bluuebunny/crossref_metadata_2025 huggingface dataset:
Environmental factors and host sex influence the skin microbiome structure of Hong Kong newt (Paramesotriton hongkongensis) in a coldspot of chytridiomycosis in subtropical East Asia
Authors: Wan Bowen , Chen Guoling , Poon Emily Shui Kei , Fung Hon Shing , Lau Anthony , Sin Simon Yung Wa
Published: February 2024

Chytridiomycosis, an infectious skin disease caused by the chytrid fungi,Batrachochytrium dendrobatidisandB. salamandrivorans, has been threatening global amphibian biodiversity. On the skin of chytrid-resistant amphibians, some antifungal bacteria likely defend them against chytridiomycosis, reducing the mortality of resistant amphibians. The Hong Kong newt (Paramesotriton hongkongensis) inhabits East Asia which is a suspected origin of chytrids. Asymptomatic infection in the newts suggests their long-term coexistence with chytrids. Thus, the skin microbiomes of this resistant species warrant investigation, along with other factors that can affect the microbiome. Among the 149 newts sampled in their natural habitats in Hong Kong, putative antifungal bacteria were found on all newts. There were 314 amplicon sequence variants distributed over 25 genera of putative antifungal bacteria, abundant ones includedAcinetobacter,Flavobacterium, andNovosphingobiumspp. The skin microbiome compositions were strongly influenced by the inter-site geographical distances. Despite inter-site differences, we identified some core skin microbes across sites, which could be vital toP. hongkongensis. The dominant cores included family Comamonadaceae, family Chitinophagaceae, and class Betaproteobacteria. Moreover, habitat elevation and host sex also exhibited significant effects on skin microbiome compositions. The antifungal bacteria found on these newts offer an important resource for conservation against chytridiomycosis, such as probiotic treatments for susceptible species.
Genetic barcodes for ash (Fraxinus) species and generation of new wide hybrids
Authors: Plumb William J. , Kelly Laura J. , Mullender Joe , Powell Robyn F. , Csiba Laszlo , Nemesio-Gorriz Miguel , Carey David , Mason Mary E. , Crowther William , Koch Jennifer , Douglas Gerry C. , Buggs Richard J. A.
Published: February 2024

Native ash tree species in Europe and North America are being devastated by ash dieback and the emerald ash borer, respectively. As worldwide ash species differ in their level of susceptibility to these threats, hybrid breeding may allow resistance to be transferred among species. However, we do not know the extent to which distantly related ash species can be crossed, and many ash species are difficult to identify from morphology alone leading to some mislabelling in living collections. Here, we develop a genetic barcode system for the identification ofFraxinusspecies based on three low-copy-number protein coding genes. We also conduct experimental crosses among ash species in different sections.

Our barcodes are effective in identifying ash samples to sectional level and in some cases to species level, and can also identify hybrids. They highlight thatF. mandshurica, F. platypodaandF. chiisanensismay be frequently mistaken for one another in living collections. We succeeded in generating ten wide hybrid plants: two of sectionMelioides(species:F. pennsylvanica) □ sectionFraxinus(species:F. excelsior) and eight of sectionOrnus(species unclear) □ sectionFraxinus(species:F. excelsior). One hybrid from each of our crosses has survived natural infection with the ash dieback pathogen in Ireland. We also discovered a hybrid between sectionMelioides(species:F. latifolia) □ sectionFraxinus(species:F. excelsior) formed spontaneously in the ash collection at Kew. Our findings facilitate the deployment of global ash species diversity in response to alien pests and pathogens.

Societal impact statement

The world-wide diversity of ash trees includes genetic information encoding resistance to the ash dieback fungus and the emerald ash borer beetle, which are currently devastating ash populations in Europe and North America. In order to mobilise this genetic diversity in conventional breeding programmes we need to be able to accurately identify ash species from around the world, and cross them with one another. Here, we present a genetic barcoding system for ash species, and a series of hybridisation experiments between European ash and other species. Two of the hybrids show early promise against ash dieback.
Evidence of sensory error threshold in triggering locomotor adaptations in humans
Authors: Herrick E. , Yakovenko S.
Published: February 2024

Changing body biomechanics or external conditions trigger neural adaptations to optimize motor behavior. While the adaptations appear continuous to minimize movement errors, not all errors necessarily initiate sensorimotor adaptations. The locomotor system exhibits resilience to change and rehabilitation. This suggests the presence of an error threshold to trigger the adaptation mechanism. Here, we imposed kinematic and kinetic constraints of stepping using a passive orthosis and real-time feedback about limb loading. We aimed to manipulate stepping asymmetry and explore the interplay between adaptation and locomotor error magnitude. Uninjured healthy adults were tested in three locomotor conditions: unconstrained, constrained, and washout unconstrained walking. Surprisingly, kinematic asymmetry alone did not induce persistent adaptation. However, the addition of asymmetric interlimb loading triggered the expected adaptation. Our finding suggests that uninjured locomotor systems can cope with a specific range of kinematic asymmetries without initiating persistent adaptations that lead to aftereffects, and that loading may be a key variable for evoking the adaptation. The presence of an error threshold may mitigate possible disruption of vital motor functions and contribute to locomotor adaptation during walking. These insights elucidate the mechanism of neural plasticity and have implications for rehabilitation.
Multiparameter Quantitative Analyses of Diagnostic Cells in Brain Tissues from Tuberous Sclerosis Complex
Authors: Arceneaux Jerome S. , Brockman Asa A. , Khurana Rohit , Chalkley Mary-Bronwen L. , Geben Laura C. , Vestal Matthew , Zafar Muhammad , Weatherspoon Sarah , Mobley Bret C. , Ess Kevin C. , Ihrie Rebecca A.
Published: February 2024

