geert-Jan , Wilson Ian A. , de Vries Robert P.
Published: January 2025

Abstract

H5Nx viruses continue to wreak havoc in avian and mammalian species worldwide. The virus distinguishes itself by the ability to replicate to high titers and transmit efficiently in a wide variety of hosts in diverse climatic environments. Fortunately, transmission to and between humans is scarce. Yet, if such an event were to occur, it could spark a pandemic as humans are immunologically naïve to H5 viruses. A significant determinant of transmission to and between humans is the ability of the influenza A virus hemagglutinin (HA) protein to shift from an avian-type to a human-type receptor specificity. Here, we demonstrate that a 2016 2.3.4.4e virus HA can convert to human-type receptor binding via a single Q226L mutation, in contrast to a cleavage-modified 2016 2.3.4.4b virus HA. Using glycan arrays, x-ray structural analyses, tissue- and direct glycan binding, we show that L133aΔ and 227Q are vital for this phenotype. Thus, whereas the 2.3.4.4e virus HA only needs a single amino acid mutation, the modified 2.3.4.4b HA was not easily converted to human-type receptor specificity.
Chemoproteomic Profiling ofC. albicansfor Characterization of Anti-fungal Kinase Inhibitors
Authors: Shirley David J. , Nandakumar Meganathan , Cabrera Aurora , Yiu Bonnie , Puumala Emily , Liu Zhongle , Robbins Nicole , Whitesell Luke , Smith Jeffrey L. , Lyons Scott P. , Mordant Angie L. , Herring Laura E. , Graves Lee M. , Couñago Rafael M. , Drewry David H. , Cowen Leah E. , Willson Timothy M.
Published: January 2025

Candida albicansis a growing health concern as the leading causal agent of systemic candidiasis, a life-threatening fungal infection with a mortality rate of ∼40% despite best available therapy. Yck2, a fungal casein kinase 1 (CK1) family member, is the cellular target of inhibitors YK-I-02 (YK) and MN-I-157 (MN). Here, multiplexed inhibitor beads paired with mass spectrometry (MIB/MS) employing ATP-competitive kinase inhibitors were used to define the selectivity of these Yck2 inhibitors across the globalC. albicansproteome. The MIB matrix captured 89% of the known and predictedC. albicansprotein kinases present in cell lysate. In MIB/MS competition assays, YK and MN demonstrated exquisite selectivity across theC. albicansfungal kinome with target engagement of only three CK1 homologs (Yck2, Yck22, and Hrr25) and a homolog of human p38α (Hog1). Additional chemoproteomics using a custom MN-kinobead identified only one additionalC. albicansprotein, confirming its remarkable fungal proteome-wide selectivity. To identify new Yck2 inhibitors with selectivity over Hog1, thirteen human CK1 kinase inhibitors were profiled for fungal kinase-binding activity using MIB/MS competition assays and in-cell NanoBRET target engagement assays. A new chemotype of family-selective Yck2 inhibitors with antifungal activity was identified. Together, these findings expand the application of MIB/MS proteomic profiling for non-human kinomes and demonstrate its utility in the discovery and development of selective inhibitors of fungal kinases with potential antimicrobial activity.

GRAPHICAL ABSTRACT
Single-molecule assay reveals the impact of composition, RNA duplex, and inhibitors on the binding dynamics of SARS-CoV-2 polymerase complex
Authors: Lovell Terri C. , Dewling Heidi A. F. , Li Cynthia X. , Lee Hery W. , Gordon Calvin J. , Kocincova Dana , Badmalia Maulik D. , Tchesnokov Egor P. , Götte Matthias , Cosa Gonzalo
Published: January 2025

