bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chk2 sustains PLK1 activity in mitosis to ensure proper chromosome segregation
Authors: Black Elizabeth M. , Ramírez Parrado Carlos Andrés , Trier Isabelle , Li Wenxue , Joo Yoon Ki , Pichurin Jennifer , Liu Yansheng , Kabeche Lilian 
Published: March 2024

SummaryPolo-like kinase 1 (PLK1) protects against genome instability by ensuring timely and accurate mitotic cell division. PLK1 activity is tightly regulated throughout the cell cycle. Although the pathways that initially activate PLK1 in G2 are well-characterized, the factors that directly regulate PLK1 in mitosis remain poorly understood. Here, we identify that human PLK1 activity is sustained by the DNA damage response kinase Checkpoint kinase 2 (Chk2) in mitosis. Chk2 directly phosphorylates PLK1 T210, a residue on its T-loop whose phosphorylation is essential for full PLK1 kinase activity. Loss of Chk2-dependent PLK1 activity causes increased mitotic errors, including chromosome misalignment, chromosome missegregation, and cytokinetic defects. Moreover, Chk2 deficiency increases sensitivity to PLK1 inhibitors, suggesting that Chk2 status may be an informative biomarker for PLK1 inhibitor efficacy. This work demonstrates that Chk2 sustains mitotic PLK1 activity and protects genome stability through discrete functions in interphase DNA damage repair and mitotic chromosome segregation.
Non-endothelial expression of Endomucin in the mouse and human choroid
Authors: Brookins Elysse , Serrano Sophia E. , Yacu George S. , Finer Gal , Thomson Benjamin R 
Published: March 2024

AbstractEndomucin (EMCN) is a 261 AA transmembrane glycoprotein that is highly expressed by venous and capillary endothelial cells where it plays a role in VEGF-mediated angiogenesis and regulation of immune cell recruitment. However, it is better known as a histological marker, where it has become widespread due to the commercial availability of high-quality antibodies that work under a wide range of conditions and in many tissues. The specificity of EMCN staining has been well-validated in retinal vessels, but while it has been used extensively as a marker in other tissues of the eye, including the choroid, the pattern of expression has not been described in detail. Here, in addition to endothelial expression in the choriocapillaris and deeper vascular layers, we characterize a population of EMCN-positive perivascular cells in the mouse choroid that did not co-localize with cells expressing other endothelial markers such as PECAM1 or PODXL. To confirm that these cells represented a new population of EMCN-expressing stromal cells, we then performed single cell RNA sequencing in choroids from adult wild-type mice. Analysis of this new dataset confirmed that, in addition to endothelial cells,EmcnmRNA expression was present in choroidal pericytes and a subset of fibroblasts, but not vascular smooth muscle cells. BesidesEmcn, no known endothelial gene expression was detected in these cell populations, confirming that they did not represent endothelial-stromal doublets, a common technical artifact in single cell RNA seq datasets. Instead, choroidalEmcn-expressing fibroblasts exhibited high levels of chemokine and interferon signaling genes, whileEmcn-negative fibroblasts were enriched in genes encoding extracellular matrix proteins.Emcnexpressing fibroblasts were also detected in published datasets from mouse brain and human choroid, suggesting that stromalEmcnexpression was not unique to the choroid and was evolutionarily conserved. Together, these findings highlight unique fibroblast and pericyte populations in the choroid and provide new context for the role of EMCN in angiogenesis and immune cell recruitment.
Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases
Authors: Gizzio Joan , Thakur Abhishek , Haldane Allan , Post Carol Beth , Levy Ronald M. 
Published: March 2024