The advent of high-dimensional imaging approaches offers innovative opportunities to molecularly characterize diagnostic cells in disorders that have previously relied on histopathological definitions. One example of such disorders is tuberous sclerosis complex (TSC), a developmental disorder characterized by systemic growth of benign tumors. Within resected brain tissues from patients with TSC, detection of abnormally enlarged balloon cells (BCs) is pathognomonic for this disorder. Though BCs can be identified by an expert neuropathologist, little is known about the specificity and broad applicability of protein markers for these cells, complicating classification of proposed BCs identified in experimental models of this disorder. Here, we report the development of a customized machine-learning workflow (BalloonIdentifier; BAIDEN) that was trained to prospectively identify BCs in tissue sections using a histological stain compatible with high-dimensional cytometry. This approach was coupled to a custom antibody panel and 36-parameter imaging mass cytometry (IMC) to explore the expression of multiple previously proposed BC markers and develop a descriptor of BC features conserved across multiple tissue samples from patients with TSC. These findings comprise a toolbox and dataset for understanding the abundance, structure, and signaling activity of these histopathologically abnormal cells, and an example case of how such tools can be developed and applied within human tissues.
Gene expression signatures of response to fluoxetine treatment: systematic review and meta-analyses
Authors: Cooper David G. , Cowden J. Paige , Stanley Parker A. , Karbowski Jack T. , Gaertig Victoria S. , Lukan Caiden J. , Vo Patrick M. , Worthington Ariel D. , Class Caleb A.
Published: February 2024

Background

Selecting the best antidepressant for a patient with major depressive disorder (MDD) remains a challenge, and some have turned to genomic (and other ‘omic) data to identify an optimal therapy. In this work, we synthesized gene expression data for fluoxetine treatment in both human patients and rodent models, to better understand biological pathways affected by treatment, as well as those that may distinguish clinical or behavioral response.

Methods

Following the PRISMA guidelines, we searched the Gene Expression Omnibus (GEO) for studies profiling humans or rodent models with treatment of the antidepressant fluoxetine, excluding those not done in the context of depression or anxiety, in an irrelevant tissue type, or with fewer than three samples per group. Included studies were systematically reanalyzed by differential expression analysis and Gene Set Enrichment Analysis (GSEA). Individual pathway and gene statistics were synthesized across studies by three p-value combination methods, and then corrected for false discovery.

Results

Of the 74 data sets that were screened, 20 were included: 18 in rodents, and two in tissue from human patients. Studies were highly heterogeneous in the comparisons of both treated vs. control samples and responders vs. non-responders, with 737 and 356 pathways, respectively, identified as significantly different between groups in at least one study. However, 19 pathways were identified as consistently different in responders vs. non-responders, including toll-like receptor (TLR) and other immune pathways. Signal transduction pathways were identified as consistently affected by fluoxetine treatment in depressed patients and rodent models.

Discussion

These meta-analyses confirm known pathways and provide new hints toward antidepressant resistance, but more work is needed. Most included studies involved rodent models, and both patient studies had small cohorts. Additional large-cohort studies applying additional ‘omics technologies are necessary to understand the intricacies and heterogeneity of antidepressant response.
The sperm hook in house mice: a functional adaptation for migration and self-organised behaviour
Authors: Ryu Heungjin , Nam Kibum , Lee Byeong Eun , Jeong Yundon , Lee Seunghun , Kim Jeongmo , Hyun Young-Min , Kim Jae-Ick , Park Jung-Hoon
Published: February 2024

In most murine species, spermatozoa exhibit a falciform apical hook at the head end. The function of the sperm hook is not yet clearly understood. In this study, we investigate the role of the sperm hook in the migration of spermatozoa through the female reproductive tract inMus musculus(C57BL/6), using a deep tissue imaging custom-built two-photon microscope. Through live reproductive tract imaging, we found evidence indicating that the sperm hook aids in the attachment of spermatozoa to the epithelium and facilitates interactions between spermatozoa and the epithelium during migration in the uterus and oviduct. We also observed synchronised sperm beating, which resulted from the spontaneous unidirectional rearrangement of spermatozoa in the uterus. Based on live imaging of spermatozoa-epithelium interaction dynamics, we propose that the sperm hook plays a crucial role in successful migration through the female reproductive tract by providing anchor-like mechanical support and facilitating interactions between spermatozoa and the female reproductive tract in the house mouse.
Sniffing can be initiated by dopamine’s actions on ventral striatum neurons
Authors: Johnson Natalie L. , Cotelo-Larrea Anamaria , Stetzik Lucas A. , Akkaya Umit M. , Zhang Zihao , Gadziola Marie A. , Varga Adrienn G. , Ma Minghong , Wesson Daniel W.
Published: February 2024

