bluuebunny/crossref_metadata_2025 huggingface dataset:
Modulatory feedback determines attentional object segmentation in a model of the ventral stream
Authors: Papale Paolo , Williford Jonathan R. , Balk Stijn , Roelfsema Pieter R.
Published: January 2023

Studies in neuroscience inspired progress in the design of artificial neural networks (ANNs), and, vice versa, ANNs provide new insights into the functioning of brain circuits. So far, the focus has been on how ANNs can help to explain the tuning of neurons at various stages of the visual cortical hierarchy. However, the role of modulatory feedback connections, which play a role in attention and perceptual organization, has not been resolved yet. The present study presents a biologically plausible neural network that performs scene segmentation and can shift attention using modulatory feedback connections from higher to lower brain areas. The model replicates several neurophysiological signatures of recurrent processing. Specifically, figural regions elicit more activity in model units than background regions. The modulation of activity by figure and ground occurs at a delay after the first feedforward response, because it depends on a loop through the higher model areas. Importantly, the figural response enhancement is enhanced by object-based attention, which stays focused on the figural regions and does not spill over to the adjacent background, just as is observed in the visual cortex. Our results indicate how progress in artificial intelligence can be used to garner insight into the recurrent cortical processing for scene segmentation and object-based attention.

Author Summary

Recent feedforward networks in artificial intelligence provide unmatched models of tuning of neurons in the visual cortex. However, these feedforward models do not explain the influences of object-based attention and image segmentation on neuronal responses, which rely on feedback interactions between cortical regions that are not included in the feedforward networks. In particular, the role of feedback connections from higher brain regions that modulate neural activity in lower cortical regions has not yet been studied extensively so that we still lack anin silicomodel of the role of these connections. Here, we present a biologically plausible neural network that successfully performs image segmentation and can shift object-based attention using modulatory feedback connections. The model evolved representations that mirror the properties of neurons in the visual cortex, including orientation tuning, shape-selectivity, surround suppression and a sensitivity to figure-ground organization, while trained only on a segmentation task. The new model provides insight into how the perception of coherent objects can emerge from the interaction between lower and higher visual cortical areas.
Resistance to vincristine in cancerous B-cells by disruption of p53-dependent mitotic surveillance
Authors: Rovsing Anne Bruun , Thomsen Emil Aagaard , Nielsen Ian , Skov Thomas Wisbech , Luo Yonglun , Dybkær Karen , Mikkelsen Jacob Giehm
Published: January 2023

The frontline therapy R-CHOP for patients with diffuse large B-cell lymphoma (DLBCL) has remained unchanged for two decades despite numerous phase III clinical trials investigating new alternatives. Multiple large studies have uncovered genetic subtypes of DLBCL enabling a targeted approach. To further pave the way for precision oncology, we perform genome-wide CRISPR screening to uncover the cellular response to one of the components of R-CHOP, vincristine, in the DLBCL cell line SU-DHL-5. We discover important pathways and subnetworks using gene-set enrichment analysis and protein-protein interaction networks and identify genes related to mitotic spindle organization that are essential during vincristine treatment. Inhibition of KIF18A, a mediator of chromosome alignment, using the small molecule inhibitor BTB-1 causes complete cell death in a synergistic manner when administered together with vincristine. We also identify the genesKIF18BandUSP28for which CRISPR/Cas9-directed knockout induces vincristine resistance across two DLBCL cell lines. Mechanistic studies show that lack ofKIF18BorUSP28counteracts a vincristine-induced p53 response involving the mitotic surveillance pathway (USP28-53BP1-p53). Collectively, our CRISPR screening data uncover potential drug targets and mechanisms behind vincristine resistance, which may support the development of future drug regimens.

Key points

Inhibition of the mitotic surveillance pathway (USP28-53BP1-p53) and KIF18B induces resistance to vincristine

Substantial synergistic effects observed when using the KIF18A-inhibitor BTB-1 with vincristine in eradicating GCB-subtype DLBCL cells
Ferroptosis Integrates Mitochondrial Derangements and Pathological Inflammation to Promote Pulmonary Hypertension
Authors: Kazmirczak Felipe , Vogel Neal T. , Prisco Sasha Z. , Patterson Michael T. , Annis Jeffrey , Moon Ryan T. , Hartweck Lynn M , Mendelson Jenna B. , Kim Minwoo , Calixto Mancipe Natalia , Markowski Todd , Higgins LeAnn , Guerrero Candace , Kremer Ben , Blake Madelyn L. , Rhodes Christopher J. , Williams Jesse W. , Brittain Evan L. , Prins Kurt W.
Published: January 2023

Background

Mitochondrial dysfunction, characterized by impaired lipid metabolism and heightened reactive oxygen species (ROS) generation, results in lipid peroxidation and ferroptosis. Ferroptosis is an inflammatory mode of cell death that promotes complement activation and macrophage recruitment. In pulmonary arterial hypertension (PAH), pulmonary arterial endothelial cells (PAEC) exhibit cellular phenotypes that promote ferroptosis. Moreover, there is ectopic complement deposition and inflammatory macrophage accumulation in the pulmonary vasculature. However, the effects of ferroptosis inhibition on these pathogenic mechanisms and the cellular landscape of the pulmonary vasculature are incompletely defined.