AbstractProtein kinases are molecular machines with rich sequence variation that distinguishes the two main evolutionary branches – tyrosine kinases (TKs) from serine/threonine kinases (STKs). Using a sequence co-variation Potts statistical energy model we previously concluded that TK catalytic domains are more likely than STKs to adopt an inactive conformation with the activation loop in an autoinhibitory “folded” conformation, due to intrinsic sequence effects. Here we investigated the structural basis for this phenomenon by integrating the sequence-based model with structure-based molecular dynamics (MD) to determine the effects of mutations on the free energy difference between active and inactive conformations, using a novel thermodynamic cycle involving many (n=108) protein-mutation free energy perturbation (FEP) simulations in the active and inactive conformations. The sequence and structure-based results are consistent and support the hypothesis that the inactive conformation “DFG-out Activation Loop Folded”, is a functional regulatory state that has been stabilized in TKs relative to STKs over the course of their evolution via the accumulation of residue substitutions in the activation loop and catalytic loop that facilitate distinct substrate binding modesin transand additional modes of regulationin cisfor TKs.
Adaptive generalization in pollinators: hawkmoths increase fitness to long-tubed flowers, but secondary pollinators remain important
Authors: Wenzell Katherine E. , Zhang Johnathan Y. , Skogen Krissa A. , Fant Jeremie B. 
Published: March 2024

AbstractSelection on floral traits by animal pollinators is important in the evolution of flowering plants, yet whether floral divergence requires specialized pollination remains uncertain. Longer floral tubes, a trait associated with long-tongued pollinators, can also exclude other pollinators from accessing rewards, a potential mechanism for specialization. Across most of its range,Castilleja sessilifloradisplays much longer corollas than mostCastillejaspecies, though tube length varies geographically and correlates partially with hawkmoth visitation. To assess if long corolla tubes reflect adaptation to hawkmoth pollinators, we performed a day/night pollinator exclusion experiment in nine natural populations that varied in corolla length across the range ofC. sessilifloraand short-tubed members of the parapatricC. purpureacomplex. We compared the fitness contributions of nocturnal and diurnal visitors, revealing that long-tubed populations visited predominantly by hawkmoths experienced greater fruit set at night, in contrast with short-tubed populations or those visited mainly by diurnal pollinators. Next, leveraging a range-wide multi-year dataset of pollinator visitation to these species, we identify that hawkmoth visitation is associated with increased fitness in long-tubed populations overall, and that long tubes are associated with less diverse visitor assemblages. Thus, long corollas represent an adaptation to hawkmoth pollination at the exclusion of diverse pollinators. Nonetheless, while hawkmoths were scarce in the northern range, secondary diurnal pollinators contributed to fruit set across the range, providing reproductive assurance despite possible trait mismatch. This study illustrates adaptive generalization in pollination modes and that floral divergence may proceed along a continuum of generalized and specialized pollinator interactions.
Nurture Early for Optimal Nutrition (NEON) Pilot Randomised Controlled Trial: Qualitative study of community facilitators and attendees’ perspective on intervention delivery
Authors: Manikam Logan , Patil Priyanka , Bello Ummi , Chakraborty Subarna , Fujita Sumire , Dwardzweska Joanna , Oyebode Oyinlola , Llewellyn Clare H. , Webb-Martin Kelley , Irish Carol , Archibong Mfon , Gilmour Jenny , Kalungi Phoebe , Batura Neha , Conway Rana , Lakhanpaul Monica , Heys Michelle 
Published: March 2024

AbstractBackgroundAppropriate and healthy feeding practices can enhance a child’s health, prevent obesity, and reduce chronic metabolic disease risks. Given the ethnic variations in feeding practices and metabolic risk, interventions must be community specific. Culturally tailored, grassroots interventions targeting infant feeding can induce behavioural changes, mitigating chronic metabolic disease risks in later life.AimThe aim of this study was to explore participant feedback and inform intervention delivery methods within marginalised communities.MethodsA pilot three-arm cluster randomised controlled trial was conducted in London’s Tower Hamlets and Newham boroughs, involving community participatory learning and action groups. The study recruited 186 South Asian (Indian, Bangladeshi, Pakistani, and Sri Lankan) mothers or carers of 0-2-year-old children. Attendees were invited to either face-to-face or online intervention arms, facilitated by trained multilingual community facilitators, offering culturally informed discussions on child nutrition and care practices. Qualitative feedback was collected from attendees and facilitators, with thematic analysis identifying key themes, underscoring intervention fidelity and acceptance.ResultsOf the initial attendees, 42 (from the remaining 153 at the study’s conclusion) and 9 community facilitators offered feedback on the intervention’s delivery and suggestions for enhancing community-based interventions’ success. Key findings highlighted the need for a more flexible approach to boost participation and the significance of providing accessible, translated documents and resources.ConclusionParenting interventions, particularly for new mothers, should adopt a hybrid design. This would provide attendees with the flexibility to select the delivery method, session timings, and the option to participate at any stage of the intervention.
Brain State-dependent Repetitive Transcranial Magnetic Stimulation for Motor Stroke Rehabilitation: A Proof of Concept Randomized Controlled Trial
Authors: Mahmoud Wala , Baur David , Zrenner Brigitte , Brancaccio Arianna , Belardinelli Paolo , Ramos-Murguialday Ander , Zrenner Christoph , Ziemann Ulf 
Published: March 2024