Sniffing is a motivated behavior displayed by nearly all terrestrial vertebrates. While sniffing is associated with acquiring and processing odors, sniffing is also intertwined with affective and motivated states. The neuromodulatory systems which influence the display of sniffing are unclear. Here, we report that dopamine release into the ventral striatum is coupled with bouts of sniffing and that stimulation of dopaminergic terminals in these regions drives increases in respiratory rate to initiate sniffing whereas inhibition of these terminals reduces respiratory rate. Both the firing of individual neurons and the activity of post-synaptic D1 and D2 receptor-expressing neurons in the ventral striatum are also coupled with sniffing and local antagonism of D1 and D2 receptors squelches sniffing. Together, these results support a model whereby sniffing can be initiated by dopamine’s actions upon ventral striatum neurons. The nature of sniffing being integral to both olfaction and motivated behaviors implicates this circuit in a wide array of functions.
Altered NRG1/ErbB4 signaling and cholesterol metabolism dysregulation are key pathomechanisms in VRK1-related motor neuropathies and motor neuron diseases
Authors: Hamzé Zeinab , Humbert Camille , Rihan Khalil , Roeckel-Trévisiol Nathalie , Castro Christel , Lenfant Nicolas , Aubert Catherine , Bertaux Karine , Jabbour Rosette , Bernard-Marissal Nathalie , Mégarbané André , Delague Valérie
Published: February 2024

Hereditary Motor and Sensory Neuropathy (HMSN), or Charcot-Marie-Tooth disease (CMT), are the most common group of Inherited peripheral neuropathies (IPN), characterized by a strong clinical and genetic heterogeneity. Among them, distal Hereditary Motor Neuropathy (dHMN), also known as neuronopathy, is a subgroup, where only motor nerves are affected. This subgroup is also genetically heterogeneous, with 25 genes described to date, of which VRK1, that we have recently described as responsible for dHMN, associated to upper motor neuron signs. There are now more than thirty mutations in VRK1, which cause a range of neurological diseases affecting motor neurons (mainly lower, but also upper) or their axons in the peripheral nervous system, that we design as VRK1-related motor neuron diseases.

In two previous studies, we have demonstrated that dHMN due to VRK1 mutations lead to reduced levels of VRK1 in the nucleus, and that this depletion alters the dynamics of coilin, a phosphorylation target of VRK1. hiPSC-derived Motor Neurons (hiPSC-MN) from these patients, display Cajal Bodies (CBs) disassembly and defects in neurite outgrowth and branching, altered Action Potential (AP) waveform and decreased Axonal Initial Segment (AIS) length.

In this study, we have further studied the link between the loss of VRK1 function and the defects observed in hiPSC-MNs, by realizing bulk mRNA-Seq sequencing in this in vitro model of the disease. Our results evidenced altered NRG1/ERBB4 signaling, leading to cholesterol metabolism dysregulation and deregulation of genes encoding the glutamate receptors AMPAR and NMDAR, which role in the Axonal Initial Segment and abnormal AP initiation in hiPSC-MNs remains to be investigated.
Pathogenic tau induces an adaptive elevation in mRNA translation rate at early stages of disease
Authors: Zuniga Gabrielle , Katsumura Sakie , Mange Jasmine De , Ramirez Paulino , Atrian Farzaneh , Morita Masahiro , Frost Bess
Published: February 2024

Alterations in the rate and accuracy of messenger RNA (mRNA) translation are associated with aging and several neurodegenerative disorders, including Alzheimer’s disease and related tauopathies. We previously reported that error-containing RNA that are normally cleared via nonsense-mediated mRNA decay (NMD), a key RNA surveillance mechanism, are translated in the adult brain of aDrosophilamodel of tauopathy. In the current study, we find that newly-synthesized peptides and translation machinery accumulate within nuclear envelope invaginations that occur as a consequence of tau pathology, and that the rate of mRNA translation is globally elevated in early stages of disease in adult brains ofDrosophilamodels of tauopathy. Polysome profiling from adult heads of tau transgenicDrosophilareveals the preferential translation of specific mRNA that have been previously linked to neurodegeneration. Unexpectedly, we find that panneuronal elevation of NMD further elevates the global translation rate in tau transgenicDrosophila, as does treatment with rapamycin. As NMD activation and rapamycin both suppress tau-induced neurodegeneration, their shared effect on translation suggests that elevated rates of mRNA translation are an early adaptive mechanism to limit neurodegeneration. Our work provides compelling evidence that tau-induced deficits in NMD reshape the tau translatome by increasing translation of RNA that are normally repressed in healthy cells.
The genomic and cultural diversity of the Inka Qhapaq hucha ceremony in Chile and Argentina
Authors: de la Fuente Castro Constanza , Cortés Constanza , Raghavan Maanasa , Castillo Daniela , Castro Mario , Verdugo Ricardo , Moraga Mauricio
Published: February 2024

The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly-generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies the Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.
Retention of the full visual opsin repertoire in Australia’s cryptozoic lizards
Authors: Ford Matthew J.R. , Ludington Alastair J. , Bradford Tessa , Sanders Kate L. , Hutchinson Mark N. , Simões Bruno F.
Published: February 2024