Methods

Multi-omics and physiological analyses evaluated how ferroptosis inhibition modulated preclinical PAH. The impact of AAV1-mediated expression of the pro-ferroptotic protein ACSL4 on PAH was determined, and a genetic association study in humans further probed the relationship between ferroptosis and pulmonary hypertension (PH).

Results

Ferrostatin-1, a small-molecule ferroptosis inhibitor, mitigated PAH severity in monocrotaline rats. RNA-seq and proteomics analyses demonstrated ferroptosis was associated with PAH severity. RNA-seq, proteomics, and confocal microscopy revealed complement activation and pro-inflammatory cytokines/chemokines were suppressed by ferrostatin-1. Additionally, ferrostatin-1 combatted changes in endothelial, smooth muscle, and interstitial macrophage abundance and gene activation patterns as revealed by deconvolution RNA-seq. Ferroptotic PAEC damage associated molecular patterns restructured the transcriptomic signature, mitochondrial morphology, and promoted proliferation of pulmonary artery smooth muscle cells, and created a pro-inflammatory phenotype in monocytesin vitro. AAV1-Acsl4induced an inflammatory PAH phenotype in rats. Finally, single-nucleotide polymorphisms in six ferroptosis genes identified a potential link between ferroptosis and PH severity in the Vanderbilt BioVU repository.

Conclusions

Ferroptosis promotes PAH through metabolic and inflammatory mechanisms in the pulmonary vasculature.
Effects of Inbreeding on Microbial Community Diversity ofZea mays
Authors: Schultz Corey R , Johnson Matthew , Wallace Jason G
Published: January 2023

Heterosis, also known as hybrid vigor, is the basis of modern maize production. The effect of heterosis on maize phenotypes has been studied for decades, but its effect on the maize-associated microbiome is much less characterized. To determine the effect of heterosis on the maize microbiome, we sequenced and compared the bacterial communities of inbred, open pollinated, and hybrid maize. Samples covered three tissue types (Stalk, Root, and Rhizosphere) in two field experiments and one greenhouse experiment. Bacterial diversity was affected by location and tissue type, but not genetic background, for both within-sample (alpha) and between-sample (beta) diversity. PERMANOVA analysis similarly showed that tissue type and location had significant effects on the overall community structure, whereas the genetic background and individual plant genotypes did not. Differential abundance analysis identified only 18 bacterial ASVs that significantly differed between inbred and hybrid maize. Predicted metagenome content was inferred with Picrust2, and it also showed a significantly larger effect of tissue and location than genetic background. Overall, these results indicate that the bacterial communities of inbred and hybrid maize are often more similar than they are different, and that non-genetic effects are generally the largest influences on the maize microbiome.
Gut-associated lymphoid tissue attrition associates with response to anti-α4β7 therapy in ulcerative colitis
Authors: Canales-Herrerias Pablo , Uzzan Mathieu , Seki Akihiro , Czepielewski Rafael S. , Verstockt Bram , Livanos Alexandra , Raso Fiona , Dunn Alexandra , Dai Daniel , Wang Andrew , Al-taie Zainab , Martin Jerome , Ko Huaibin M. , Tokuyama Minami , Tankelevich Michael , Meringer Hadar , Cossarini Francesca , Jha Divya , Krek Azra , Paulsen John D. , Nakadar M. Zuber , Wong Joshua , Erlich Emma C. , Onufer Emily J. , Helmink Beth A. , Sharma Keshav , Rosenstein Adam , Chung Grace , Dawson Travis , Juarez Julius , Yajnik Vijay , Cerutti Andrea , Faith Jeremiah , Suarez-Farinas Mayte , Argmann Carmen , Petralia Francesca , Randolph Gwendalyn J. , Polydorides Alexandros D. , Reboldi Andrea , Colombel Jean Frederic , Mehandru Saurabh
Published: January 2023

Targeting the α4β7-MAdCAM-1 axis with vedolizumab (VDZ) is a front-line therapeutic paradigm in ulcerative colitis (UC). However, mechanism(s) of action (MOA) of VDZ remain relatively undefined. Here, we examined three distinct cohorts of patients with UC (n=83, n=60, and n=21), to determine the effect of VDZ on the mucosal and peripheral immune system. Transcriptomic studies with protein level validation were used to study drug MOA using conventional and transgenic murine models. We found a significant decrease in colonic and ileal naïve B and T cells and circulating gut-homing plasmablasts (β7+) in VDZ-treated patients, pointing to gut-associated lymphoid tissue (GALT) targeting by VDZ. Murine Peyer’s patches (PP) demonstrated a significant loss cellularity associated with reduction in follicular B cells, including a unique population of epithelium-associated B cells, following anti-α4β7 antibody (mAb) administration. Photoconvertible (KikGR) mice unequivocally demonstrated impaired cellular entry into PPs in anti-α4β7 mAb treated mice. In VDZ-treated, but not anti-tumor necrosis factor-treated UC patients, lymphoid aggregate size was significantly reduced in treatment responders compared to non-responders, with an independent validation cohort further confirming these data. GALT targeting represents a novel MOA of α4β7-targeted therapies, with major implications for this therapeutic paradigm in UC, and for the development of new therapeutic strategies.
Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes
Authors: Núñez-Carpintero Iker , O’Connor Emily , Rigau Maria , Bosio Mattia , Spendiff Sally , Azuma Yoshiteru , Topf Ana , Thompson Rachel , ’t Hoen Peter A.C. , Chamova Teodora , Tournev Ivailo , Guergueltcheva Velina , Laurie Steven , Beltran Sergi , Capella Salvador , Cirillo Davide , Lochmüller Hanns , Valencia Alfonso
Published: January 2023