AbstractBackgroundIn healthy subjects, repetitive transcranial magnetic stimulation (rTMS) targeting the primary motor cortex (M1) demonstrated plasticity effects contingent on electroencephalography (EEG)-derived excitability states, defined by the phase of the ongoing sensorimotor μ-oscillation. The therapeutic potential of brain state-dependent rTMS in the rehabilitation of upper limb motor impairment post-stroke remains unexplored.ObjectiveProof-of-concept trial to assess the efficacy of rTMS, synchronized to the sensorimotor µ-oscillation, in improving motor function and reducing upper-limb spasticity in stroke patients.MethodsWe conducted a parallel group, randomized double-blind controlled trial in 30 chronic stroke patients. The experimental intervention group received EEG-triggered rTMS of the ipsilesional M1 (1,200 pulses; 0.33 Hz; 90% of the resting motor threshold (RMT)), while the control group received low-frequency rTMS of the contralesional motor cortex (1,200 pulses; 1 Hz, 115% RMT), i.e., an established treatment protocol. Both groups received 12 rTMS sessions (20 min, 3x per week, 4 weeks) followed by 50 min of physiotherapy. The primary outcome measure was the change in upper-extremity Fugl-Meyer assessment (FMA-UE) scores between baseline, immediately post-treatment and 3 months’ follow-up.ResultsBoth groups showed significant FMA-UE improvement and spasticity reduction (clinical and objective measures). There were no significant differences between the groups in any of the outcome measures.ConclusionsThe application of brain state-dependent rTMS for rehabilitation in chronic stroke patients is feasible. This pilot study demonstrated that the brain oscillation-synchronized rTMS protocol produced beneficial effects on motor disability and spasticity that were comparable to those observed with an established therapeutic rTMS protocol.
High fat and low carbohydrate supplies are linked to decreased epilepsy disease burden globally
Authors: Ni Duan , Senior Alistair , Raubenheimer David , Simpson Stephen J. , Nanan Ralph 
Published: March 2024

AbstractObjectivesEpilepsy is one of the major neural disorders globally. Ketogenic diets with high fat, low carbohydrate and moderate to low protein contents are well-established as interventions for epilepsy, particularly the intricate ones, exemplifying that modifying dietary compositions might have profound effects on established epilepsy. However, most of the diet-related epilepsy interventions have focused on dividual nutrients or specific diets with set nutrient compositions. An important unanswered question is whether specific macronutrient exposure through diets and food environments are linked to epilepsy and could potentially extend to primary preventive qualities.MethodsMacronutrient supply, gross domestic product (GDP), and epilepsy disease burden data were collated from more than 150 countries spanning from 1990 to 2018. Nutritional geometry generalized additive mixed models (GAMMs) were carried out for analysis.ResultsGAMM modelling unravelled the interactive effects of nutrient supplies and socioeconomic status on epilepsy disease burden. Carbohydrate supply was associated with increased epilepsy while fat supply had the opposite effect. A high fat low carbohydrate supplies dietary environment, similar to ketogenic diets, was linked to the lowest epilepsy disease burden. These associations were conserved across sexes and were not confounded by the total energy supply.ConclusionsA high fat low carbohydrate supplies dietary environment is associated with decreased epilepsy disease burden, hinting a plausible primary preventive role. This might expand the clinical application of ketogenic diets and inform future nutrient-based epilepsy treatment and/or prevention.
Dorsal hippocampus represents locations to avoid as well as locations to approach during approach-avoidance conflict
Authors: Calvin Olivia L. , Erickson Matthew T. , Walters Cody J. , David Redish A. 
Published: March 2024