The genome replication of SARS-CoV-2, the causative agent of COVID-19, involves a multi-subunit replication complex consisting of non-structural proteins (nsps) 12, 7 and 8. While the structure of this complex is known, the dynamic behavior of the subunits interacting with RNA is missing. Here we report a single-molecule protein-induced fluorescence enhancement (SM-PIFE) assay to monitor binding dynamics between the reconstituted or co-expressed replication complex and RNA. Increasing binding times were observed, in this order, with nsp7 (none) nsp8 and nsp12, in nsp8-nsp12 mixtures and in reconstituted mixtures bearing all three proteins. Unstable, transient, and stable binding modes were recorded in the latter case, indicating that complexation is dynamic, and the correct conformation must be achieved before stable RNA binding can occur. Notably, the co-expressed protein yields mostly stable binding even at low concentrations, while the reconstituted proteins exhibit unstable binding indicating inefficient complexation with reduced protein. The SM-PIFE assay distinguishes inhibitors that impact protein binding from those that prevent replication, as demonstrated with suramin and remdesivir, respectively. The data reveals a correlation between binding lifetime/affinity, and protein activity, and underscores differences between co-expressed vs reconstituted mixtures, suggesting the existence of trapped conformations that may not evolve to productive binding.
Scaling of mouse somitogenesis by coupling of cell cycle to segmentation clock oscillations
Authors: van Oostrom Marek J. , Li Yuting I. , Meijer Wilke H. M. , Noordzij Tomas E. J. C. , Fountas Charis , Timmers Erika , Korving Jeroen , Thomas Wouter M. , Simons Benjamin D. , Sonnen Katharina F.
Published: January 2025

Somitogenesis is the periodic segmentation of a continuously growing tissue in vertebrate embryos1. Timing and spacing of somitogenesis is regulated by the segmentation clock, oscillations in Notch, Wnt and FGF signalling in mice, and FGF and Wnt morphogen gradients2–4. The size of nascent somites scales with the size of the unsegmented region, the presomitic mesoderm (PSM), over developmental time and upon experimental perturbation of PSM size5–7. Here, we addressed how scaling is ensured in the developing mouse embryo. We found that the entire oscillating presomitic mesoderm proliferates. Quantifying the dynamics of signalling and cell cycle progression in single cells, we detected a correlation between the two. Using a microfluidics-based entrainment approach, we showed that signalling oscillations and cell cycle are coupled, likely via periodic induction of S phase-inducing Cyclins. An updated theoretical somitogenesis model incorporating this coupling suggests that this correlation ensures uniform PSM growth and uniform dilution of morphogen gradients by cell divisions, thereby directly affecting somite formation. Indeed, when blocking cell proliferation, gradient spreading and somite formation as well as somite scaling are impaired. Our data suggests a mechanism by which coupling signalling oscillations to cell proliferation ensures formation of properly sized somites and scaling of somite size.
A post-assembly conformational change makes the SARS-CoV-2 polymerase elongation-competent
Authors: Klein Misha , Das Arnab , Bera Subhas C. , Anderson Thomas K. , Kocincova Dana , Lee Hery W. , Wang Bing , Papini Flavia S. , Marecki John C. , Arnold Jamie J. , Cameron Craig E. , Raney Kevin D. , Artsimovitch Irina , Götte Mathias , Kirchdoerfer Robert N. , Depken Martin , Dulin David
Published: January 2025

Coronaviruses (CoV) encode sixteen non-structural proteins (nsps), most of which form the replication-transcription complex (RTC). The RTC contains a core composed of one nsp12 RNA-dependent RNA polymerase (RdRp), two nsp8s and one nsp7. The core RTC recruits other nsps to synthesize all viral RNAs within the infected cell. While essential for viral replication, the mechanism by which the core RTC assembles into a processive polymerase remains poorly understood. We show that the core RTC preferentially assembles by first having nsp12-polymerase bind to the RNA template, followed by the subsequent association of nsp7 and nsp8. Once assembled on the RNA template, the core RTC requires hundreds of seconds to undergo a conformational change that enables processive elongation. In the absence of RNA, the (apo-)RTC requires several hours to adopt its elongation-competent conformation. We propose that this obligatory activation step facilitates the recruitment of additional nsp’s essential for efficient viral RNA synthesis and may represent a promising target for therapeutic interventions.
Infectome analysis of bat kidneys from Yunnan province, China, reveals close relatives of Hendra-Nipah viruses and prevalent bacterial and eukaryotic pathogens
Authors: Kuang Guopeng , Yang Tian , Yang Weihong , Wang Jing , Pan Hong , Pan Yuanfei , Gou Qin-yu , Wu Wei-chen , Wang Juan , Yang Lifeng , Han Xi , Chen Yao-qing , Eden John-Sebastian , Holmes Edward C. , Shi Mang , Feng Yun
Published: January 2025