Exploring the molecular basis of disease severity in rare disease scenarios is a challenging task provided the limitations on data availability. Causative genes have been described for Congenital Myasthenic Syndromes (CMS), a group of diverse minority neuromuscular junction (NMJ) disorders; yet a molecular explanation for the phenotypic severity differences remains unclear. Here, we present a workflow to explore the functional relationships between CMS causal genes and altered genes from each patient, based on multilayer network analysis of protein-protein interactions, pathways and metabolomics.

Our results show that CMS severity can be ascribed to the personalized impairment of extracellular matrix components and postsynaptic modulators of acetylcholine receptor (AChR) clustering. We explore this in more detail for one of the proteins not previously associated with the NMJ, USH2A. Loss of the zebrafish USH2A ortholog revealed some effects on early movement and gross NMJ morphology.

This work showcases how coupling multilayer network analysis with personalized -omics information provides molecular explanations to the varying severity of rare diseases; paving the way for sorting out similar cases in other rare diseases.
The effectiveness of pseudomagic traits in promoting premating isolation
Authors: Aubier Thomas G. , Bürger Reinhard , Servedio Maria R.
Published: January 2023

Upon the secondary contact of populations, speciation with gene flow is greatly facilitated when the same pleiotropic loci are both subject to divergent ecological selection and induce non-random mating, leading to loci with this fortuitous combination of functions being referred to as “magic trait” loci. We use a population genetics model to examine whether “pseudomagic trait” complexes, composed of physically linked loci fulfilling these two functions, are as efficient in promoting premating isolation as magic traits. We specifically measure the evolution of choosiness, which controls the strength of assortative mating. We show that, surprisingly, pseudomagic trait complexes, and to a lesser extent also physically unlinked loci, can lead to the evolution of considerably stronger assortative mating preferences than do magic traits, provided polymorphism at the involved loci is maintained. This is because assortative mating preferences are generally favored when there is a risk of producing maladapted recombinants, as occurs with nonmagic trait complexes but not with magic traits (since pleiotropy precludes recombination). Contrary to current belief, magic traits may not be the most effective genetic architecture for promoting strong premating isolation. Distinguishing between magic traits and pseudomagic trait complexes is therefore important when inferring their role in premating isolation. This calls for further fine-scale genomic research on speciation genes.
Graph-pMHC: Graph Neural Network Approach to MHC Class II Peptide Presentation and Antibody Immunogenicity
Authors: Thrift William John , Perera Jason , Cohen Sivan , Lounsbury Nicolas W. , Gurung Hem , Rose Chris , Chen Jieming , Jhunjhunwala Suchit , Liu Kai
Published: January 2023

Antigen presentation on MHC Class II (pMHCII presentation) plays an essential role in the adaptive immune response to extracellular pathogens and cancerous cells. But it can also reduce the efficacy of large-molecule drugs by triggering an anti-drug response. Significant progress has been made in pMHCII presentation modeling due to the collection of large-scale pMHC mass spectrometry datasets (ligandomes) and advances in deep machine learning. Here, we develop graph-pMHC, a graph neural network approach to predict pMHCII presentation. We derive adjacency matrices for pMHCII using Alphafold2-multimer, and address the peptide-MHC binding groove alignment problem with a simple graph enumeration strategy. We demonstrate that graph-pMHC dramatically outperforms methods with suboptimal inductive biases, such as the multilayer-perceptron-based NetMHCIIan-4.0 (+22.84% average precision). Finally, we create an antibody drug immunogenicity dataset from clinical trial data, and develop a method for measuring anti-antibody immunogenicity risk using pMHCII presentation models. In comparison with BioPhi’s Sapiens score, a deep learning based measure of the humanness of an antibody drug, our strategy achieves a 7.14% ROC AUC improvement in predicting antibody drug immunogenicity.
The mechanics of cephalic furrow formation in theDrosophilaembryo
Authors: Niloy Redowan A. , Holcomb Michael C. , Thomas Jeffrey H. , Blawzdziewicz Jerzy
Published: January 2023

Cephalic furrow formation (CFF) is a major morphogenetic movement during gastrulation inDrosophila melanogasterembryos that gives rise to a deep, transitory epithelial invagination. Recent studies have identified the individual cell shape changes that drive the initiation and progression phases of CFF; however, the underlying mechanics of these changes are not yet well understood. During the progression phase, the furrow deepens as columnar cells from both the anterior and posterior directions fold inwards rotating by 90°. To analyze the mechanics of this process, we have developed an advanced 2D vertex model, which introduces multi-node representation of cellular membranes and allows us to capture the membrane curvature associated with pressure variation. Our investigations reveal some key mechanical features of CFF. As cells begin to roll over the cephalic furrow cleft, they become wedge-shaped as their apical cortices and overlying membranes expand, lateral cortices and overlying membranes release tension, internal pressures drop, and basal cortices and membranes contract. Cells then reverse the process by shortening apical cortices and membranes, increasing lateral tension, and causing internal pressures to rise. Since the basal membranes expand, the cells recover a rotated columnar shape at the end of this process. Interestingly, our findings indicate that the basal membranes may be passively reactive throughout the progression phase. We also find that the smooth rolling of cells over the cephalic furrow cleft necessitates that internalized cells provide a solid base through high membrane tensions and internal pressure levels, which allows transmission of tensile force that pulls new cells into the furrow. These results lead us to suggest that CFF may help establish a baseline tension across the apical surface of the embryo that would facilitate cellular coordination of other morphogenetic movements via mechanical stress feedback mechanisms.

