bluuebunny/crossref_metadata_2025 huggingface dataset:
Clostridium tetanibacteraemia in the plague area in France: two cases
Authors: Boualam M.A. , Bouri A. , Signoli M. , Drancourt M. , Caputo A. , Terrerzz E. , Aboudharam G.
Published: February 2024

Background

Paleoculturomics aims to culture ancient pathogens from human remains such as dental pulp, which traps a drop of blood at the time of the death, to diagnose bacteraemia.Clostridium tetani(C. tetani) bacteraemia is a rare situation, with only four case reports in the literature.

Methods

Fourteen teeth collected from 14 individuals buried at the site of the 1590 plague in Fedons, France, were surface decontaminated before the pulp was cultured under strict anaerobiosis with negative controls. Colonies were identified by mass spectrometry and whole genome sequencing, andC. tetani-specific PCR was performed using DNA extracted from dental pulps, calculus and sediments.

Results

C. tetanicultured in two dental pulp specimens from two individuals was firmly identified by MALDI-TOF mass spectrometry, and whole genome sequencing confirmed toxigenicC. tetani. In the remaining twelve individuals, no suchC. tetaniwas recovered and further detection by PCR and palaeoculturomics of dental calculus and sediments surrounding the teeth in these two individuals remained negative.

Conclusion

ToxigenicC. tetaniwhich did not result from mere environmental contamination, caused bacteraemia in two individuals from a modern time plague site in France.
Frequency of lipoprotein(a) testing and its levels in Pakistani population
Authors: Batool Hijab , Khan Madeeha , Ain Quratul , Chughtai Omar R. , Khan Muhammad D. , Khan Mohammad I. , Sadiq Fouzia
Published: February 2024

Background

Lipoprotein(a) [Lp(a)] is a highly atherogenic particle identified as an independent risk factor for the development of atherosclerotic cardiovascular disease (ASCVD). This study aimed to investigate the frequency of Lp(a) testing and incidence of elevated Lp(a) in the Pakistani population.

Methods

For this observational study, Lp(a) and lipid profile data from five years (June 2015 to October 2020) were acquired from the electronic patient records of a diagnostic laboratory (Chughtai Laboratories, Lahore). The association of age, total cholesterol (TC), high-density lipoprotein (HDL), low-density lipoprotein cholesterol (LDL-C), non-HDL, and triglyceride (TG) levels with two thresholds for Lp(a), that is, <30 mg/dL and ≥30 mg/dL, was calculated using the Kruskal Wallis test, while the association between Lp(a) levels and lipid variables was calculated using Spearman correlation.

Results

For five years, 1060 tests were conducted, averaging 212 tests per year. Of these tests, 37.2% showed Lp(a) levels above 30 mg/dL. There were no significant differences observed in the results between males and females. However, younger individuals displayed significantly higher Lp(a) levels. Additionally, there was only a weak correlation between Lp(a) levels and other lipid variables.

Conclusion

Despite being recognized as a risk factor for ASCVD in the Pakistani population, only a small proportion of the large population had their Lp(a) tested. Moreover, a significant proportion of the population lies above the threshold.
Use of a Continuous Single Lead Electrocardiogram Analytic to Predict Patient Deterioration Requiring Rapid Response Team Activation
Authors: Lee Sooin , Benson Bryce , Belle Ashwin , Medlin Richard P. , Jerkins David , Goss Foster , Khanna Ashish K. , DeVita Michael A. , Ward Kevin R.
Published: February 2024

Identifying the onset of patient deterioration is challenging despite the potential to respond to patients earlier with better vital sign monitoring and rapid response team (RRT) activation. In this study an ECG based software as a medical device, the Analytic for Hemodynamic Instability Predictive Index (AHI-PI), was compared to the vital signs of heart rate, blood pressure, and respiratory rate, evaluating how early it indicated risk before an RRT activation. A higher proportion of the events had risk indication by AHI-PI (92.71%) than by vital signs (41.67%). AHI-PI indicated risk early, with an average of over a day before RRT events. In events whose risks were indicated by both AHI-PI and vital signs, AHI-PI demonstrated earlier recognition of deterioration compared to vital signs. A case-control study showed that situations requiring RRTs were more likely to have AHI-PI risk indication than those that did not. The study derived several insights in support of AHI-PI’s efficacy as a clinical decision support system. The findings demonstrated AHI-PI’s potential to serve as a reliable predictor of future RRT events. It could potentially help clinicians recognize early clinical deterioration and respond to those unnoticed by vital signs, thereby helping clinicians improve clinical outcomes.

Author Summary

Recognizing patient deterioration remains challenging even for experienced clinicians and nurses. RRTs can help mobilize resources to respond to patients earlier. However, determining when to activate RRTs is difficult. We retrospectively evaluated a software as a medical device, AHI-PI, compared the vital signs of heart rate, blood pressure, and respiratory rate to understand if AHI-PI could provide an earlier indicator of patient deterioration than vital signs. Our findings demonstrated AHI-PI’s potential to serve as a reliable predictor of future RRT events, before vital sign changes occur. This could potentially help clinicians recognize patients at risk for clinical deterioration and improve clinical outcomes through early targeted therapy or interventions.
Myocardial-derived small extracellular vesicles spontaneously released from living myocardial slices under biomimetic culture conditions regulate contractility and cardiac remodelling
Authors: Nicastro L. , Lal A. , Kyriakou A. , Kholia S. , Toldra R. Nunez , Downing B. , Kermani F. , Anwar M. , Martino F. , Chokron D. , Sarathchandra P. , Sarkar M. , Emanueli C. , Terracciano C.M.
Published: February 2024

BACKGROUND

Small extracellular vesicles (sEVs) released in the cardiac microenvironment are reported to regulate cardiac remodelling, partially via microRNA transfer. Harvesting sEVs produced exclusively from the myocardium remains challenging and a solid research platform for sEV cardiovascular testing needs to be established. Organotypic living myocardial slices (LMS) allow to mimic cardiac disease and to record electrophysiological responses to biological and pharmacological stimuli. This study aims at understanding how cardiac sEVs obtained from donor and failing human LMS and rat LMS under physiological or heart failure-mimicking conditions impact myocardial function and remodelling.