Australian scincid lizards in the sister-generaLeristaandCtenotusare a prominent system for understanding adaptation in the transition from surface to fossorial life. The approximately 205 species in this group exhibit extreme diversity in morphology and ecology.LeristaandCtenotusboth include diurnal and surface-active species that are fully pentadactyl, andLeristaalso contains many specialised limb-reduced and limbless sand-swimmers. To understand how the visual systems of these lizards have responded to their varied photic environments, we examined the five opsin genes encoding the pigments that mediate colour and dim-light vision. These genes were sequenced for 59 species ofLeristaandCtenotusand analysed for variation in selection pressures among amino acid sites and across branches in the species tree. All five opsins are present and intact in all species ofLeristaandCtenotusexamined, and we identified signals of positively selected substitutions in all five opsin genes –RH1, which mediates scotopic vision, and four cone opsins associated with photopic vision (SWS1, SWS2, RH2, LWS). Most comparisons of selection pressures did not show significant differences according to broad ecological divisions. Only LWS showed a signal of relaxed selection in sand-swimming (limb reduced) versus less fossorial (fully limbed)Lerista. These results suggest that photopic abilities are retained across both clades, even in the most fossorial species, highlighting a need for studies of visual ecology of Australian skinks, and prompts caution with regards to generalisations about degenerate vision in fossorial squamates.
Plk3 Regulates Bacteremia and Supports Sepsis
Authors: Kostyak John C , Sarojini Sharath S , Naik Meghna U , Dai Wei , Michael James V , McKenzie Steven E , Naik Ulhas P
Published: February 2024

Objective

Sepsis, which is the body’s response to overwhelming infection, can lead to septic shock, characterized by thrombocytopenia, hypotension, and organ damage. Polo-like kinase 3 (Plk3) is a ubiquitously expressed serine/threonine kinase, but its exact role in immune function is unknown.

Approach and Results

We usedPlk3−/−and WT mice to evaluate the function of Plk3 in several models of severe sepsis. We found that WT mice die within 48 hours of 100% cecal ligation and puncture (CLP), whilePlk3−/−mice survive. Survival following cecal slurry (CS) injection mirrored that of CLP as recipient WT mice succumbed, while recipientPlk3−/−mice survived. Analysis of bacterial load 24 hours after CLP revealed that WT blood and peritonea were loaded with bacteria, but bacteria were virtually undetectable in the peritonea or blood ofPlk3−/−mice. To determine if bacteria infiltrate the blood ofPlk3−/−mice shortly after infection, we measured bacteria 1 and 3 hours after CS injection. We found a time-dependent increase in bacteria in the blood of WT mice that was not observed inPlk3−/−mice. To determine if the lack of bacteria in the blood ofPlk3−/−mice is due to enhanced clearance, we injectedE. coliIV into WT andPlk3−/−mice. We found 75% mortality for both WT andPlk3−/−mice within 72 hours following IV injection suggesting that survival ofPlk3−/−mice following enteric infection is likely due to reduced bacteremia.

Conclusion

Collectively our data suggest that Plk3 supports the systemic dissemination of bacteria and subsequent sepsis following enteric infection.
Sucrose-responsive osmoregulation of plant cell size by a long non-coding RNA
Authors: Hajný Jakub , Trávníčková Tereza , Rony R. M. Imtiaz Karim , Sacharowski Sebastian , Krzyszton Michal , Zalabák David , Hardtke Christian S. , Pečinka Aleš , Swiezewski Szymon , van Norman Jaimie M. , Novák Ondřej
Published: February 2024

The shoot of green plants is the primary site of carbon assimilation into sugars, the key source of energy and metabolic building blocks. The systemic transport of sugars is essential for plant growth and morphogenesis. Plants evolved intricate networks of molecular players to effectively orchestrate the subcellular partitioning of sugars. Dynamic distribution of these osmotically active compounds is a handy tool to regulate cell turgor pressure. Pressure-induced mechanical forces play an instructive role in developmental biology across kingdoms. Here, we functionally characterized a long non-coding RNA,CARMA,as a negative regulator of a receptor-like kinase, CANAR. Sugar-responsiveCARMAspecifically fine-tunesCANARexpression in the phloem, the route of sugar transport. By controlling sugar distribution, the CARMA-CANAR module allows cells to flexibly adapt to the external osmolality and adjust the size of vascular cell types during organ growth and development. We identify a nexus of plant vascular tissue formation with cell internal pressure monitoring and reveal a novel functional aspect of long non-coding RNAs in developmental biology.
Microglia are not necessary for maintenance of blood-brain barrier properties in health, but PLX5622 alters brain endothelial cholesterol metabolism
Authors: Profaci CP , Harvey SS , Bajc K , Zhang TZ , Zhang AZ , Nemec KM , McKinsey GL , Longworth A , McMullen TP , Arnold TD , Lawson DA , Bennett FC , Davalos D , Daneman R
Published: February 2024

