bluuebunny/crossref_metadata_2025 huggingface dataset:
Cognitive control activity is enhanced by single pulse transcranial magnetic stimulation over prefrontal and premotor areas
Authors: Cespón Jesús , Pellicciari Maria Concetta , Miniussi Carlo
Published: February 2023

Cognitive control, which includes a set of processes to implement goal directed actions and flexible behaviour, is related to a set of brain areas comprising prefrontal, premotor, and parietal cortex. However, the functional relationships between these areas and the neural correlates underlying the specific cognitive processes linked to cognitive control (e.g., inhibition and working memory update) are still unclear. In the present study, participants performed a spatial cognitive control task (i.e., a Simon task) during a transcranial magnetic stimulation electroencephalogram (TMS-EEG) co-registration. In different blocks of the task, single pulse TMS was applied over the left prefrontal, premotor, and parietal regions (a sham TMS condition was also included) at 180ms after the stimulus onset. Behavioural differences between the four TMS conditions were not observed. Accordingly, activity to inhibit the response toward the attended location was not modulated by TMS, as indexed by the contralateral central negativity (N2cc), even if TMS over parietal regions accelerated the visuospatial processing, as evidenced by faster contralateral posterior negativity (N2pc). Importantly, we observed larger P300 amplitude when delivering TMS over prefrontal and premotor cortex compared to the sham condition. These results suggest that TMS applied over the left prefrontal and premotor regions could enhances working memory processes linked to switch-and-update of the stimulus-response binding and align with the existence of prefrontal-premotor connections.
Erasable Hippocampal Neural Signatures Predict Memory Discrimination
Authors: Kinsky Nathaniel R. , Orlin Daniel J. , Ruesch Evan A. , Kim Brian , Coello Siria , Diba Kamran , Ramirez Steve
Published: February 2023

Memories involving the hippocampus can take several days to consolidate, challenging efforts to uncover the neuronal signatures underlying this process. Using calcium imaging in freely moving mice, we tracked the hippocampal dynamics underlying memory formation across a ten-day contextual fear conditioning (CFC) task. Following learning, context-specific place field remapping correlated with memory performance. To causally test whether these hippocampal dynamics support memory consolidation, we induced amnesia in a group of mice by pharmacologically blocking protein synthesis immediately following learning. We found that halting protein synthesis following learning paradoxically accelerated cell turnover and also arrested learning-related remapping, paralleling the absence of remapping observed in untreated mice that exhibited poor memory expression. Finally, coordinated neural activity that emerged following learning was dependent on intact protein synthesis and predicted memory-related freezing behavior. We conclude that context-specific place field remapping and the development of coordinated ensemble activity require protein synthesis and underlie contextual fear memory consolidation.
Paired single-cell multi-omics data integration with Mowgli
Authors: Huizing Geert-Jan , Deutschmann Ina Maria , Peyré Gabriel , Cantini Laura
Published: February 2023

The profiling of multiple molecular layers from the same set of cells has recently become possible. There is thus a growing need for multi-view learning methods able to jointly analyze these data. We here present Multi-Omics Wasserstein inteGrative anaLysIs (Mowgli), a novel method for the integration of paired multi-omics data with any type and number of omics. Of note, Mowgli combines integrative Nonnegative Matrix Factorization (NMF) and Optimal Transport (OT), enhancing at the same time the clustering performance and interpretability of integrative NMF. We apply Mowgli to multiple paired single-cell multi-omics data profiled with 10X Multiome, CITE-seq and TEA-seq. Our in depth benchmark demonstrates that Mowgli’s performance is competitive with the state-of-the-art in cell clustering and superior to the state-of-the-art once considering biological interpretability. Mowgli is implemented as a Python package seamlessly integrated within the scverse ecosystem and it is available athttp://github.com/cantinilab/mowgli.
Bayesian optimization for design of multiscale biological circuits
Authors: Merzbacher Charlotte , Mac Aodha Oisin , Oyarzún Diego A.
Published: February 2023

Recent advances in synthetic biology have enabled the construction of molecular circuits that operate across multiple scales of cellular organization, such as gene regulation, signalling pathways and cellular metabolism. Computational optimization can effectively aid the design process, but current methods are generally unsuited for systems with multiple temporal or concentration scales, as these are slow to simulate due to their numerical stiffness. Here, we present a machine learning method for the efficient optimization of biological circuits across scales. The method relies on Bayesian Optimization, a technique commonly used to fine-tune deep neural networks, to learn the shape of a performance landscape and iteratively navigate the design space towards an optimal circuit. This strategy allows the joint optimization of both circuit architecture and parameters, and hence provides a feasible approach to solve a highly non-convex optimization problem in a mixed-integer input space. We illustrate the applicability of the method on several gene circuits for controlling biosynthetic pathways with strong nonlinearities, multiple interacting scales, and using various performance objectives. The method efficiently handles large multiscale problems and enables parametric sweeps to assess circuit robustness to perturbations, serving as an efficientin silicoscreening method prior to experimental implementation.
Finding phylogeny-aware and biologically meaningful averages of metagenomic samples:L2UniFrac
Authors: Wei Wei , Millward Andrew , Koslicki David
Published: February 2023