SIGNIFICANCE

Mechanical forces and stress feedback are essential for the development of morphology and structure in the embryo. Although great progress has been made in understanding the genetic control of patterning and cell fate, mechanical stress contributions are not as well understood. Mechanical analyses of the apical constrictions initiating ventral furrow formation and subsequent invagination dynamics inDrosophilahave shed considerable light on these processes; however, ventral furrow formation is only one of many morphogenetic movements. Cephalic furrow formation occurs simultaneously with ventral furrow formation, but its cell shape changes and invagination dynamics are radically different. This study shows that mechanical forces and feedback operating in cephalic furrow formation also differ considerably from those in ventral furrow, demonstrating a potentially wide array of mechanical processes in morphogenesis.
TCF4 mutations disrupt synaptic function through dysregulation of RIMBP2 in patient-derived cortical neurons
Authors: Davis Brittany A. , Chen Huei-Ying , Ye Zengyou , Ostlund Isaac , Tippani Madhavi , Das Debamitra , Sripathy Srinidhi Rao , Wang Yanhong , Martin Jacqueline M. , Shim Gina , Panchwagh Neel M. , Moses Rebecca L. , Farinelli Federica , Bohlen Joseph F. , Li Meijie , Luikart Bryan W. , Jaffe Andrew E. , Maher Brady J.
Published: January 2023

Genetic variation in the transcription factor 4 (TCF4)gene is associated with risk for a variety of developmental and psychiatric conditions, which includes a syndromic form of ASD called Pitt Hopkins Syndrome (PTHS).TCF4encodes an activity-dependent transcription factor that is highly expressed during cortical development and in animal models is shown to regulate various aspects of neuronal development and function. However, our understanding of how disease-causing mutations in TCF4 confer pathophysiology in a human context is lacking. Here we show that cortical neurons derived from patients withTCF4mutations have deficits in spontaneous synaptic transmission, network excitability and homeostatic plasticity. Transcriptomic analysis indicates these phenotypes result from altered expression of genes involved in presynaptic neurotransmission and identifies the presynaptic binding protein, RIMBP2 as the most differentially expressed gene in PTHS neurons. Remarkably, TCF4-dependent deficits in spontaneous synaptic transmission and network excitability were rescued by increasing RIMBP2 expression in presynaptic neurons. Together, these results identify TCF4 as a critical transcriptional regulator of human synaptic development and plasticity and specifically identifies dysregulation of presynaptic function as an early pathophysiology in PTHS.
Novel genetically encoded tools for imaging or silencing neuropeptide release from presynaptic terminalsin vivo
Authors: Kim Dong-Il , Park Sekun , Ye Mao , Chen Jane Y. , Jhang Jinho , Hunker Avery C. , Zweifel Larry S. , Palmiter Richard D. , Han Sung
Published: January 2023

Neurons produce and release neuropeptides to communicate with one another. Despite their profound impact on critical brain functions, circuit-based mechanisms of peptidergic transmission are poorly understood, primarily due to the lack of tools for monitoring and manipulating neuropeptide releasein vivo. Here, we report the development of two genetically encoded tools for investigating peptidergic transmission in behaving mice: a genetically encoded large dense core vesicle (LDCV) sensor that detects the neuropeptides release presynaptically, and a genetically encoded silencer that specifically degrades neuropeptides inside the LDCV. Monitoring and silencing peptidergic and glutamatergic transmissions from presynaptic terminals using our newly developed tools and existing genetic tools, respectively, reveal that neuropeptides, not glutamate, are the primary transmitter in encoding unconditioned stimulus during Pavlovian threat learning. These results show that our sensor and silencer for peptidergic transmission are reliable tools to investigate neuropeptidergic systems in awake behaving animals.
Damage-induced pyroptosis drives endogenous thymic regeneration via induction of Foxn1 by purinergic receptor activation
Authors: Kinsella Sinéad , Evandy Cindy A. , Cooper Kirsten , Cardinale Antonella , Iovino Lorenzo , deRoos Paul , Hopwo Kayla S. , Smith Colton W. , Granadier David , Sullivan Lucas B. , Velardi Enrico , Dudakov Jarrod A.
Published: January 2023

Endogenous thymic regeneration is a crucial process that allows for the renewal of immune competence following stress, infection or cytoreductive conditioning. Fully understanding the molecular mechanisms driving regeneration will uncover therapeutic targets to enhance regeneration. We previously demonstrated that high levels of homeostatic apoptosis suppress regeneration and that a reduction in the presence of damage-induced apoptotic thymocytes facilitates regeneration. Here we identified that cell-specific metabolic remodeling after ionizing radiation steers thymocytes towards mitochondrial-driven pyroptotic cell death. We further identified that a key damage-associated molecular pattern (DAMP), ATP, stimulates the cell surface purinergic receptor P2Y2 on cortical thymic epithelial cells (cTECs) acutely after damage, enhancing expression ofFoxn1, the critical thymic transcription factor. Targeting the P2Y2 receptor with the agonist UTPγS promotes rapid regeneration of the thymusin vivofollowing acute damage. Together these data demonstrate that intrinsic metabolic regulation of pyruvate processing is a critical process driving thymus repair and identifies the P2Y2 receptor as a novel molecular therapeutic target to enhance thymus regeneration.