METHODS & RESULTS

Human LMS were obtained from the left ventricle (LV) of human donor non-failing and end-stage failing hearts and cultured at 2.2 µm sarcomere length (SL). Rat LV LMS from healthy Sprague-Dawley rats were cultured at a preload of 2.2 or 2.4 µm SL, to recapitulate physiological load and overload, respectively. Following 48-hours biomimetic culture, sEVs were isolated from the culture media by size exclusion chromatography and characterized for their size, concentration, and expression of exosome markers. LMS from human failing hearts presented impaired contractility (P<0.05 vs donor-LMS), which was improved by application of donor heart-derived sEVs at 15 and 20% stretch. Whilst rat overloaded sEVs did not alter the force production of physiological LMS, physiological sEVs significantly increased the active force and decreased their passive force. In rat LMS, 1×108physiological EVs/slice restored the contractility of overloaded slices, reduced apoptosis, fibrosis-related gene expression and promoted angiogenesis. microRNAs analysis showed significant upregulation of miR-23a-3p and miR-378a-3p in rat physiological sEVs. Finally, to test whether sEVs have a direct effect on cardiomyocytes, we applied sEVs on cultured induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). sEVs did not affect the contractility of iPSC-CM monoculture but increased the contractility of iPSC-CM co-cultured with human microvasculature endothelial cells (MVECs).

CONCLUSIONS

Cardiac sEVs isolated from healthy hearts increase the contractility of failing LMS. This effect is associated with, and possibly brought about by, a combination of inhibition of apoptosis, reduction of fibrosis and increased microvascular density, and could involve the transfer of sEV-microRNA into myocardial cells. Our data support the hypothesis that the sEV inotropic action is mediated by endothelial cells.
Real-time Imaging of Decompression Gas Bubble Growth in the Spinal Cord of Live Rats
Authors: Alvarado Roman , Scheven Ulrich M. , Meiners J.-C.
Published: February 2024

1)

Structured Abstract

Purpose

To observe the growth and resolution of decompression gas bubbles in the spinal cord of live rats in real time using magnetic resonance imaging (MRI).

Methods

We constructed an MRI-compatible pressure chamber system to visualize gas bubble dynamics in deep tissues in real time. The system pressurizes and depressurizes rodents inside an MRI scanner and monitors their respiratory rate, heart rate, and body temperature while providing gaseous anesthesia under pressure during the experiments.

Results

We observed the formation of decompression gas bubbles in the spinal cord of rats after compression to 7.1 bar absolute and rapid decompression inside the MRI scanner while maintaining continuous gaseous anesthesia and vital monitoring.

Conclusion

We have shown the direct observation of decompression gas bubble formation in real time by MRI in live, anesthetized rats.
Ubiquity of inverted ’gelatinous’ ecosystem pyramids in the global ocean
Authors: Fabien Lombard , Lionel Guidi , Brandão Manoela C. , Pedro Coelho Luis , Sébastien Colin , Richard Dolan John , Amanda Elineau , Gasol Josep M , Luc Grondin Pierre , Nicolas Henry , Ibarbalz Federico M , Laëtitia Jalabert , Michel Loreau , Séverinne Martini , Zoé Mériguet , Marc Picheral , Pierella Karlusich Juan José , Pepperkok Rainer , Jean-Baptiste Romagnan , Lucie Zinger ,   Tara Oceans Coordinators, Lars Stemmann , Acinas Silvia G , Lee Karp-Boss , Emmanuel Boss , Sullivan Matthew B. , de Vargas Colomban , Chris Bowler , Eric Karsenti , Gabriel Gorsky
Published: February 2024

Summary paragraph

Plankton are essential in marine ecosystems. However, our knowledge of overall community structure is sparse due to inconsistent sampling across their very large organismal size range. Here we use diverse imaging methods to establish complete plankton inventories of organisms spanning five orders of magnitude in size. Plankton community size and trophic structure variation validate a long-held theoretical link between organism size-spectra and ecosystem trophic structures. We found that predator/grazer biomass and biovolume unexpectedly exceed that of primary producers at most (55%) locations, likely due to our better quantification of gelatinous organisms. Bottom- heavy ecosystems (the norm on land) appear to be rare in the ocean. Collectively, gelatinous organisms represent 30% of the total biovolume (8-9% of carbon) of marine plankton communities from tropical to polar ecosystems. Communities can be split into three extreme typologies: diatom/copepod-dominated in eutrophic blooms, rhizarian/chaetognath-dominated in oligotrophic tropical oceans, and gelatinous-dominated elsewhere. While plankton taxonomic composition changes with latitude, functional and trophic structures mostly depend on the amount of prey available for each trophic level. Given future projections of oligotrophication of marine ecosystems, our findings suggest that rhizarian and gelatinous organisms will increasingly dominate the apex position of planktonic ecosystems, leading to significant changes in the ocean’s carbon cycle.
Olive mill solid waste induces beneficial mushroom-specialized metabolite diversity revealed by computational metabolomics strategies
Authors: Khatib Soliman , Pereman Idan , Kostanda Elizabeth , Zdouc Mitja M. , Ezov Nirit , Schweitzer Ron , van der Hooft Justin J. J.
Published: February 2024