Microglia are resident immune cells of the central nervous system, yet their functions far exceed those related to immunology. From pruning neural synapses during development to preventing excessive neural activity throughout life, microglia are intimately involved in the brain’s most basic processes. Studies have reported a close interaction between microglia and endothelial cells, as well as both helpful and harmful roles for microglia at the blood-brain barrier (BBB) in the context of disease. However, much less work has been done to understand microglia-endothelial cell interactions in the healthy brain. Here, we aim to determine the role of microglia at the healthy BBB. We used the colony-stimulating factor 1 receptor (CSF1R) inhibitor PLX5622 to deplete microglia and analyzed BBB ultrastructure, permeability, and transcriptome. Interestingly, we found that, despite their direct contact with endothelial cells, microglia are not necessary for maintenance of BBB structure, function, or gene expression in the healthy brain. However, we found that PLX5622 treatment alters brain endothelial cholesterol metabolism, and this effect was independent from microglial depletion, suggesting PLX5622 has off-target effects on brain vasculature.
Lipid membrane topographies are regulators for the spatial distribution of liquid protein condensates
Authors: Kang Chae Yeon , Chang Yoohyun , Zieske Katja
Published: February 2024

Liquid protein condensates play important roles in orchestrating subcellular organization and in serving as hubs for biochemical reactions. Recent studies have established associations between lipid membranes and proteins capable of forming liquid condensates, and shown that liquid protein condensates can remodel lipid membranes. However, little is known about how the topography of membranes affects liquid condensates. Here, we devised a cell-free system to reconstitute liquid condensates on lipid membranes with microstructured topographies and demonstrated an important role of lipid membranes topography as a biophysical regulator. By employing membrane surfaces designed with microwells, we found that liquid condensates assemble into orderly patterns. Furthermore, we demonstrated that membrane topographies influence the shape of liquid condensates. Finally, we showed that capillary forces, mediated by membrane topographies, led to the directed fusion of liquid condensates. Our results demonstrate that membrane topography is a potent biophysical regulator for the localization and shape of mesoscale liquid protein condensates.
Algorithmic construction of topologically complex biomineral lattices via cellular syncytia
Authors: Vyas Pranav , Brannon Charlotte , Formery Laurent , Lowe Christopher J. , Prakash Manu
Published: February 2024

Biomineralization is ubiquitous in both unicellular and multicellular living systems [1, 2] and has remained elusive due to a limited understanding of physicochemical and biomolecular processes [3]. Echinoderms, identified with diverse architectures of calcite-based structures in the dermis[4], present an enigma of how cellular processes control shape and form of individual structures. Specifically, in holothurians (sea cucumbers), multi-cellular clusters construct discrete single-crystal calcite ‘ossicles’ (∼100µm length scale), with diverse morphologies both across species and even within an individual animal [5]. The local rules that might encode these unique morphologies in calcite ossicles in holothurians remain largely unknown. Here we show how transport processes in a cellular syncytium impart a top-down control on ossicle geometry via symmetry breaking, branching, and fusion in finite cellular clusters. As a unique example of cellular masonary, we show how coordination within a small cluster of cells builds calcite structures about an order of magnitude larger than any individual participating cell. We establish live imaging of ossicle growth inApostichopus parvimensisjuveniles revealing how individual crystalline seeds (∼1−2µm) grow inside a multi-cellular syncytial complex with the biomineral completely wrapped within a membrane-bound cytoplasmic sheath. Constructing a topological description of ossicle geometries from 3D micro-CT (computational tomography) data reveals the hidden growth history and conserved patterns across ossicle types. We further demonstrate vesicle transport on the surface of the ossicle, rather than cell motility, regulates material transport to the ossicle tips via a unique cytoskeletal architecture. Finally, using reduced order models of conserved transport on self-closing active branching networks, we highlight the hidden universality in the growth process of distinct ossicles. The system presented here serves as a unique playground merging top-down cellular physiology and classical branching morphogenesis [6] with bottom-up non-equilibrium mineralization [7] processes at the interface of living and non-living matter [8].
Time-restricted feeding leads to sex- and organ-specific responses in the murine digestive system
Authors: Oparija-Rogenmozere Lalita , Di Natale Madeleine R. , Hunne Billie , Koo Ada , Ringuet Mitchell , Fazio Coles Therese E. , Fothergill Linda J. , McQuade Rachel , Furness John B.
Published: February 2024

Food intake is one of the main zeitgebers in the digestive system; however, little is known about organ- and sex-specific differences in food-driven regulation. We placed male and female C57Bl/6 mice on time-restricted feeding (TRF), limiting the food intake period to 8 hours. Food was added either at dark (ZT12) or light (ZT0) onset for 14 days. Afterwards, an additional 4-hour delay in the feeding period was introduced for half of the mice, and the TRF regime continued for another 14 days.

TRF from ZT12 to ZT20 led to the highest weight gain in females but the lowest in males while improving intestinal transepithelial resistance (TEER) in both sexes. However, it also led to the disappearance of food-anticipatory response in several hepatic genes. Delaying the start of TRF until ZT16 led to an increase in weight gain and a decrease in fasting plasma glucose levels in male mice, as well as to strong entrainment of metabolism-related hepatic and duodenal genes in both sexes.

The alignment of food intake with the early lights-on phase (ZT0-ZT8) caused only minor changes in physiological responses. However, it did lead to an overall downregulation of hepatic and an upregulation of duodenal and gastric genes, with additional loss of food-anticipatory gene expression in both sexes. Delaying the start of food intake until ZT4 was highly detrimental, causing an increase in fasting blood glucose levels, a decrease in TEER, and further disruptions in gene expression patterns in the stomach and liver. In contrast, the duodenum was able to restore its food-driven gene expression.