Metagenomic samples have high spatiotemporal variability. Hence, it is useful to summarize and characterize the microbial makeup of a given environment in a way that is biologically reasonable and interpretable. The UniFrac metric has been a robust and widely-used metric for measuring the variability between metagenomic samples. We propose that the characterization of metagenomic environments can be achieved by finding the average, a.k.a. the barycenter, among the samples with respect to the UniFrac distance. However, it is possible that such a UniFrac-average includes negative entries, making it no longer a valid representation of a metagenomic community. To overcome this intrinsic issue, we propose a special version of the UniFrac metric, termedL2UniFrac, which inherits the phylogenetic nature of the traditional UniFrac and with respect to which one can easily compute the average, producing biologically meaningful environment-specific “representative samples”. We demonstrate the usefulness of such representative samples as well as the extended usage ofL2UniFrac in efficient clustering of metagenomic samples, and provide mathematical characterizations and proofs to the desired properties ofL2UniFrac. A prototype implementation is provided at:https://github.com/KoslickiLab/L2-UniFrac.git.
Bioinformatic identification of ClpI, a class of Clp unfoldase in Actinomycetota
Authors: Jiang Jialiu , Schmitz Karl R.
Published: February 2023

All clades of bacteria possess Hsp100/Clp family unfoldase enzymes that contribute to aspects of protein quality control. In Actinomycetota, these include ClpB, which functions as an independent chaperone and disaggregase, and ClpC, which cooperates with the ClpP1P2 peptidase to carry out regulated proteolysis of client proteins. We initially sought to algorithmically catalog Clp unfoldase orthologs from Actinomycetota into ClpB and ClpC categories. In the process, we uncovered a phylogenetically distinct third group of double-ringed Clp enzymes, which we term ClpI. ClpI enzymes are architecturally similar to ClpB and ClpC, with intact ATPase modules and motifs associated with substrate unfolding and translation. While ClpI possess an M-domain similar in length to that of ClpC, their N-terminal domain is more variable than the strongly conserved N-terminal domain of ClpC. Surprisingly, we identified separate sets of ClpI sequences that possess or lack the LGF-motifs required for stable assembly with ClpP1P2. In species where they occur, we suggest that ClpI enzymes provides additional pathways and points of regulatory control over protein quality control programs, supplementing the conserved roles of ClpB and ClpC.
Xenopus laevislack the critical sperm factor PLCζ
Authors: Bainbridge Rachel E. , Rosenbaum Joel C. , Sau Paushaly , Carlson Anne E.
Published: February 2023

Fertilization of eggs from the African clawed frogXenopus laevisis characterized by an increase in cytosolic calcium, a phenomenon that is also observed in other vertebrates such as mammals and birds. During fertilization in mammals and birds, the transfer of the soluble PLCζ from sperm into the egg is thought to trigger the release of calcium from the endoplasmic reticulum (ER). Injecting sperm extracts into eggs reproduces this effect, reinforcing the hypothesis that a sperm factor is responsible for calcium release and egg activation. Remarkably, this occurs even when sperm extracts fromX. laevisare injected into mouse eggs, suggesting that mammals andX. laevisshare a sperm factor. However,X. laevislacks an annotatedPLCZ1gene, which encodes the PLCζ enzyme. In this study, we attempted to determine whether sperm fromX. laevisexpress an unannotatedPLCZ1ortholog. We identifiedPLCZ1orthologs in 11 amphibian species, including 5 that had not been previously characterized, but did not find any in eitherX. laevisor the closely relatedXenopus tropicalis. Additionally, we performed RNA sequencing on testes obtained from adultX. laevismales and did not identify potential PLCZ1 orthologs in our dataset or in previously collected ones. These findings suggest that PLCZ1 may have been lost in theXenopuslineage and raise the question of how fertilization triggers calcium release and egg activation in these species.
Rosuvastatin-Eluting Gold Nanoparticle-Loaded Perivascular Implantable Wrap for Enhanced Arteriovenous Fistula Maturation in a Murine Model
Authors: Klusman Carleigh , Martin Benjamin , Perez Joy Vanessa D. , Barcena Allan John R. , Bernardino Marvin R. , San Valentin Erin Marie D. , Damasco Jossana A. , Mundo Huckie C. Del , Court Karem , Godin Biana , Fowlkes Natalie , Bouchard Richard , Cheng Jizhong , Huang Steven Y. , Melancon Marites P.
Published: February 2023

Background

Arteriovenous fistulas (AVFs) are a vital intervention for patients requiring hemodialysis, but they also contribute to overall mortality due to access malfunction. The most common cause of both AVF non-maturation and secondary failure is neointimal hyperplasia (NIH). Absorbable polycaprolactone (PCL) perivascular wraps can address these complications by incorporating drugs to attenuate NIH, such as rosuvastatin (ROSU), and metallic nanoparticles for visualization and device monitoring.