Introduction

Mushrooms contain besides proteins a diverse pallet of specialized metabolites bioactive in either beneficial or harmful manner. Therefore, mushrooms have been exploited by humans for centuries for dietary or medical purposes. For example, the edible and medicinal mushroomsHericium erinaceusandPleurotus eryngiiare grown commercially around the world. In nature,H. erinaceusgrows on old or dead tree trunks, andP. eryngiigrows on Apiaceae plant roots, whereas in cultivation, they grow on substrates mainly consisting of dry wood chips, straw, and cereals. To make their farming more sustainable, supplements such as olive mill solid waste (OMSW) have been added to support mushroom development. However, so far, the impact of substrate additives on the edible mushroom metabolic content has not been assessed.

Methods

Here, we examined the effect of different proportions of OMSW added to the substrate on the metabolic profiles of the fruiting body (FB) and mycelium ofH. erinaceusandP. eryngiimushrooms. We used computational metabolomics strategies including GNPS molecular networking, MS2Query, and the FERMO dashboard, to organize, annotate, and prioritize metabolite features from the untargeted Q-Exactive Plus HR-LC-MS/MS metabolomics data. Following chromatography-based fractionation, the metabolite annotation of four metabolite features was further validated or fine-tuned using1H-NMR, to resolve structural isomers.

Results & Discussion

Our computational metabolomics strategies showed several annotated metabolite features to be affected by OSMW concentration. In general, the methanolic extracts ofH. erinaceusFB and mycelium were more highly enriched with specialized metabolites than those ofP. eryngii. Interestingly, OMSW increased several hericenone analogues in theH. erinaceusFB, to which beneficial properties, such as anti-inflammatory, anticancer and neuroprotective properties are assigned, as well as several erinacerin metabolites from the mycelium. In addition, high concentrations of OMSW decreased the toxic enniatin metabolite abundance. In conclusion, we demonstrate how a change in substrate composition affects the mushroom’s specialized metabolome and can induce beneficial mushroom metabolite diversity. These results highlight the importance of including computational metabolomic strategies to investigate new sustainable growth options for edible mushrooms and other natural foods.
Regulation of IFNγ production by ZFP36L2 in T cells is context-dependent
Authors: Zandhuis Nordin D. , Guislain Aurélie , Popalzij Abeera , Engels Sander , Popović Branka , Turner Martin , Wolkers Monika C.
Published: February 2024

CD8+T cells kill target cells by releasing cytotoxic molecules and pro-inflammatory cytokines, such as TNF and IFNγ. The magnitude and duration of cytokine production is defined by post-transcriptional regulation, and a critical regulator herein are RNA-binding proteins (RBPs). Although the functional importance of RBPs in regulating cytokine production is established, the kinetics and mode of action through which RBPs control cytokine production is not well understood. Previously, we showed that the RBP ZFP36L2 blocks translation of pre-formed cytokine encoding mRNA in quiescent memory T cells. Here, we uncover that ZFP36L2 regulates cytokine production in a context-dependent manner. T cell-specific deletion of ZFP36L2 (CD4-cre) had no effect on T cell development, or on cytokine production during early time points (2-6h) of T cell activation. In contrast, ZFP36L2 specifically dampened the production of IFNγ during prolonged T cell activation (20-48h). ZFP36L2 deficiency also resulted in increased production of IFNγ production in tumour-infiltrating T cells that are chronically exposed to antigen. Mechanistically, ZFP36L2 regulates IFNγ production at late time points of activation by destabilizingIfngmRNA in an AU-rich element-dependent manner. Together, our results reveal that ZFP36L2 employs different regulatory nodules in effector and memory T cells to regulate cytokine production.
Synthesis and Biological Evaluation of Novel MB327 Analogs as Resensitizers for Desensitized Nicotinic Acetylcholine Receptors after Intoxication with Nerve Agents
Authors: Bernauer Tamara , Nitsche Valentin , Kaiser Jesko , Gertzen Christoph G.W. , Höfner Georg , Niessen Karin V. , Seeger Thomas , Steinritz Dirk , Worek Franz , Gohlke Holger , Wanner Klaus T. , Paintner Franz F.
Published: February 2024