These results demonstrate that the adjustment to food intake time in mice is highly sex- and organ-specific. Our chosen TRF regimes were not able to synchronize food-anticipatory responses between the liver and gut. Instead, we observed that organs entrain to food intake at different rates.
Effects of head-only exposure to 900 MHz GSM electromagnetic fields in rats : changes in neuronal activity as revealed by c-Fos imaging without concomitant cognitive impairments
Authors: Bontempi Bruno , Lévêque Philippe , Dubreuil Diane , Jay Thérèse M. , Edeline Jean-Marc
Published: February 2024

Over the last decade, animal models have been used to evaluate the physiological and cognitive effects of mobile phone exposures. Here, we used a head-only exposure system in rats to determine whether exposure to 900MHz GSM electromagnetic fields (EMF) induces regional changes in neuronal activation as revealed by c-Fos imaging. In a first study, rats were exposed for 2h to brain average specific absorption rates (BASARs) ranging from 0.5 to 6W/kg. Changes in neuronal activation were found to be dose-dependent with significant increases in c-Fos expression occurring at BASAR of 1W/kg in prelimbic, infralimbic, frontal and cingulate cortices. In a second study, animals were submitted to either a spatial working memory (WM) task in a radial maze or a spatial reference memory (RM) task in an open field arena. Exposures (45min) were conducted before each training session (BASARs of 1 and 3.5W/kg). Control groups included sham-exposed and control cage animals. In both tasks, behavioral performance evolved similarly in the four groups over testing days. However, c-Fos staining was significantly reduced in cortical areas (prelimbic, infralimbic, frontal, cingulate and visual cortices) and in hippocampus of animals engaged in the WM task (BASARs of 1 and 3.5W/kg). In the RM task, EMF exposure-induced decreases were limited to temporal and visual cortices (BASAR of 1W/kg). These results demonstrate that both acute and subchronic exposures to 900MHz EMFs can produce biological effects, but these effects were not sufficient to induce detectable cognitive deficits in the tasks used here.
NR4A3 deficiency ameliorates contact hypersensitivity and exacerbates psoriasis by regulating gene expression in dendritic cells
Authors: Katagiri Mayuka , Ito Naoto , Nagata Kazuki , Nakano Shiori , Minamikawa Natsuki , Yamashita Niya , Takahashi Miki , Kurihara Masami , Nagaoka Masanori , Ando Miki , Ito Tomoka , Yashiro Takuya , Yoshimura Akihiko , Nishiyama Chiharu
Published: February 2024

NR4A3 is a transcription factor that belongs to the nuclear receptor superfamily. To reveal the roles of NR4A3 in skin diseases, we constructed contact hypersensitivity (CHS)- and imiquimod-induced psoriasis models inNr4a3-/-mice. In the CHS inducedNr4a3-/-mice, ear swelling was significantly reduced, accompanied by suppressed migration of dendritic cells (DCs), in which CCR7 expression was reduced. In contrast, ear swelling in psoriasis modelNr4a3-/-mice was enhanced. The expression levels of inflammatory cytokines in psoriasis skin lesions and in TLR7-ligand-stimulated DCs were increased by NR4A3 deficiency. Subcutaneous (s.c.) injection of hapten-treatedNr4a3+/+DCs induced ear swelling inNr4a3-/-mice, and s.c. injection of TLR7-ligand-stimulatedNr4a3-/-DCs caused significant ear swelling. Compared withNr4a3+/+DCs,Nr4a3-/-DCs expressed lower levels of CCR7 and IRF4, and higher levels of TLR7, IRF7, IFN-β, and PU.1. Taken together, NR4A3 deficiency ameliorates CHS and exacerbates psoriasis by regulating the expression of CCR7, TLR7, and related transcription factors in DCs.
The Alexander Disease Protein GFAP Drives Mitochondrial Fission
Authors: Xiong Ding , Kong Linghai , Tan Ye Sing , Yuan Fang , Sun Zijun , Li Xueyan , Abella Emily , Messing Albee , Zhang Su-Chun
Published: February 2024

Mitochondrial plasticity, coordinated by fission and fusion, is crucial to ensure cellular functions. Mitochondrial fission is mediated by the GTPase Drp1 at the constriction site, which is proposed to be driven by the actin-myosin contractile force. However, the mechanism that propels constriction remains unclear, and the potential involvement of additional mechanisms in this process remains an open question. Here, using structured illumination microscopy and electron microscopy, we show that the type-III intermediate filament glial fibrillary acidic protein (GFAP) closely surrounds mitochondria fission sites and associates with accumulated Drp1 molecules. Remarkably, loss of GFAP results in hyperfused mitochondria under physiological condition and even Ca2+-induced mitochondrial fission. Additionally, mutations of GFAP, the cause of Alexander disease, result in an elevated recruitment of Drp1 to GFAP, leading to significantly increased mitochondrial fissions. Taking together, these findings suggest a novel mechanism of mitochondrial division mediated by type-III intermediate filaments.
Purging viral latency by a bifunctional HSV-vectored therapeutic vaccine in chronically SIV-infected macaques
Authors: Wen Ziyu , Li Pingchao , Yuan Yue , Wang Congcong , Li Minchao , Wang Haohang , Shi Minjuan , He Yizi , Cui Mingting , Chen Ling , Sun Caijun
Published: February 2024