Objectives

This study aimed to assess the impacts of gold nanoparticle (AuNP) and ROSU-loaded perivascular wraps on vasculature NIH and AVF maturation and patency in a chronic kidney disease rat model.

Methods

Electrospun wraps containing combinations of PCL, AuNP, and ROSU were monitored forin vitrodrug elution, nanoparticle release, tensile strength, and cell viability. Perivascular wraps were implanted in chronic kidney disease rats forin vivoultrasound (US) and micro-computed tomography (mCT) imaging. AVF specimens were collected for histological analyses.

Results

No difference in cell line viability was observed in ROSU-containing grafts.In vitrorelease studies of ROSU and AuNPs correlated with decreasing radiopacity over time onin vivomCT analysis. The mCT study also demonstrated increased radiopacity in AuNP-loaded wraps compared with PCL and control. The addition of ROSU demonstrated decreased US and histologic measurements of NIH.

Conclusions

The reduced NIH seen with ROSU-loading of perivascular wraps suggests a synergistic effect between mechanical support and anti-hyperplasia medication. Furthermore, the addition of AuNPs increased wrap radiopacity. Together, our results show that radiopaque, AuNP-, and ROSU-loaded PCL grafts induce AVF maturation and suppress NIH while facilitating optimal implanted device visualization.
Theoretical understanding of evolutionary dynamics on inhomogeneous networks
Authors: Teimouri Hamid , Khavas Dorsa Sattari , Spaulding Cade , Li Christopher , Kolomeisky Anatoly B.
Published: February 2023

Evolution is the main feature of all biological systems that allows populations to change their characteristics over successive generations. A powerful approach to understand evolutionary dynamics is to investigate fixation probabilities and fixation times of novel mutations on networks that mimic biological populations. It is now well established that the structure of such networks can have dramatic effects on evolutionary dynamics. In particular, there are population structures that might amplify the fixation probabilities while simultaneously delaying the fixation events. However, the microscopic origins of such complex evolutionary dynamics remain not well understood. We present here a theoretical investigation of the microscopic mechanisms of mutation fixation processes on inhomogeneous networks. It views evolutionary dynamics as a set of stochastic transitions between discrete states specified by different numbers of mutated cells. By specifically considering star networks, we obtain a comprehensive description of evolutionary dynamics. Our approach allows us to employ physics-inspired free-energy landscape arguments to explain the observed trends in fixation times and fixation probabilities, providing a better microscopic understanding of evolutionary dynamics in complex systems.
Maternal Aggression Driven by the Transient Mobilisation of a Dormant Hormone-Sensitive Circuit
Authors: Stagkourakis Stefanos , Williams Paul , Spigolon Giada , Khanal Shreya , Ziegler Katharina , Heikkinen Laura , Fisone Gilberto , Broberger Christian
Published: February 2023

Aggression, a sexually dimorphic behaviour, is prevalent in males and typically absent in virgin females. Following parturition, however, the transient expression of aggression in adult female mice protects pups from predators and infanticide by male conspecifics. While maternal hormones are known to elicit nursing, their potential role in maternal aggression remains elusive. Here, we show in mice that a molecularly defined subset of ventral premammillary (PMvDAT) neurons, instrumental for intermale aggression, switch from quiescence to a hyperexcitable state during lactation. We identify that the maternal hormones prolactin and oxytocin excite these cells through actions that include T-type Ca2+channels. Optogenetic manipulation or genetic ablation of PMvDATneurons profoundly affects maternal aggression, while activation of these neurons impairs the expression of non-aggression-related maternal behaviours. This work identifies a monomorphic neural substrate that can incorporate hormonal cues to enable the transient expression of a dormant behavioural program in lactating females.
Phenelzine-based probes reveal Secernin-3 is involved in thermal nociception
Authors: Bustin Katelyn A. , Shishikura Kyosuke , Chen Irene , Lin Zongtao , McKnight Nate , Chang Yuxuan , Wang Xie , Li Jing Jing , Arellano Eric , Pei Liming , Morton Paul D. , Gregus Ann M. , Buczynski Matthew W. , Matthews Megan L.
Published: February 2023