Poisoning with organophosphorus compounds, which can lead to a cholinergic crisis due to the inhibition of acetylcholinesterase and the subsequent accumulation of acetylcholine (ACh) in the synaptic cleft, is a serious problem for which treatment options are currently insufficient. Our approach to broadening the therapeutic spectrum is to use agents that interact directly with desensitized nicotinic acetylcholine receptors (nAChRs) in order to induce functional recovery after ACh overstimulation. Although MB327, one of the most prominent compounds investigated in this context, has already shown positive properties in terms of muscle force recovery, this compound is not suitable for use as a therapeutic agent due to its insufficient potency. By means ofin silicostudies based on our recently presented allosteric binding pocket at the nAChR, i.e. the MB327-PAM-1 binding site, three promising 4-aminopyridinium ion-substituted MB327 analogs (PTM0056, PTM0062 and PTM0063) were identified. In this study, we present the synthesis and biological evaluation of a series of new 4-aminopyridinium ion-substituted analogs of the aforementioned compounds (PTM0064-PTM0072), as well as hydroxy-substituted analogs of MB327 (PTMD90-0012 and PTMD90-0015) designed to substitute energetically unfavorable water clusters identified during molecular dynamics simulations. The compounds were characterized in terms of their binding affinity towards the aforementioned binding site by applying the UNC0642 MS Binding Assays and in terms of their muscle force reactivation in rat diaphragm myography. More potent compounds were identified compared to MB327, as some of them showed a higher affinity towards MB327-PAM-1 and also a higher recovery of neuromuscular transmission at lower compound concentrations. To improve the treatment of organophosphate poisoning, direct targeting of nAChRs with appropriate compounds is a key step, and this study is an important contribution to this research.
Cell state transition analysis reveals a causal network that controls critical limb ischemia
Authors: Rukhlenko Oleksii S. , McClung Joseph M. , Tuliakova Anna , Annex Brian H. , Kholodenko Boris N.
Published: February 2024

Increased endothelial cell (EC) permeability significantly contributes to peripheral arterial disease and its severe manifestation, critical limb ischemia (CLI). CLI remains refractory to current pharmacological interventions, often requiring limb amputation and showing how limited our knowledge is about signaling pathways that control EC states. Here, we utilize a two-pronged approach, employing cell State Transition Assessment and Regulation (cSTAR) analyses to both the published knowledge (e.g., LINCS data portal) and our own transcriptomics data collected from CLI patients and healthy adult (HA) control. We identified CLI and HA transcriptomics patterns and reconstructed causal network that controls transitions between EC states associated with CLI and HA. Contrary to general belief, our study demonstrates that VEGF administration slightly promotes the CLI EC states, indicating VEGF ineffectiveness in enhancing perfusion of CLI tissue.

Based on the unveiled control network, we suggest targets whose inhibition would reverse CLI EC states closer to HA states.
Closed-loop electrical stimulation to prevent focal epilepsy progression and long-term memory impairment
Authors: Ferrero Jose J. , Hassan Ahnaf R. , Yu Zelin , Zhao Zifang , Ma Liang , Wu Cynthia , Shao Shan , Kawano Takeshi , Engel Judah , Doyle Werner , Devinsky Orrin , Khodagholy Dion , Gelinas Jennifer N.
Published: February 2024

Interictal epileptiform discharges (IEDs) are ubiquitously expressed in epileptic networks and disrupt cognitive functions. It is unclear whether addressing IED-induced dysfunction could improve epilepsy outcomes as most therapeutics target seizures. We show in a model of progressive hippocampal epilepsy that IEDs produce pathological oscillatory coupling which is associated with prolonged, hypersynchronous neural spiking in synaptically connected cortex and expands the brain territory capable of generating IEDs. A similar relationship between IED-mediated oscillatory coupling and temporal organization of IEDs across brain regions was identified in human subjects with refractory focal epilepsy. Spatiotemporally targeted closed-loop electrical stimulation triggered on hippocampal IED occurrence eliminated the abnormal cortical activity patterns, preventing spread of the epileptic network and ameliorating long-term spatial memory deficits in rodents. These findings suggest that stimulation-based network interventions that normalize interictal dynamics may be an effective treatment of epilepsy and its comorbidities, with a low barrier to clinical translation.

One-Sentence Summary

Targeted closed-loop electrical stimulation prevents spread of the epileptic network and ameliorates long-term spatial memory deficits.
Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex
Authors: Huuki-Myers Louise A. , Montgomery Kelsey D. , Kwon Sang Ho , Cinquemani Sophia , Eagles Nicholas J. , Gonzalez-Padilla Daianna , Maden Sean K. , Kleinman Joel E. , Hyde Thomas M. , Hicks Stephanie C. , Maynard Kristen R. , Collado-Torres Leonardo
Published: February 2024

Background

Cellular deconvolution of bulk RNA-sequencing (RNA-seq) data using single cell or nuclei RNA-seq (sc/snRNA-seq) reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as human brain. Computational methods for deconvolution have been developed and benchmarked against simulated data, pseudobulked sc/snRNA-seq data, or immunohistochemistry reference data. A major limitation in developing improved deconvolution algorithms has been the lack of integrated datasets with orthogonal measurements of gene expression and estimates of cell type proportions on the same tissue sample. Deconvolution algorithm performance has not yet been evaluated across different RNA extraction methods (cytosolic, nuclear, or whole cell RNA), different library preparation types (mRNA enrichment vs. ribosomal RNA depletion), or with matched single cell reference datasets.

Results

A rich multi-assay dataset was generated in postmortem human dorsolateral prefrontal cortex (DLPFC) from 22 tissue blocks. Assays included spatially-resolved transcriptomics, snRNA-seq, bulk RNA-seq (across six library/extraction RNA-seq combinations), and RNAScope/Immunofluorescence (RNAScope/IF) for six broad cell types. TheMean Ratiomethod, implemented in theDeconvoBuddiesR package, was developed for selecting cell type marker genes. Six computational deconvolution algorithms were evaluated in DLPFC and predicted cell type proportions were compared to orthogonal RNAScope/IF measurements.