Thymocytes rapidly and transiently undergo pyroptosis after acute thymic damage and promote regeneration.

Damage-induced redirection of pyruvate acutely enhances mitochondrial OXPHOS in thymocytes.

Elevated mitochondrial ROS promotes pyroptosis in thymocytes after acute insult by driving caspase 1 cleavage.

Extracellular ATP release promotesFoxn1expression in cTECs via activation of P2Y2

Therapeutic targeting of the P2Y2 receptor promotes thymic regeneration.
Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment
Authors: Pineau Rozenn M. , Demory David , Libby Eric , Lac Dung T. , Day Thomas C. , Bravo Pablo , Yunker Peter J. , Weitz Joshua S. , Bozdag G. Ozan , Ratcliff William C.
Published: January 2023

The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth’s ecosystems. Yet little is known about how early steps in the evolution of multicellularity transform eco-evolutionary dynamics, e.g., via niche expansion processes that may facilitate coexistence. Using long-term experimental evolution in the snowflake yeast model system, we show that the evolution of multicellularity drove niche partitioning and the adaptive divergence of two distinct, specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subject to selection for rapid growth in rich media, followed by selection favoring larger group size. Both small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations. These small and large sized snowflake yeast lineages specialized on divergent aspects of a trade-off between growth rate and survival, mirroring predictions from ecological theory. Through modeling and experimentation, we demonstrate that coexistence is maintained by a trade-off between organismal size and competitiveness for dissolved oxygen. Taken together, this work shows how the evolution of a new level of biological individuality can rapidly drive adaptive diversification and the expansion of a nascent multicellular niche, one of the most historically-impactful emergent properties of this evolutionary transition.
Plasticity in the functional properties of NMDA receptors improves network stability during severe energy stress
Authors: Bueschke Nikolaus , Amaral-Silva Lara , Hu Min , Alvarez Alvaro , Santin Joseph M.
Published: January 2023

Brain energy stress leads to neuronal hyperexcitability followed by a rapid loss of function and cell death. In contrast, the frog brainstem switches into a state of extreme metabolic resilience that allows them to maintain motor function during hypoxia as they emerge from hibernation. NMDA receptors (NMDARs) are Ca2+-permeable glutamate receptors that contribute to the loss of homeostasis during hypoxia. Therefore, we hypothesized that hibernation leads to plasticity that reduces the role of NMDARs within neural networks to improve function during energy stress. To test this, we assessed a circuit with a large involvement of NMDAR synapses, the brainstem respiratory network of female bullfrogs,Lithobates catesbeianus. Contrary to our expectations, hibernation did not alter the role of NMDARs in generating network output, nor did it affect the amplitude, kinetics, and hypoxia sensitivity of NMDAR currents. Instead, hibernation strongly reduced NMDAR Ca2+permeability and enhanced desensitization during repetitive stimulation. Under severe hypoxia, the normal NMDAR profile caused network hyperexcitability within minutes, which was mitigated by blocking NMDARs. After hibernation, the modified complement of NMDARs protected against hyperexcitability, as disordered output did not occur for at least one hour in hypoxia. These findings uncover state-dependence in the plasticity of NMDARs, whereby multiple changes to receptor function improve neural performance during energy stress without interfering with its normal role during healthy activity.

Significance Statement

Neural circuits lose homeostasis during severe energy stress, and NMDA-glutamate receptors play a major role in this response. In contrast, frogs have the remarkable capacity to use plasticity that improves circuit function from minutes to hours during hypoxia, likely as an adaptation to survive emergence from hibernation. We found this occurs, in part, through modification of NMDA receptors that renders them less permeable to Ca2+and more likely to desensitize during high activity states. These NMDA receptor modifications do not influence normal network function but protect against hyperexcitability caused by hypoxia. This work points to endogenous plasticity mechanisms that improve network function during energy stress without altering circuit function when the brain is well-oxygenated.
Myxosortases process MYXO-CTERM and other bacterial C-terminal protein-sorting signals that have invariant Cys residues
Authors: Haft Daniel H
Published: January 2023