Bats are natural reservoirs for a wide range of microorganisms, including many notable zoonotic pathogens. However, the infectome of bat kidneys remains poorly understood. To address this gap, we performed meta-transcriptomic sequencing on kidney tissues from 142 bats, spanning ten species sampled at five locations in Yunnan province, China. This analysis identified 22 viral species, including 20 novel viruses, two of which represented newly discovered henipaviruses closely related to the highly pathogenic Hendra and Nipah viruses. These henipaviruses were found in the kidneys of bats inhabiting an orchard near villages, raising concerns about potential fruit contamination via bat urine and transmission risks to livestock or humans. Additionally, we identified a novel protozoan parasite, tentatively namedKlossiella yunnanensis, along with two highly abundant bacterial species, one of which is a newly discovered species—Flavobacterium yunnanensis. These findings broaden our understanding of the bat kidney infectome, underscore critical zoonotic threats, and highlight the need for comprehensive, full-spectrum microbial analyses of previously understudied organs to better assess spillover risks from bat populations.
Monocarboxylate transporter 2 is required for the maintenance of myelin and axonal integrity by oligodendrocytes
Authors: Izagirre-Urizar Leire , Mora-Huerta Luna , Soler-Saez Irene , Morales-Gallel Raquel , Ulloa-Navas Maria-Jose , Chara Juan-Carlos , Calovi Stefano , Deboux Cyrille , Merino-Cacho Laura , Netzahualcoyotzi Citlalli , Domercq Maria , Zugaza José L. , Pellerin Luc , Garcia-Garcia Francisco , Garcia-Verdugo Jose-Manuel , Matute Carlos , Nait-Oumesmar Brahim , Tepavcevic Vanja
Published: January 2025

Neurodegenerative pathologies including multiple sclerosis (MS) are consistently associated with energy deficit in the central nervous system (CNS). This might directly impact myelinating oligodendrocytes as these are particularly vulnerable to metabolic insults. Importantly, oligodendroglial dysfunction and myelin alterations occur in most, if not all neurodegenerative diseases, and are associated with axonal pathology/loss. Thus, elucidating metabolic mechanisms required for oligodendroglial myelin maintenance and axonal support might be crucial to identify therapeutic targets to achieve neuroprotection. While monocarboxylates are important energy fuels for the CNS, their role in myelinating oligodendrocyte function remains unclear. Here we show that, just like neurons, myelinating oligodendrocytes express high affinity monocarboxylate transporter 2 (MCT2) both in mice and humans, which is downregulated in progressive MS. While deletion of MCT2 in mouse oligodendrocytes did not affect the survival of these cells, it resulted in downregulation of lipid synthesis-associated enzymes and failure of myelin maintenance. Moreover, axonal upregulation of lactate dehydrogenase A concomitant with axonal damage was observed but could be alleviated by ketogenic diet. We conclude that oligodendroglial MCT2 is required for myelin maintenance and axonal support, which becomes altered in progressive MS, but may be compensated for by specific metabolic therapies.

Graphical abstract
Recreating coronary vascularization and sympathetic innervation of myocardium on a human pluripotent stem cell-derived heart organoid
Authors: Branco Mariana A. , Nunes Mafalda Marques , Rayagra Ana Luísa , Tenreiro Miguel F. , Cabral Joaquim M.S. , Diogo Maria Margarida
Published: January 2025