Conclusions

Bisqueandhspewere the most accurate methods, were robust to differences in RNA library types and extractions. This multi-assay dataset showed that cell size differences, marker genes differentially quantified across RNA libraries, and cell composition variability in reference snRNA-seq impact the accuracy of current deconvolution methods.
Genome-wide Nucleosome Positioning and Associated Features uncovered with Interpretable Deep Residual Networks
Authors: Masoudi-Sobhanzadeh Yosef , Li Shuxiang , Peng Yunhui , Panchenko Anna R
Published: February 2024

Nucleosomes represent elementary building units of eukaryotic chromosomes and consist of DNA wrapped around a histone octamer flanked by linker DNA segments. Nucleosomes are central in epigenetic pathways and their genomic positioning is associated with regulation of gene expression, DNA replication, DNA methylation and DNA repair, among other functions. Building on prior discoveries, that DNA sequences noticeably affect nucleosome positioning, our objective is to identify nucleosome positions and related features across entire genome. Here we introduce an interpretable framework based on the concepts of deep residual networks (NuPose). Trained on high-coverage human experimental MNase-seq data, NuPose is able to learn sequence and structural patterns and their dependencies associated with nucleosome organization in human genome. NuPoSe can be used to identify nucleosomal regions, not covered by experiments, and be applied to unseen data from different organisms and cell types. Our findings point to 43 informative DNA sequence features, most of them constitute tri-nucleotides, di-nucleotides and one tetra-nucleotide. Most features are significantly associated with the structural characteristics, namely, periodicity of nucleosomal DNA and its location with respect to a histone octamer. Importantly, we show that linker DNA features contribute ∼10% to the quality of the prediction model, which together with comprehensive training sets, deep-learning architecture and feature selection may explain the advanced performance of NuPose of 80-89% accuracy.
Determination of Absolute Intramolecular Distances in Proteins by Anomalous X-ray Scattering Interferometry
Authors: Stubhan Samuel , Baptist Anna V. , Körösy Caroline , Narducci Alessandra , Moya Muñoz Gustavo Gabriel , Wendler Nicolas , Lak Aidin , Sztucki Michael , Cordes Thorben , Lipfert Jan
Published: February 2024

Biomolecular structures are typically determined using frozen or crystalline samples. Measurement of intramolecular distances in solution can provide additional insights into conformational heterogeneity and dynamics of biological macromolecules and their complexes. The established molecular ruler techniques used for this (NMR, FRET, and EPR) are, however, limited in their dynamic range and require model assumptions to determine absolute distance (distributions). Here, we introduce anomalous X-ray scattering interferometry (AXSI) for intramolecular distance measurements in proteins, which are labeled at two sites with small gold nanoparticles of 0.7 nm radius. We apply AXSI to two different cysteine-variants of maltose binding protein in the presence and absence of its ligand maltose and find distances in quantitative agreement with single-molecule FRET experiments. Our study shows that AXSI enables determination of absolute intramolecular distance distributions under virtually arbitrary solution conditions and we anticipate its broad use to characterize protein conformational ensembles and dynamics.
Medulloblastoma oncogene aberrations are not involved in tumor initiation, but essential for disease progression and therapy resistance
Authors: Okonechnikov Konstantin , Joshi Piyush , Körber Verena , Rademacher Anne , Bortolomeazzi Michele , Mallm Jan-Philipp , da Silva Patricia Benites Goncalves , Statz Britta , Sepp Mari , Sarropoulos Ioannis , Yamada-Saito Tetsuya , Vaillant Jan , Wittmann Andrea , Schramm Kathrin , Blattner-Johnson Mirjam , Fiesel Petra , Jones Barbara , Milde Till , Pajtler Kristian , van Tilburg Cornelis M. , Witt Olaf , Bochennek Konrad , Weber Katharina Johanna , Nonnenmacher Lisa , Reimann Christian , Schüller Ulrich , Mynarek Martin , Rutkowski Stefan , Jones David T.W. , Korshunov Andrey , Rippe Karsten , Westermann Frank , Thongjuea Supat , Höfer Thomas , Kaessmann Henrik , Kutscher Lena M. , Pfister Stefan M.
Published: February 2024

Despite recent advances in understanding disease biology, treatment of Group 3/4 medulloblastoma remains a therapeutic challenge in pediatric neuro-oncology. Bulk-omics approaches have identified considerable intertumoral heterogeneity in Group 3/4 medulloblastoma, including the presence of clear single-gene oncogenic drivers in only a subset of cases, whereas in the majority of cases, large-scale copy-number aberrations prevail. However, intratumoral heterogeneity, the role of oncogene aberrations, and broad CNVs in tumor evolution and treatment resistance remain poorly understood. To dissect this interplay, we used single-cell technologies (snRNA-seq, snATAC-seq, spatial transcriptomics) on a cohort of Group 3/4 medulloblastoma with known alterations in the oncogenesMYC, MYCN, andPRDM6. We show that large-scale chromosomal aberrations are early tumor initiating events, while the single-gene oncogenic events arise late and are typically sub-clonal, butMYCcan become clonal upon disease progression to drive further tumor development and therapy resistance. We identify that the subclones are mostly interspersed across tumor tissue using spatial transcriptomics, but clear segregation is also present. Using a population genetics model, we estimate medulloblastoma initiation in the cerebellar unipolar brush cell-lineage starting from the first gestational trimester. Our findings demonstrate how single-cell technologies can be applied for early detection and diagnosis of this fatal disease.
A long non-coding RNA at thecortexlocus controls adaptive colouration in butterflies
Authors: Livraghi Luca , Hanly Joseph J. , Evans Elizabeth , Wright Charlotte J. , Loh Ling S. , Mazo-Vargas Anyi , Kamrava Kiana , Carter Alexander , van der Heijden Eva S.M. , Reed Robert D. , Papa Riccardo , Jiggins Chris D. , Martin Arnaud
Published: February 2024