The LPXTG protein-sorting signal, found in surface proteins of various Gram-positive pathogens, was the founding member of a growing panel of prokaryotic small C-terminal sorting domains. Sortase A (SrtA) cleaves LPXTG, exosortases (XrtA and XrtB) cleave the PEP-CTERM sorting signal, archaeosortase A (ArtA) cleaves PGF-CTERM, and rhombosortase (RrtA) cleaves GlyGly-CTERM domains. Three sorting signal domains without previously known processing proteases are the MYXO-CTERM, JDVT-CTERM, and SYNERG-CTERM domains. These exhibit the standard tripartite architecture of short signature motif, then a hydrophobic transmembrane segment, then an Arg-rich cluster. Each has an invariant cysteine in its signature motif. Here, we show computational evidence that these three Cys-containing sorting signals are processed by corresponding subfamilies of glutamic-type intramembrane proteases, related to type II CAAX-processing proteases found in eukaryotes. We name these sorting enzymes generally as myxosortases, and identify MXAN_2755 from Myxococcus xanthus as MrtX (myxosortase X). Additional myxosortases families MrtC and MrtP have radically different N-terminal domains, suggesting most myxosortases act as bifunctional enzymes. Myxosortase-like processing enzymes are identified also for the JDVT-CTERM (MrtJ) and SYNERG-CTERM (MrtS). This work establishes a major new family of protein-sorting housekeeping enzymes for the surface attachment of proteins on bacterial outer membranes.
Fusidic acid-based drug combinations exhibit enhanced activity againstMycobacterium tuberculosis
Authors: Omollo Charles , Moosa Atica , Chibale Kelly , Warner Digby F.
Published: January 2023

Tuberculosis (TB) imposes a major burden on global public health which is exacerbated by the escalating number of multidrug-resistant (MDR)-TB cases. There is consequently an urgent need for new anti-TB drugs and combination regimens. We have investigated the natural product antibiotic fusidic acid (FA) for repurposing againstMycobacterium tuberculosis, the causative agent of TB. Here, we report the results of synergy screens combining FA with a panel of approved anti-TB agents. Checkerboard and time-kill kinetics assays identified seven compounds from different chemical classes that synergized with FA in inhibiting the growth ofM. tuberculosis in vitro: rifampicin (RIF), a rifamycin and frontline anti-TB drug; the macrolides, erythromycin (ERY), clarithromycin (CLR), and roxythromycin (ROX); the oxazolidinone, linezolid (LZD); the aminoglycoside, streptomycin (STR); and the aminocyclitol, spectinomycin (SPC). Among these, the strongest synergies were observed where FA was combined with SPC and ERY. Moreover, the FA-RIF combination was cidal, while all other FA combinations were bacteriostatic. These results providein vitroevidence of the potential utility of FA-containing combinations againstM. tuberculosis.
Novel keto-alkyl-pyridinium antifungal molecules active in models of in vivoCandida albicansvascular catheter infection and ex vivoCandida aurisskin colonization
Authors: Beattie Sarah R. , Esan Taiwo , Zarnowski Robert , Eix Emily , Nett Jeniel E. , Andes David R. , Hagen Timothy , Krysan Damian J.
Published: January 2023

New antifungal therapies are needed for both systemic, invasive infections as well as superficial infections of mucosal and skin surfaces as well as biofilms associated with medical devices. The resistance of biofilm and biofilm-like growth phases of fungi contributes to the poor efficacy of systemic therapies to non-systemic infections. Here, we describe the identification and characterization of a novel keto-alkyl-pyridinium scaffold with broad spectrum activity (2-16 µg/mL) against medically important yeasts and moulds, including clinical isolates resistant to azoles and/or echinocandins. Furthermore, these keto-alkyl-pyridinium agents retain substantial activity against biofilm phase yeast and have direct activity against hyphalA. fumigatus. Although their toxicity precludes use in systemic infections, we found that the keto-alkyl-pyridinium molecules reduceC. albicansfungal burden in a rat model of vascular catheter infection and reduceCandida auriscolonization in a porcine ex vivo model. These initial pre-clinical data suggest that molecules of this class may warrant further study and development.
Platelet activation with the Aeson Bioprosthetic Total Artificial Heart: insight from aspirin treatment and outcomes
Authors: Smadja David M. , Peronino Christophe , Jilet Léa , Ivak Peter , Pya Yuri , Philippe Aurélien , Latremouille Christian , Gustafsson Finn , Ramjankhan Faiz Z. , Roussel Jean Christian , Vincentelli André , Flecher Erwan , Gaussem Pascale , Jansen Piet , Netuka Ivan
Published: January 2023

Introduction

The Aeson bioprosthetic total artificial heart (A-TAH) is a pulsatile and autoregulated device. The aim of this study was to evaluate the level of platelet activation secondary to A-TAH implantation.

Methods

We examined the level of platelet activation markers in adult patients receiving A-TAH support (n=16) during clinical follow-up by quantifying sP-selectin (sP-sel) and sCD40L in plasma.

Results

The cumulative duration of A-TAH support was 3587 days. Before implantation, sCD40L was 2684.6 pg/mL (954.0-16706.1) and remained steady after implantation [3305.8 pg/mL (1234.2-12327.5), 3300.5 pg/mL (1041.5-8370.1), and 2560.0 pg/mL (1325.5-14039.5), respectively, at <3 months, 3–6 months and >6 months; non-significant difference along time-period]. sP-sel was 33997.0 pg/mL (16019.6-73377.6) and remained steady after implantation [33580.1 pg/mL (13979.8-53395.2), 33204.9 pg/mL (15332.6-67263.4), and 34684.5 pg/mL (14084.9-49206.0), respectively, at <3 months, 3–6 months and >6 months; non-significant difference along time-period]. Levels sP-sel and sCD40L analysed according to aspirin or heparin use did not change. Finally, no relation existed between pericardial effusion and aspirin use according to timing of aspirin start and drain removal.