Coronary vascularization and sympathetic innervation of the myocardium is a concomitant event during embryonic heart development and both systems are crucial to ensure normal adult heart function. Here we describe a self-organized hiPSC-derived heart organoid that recreates both the coronary vascular plexus and the sympathetic neuronal network of the ventricle myocardium, with a physiologically relevant in-vivo-like structural organization and function. Through modulation of PDGF-β and VEGF signalling pathways, we attained a heart organoid that incorporates 1) an external epicardial layer (mesothelium) of DACH1, NR2F2 and WT1 positive cells, 2) a sub-epicardial space from where a functional primary coronary vascular plexus of CD31+/DACH1+cells emerge, 3) a compact myocardial region adjacent to the epicardium, enriched in proliferative cardiomyocytes and ECM deposition, and 4) a sympathetic neuronal network that controls heart organoid contraction. Therefore, the human heart organoid described herein, is a unique model to study new regenerative medicine-based approaches to restore innervation and promote re-vascularization in adult heart after ischemic events and to perform adult and developmental cardiotoxicity studies.
Collateral connectomes of Esr1-positive hypothalamic neurons modulate defensive behavior plasticity
Authors: Csillag Veronika , Forastieri Chiara , Szucs Greta Martina , Vidal Ines Talaya , Hiriart Marianne Bizzozzero , Lavis Luke D. , Calvigioni Daniela , Fuzik Janos
Published: January 2025

The ventromedial hypothalamus (VMH) projects to the periaqueductal gray (PAG) and anterior hypothalamic nucleus (AHN), mediating freezing and escape behaviors, respectively. We investigated VMH collateral (VMH-coll) neurons, which innervate both PAG and AHN, to elucidate their role in postsynaptic processing and defensive behavior plasticity. Using all-optical voltage imaging of 22,151 postsynaptic neurons ex vivo, we found that VMH-coll neurons engage inhibitory mechanisms at both synaptic ends and can induce synaptic circuit plasticity. In vivo optogenetic activation of the VMH-coll somas induced escape behaviors. We identified an Esr1-expressing VMH-coll subpopulation with postsynaptic connectome resembling that of wild-type collaterals on the PAG side. Activation of Esr1+VMH-coll neurons evoked freezing and unexpected flattening behavior, previously not linked to the VMH. Neuropeptides such as PACAP and dynorphin modulated both Esr1+VMH-coll connectomes. In vivo kappa-opioid receptor antagonism impaired Esr1+VMH-coll-mediated defensive behaviors. These findings unveiled the central role of VMH-coll pathways in innate defensive behavior plasticity.
Developmental axon diameter growth of central nervous system axons does not depend on ensheathment or myelination by oligodendrocytes
Authors: Bin Jenea M , Emberley Katie , Buscham Tobias J , Eichel-Vogel Maria A , Doan Ryan A , Steyer Anna M , Nolan Matthew F , Möbius Wiebke , Monk Kelly R , Werner Hauke B , Emery Ben , Lyons David A
Published: January 2025

Myelination facilitates the rapid conduction of action potentials along axons. In the central nervous system (CNS), myelinated axons vary over 100-fold in diameter, with conduction speed scaling linearly with increasing diameter. Axon diameter and myelination are closely interlinked, with axon diameter exerting a strong influence on myelination. Conversely, myelinating Schwann cells in the peripheral nervous system can both positively and negatively affect axon diameter. However, whether axon diameter is regulated by CNS oligodendrocytes is less clear. Here, we investigated CNS axon diameter growth in the absence of myelin using mouse (Mbpshi/shiand Myrfconditional knockout) and zebrafish (olig2morpholino) models. We find that neither the ensheathment of axons, nor the formation of compact myelin are required for CNS axons to achieve appropriate and diverse diameters. This indicates that developmental CNS axon diameter growth is independent of myelination, and shows that myelinating cells of CNS and PNS differentially influence axonal morphology.
Resolving forebrain developmental organisation by analysis of differential growth patterns
Authors: Manning Elizabeth , Chinnaiya Kavitha , Furley Caitlyn , Kim Dong Won , Blackshaw Seth , Placzek Marysia , Place Elsie
Published: January 2025

The forebrain is the most complex region of the vertebrate CNS, and its developmental organisation is controversial. We fate-mapped the embryonic chick forebrain using lipophilic dyes and Cre-recombination lineage tracing, and built a 4D model of brain growth. We reveal modular patterns of anisotropic growth, ascribed to progenitor regions through multiplex HCR. Morphogenesis is dominated by directional growth towards the eye, more isometric expansion of the prethalamus and dorsal telencephalon, and anterior movement of ventral cells into the hypothalamus. Fate conversion experiments in chick and comparative gene expression analysis in chick and mouse support placement of the hypothalamus ventral to structures extending from the telencephalon up to and including the zona limitans intrathalamica (ZLI), with the dorsoventral axis becoming distorted at the base of the ZLI. Our findings challenge the widely accepted prosomere model of forebrain organisation, and we propose an alternative ‘tripartite hypothalamus’ model.
A zebrafish model of nicotinamide adenine dinucleotide (NAD+) deficiency-derived congenital disorders
Authors: Tsurho Visakuo , Gilliland Carla , Ensing Jessica , Vansickle Elizabeth , Lanning Nathan J. , Mark Paul R. , Grainger Stephanie
Published: January 2025