Evolutionary variation in the wing pigmentation of butterflies and moths offers striking examples of adaptation by crypsis and mimicry. Thecortexlocus has been independently mapped as the locus controlling colour polymorphisms in 14 lepidopteran species, suggesting it acts as a genomic hotspot for the diversification of wing patterns, but functional validation through protein-coding knockouts has proven difficult to obtain. Our study unveils the role of a novel long non-coding RNA (lncRNA) which we nameivory, transcribed from thecortexlocus, in modulating colour patterning in butterflies. Strikingly,ivoryexpression prefigures most melanic patterns during pupal development, suggesting an early developmental role in specifying scale identity. To test this, we generated CRISPR mosaic knock-outs in five nymphalid butterfly species and show thativorymutagenesis yields transformations of dark pigmented scales into white or light-coloured scales. Genotyping ofVanessa carduigermline mutants associates these phenotypes to small on-target deletions at the conserved first exon ofivory. In contrast,cortexgermline mutant butterflies with confirmed null alleles lack any wing phenotype, and exclude a colour patterning role for this adjacent gene. Overall, these results show that a lncRNA acts as a master switch of colour pattern specification, and played key roles in the adaptive diversification of colour patterns in butterflies.

Significance statement

Deciphering the genetic underpinnings of adaptive variation is fundamental for a comprehensive understanding of evolutionary processes. Long non-coding RNAs (lncRNAs) represent an emerging category of genetic modulators within the genome, yet they have been overlooked as a source of phenotypic diversity. In this study, we unveil the pivotal role of a lncRNA in orchestrating colour transitions between dark and light patterns during butterfly wing development. Remarkably, this lncRNA gene is nested within thecortexlocus, a genetic region known to control multiple cases of adaptive variation in butterflies and moths, including iconic examples of natural selection. These findings highlight the significant influence of lncRNAs in developmental regulation, and also underscore their potential as key genetic players in the evolutionary process itself.
Chondroitin sulfate glycan sulfation patterns influence histochemical labeling of perineuronal nets: a comparative study of interregional distribution in human and mouse brain
Authors: Belliveau Claudia , Théberge Stéphanie , Netto Stefanie , Rahimian Reza , Fakhfouri Gohar , Hosdey Clémentine , Davoli Maria Antonietta , Hendrickson Aarun , Hao Kathryn , Giros Bruno , Turecki Gustavo , Alonge Kimberly M. , Mechawar Naguib
Published: February 2024

Perineuronal nets (PNNs) are a condensed subtype of extracellular matrix that form a net-like coverings around certain neurons in the brain. PNNs are primarily composed of chondroitin sulfate (CS) proteoglycans from the lectican family that consist of CS-glycosaminoglycan (CS-GAG) side chains attached to a core protein. CS disaccharides can exist in various isoforms with different sulfation patterns. Literature suggests that CS disaccharide sulfation patterns can influence the function of PNNs as well as their labeling. This study was conducted to characterize such interregional CS disaccharide sulfation pattern differences in adult human (N = 81) and mouse (N = 19) brains. Liquid chromatography tandem mass spectrometry was used to quantify five different CS disaccharide sulfation patterns, which were then compared to immunolabeling of PNNs usingWisteria Floribunda Lectin(WFL) to identify CS-GAGs and anti-aggrecan to identify CS proteoglycans. In healthy brains, significant regional and species-specific differences in CS disaccharide sulfation and single versus double-labeling pattern were identified. A secondary analysis to investigate how early-life stress (ELS) impacts these PNN features discovered that although ELS increases WFL+ PNN density, the CS-GAG sulfation code and single versus double PNN-labeling distributions remained unaffected in both species. These results underscore PNN complexity in traditional research, emphasizing the need to consider their heterogeneity in future experiments.
Increased excitability of dentate gyrus mossy cells occurs early in life in the Tg2576 model of Alzheimer’s disease
Authors: Alcantara-Gonzalez David , Kennedy Meghan , Criscuolo Chiara , Botterill Justin , Scharfman Helen E
Published: February 2024

INTRODUCTION

Hyperexcitability in Alzheimer’s disease (AD) emerge early and contribute to disease progression. The dentate gyrus (DG) is implicated in hyperexcitability in AD. We hypothesized that mossy cells (MCs), regulators of DG excitability, contribute to early hyperexcitability in AD. Indeed, MCs generate hyperexcitability in epilepsy.

METHODS

Using the Tg2576 model and WT mice (∼1month-old), we compared MCs electrophysiologically, assessed c-Fos activity marker, Aβ expression and mice performance in a hippocampal-dependent memory task.

RESULTS

Tg2576 MCs exhibit increased spontaneous excitatory events and decreased inhibitory currents, increasing the charge transfer excitation/inhibition ratio. Tg2576 MC intrinsic excitability was enhanced, and showed higher c-Fos, intracellular Aβ expression, and axon sprouting. Granule cells only showed changes in synaptic properties, without intrinsic changes. The effects occurred before a memory task is affected.

DISCUSSION

Early electrophysiological and morphological alterations in Tg2576 MCs are consistent with enhanced excitability, suggesting an early role in DG hyperexcitability and AD pathophysiology.