The persistence of latent viral reservoirs remains the major obstacle to eradicating human immunodeficiency virus (HIV). We herein found that ICP34.5 can act as an antagonistic factor for the reactivation of HIV latency by herpes simplex virus type I (HSV-1), and thus recombinant HSV-1 with ICP34.5 deletion could more effectively reactivate HIV latency than its wild-type counterpart. Mechanistically, HSV-ΔICP34.5 promoted the phosphorylation of HSF1 by decreasing the recruitment of protein phosphatase 1 (PP1α), thus effectively binding to the HIV LTR to reactivate the latent reservoirs. In addition, HSV-ΔICP34.5 enhanced the phosphorylation of IKKα/β through the degradation of IκBα, leading to p65 accumulation in the nucleus to elicit NF-κB pathway-dependent reactivation of HIV latency. Then, we constructed the recombinant HSV-ΔICP34.5 expressing simian immunodeficiency virus (SIV) env, gag, or the fusion antigen sPD1-SIVgag as a therapeutic vaccine, aiming to achieve a functional cure by simultaneously reactivating viral latency and eliciting antigen-specific immune responses. Results showed that these constructs effectively elicited SIV-specific immune responses, reactivated SIV latency, and delayed viral rebound after the interruption of antiretroviral therapy (ART) in chronically SIV-infected rhesus macaques. Collectively, these findings provide insights into the rational design of HSV-vectored therapeutic strategies for pursuing an HIV functional cure.
Trapped in translocation – Stalling of XPD on a crosslinked DNA substrate
Authors: Kuper Jochen , Hove Tamsanqa , Maidl Sarah , Sauer Florian , Kempf Maximilian , Greiter Elke , Neitz Hermann , Höbartner Claudia , Kisker Caroline
Published: February 2024

The super family 2 (SF2) helicase XPD is a central component of the general transcription factor II H (TFIIH) which is essential for transcription and nucleotide excision DNA repair (NER)1. Within these two processes XPDs helicase function is vital for NER but not for transcription initiation, where XPD only acts as a scaffold for other factors2. We deciphered one of the most enigmatic steps in XPD helicase action: the active separation of dsDNA and its stalling upon approaching an interstrand crosslink, one of the most severe DNA damages in the cell, using cryo EM. Furthermore, the structure clearly shows how dsDNA is separated and reveals a highly unusual involvement of the Arch domain in active dsDNA separation. Combined with mutagenesis and biochemical analyses, we identify distinct functional residues important for helicase activity. Surprisingly, those areas also affect core TFIIH translocase activity, revealing a yet unencountered function of XPD within the TFIIH scaffold. Importantly, our structure provides a basis for XPD damage recognition and further suggests how the NER bubble could be formed, leading to a model for the location of the XPG nuclease relative to the excised damage.
Design and optimization of novel succinate dehydrogenase inhibitors against agricultural fungi based on Transformer model
Authors: Zhang Yuan , Chai Jianqi , Li Ling , Zhao Wenqian , Chen Yuanyuan , Zhang Liangyun , Xu Zhihui , Yang Chunlong , Pian Cong
Published: February 2024

Succinate dehydrogenase inhibitors (SDHIs) are a promising class of fungicides targeting the energy production pathway of pathogenic fungi. However, overuse has led to resistance, necessitating the development of new and effective SDHIs. This study takes the Transformer model to generate a customized virtual library of potential SDHIs. These candidates were then meticulously screened based on expert knowledge and synthetic feasibility, ultimately yielding several pyrazole carboxamide derivatives as the promising leads. Subsequent synthesis, antifungal activity testing, and structural optimization further refined these leads into potent SDHI candidates. This work marks the first application of a generative model to SDHI design, establishing a robust workflow for virtual library generation, screening, activity evaluation, and structure optimization. This provides one way for the rational design of future SDHIs, not only against fungi, but potentially other agricultural pathogens as well.
Spatiotemporal observation reveals metastatic tumor-driven vascular remodeling as a potential route to polyclonal colonization
Authors: Ikeda Yukinori , Oshima Hiroko , Kok Sau Yee , Oshima Masanobu , Matsunaga Yukiko T.
Published: February 2024

Polyclonal metastasis, which arises from clusters of circulating tumor cells, promotes metastasis development and has become a major target of metastasis inhibition. Mouse experiments have clearly verified that nonmetastatic and metastatic tumors coexist and form metastatic nests, but the detailed mechanism of extravasation remains unclear. We established a three-dimensional tumor microvessel model to investigate extravasation between nonmetastatic tumors, metastatic tumors, and mosaic tumor organoids in a mixed state by time-lapse imaging and to determine the sequential steps of the extravasation of tumor cells via vascular remodeling. This comparison revealed a new concept of extravascular invasion via vascular remodeling in metastatic carcinoma. Furthermore, the involvement of liver host cells, the hepatic stellate cells, demonstrated an interaction with metastatic cells to facilitate metastatic foci formation. Moreover,Adam28was highly expressed exclusively in metastatic tumor cells, suggesting its involvement in vascular remodeling. These results demonstrate the ability of metastatic tumor cells for extravasation in polyclonal metastasis, which may lead to the development of new therapeutic targets.
Automated high-throughput biological sex identification from archaeological human dental enamel using targeted proteomics
Authors: Koenig Claire , Bortel Patricia , Paterson Ryan S. , Rendl Barbara , Madupe Palesa P. , Troché Gaudry B. , Hermann Nuno Vibe , Martínez de Pinillos Marina , Martinón-Torres María , Mularczyk Sandra , Jørkov Marie Louise Schjellerup , Gerner Christopher , Kanz Fabian , Martinez-Val Ana , Cappellini Enrico , Olsen Jesper V.
Published: February 2024