Conclusions

We demonstrated that A-TAH does not induce significant platelet activation. Absence of relationship between aspirin and platelet activation levels or pericardial effusion may support potential for withdrawal of antiplatelet therapy after A-TAH implantation in the future.
A rare gain of function HCN4 gene mutation is responsible for inappropriate sinus tachycardia in a Spanish family
Authors: Cámara-Checa Anabel , Perin Francesca , Rubio-Alarcón Marcos , Dago María , Crespo-García Teresa , Rapún Josu , Marín María , Cebrián Jorge , Bermúdez-Jiménez Francisco , Monserrat Lorenzo , Tamargo Juan , Caballero Ricardo , Jiménez-Jáimez Juan , Delpón Eva
Published: January 2023

Background

In a family with inappropriate sinus tachycardia (IST) we identified a novel mutation (p.V240M) of the hyperpolarization-activated cyclic nucleotide-gated type 4 (HCN4) channel, which contributes to the pacemaker current (If) in human sinoatrial node cells. Here we clinically study the family and functionally analyze the p.V240M variant.

Methods

Macroscopic (IHCN4) and single-channel currents were recorded using patch-clamp in cells expressing human native (WT) and/or p.V240M HCN4 channels.

Results

All p.V240M mutation carriers exhibited IST (mean heart rate 113[7] bpm, n=9), that in adults, was accompanied by cardiomyopathy. IHCN4generated by p.V240M channels either alone or in combination with WT was significantly greater than that generated by WT channels. The variant, which lies in the N-terminal HCN domain, increased single-channel conductance and opening frequency and probability of HCN4 channels. Conversely, it did not modify channel sensitivity for cAMP and ivabradine or the level of expression at the membrane. Treatment with ivabradine based on functional data reversed the IST and the cardiomyopathy of the carriers.

Conclusions

The p.V240M gain-of-function variant increases Ifduring diastole, which explains the IST of the carriers. The results demonstrate the importance of the unique HCN domain in HCN4 which stabilizes the channels in the closed state.

Funding

Ministerio de Ciencia e Innovación (PID2020-118694RB-I00); Comunidad Autónoma de Madrid (P2022/BMD-7229), European Structural and Investment Funds); and Instituto de Salud Carlos III (CIBERCV; CB16/11/00303).
Evaluation of the Curitiba University intern medical students’ hability in breaking bad news in a OSCE test
Authors: Silva Thiago Ribeiro E , De Lara João Paulo Zanardini , Prado Oliveira Leonardo Ajuz Do , Baggio Lucas , Freitas Matheus Pisa , Ribeiro E Silva Rodrigo , Baptista João Pedro Ribeiro , Takimura Marcos , Okamoto Cristina Terumy
Published: January 2023

Objective

Breaking bad news (BBN) has a big influence in patients’ lives, but still a lot of health care providers struggle when doing it with efficiency and empathy.

Methods

This study is a prospective cohort that evaluated the knowledge and the evolution of fifth year medical students in breaking bad news, and investigated which factors had a positive or negative influence on their scores. Two simulations were conducted during the year in the model of Objective Structured Clinical Examination (OSCE), the students’ scores were acquired through a checklist based on the SPIKES protocol. Posteriorly, an online questionnaire was filled by the students, containing objective and open questions relevant to the BBN scenario.

Results

Participated in this study 85 undergraduates, in the first OSCE 52% (n = 44) scored above the minimum institutional average, in the second OSCE 59% (n = 50) scored above the minimum institutional average. Comparing both activities there were isolated differences between isolated items at the checklist, but without statistical significance. The factor that had a positive influence for scoring higher was having previous experience in BBN, during the second OSCE the group that had experience scored an average of 3,11 points, the other group had an average of 2,57 only (p = 0,012).

Conclusion

The performance was median, and no score evolution was observed between the activities. Previous experience was the more important factor for a better score.

ILUSTRATIONS’ LIST

Table 1 Number of students’ right scores, per criteria in both of simulations
Causal relevance of different blood pressure traits on risk of cardiovascular diseases: GWAS and Mendelian randomisation in 100,000 Chinese adults
Authors: Pozarickij Alfred , Gan Wei , Lin Kuang , Clarke Robert , Fairhurst-Hunter Zammy , Koido Masaru , Kanai Masahiro , Okada Yukinori , Kamatani Yoichiro , Guo Yu , Bennett Derrick , Du Huaidong , Chen Yiping , Yang Ling , Avery Daniel , Yu Min , Yu Canqing , Valle Dan Schmidt , Lv Jun , Chen Junshi , Peto Richard , Collins Rory , Li Liming , Chen Zhengming , Millwood Iona Y , Walters Robin G
Published: January 2023