HIGHLIGHTS

∘

MCs from 1 month-old Tg2576 mice had increased spontaneous excitatory synaptic input.

∘

Tg2576 MCs had reduced spontaneous inhibitory synaptic input.

∘

Several intrinsic properties were abnormal in Tg2576 MCs.

∘

Tg2576 GCs had enhanced synaptic excitation but no changes in intrinsic properties.

∘

Tg2576 MCs exhibited high c-Fos expression, soluble Aβ and axonal sprouting.
Inferring Metabolic Objectives and Tradeoffs in Single Cells During Embryogenesis
Authors: Lin Da-Wei , Zhang Ling , Zhang Jin , Chandrasekaran Sriram
Published: February 2024

While proliferating cells optimize their metabolism to produce biomass, the metabolic objectives of cells that perform non-proliferative tasks are unclear. The opposing requirements for optimizing each objective results in a trade-off that forces single cells to prioritize their metabolic needs and optimally allocate limited resources. To define metabolic objectives and tradeoffs in biological systems mathematically, we integrated bulk and single-cell omics data with a novel framework to infer cell objectives using metabolic modeling and machine learning. We validated this framework by identifying essential genes from CRISPR-Cas9 screens in embryonic stem cells, and by inferring the metabolic objectives of quiescent cells and during different cell-cycle phases. Applying this to embryonic cell states, we observed a decrease in metabolic entropy upon development. We further uncovered a trade-off between glutathione and biosynthetic precursors in 1-cell zygote, 2-cell embryo, and blastocyst cells, potentially representing a trade-off between pluripotency and proliferation.
British Oncology Pharmacy Association Delphi Consensus Guidelines: co-infusion of trometamol-containing calcium folinate (Leucovorin) with Systemic Anti-Cancer Treatments
Authors: Polwart Calum , Root Tim , Tezcan Songül , Meehan Sharon , Wetherill Bill , Waterson Chloë , Burnett Bruce , Chauhan Rena , Al-Modaris Ibrahim , Walters-Davies Rhiannon
Published: February 2024

Drug stability and compatibility are critical factors influencing cost and logistics of treatment delivery, therapeutic effectiveness, and patient safety. This is particularly significant in the realm of cancer chemotherapeutics, where stability and compatibility studies play a vital role in ensuring rational and safe medicine administration. Oxaliplatin, fluorouracil, and irinotecan, commonly used in various combination for gastrointestinal cancers, are complemented by co-administration of folinic acid in certain protocols. Notably, some folinic acid preparations include trometamol as an excipient, potentially impacting the stability of the chemotherapeutic agentsif infused concomitantly. This study seeks to establish guidelines for oncology multidisciplinary teams, addressing potential risks associated with the combination of trometamol-containing folinic acid and chemotherapeutics. To achieve this, a quantitative questionnaire was distributed to members of the British Oncology Pharmacy Association (BOPA) and non-BOPA members through an online survey. Nineteen healthcare professionals with oncology experience, comprising 18 pharmacists and 1 nurse, completed the questionnaires. Each participant rated the validity and clarity of statements on a 5-point scale. The Delphi process concluded after the fourth round, consolidating the findings and recommendations from the multidisciplinary team. Twelve recommendations for safe practice have been made.
Clinical prediction model performance in differentiating septic arthritis from transient synovitis: A multi-center study
Authors: Qiu Xin , Deng Han-Sheng , Tang Gen , Su Yu-Xi , Chen Xiao-Liang , Liu Yao-Xi , Li Jing-Chun , Wu Xin-Wu , Guo Jia-Chao , Jiang Fei , Su Qi-Ru , Tang Sheng-Ping , Xiong Zhu ,   Chinese Multi-center Pediatric Orthopedic Study Group (CMPOS)
Published: February 2024

Objective

Differentiating septic arthritis from transient synovitis in children is challenging. This study aimed to determine the diagnostic value for distinguishing these two conditions and to develop an effective clinical prediction model based on multi-center clinical data.

Methods

We retrospectively analyzed data of children aged under 18 years who were hospitalized in eight specialized children’s hospitals in China from 2013 to 2021. To ensure the prediction model’s reliability, we established three clinical prediction models.

Results

This study collected data of 819 children from 8 tertiary children’s hospitals, including 265 patients with septic arthritis and 554 patients with transient synovitis.

We established three clinical prediction models. For septic hip arthritis, a retrospective study based on six clinical predictors was a history of prodromal respiratory tract infection (HRTI), temperature>37.5 °C, ESR>20 mm/h, CRP>10 mg/L, red blood cell distribution width (RDW)>50%, and WBC>11×109 /L. When these six factors were present, the probability of septic hip arthritis was 99.99%.

For septic knee arthritis, a retrospective study based on three clinical predictors, the predictors were ESR>20 mm/h, CRP>10 mg/L, and absolute monocyte count (AMONO)>0.74×109/L. When these three factors were present, the probability of having septic knee arthritis was 94.68%. For septic arthritis (septic hip arthritis or septic knee arthritis), a retrospective study based on six clinical predictors, the predictors were male children, history of HRTI), temperature>37.5 °C, ESR>20 mm/hr, PC > 407 × 109/L and CRP>10 mg/L. When these six factors were present, the probability of septic arthritis was 99.65%.

Conclusion

This study used multi-center clinical data to construct a new clinical prediction model for children with septic arthritis. In addition we identified new clinical predictors such as sex, history of HRTI, RDW, PC and AMONO.