Congenital NAD deficiency disorder (CNDD) is a multisystem condition in which cardiac, renal, vertebral, and limb anomalies are most common, but anomalies in all organ systems have been identified. Patients with this condition have biallelic pathogenic variants involving genes in the nicotinamide adenine dinucleotide (NAD+) synthesis pathway leading to decreased systemic NAD+levels. CNDD anomalies mimic the clinical features described in vertebral-anal-cardiac-tracheoesophageal fistula-renal-limb (VACTERL) association raising the possibility that CNDD and VACTERL association possess similar underlying causes. However, the mechanism by which NAD+deficiency causes CNDD developmental anomalies has not been determined, nor has NAD+deficiency been definitively linked to VACTERL association. Therefore, additional animal models amenable to detailed observation of embryonic development are needed to address the causes and progression of congenital anomalies in both CNDD and VACTERL association. Here, we describe a zebrafish model of NAD+disruption to begin to model CNDD and VACTERL association phenotypes, assessing developmental anomalies in real-time. Treatment of zebrafish embryos with 2-amino-1,3,4-thiadiazole (ATDA), a teratogen known to disrupt NAD+metabolism, resulted in neural tube, craniofacial, cardiac, and tail defects. These defects were rescued by the administration of nicotinamide (NAM) in a dose-dependent manner. Our work establishes zebrafish as a useful model for investigating the mechanistic causes and developmental dynamics of CNDD and VACTERL association. Further, as VACTERL association has been linked to teratogens, our zebrafish model provides a platform to assess these agents.

One sentence summary

NAD(H) deficiency causes multiple congenital anomalies in zebrafish.
Uptake of Prochlorococcus-derived metabolites byAlteromonas macleodiiMIT1002 shows high levels of substrate specificity
Authors: Halloran Kathryn H. , Braakman Rogier , Coe Allison , Swarr Gretchen , Kido Soule Melissa C. , Chisholm Sallie W. , Kujawinski Elizabeth B.
Published: January 2025

Seawater contains an abundance of small biomolecules, or metabolites, that are highly labile components of dissolved organic matter (DOM). Marine microbes interact by exchanging metabolites, thus shaping marine microbial ecology, DOM composition, and global carbon cycling. To better constrain one set of microbe-metabolite interactions, we cultured the marine gammaproteobacteriumAlteromonas macleodiiMIT1002 on a range of compounds excreted by a sympatric cyanobacterium,Prochlorococcus.Alteromonascould assimilate the branched chain amino acids leucine, isoleucine, and valine, as well as 3-methyl-2-oxobutanoic acid (a branched chain ketoacid intermediate of valine metabolism), but not thymidine, kynurenine, 4-hydroxybenzoic acid, or the other branched chain ketoacids. The assimilation of branched chain amino acids indicates thatAlteromonascan metabolically process each corresponding ketoacid, suggesting that transporter specificity underlies the observed substrate specificity for 3-methyl-2-oxobutanoic acid. These experiments show that even subtle changes in chemical structure can result in different microbial interactions and different fates for dissolved metabolites.