AbstractWorrying about perceived threats is a hallmark of multiple psychological disorders including anxiety. This concern about future events is particularly important when an individual is faced with an approach-avoidance conflict. Potential goals to approach are known to be represented in the dorsal hippocampus during theta sweeps. Similarly, important non-local information is represented during hippocampal high synchrony events (HSEs), which are correlated with sharp-wave ripples (SWRs). It is likely that potential future threats may be similarly represented. We examined how threats and rewards were represented within the hippocampus during approach-avoidance conflicts in rats faced with a predator-like robot guarding a food reward. We found representations of the pseudo-predator during HSEs when hesitating in the nest, and during theta prior to retreating as the rats approached the pseudo-predator. After the first attack, we observed new place fields appearing at the location of the robot (not the location the rat was when attacked). The anxiolytic diazepam reduced anxiety-like behavior and altered hippocampal local field potentials, including reducing SWRs, suggesting that one potential mechanism of diazepam’s actions may be through altered representations of imagined threat. These results suggest that hippocampal representation of potential threats could be an important mechanism that underlies worry and a potential target for anxiolytics.
A cellular assay system revealed the deamidase-mediated regulation of the Arg-mediated N-end rule protein degradation pathway
Authors: Yoshida Shusei , Ohta Ren , Miyabe Mami , Tamura Taku 
Published: March 2024

AbstractRegulated protein production and degradation are essential for maintaining proteostasis in eukaryotic cells. The N-end rule, or N-degron pathway, is a protein degradation machinery in which the N-terminal amino acid is the mark of the protein degradation via the proteasome. The N-end rule is a conserved protein disposal machinery in eukaryotic cells. However, the precise cellular mechanisms and their physiological roles are not fully understood. Herein, we report the development of an Arg-mediated N-end rule assay system using artificial substrates expressed in cultured cell lines. We demonstrated that the N-end rule degradation is significantly influenced by the expression levels of N-terminal amino acid-modifying enzymes, including NTAN1, NTAQ1, and ATE1. In the N-terminal Asn protein pathway, an increase in NTAN1 or ATE1 expression promotes its disposal via the N-end rule degradation pathway. Interestingly, overexpression of NTAQ1 decreased the degradation of the protein bearing Gln at the N-terminus. Computational prediction of NTAQ1 and ATE1 complex formation suggests that the outer loop region of NTAQ1 is involved in its interaction with ATE1 and that the NTAQ1 overexpression may negatively affect this interaction. Our findings suggest that the degradation activity of the Arg/N-end rule pathway is positively or negatively regulated by deamidase expression levels and propose a higher degree of control of protein degradation by the Arg/N-end rule within cells.
YmoA functions as a molecular stress sensor inYersinia
Authors: Héchard Tifaine , Lu Lu , Edgren Tomas , Chi Celestine , Wang Helen 
Published: March 2024

AbstractPathogenic bacteria sense and respond to environmental fluctuations, a capability essential for establishing successful infections. The YmoA/Hha protein family are conserved transcription regulators in Enterobacteriaceae, playing a critical role in these responses. Specifically, YmoA inYersiniaadjusts the expression of virulence-associated traits upon temperature shift. Still, the molecular mechanisms transducing environmental signal through YmoA remain elusive. Our study employed nuclear magnetic resonance spectroscopy, biological assays and RNA-seq analysis to elucidate these mechanisms. We demonstrated that YmoA underwent structural fluctuations and conformational dynamics in response to temperature and osmolarity changes, correlating with changes in plasmid copy number, bacterial fitness and virulence function. Notably, chemical shift analysis identified key roles of a few specific residues and of the C-terminus region in sensing both temperature and salt-driven switch. These findings demonstrate that YmoA acts as a central stress sensor inYersinia, fine-tuning virulence gene expression and balancing metabolic trade-offs.
Stochastic Voronoi Tessellations as Models for Cellular Neighborhoods in Simple Multicellular Organisms
Authors: Srinivasan Anand , Höhn Steph S.M.H. , Goldstein Raymond E. 
Published: March 2024