Translational potential

A clinical prediction model, built on multi-center data, is capable of effectively making high-precision predictions for septic arthritis. Furthermore, based on the microbial characteristics of septic arthritis in children, we aim to develop diagnostic kits that can accurately and quickly detect infections caused by pathogens such as bacteria.
Improving research transparency with individualized report cards: A feasibility study in clinical trials at a large university medical center
Authors: Franzen Delwen L. , Salholz-Hillel Maia , Müller-Ohlraun Stephanie , Strech Daniel
Published: February 2024

Research transparency is crucial for ensuring the relevance, integrity, and reliability of scientific findings. However, previous work indicates room for improvement across transparency practices. The primary objective of this study was to develop an extensible tool to provide individualized feedback and guidance for improved transparency across phases of a study. Our secondary objective was to assess the feasibility of implementing this tool to improve transparency in clinical trials.

We developed study-level “report cards” that combine tailored feedback and guidance to investigators across several transparency practices, including prospective registration, availability of summary results, and open access publication. The report cards were generated through an automated pipeline for scalability. We also developed an infosheet to summarize relevant laws, guidelines, and resources relating to transparency. To assess the feasibility of using these tools to improve transparency, we conducted a single-arm intervention study at Berlin’s university medical center, the Charité – Universitätsmedizin Berlin. Investigators (n = 92) of 155 clinical trials were sent individualized report cards and the infosheet, and surveyed to assess their perceived usefulness. We also evaluated included trials for improvements in transparency following the intervention.

Survey responses indicated general appreciation for the report cards and infosheet, with a majority of participants finding them helpful to build awareness of the transparency of their trial and transparency requirements. However, improvement on transparency practices was minimal and largely limited to linking publications in registries. Investigators also commented on various challenges associated with implementing transparency, including a lack of clarity around best practices and institutional hurdles.

This study demonstrates the potential of developing and using tools, such as report cards, to provide individualized feedback at scale to investigators on the transparency of their study. While these tools were positively received by investigators, the limited improvement in transparency practices suggests that awareness alone is likely not sufficient to drive improvement. Future research and implementation efforts may adapt the tools to further practices or research areas, and explore integrated approaches that combine the report cards with incentives and institutional support to effectively strengthen transparency in research.
Caregiver ECHO: A Model for Delivering Virtual Behavior Management Education to Families of Children with Developmental Disabilities
Authors: Nevill Rose E. , Lovette Gail E. , Bateman Katherine J. , Badgett Natalie M. , Lyons Genevieve R. , Fuhrmann Emily C. , Bohac Genevieve E. , Orlando Karen G. , Page Keith D.
Published: February 2024

Children with developmental disabilities are at high risk of challenging behavior, yet their families experience consistent barriers to affordable parent education in behavior management. The present study tested the efficacy of a caregiver-focused Extensions of Community Health Outcomes program for delivering virtual parent education and support to familial caregivers of children with DD in behavior management. A pre-post quasi-experimental design was used to evaluate the effect of Caregiver ECHO on caregiver participants’ (n = 30) knowledge of behavior modification strategies, self-efficacy in managing challenging behavior, empowerment, and negative emotional reactions to challenging behavior. Participating in Caregiver ECHO resulted in significant increases in caregiver knowledge, self-efficacy, and empowerment, and significant reductions in certain negative emotional reactions to challenging behavior. The Caregiver ECHO model offers advantages over other parent education programs in that it emphasizes peer learning, active problem-solving, and community building as core components of its approach while using low-cost methodologies.
Macrolactin A Is an Inhibitor of Protein Biosynthesis in Bacteria
Authors: Vasilchenko Alexey S. , Lukyanov Dmitry A. , Dilbaryan Diana S. , Usachev Konstantin S. , Poshvina Darya V. , Nikandrova Arina A. , Imamutdinova Arina N. , Garaeva Natalia S. , Bikmullin Aydar G. , Klochkova Evelina A. , Taldaev Amir , Rusanov Alexander L. , Romashin Daniil D. , Luzgina Natalia G. , Osterman Ilya A. , Sergiev Petr V. , Teslya Anastasia V.
Published: February 2024

The macrolide antibiotic, macrolactin A (McA), has been known for its antimicrobial properties since the late 1980s, but the mechanism of its antibacterial activity is still unknown. In this study, we investigated the microbiological and molecular characteristics of McA antimicrobial activity. McA effect on bacteria was found to be both bacteriostatic and bactericidal, depending on species and strains. Regarding the mechanism of action of McA, the following important results were obtained: 1) usingin vivoandin vitrosystems, we showed that McA is an inhibitor of protein synthesis in bacteria; 2) the concentration of McA required to inhibit protein synthesis in theE. colicell-free model was found to be 50 times lower than the concentration required in theS. aureuscell-free model; 3) the toe-printing assay revealed that McA inhibits the first step of elongation stage of protein synthesis; 4) we identified single and multiple nucleotide polymorphisms in the gene encoding the translation elongation factor Tu (EF-Tu) by annotating the genomes of McA-resistantBacillus pumilusMcARand its parental strain. Molecular modeling showed that the McA molecule can form non-covalent bonds with amino acids at the interface of domains 1 and 2 of EF-Tu, characterized by a relatively high docking score. Overall, our study demonstrated that McA acts as an elfamycin-like antibiotic (targeting EF-Tu), addressing a substantial gap in our understanding of the mechanism of action of macrolactin A, a representative member of macrolides.