Significance Statement

Microbial interactions with dissolved organic matter are important controls on the marine carbon cycle. Dissolved organic matter is often considered in bulk, which leaves the specificity and nature of these interactions poorly constrained. Here we show that microbe-molecule interactions can be highly specific, distinguishing between molecules that are structurally and biochemically similar. This implies that small changes in this pool of carbon could have large impacts for the overall system function, and that measuring this pool of carbon with molecular-level resolution is important to characterizing microbe-molecule interactions. We further explore the mechanism underlying the observed substrate specificity and suggest that it is caused by transporter selectivity, meaning the ability of these microbes to selectively uptake specific dissolved organic molecules.
Dual-use virulence factors of the opportunistic pathogenChromobacterium haemolyticummediate haemolysis and colonization
Authors: Dumjahn Leo , Wein Philipp , Molloy Evelyn M. , Scherlach Kirstin , Trottmann Felix , Meisinger Philippe , Judd Louise M. , Pidot Sacha J. , Stinear Timothy P. , Richter Ingrid , Hertweck Christian
Published: January 2025

Chromobacterium haemolyticumis an environmental bacterium that can cause severe and fatal opportunistic infections in humans and animals. AlthoughC. haemolyticumis characterized by its strong β-haemolytic activity, the molecular basis of this phenotype has remained elusive over the more than fifteen years since the species was first described. Here, we report the discovery of a family of cyclic lipodepsipeptides that are responsible for the potent haemolytic activity ofC. haemolyticum.Comparative genomics ofChromobacteriumspp. isolated from different environments revealed a completely conserved gene locus (chl) encoding a non-ribosomal peptide synthetase (NRPS). Metabolic profiling ofC. haemolyticumDSM 19808 identified a suite of cyclic lipodepsipeptides as the products of thechllocus, with the three main congeners (jagaricin, chromolysin A and B) being elucidated by a combination of tandem mass spectrometry, chemical derivatization, and NMR spectroscopy. Significantly, aC. haemolyticum chldeletion mutant is devoid of haemolytic activity. Moreover, purified jagaricin, chromolysin A and B are haemolytic at low- micromolar concentrations in an erythrocyte lysis assay. Further bioassays demonstrated that the cyclic lipodepsipeptides are crucial for biofilm-forming and swarming behavior ofC. haemolyticum. MALDI mass spectrometry imaging showed that primarily chromolysin A and B are involved in these processesin vitro. Our data shed light on the bioactivities of chromolysin A and B, specialized metabolites that likely contribute to both successful colonization of new niches and virulence potential ofC. haemolyticum.

Importance

Despite the rising incidence ofChromobacterium haemolyticumas a serious opportunistic pathogen, there is limited information on whether the competitive traits that ensure its survival in its freshwater niche contribute to host infection. We present a case where bacterially produced specialized metabolites act as lynchpin chemical mediators that are not only responsible for the pronounced haemolytic phenotype ofC. haemolyticumbut are crucial for biofilm formation and swarming motility. These results exemplify a case of coincidental evolution, wherein the selective pressures encountered in a primary environmental niche drive the evolution of a trait impacting virulence. This knowledge provides a foundation for the development of antivirulence therapies against the emerging pathogenC. haemolyticum.
Whole-body coarticulation reflects expertise in sport climbing
Authors: Maselli Antonella , Musculus Lisa , Moretti Riccardo , d’Avella Andrea , Raab Markus , Pezzulo Giovanni
Published: January 2025

Taking sport climbing as a testbed, we explored coarticulation in naturalistic motor-behavior at the level of whole-body kinematics. Participants were instructed to execute a series of climbing routes, each composed of two initial foot-moves equal in all routes, and two subsequent hand-moves differing across routes in a set of eight possible configurations. The goal was assessing whether climbers modulate the execution of a given move depending on which moves come next in the plan. Coarticulation was assessed by training a set of classifiers and estimating how well the whole-body (or single-joint) kinematics during a given stage of the climbing execution could predict its future unfolding. Results showed that most participants engage in coarticulation, with temporal and bodily patterns that depend on expertise. Non-climbers tend to prepare the next-to-come move right before its onset and only after the end of the previous move. Rather, expert-climbers (and to a smaller extent, beginner-climbers) show early coarticulation during the execution of the previous move and engage in adjustments that involve the coordination of a larger number of joints across the body. These results demonstrate coarticulation effects in whole-body naturalistic motor behavior and as a function of expertise. Furthermore, the enhanced coarticulation found in expert-climbers provides hints for experts engaging in more refined mental processes converting abstract instructions (e.g., move the right hand to a given location) into motor simulations involving whole-body coordination. Overall, these results contribute to advancing our current knowledge of the rich interplay between cognition and motor control.