AbstractRecent work on distinct multicellular organisms has revealed a hitherto unknown type of biological noise; rather than a regular arrangement, cellular neighborhood volumes, obtained by Voronoi tessellations of the cell locations, are broadly distributed and consistent with gamma distributions. We propose an explanation for those observations in the case of the algaVolvox, whose somatic cells are embedded in an extracellular matrix (ECM) they export. Both a solvable one-dimensional model of ECM growth derived from bursty transcriptional activity and a two-dimensional “Voronoi liquid” model are shown to provide one-parameter families that smoothly interpolate between the empirically-observed near-maximum-entropy gamma distributions and the crystalline limit of Gaussian distributions governed by the central limit theorem. These results highlight a universal consequence of intrinsic biological noise on the architecture of certain tissues.
Multiple levels of transcriptional regulation control glycolate metabolism inParacoccus denitrificans
Authors: Schada von Borzyskowski Lennart , Hermann Lucas , Kremer Katharina , Barthel Sebastian , Pommerenke Bianca , Glatter Timo , Paczia Nicole , Bremer Erhard , Erb Tobias J. 
Published: March 2024

AbstractThe hydroxyacid glycolate is a highly abundant carbon source in the environment. Glycolate is produced by unicellular photosynthetic organisms and excreted at petagram scales to the environment, where it serves as growth substrate for heterotrophic bacteria. In microbial metabolism, glycolate is first oxidized to glyoxylate by the enzyme glycolate oxidase. The recently described β-hydroxyaspartate cycle (BHAC) subsequently mediates the carbon-neutral assimilation of glyoxylate into central metabolism in ubiquitous Alpha- and Gammaproteobacteria. While the reaction sequence of the BHAC was elucidated inParacoccus denitrificans, little is known about the regulation of glycolate and glyoxylate assimilation in this relevant alphaproteobacterial model organism. Here, we show that regulation of glycolate metabolism inP. denitrificansis surprisingly complex, involving two regulators, the IclR-type transcription factor BhcR that acts as an activator for the BHAC gene cluster, as well as the GntR-type transcriptional regulator GlcR, a previously unidentified repressor that controls the production of glycolate oxidase. Furthermore, an additional layer of regulation is exerted at the global level, which involves the transcriptional regulator CceR that controls the switch between glycolysis and gluconeogenesis inP. denitrificans. Together, these regulators control glycolate metabolism inP. denitrificans, allowing the organism to assimilate glycolate together with other carbon substrates in a simultaneous fashion, rather than sequentially. Our results show that the metabolic network of Alphaproteobacteria shows a high degree of flexibility to react to the availability of multiple substrates in the environment.
Disentangling the potential factors definingBacillus subtilisabundance in natural soils
Authors: Xu Xinming , Pioppi Adele , Kiesewalter Heiko T. , Strube Mikael Lenz , Kovács Ákos T. 
Published: March 2024

AbstractBacillus subtilisis ubiquitously and broadly distributed in various environments but mostly isolated from soil. Given that species ofB. subtilisare known as key plant growth-promoting rhizobacteria in agriculture, we here aimed to describe the natural distribution of this species and uncover how biotic and abiotic factors affect its distribution. When comparing different soils, we discovered thatB. subtilisis most abundant in grasslands, but can rarely be isolated from forest soil, even if the sample sites for the two types of soil are situated in proximity. Differential analysis revealed that spore-forming bacteria exhibited enrichments in the grassland, suggesting niche overlap or synergistic interactions leading to the proliferation of certainBacillusspecies in grassland environments. Network analysis further revealed thatBacillusand otherBacillotaestablished a densely interconnected hub module in the grassland soil samples, characterized by positive associations indicating co-occurrence, a pattern not observed in the forest soil. Speculating that this difference was driven by abiotic factors, we next combined amplicon sequencing with physio-chemical analysis of soil samples, and found multiple chemical variables, mainly pH, to affect microbial composition. Our study pinpoints the factors that influenceB. subtilisabundance in natural soils and, therefore, offers insights for designingB. subtilis-based biocontrol products in agricultural settings.