Biological sex is key information for archaeological and forensic studies, which can be determined by proteomics. However, lack of a standardised approach for fast and accurate sex identification currently limits the reach of proteomics applications. Here, we introduce a streamlined mass spectrometry (MS)-based workflow for determination of biological sex using human dental enamel. Our approach builds on a minimally invasive sampling strategy by acid etching, a rapid online liquid chromatography (LC) gradient coupled to high-resolution parallel reaction monitoring assay allowing for a throughput of 200 samples-per-day with high quantitative performance enabling confident identification of both males and females. Additionally, we have developed a streamlined data analysis pipeline and integrated it into an R-Shiny interface for ease-of-use. The method was first developed and optimised using modern teeth and then validated in an independent set of deciduous teeth of known sex. Finally, the assay was successfully applied to archaeological material, enabling the analysis of over 300 individuals. We demonstrate unprecedented performance and scalability, speeding up MS analysis by tenfold compared to conventional proteomics-based sex identification methods. This work paves the way for large-scale archaeological or forensic studies enabling the investigation of entire populations rather than focusing on individual high-profile specimens.
Pathological mechanisms and candidate therapeutic approaches in the hearing loss of mice carrying humanMIR96mutations
Authors: Lewis Morag A , Lachgar-Ruiz Maria , Di Domenico Francesca , Duddy Graham , Chen Jing , Fernandez Sergio , Morin Matias , Williams Gareth , Moreno Pelayo Miguel Angel , Steel Karen P
Published: February 2024

Progressive hearing loss is a common problem in the human population with no effective therapeutics currently available. However, it has a strong genetic contribution, and investigating the genes and regulatory interactions underlying hearing loss offers the possibility of identifying therapeutic candidates. Mutations in regulatory genes are particularly useful for this, and an example is the microRNA miR-96, a transcriptional regulator which controls hair cell maturation. Mice and humans carrying mutations inMir96all develop hearing loss, but different mutations result in different physiological, structural and transcriptional phenotypes.

Here we present our characterisation of two lines of mice carrying different human mutations knocked-in toMir96. While mice homozygous for either mutation are profoundly deaf from two weeks old, the heterozygous phenotypes differ markedly, with only one mutation resulting in hearing impairment in heterozygosis. Investigations of the structural phenotype showed that one mutation appears to lead to synaptic defects, while the other has a much more severe effect on the hair cell stereociliary bundles. Transcriptome analyses revealed a wide range of misregulated genes in both mutants which were notably dissimilar. We used the transcriptome analyses to investigate candidate therapeutics, and tested one, finding that it delayed the progression of hearing loss in heterozygous mice.

Our work adds further support for the importance of the gain of novel targets in microRNA mutants, and offers a proof of concept for the identification of pharmacological interventions to maintain hearing.
The polyamine transporter ATP13A3 mediates DFMO-induced polyamine uptake in neuroblastoma
Authors: Azfar Mujahid , Gao Weiman , Van den Haute Chris , Xiao Lin , Karsa Mawar , Pandher Ruby , Ronca Emma , Bongers Angelika , Karsa Ayu , Spurling Dayna , Guo Xinyi , Mayoh Chelsea , Burns Mark R. , Verhelst Steven H.L. , Norris Murray D. , Haber Michelle , Vangheluwe Peter , Somers Klaartje
Published: February 2024

High-risk neuroblastomas, often associated withMYCNoncogene amplification, are addicted to polyamines, small polycations vital for cellular functioning. We have shown that neuroblastoma cells increase polyamine uptake when exposed to the polyamine biosynthesis inhibitor DFMO, currently in clinical trial, and that this mechanism limits the efficacy of the drug. While this finding resulted in the clinical development of polyamine transport inhibitors including AMXT 1501, presently under clinical investigation in combination with DFMO, the mechanisms and transporters involved in DFMO-induced polyamine uptake are unknown. Knockdown of ATP13A3, a member of the P5B-ATPase family, limited basal and DFMO-induced polyamine uptake, attenuatedMYCN-amplified and non-MYCN-amplified neuroblastoma cell growth and potentiated the inhibitory effects of DFMO. Overexpression of ATP13A3 in neuroblastoma cells increased polyamine uptake, which was inhibited by AMXT 1501, highlighting ATP13A3 as a key target of the drug. The association between high ATP13A3 expression and poorer survival in neuroblastoma further supports a role of this transporter in neuroblastoma progression. Thus, this study identified ATP13A3 as a critical regulator of basal and DFMO-induced polyamine uptake and a novel therapeutic target for neuroblastoma.

Graphical Abstract