NEW & NOTEWORTHY

The current study explores the way in which having formed a plan for a sequential motor task affects its execution. We showed that climbing expertise increases the extent to which participants adjust their motor execution based on the moves that follow in a planned route. These results provide evidence of coarticulation in naturalistic motor behavior and suggest enhanced skills in mentalizing forward motor control and optimal-control strategies in expert climbers.
Homeostatic regulation of a motor circuit through temperature sensing rather than activity sensing
Authors: Cannon Delaney , Santin Joseph M.
Published: January 2025

Homeostasis is a driving principle in physiology. To achieve homeostatic control of neural activity, neurons monitor their activity levels and then initiate corrective adjustments in excitability when activity strays from a set point. However, fluctuations in the brain microenvironment, such as temperature, pH, and other ions represent some of the most common perturbations to neural function in animals. Therefore, it is unclear if activity sensing is a universal strategy for different types of perturbations or if stability may arise by sensing specific environmental cues. Here we show the respiratory network of amphibians mounts a fast homeostatic response to restore motor function following inactivity caused by cooling over the physiological range. This response was not initiated by inactivity, but rather, by temperature. Compensation involved cold-activation of the noradrenergic systemviamechanisms that involve inhibition of the Na+/K+ATPase, causing β-adrenoceptor signaling that enhanced network excitability. Thus, acute cooling initiates a modulatory response that opposes inactivity and enhances network excitability. As the nervous system of all animals is subjected to changes in the microenvironment, some circuits may have selected regulatory systems tuned to environmental variables in place of, or in addition to, activity-dependent control mechanisms.

Graphical Abstract
Humans can walk economically on uneven terrain without deliberative optimization with a Simple Feedback Control Policy
Authors: Darici Osman , Kuo Arthur D.
Published: January 2025

Humans proactively anticipate and adjust for uneven terrain as they traverse it. They modulate their forward speed and momentum ahead of upcoming steps, perhaps to optimize energy expenditure as they prefer to do for level ground. But actual optimization is a complex, deliberative process and seems not to describe how human act in real time during continuous walking. Here we show that human uneven walking strategies are predicted well by an control scheme that requires no deliberation yet is nearly optimal. The experimentally measured speed trajectory for a single upward step (a “kernel”) predicts the strategy for a complex terrain sequence, by repeatedly delaying and weighting (convolving) it for each step height. Conversely, the same strategy can be deconvolved to predict for six other terrains about as well as deliberative energy minimization Composability is predicted by a simple model of walking, which requires work to redirect the body center of mass velocity between pendulum-like steps. These dynamics obey linear superposition, so that a simple kernel, learnable through experience, is sufficient to compose other strategies with lookahead information about upcoming step heights. Walking dynamics may allow humans to act quickly and nearly optimally without thinking slowly.
Local erythropoiesis directs oxygen availability in bone fracture repair
Authors: Lang Annemarie , Collins Joseph M. , Nijsure Madhura P. , Belali Simin , Khan Mohd Parvez , Moharrer Yasaman , Schipani Ernestina , Yien Yvette Y. , Fan Yi , Gelinsky Michael , Vinogradov Sergei A. , Koch Cameron , Boerckel Joel D.
Published: January 2025

Bone fracture ruptures blood vessels and disrupts the bone marrow, the site of new red blood cell production (erythropoiesis). Current dogma holds that bone fracture causes severe hypoxia at the fracture site, due to vascular rupture, and that this hypoxia must be overcome for regeneration. Here, we show that the early fracture site is not hypoxic, but instead exhibits high oxygen tension (> 55 mmHg, or 8%), similar to the red blood cell reservoir, the spleen. This elevated oxygen stems not from angiogenesis but from activated erythropoiesis in the adjacent bone marrow. Fracture-activated erythroid progenitor cells concentrate oxygen through haemoglobin formation. Blocking transferrin receptor 1 (CD71)-mediated iron uptake prevents oxygen binding by these cells, induces fracture site hypoxia, and enhances bone repair through increased angiogenesis and osteogenesis. These findings upend our current understanding of the early phase of bone fracture repair, provide a mechanism for high oxygen tension in the bone marrow after injury, and reveal an unexpected and targetable role of erythroid progenitors in fracture repair.