Elevated blood pressure (BP) is major risk factor for cardiovascular diseases (CVD). Genome-wide association studies (GWAS) conducted predominantly in populations of European ancestry have identified >2,000 BP-associated loci, but other ancestries have been less well-studied. We conducted GWAS of systolic, diastolic, pulse, and mean arterial BP in 100,453 Chinese adults. We identified 128 non-overlapping loci associated with one or more BP traits, harbouring 81 novel associations. Despite strong genetic correlations between populations, we identified appreciably higher heritability and larger variant effect sizes in Chinese compared with European or Japanese ancestry populations. Using instruments derived from these GWAS, multivariable Mendelian randomisation demonstrated strong causal associations of specific BP traits with CVD, including systolic BP with intracranial haemorrhage, and pulse pressure with carotid plaque. The findings reinforce the need for studies in diverse populations to understand the genetic determinants of BP traits and their role in disease risk.
Immunogenicity, Safety and Effectiveness of COVID-19 Pfizer-BioNTech (BNT162b2) mRNA Vaccination in Immunocompromised Adolescents and Young Adults: A systematic Review and Meta-Analyses
Authors: Katoto Patrick DMC , Kakubu Mireille AM , Tamuzi Jacques L. , Brand Amanda S. , Ayuk Adaeze , Byamungu Liliane N. , Wiysonge Charles S. , Gray Glenda
Published: January 2023

People with weak immune systems are more likely to develop severe COVID-19, less likely to be included in vaccine controlled studies but more likely to be under-vaccinated. We review post-marketing studies to examine the immunogenicity, safety and effectiveness of BNT162b2 vaccine in immunocompromised adolescents and young adults (AYA). We searched more than three international databases from 2020 to 30 May 2022 and used the ROBINS-I for bias assessment. Random effect model was used to estimate pooled proportion, log RR, and mean difference. Egger’s regression and Begg’s rank correlation were used to examine publication bias. 47 full texts were reviewed, and nine were included. Conditions studied were rheumatic diseases, diabetes mellitus, Down syndrome, solid tumours, neurodisability, and cystic fibrosis. Eight studies used cohort designs and one used cross-sectional designs. Europe led most of the investigations. Most studies had unclear risk of bias and none could rule out selection bias, ascertainment bias, or selective outcome reporting. The overall estimated proportion of combined local and systemic reactions after the first BNT162b2 vaccination was 30%[95% CI: 17-42%] and slightly rose to 32% [95% CI: 19-44%] after the second dose. Rheumatic illnesses had the highest rate of AEFI (40%[95% CI: 16-65%]), while cystic fibrosis had the lowest (27%[95% CI: 17%-38%]). Hospitalizations for AEFIs were rare. Healthy controls exhibited higher levels of neutralizing antibodies and measured IgG than immunocompromised AYA, although pooled estimations did not demonstrate a statistically significant difference after primary dose. BNT162b2 is safe and effective in immunocompromised AYA, with no significant difference to healthy controls. However, current evidence is low to moderate due to high RoB. Our research advocates for improving methodology in studies including specific AYA population.
Adaptive robustness through incoherent signaling mechanisms in a regenerative brain
Authors: Bray Samuel R. , Wyss Livia S. , Chai Chew , Lozada Maria E. , Wang Bo
Published: January 2023

Animal behavior emerges from collective dynamics of interconnected neurons, making it vulnerable to connectome damage. Paradoxically, many organisms maintain significant behavioral output after large-scale neural injury. Molecular underpinnings of this extreme robustness remain largely unknown. Here, we develop a quantitative behavioral analysis pipeline to measure previously uncharacterized long-lasting latent memory states in planarian flatworms during whole-brain regeneration. By combining >20,000 animal trials with neural population dynamic modeling, we show that long-range volumetric peptidergic signals allow the planarian to rapidly reestablish latent states and restore coarse behavior after large structural perturbations to the nervous system, while small-molecule neuromodulators gradually refine the precision. The different time and length scales of neuropeptide and small-molecule transmission generate incoherent patterns of neural activity which competitively regulate behavior and memory. Controlling behavior through opposing communication mechanisms creates a more robust system than either alone and may serve as a generic approach to construct robust neural networks.
Genomic profiling and pre-clinical modelling of breast cancer leptomeningeal metastasis reveals acquisition of a lobular-like phenotype
Authors: Fitzpatrick Amanda , Iravani Marjan , Mills Adam , Vicente David , Alaguthurai Thanussuyah , Roxanis Ioannis , Turner Nicholas C. , Haider Syed , Tutt Andrew N.J. , Isacke Clare M.
Published: January 2023

Breast cancer leptomeningeal metastasis (BCLM), where tumour cells grow along the lining of the brain and spinal cord, is a devastating development for patients. Investigating this metastatic site is hampered by difficulty in accessing tumour material. Here, we utilise cerebrospinal fluid (CSF) cell-free DNA (cfDNA) and CSF disseminated tumour cells (DTCs) to explore the clonal evolution of BCLM and heterogeneity between leptomeningeal and extracranial metastatic sites. Somatic alterations with potential therapeutic actionability were detected in 81% (17/21) of BCLM cases, with 19% detectable in CSF cfDNA only. BCLM was enriched in genomic aberrations in adherens junction and cytoskeletal genes, revealing a lobular-like breast cancer phenotype. CSF DTCs were cultured in 3D to establish BCLM patient-derived organoids, and used for the successful generation of BCLMin vivomodels. These data reveal that BCLM possess a unique genomic aberration profile and highlights potential cellular dependencies in this hard-to-treat form of metastatic disease.