Chemical platforms that facilitate both the identification and elucidation of new areas for therapeutic development are necessary but lacking. Activity-based protein profiling (ABPP) leverages active site-directed chemical probes as target discovery tools that resolve activity from expression and immediately marry the targets identified with lead compounds for drug design. However, this approach has traditionally focused on predictable and intrinsic enzyme functionality. Here, we applied our activity-based proteomics discovery platform to map non-encoded and post-translationally acquired enzyme functionalities (e.g. cofactors)in vivousing chemical probes that exploit the nucleophilic hydrazine pharmacophores found in a classic antidepressant drug (e.g. phenelzine, Nardil®). We show the probes arein vivoactive and can map proteome-wide tissue-specific target engagement of the drug. In addition to engaging targets (flavoenzymes monoamine oxidase A/B) that are associated with the known therapeutic mechanism as well as several other members of the flavoenzyme family, the probes captured the previously discoveredN-terminal glyoxylyl (Glox) group of Secernin-3 (SCRN3)in vivothrough a divergent mechanism, indicating this functional feature has biochemical activity in the brain. SCRN3 protein is ubiquitously expressed in the brain, yet gene expression is regulated by inflammatory stimuli. In an inflammatory pain mouse model, behavioral assessment of nociception showedScrn3male knockout mice selectively exhibited impaired thermal nociceptive sensitivity. Our study provides a guided workflow to entangle molecular (off)targets and pharmacological mechanisms for therapeutic development.
Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps
Authors: Dai Xin , Wu Longlong , Yoo Shinjae , Liu Qun
Published: February 2023

Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3-D atomic models of biological molecules. AlphaFold-predicted models generate initial 3-D coordinates; however, model inaccuracy and conformational heterogeneity often necessitate labor-intensive manual model building and fitting into cryo-EM maps. In this work, we designed a protein modelbuilding workflow, which combines a deep-learning cryo-EM map feature enhancement tool, CryoFEM (Cryo-EM Feature Enhancement Model) and AlphaFold. A benchmark test using 36 cryo-EM maps shows that CryoFEM achieves state-of-the-art performance in optimizing the Fourier Shell Correlations between the maps and the ground truth models. Furthermore, in a subset of 17 datasets where the initial AlphaFold predictions are less accurate, the workflow significantly improves their model accuracy. Our work demonstrates that the integration of modern deep learning image enhancement and AlphaFold may lead to automated model building and fitting for the atomistic interpretation of cryo-EM maps.
Histone bivalency regulates the timing of cerebellar granule cell development
Authors: Mätlik Kärt , Govek Eve-Ellen , Paul Matthew R. , Allis C. David , Hatten Mary E.
Published: February 2023

Developing neurons undergo a progression of morphological and gene expression changes as they transition from neuronal progenitors to mature, multipolar neurons. Here we use RNA-seq and H3K4me3 and H3K27me3 ChIP-seq to analyze how chromatin modifications control gene expression in a specific type of CNS neuron, the mouse cerebellar granule cell (GC). We find that in proliferating GC progenitors (GCPs), H3K4me3/H3K27me3 bivalency is common at neuronal genes and undergoes dynamic changes that correlate with gene expression during migration and circuit formation. Expressing a fluorescent sensor for bivalent H3K4me3 and H3K27me3 domains revealed subnuclear bivalent foci in proliferating GCPs. Inhibiting H3K27 methyltransferases EZH1 and EZH2in vitroand in organotypic cerebellar slices dramatically altered the expression of bivalent genes and induced the downregulation of migration-related genes and upregulation of synaptic genes, inhibited glial-guided migration, and accelerated terminal differentiation. Thus, histone bivalency is required to regulate the timing of the progression from progenitor cells to mature neurons.
Spaces of phylogenetic diversity indices: combinatorial and geometric properties
Authors: Manson Kerry , Steel Mike
Published: February 2023

Biodiversity is a concept most naturally quantified and measured across sets of species. However, for some applications, such as prioritising species for conservation efforts, a species-by-species approach is desirable. Phylogenetic diversity indices are functions that apportion the total biodiversity value of a set of species across its constituent members. As such, they aim to measure each species’ individual contribution to, and embodiment of, the diversity present in that set. However, no clear definition exists that encompasses the diversity indices in current use. This paper presents conditions that define diversity indices arising from the phylogenetic diversity measure on rooted phylogenetic trees. In this context, the diversity index ‘score’ given to a species represents a measure of its unique and shared evolutionary history as displayed in the underlying phylogenetic tree. Our definition generalises the diversity index notion beyond the popular Fair Proportion and Equal-Splits indices. These particular indices may now be seen as two points in a convex space of possible diversity indices, for which the boundary conditions are determined by the underlying shape of each phylogenetic tree. We calculated the dimension of the convex space associated with each tree shape and described the extremal points.
Rural selection drives the evolution of an urban-rural cline in coat color in gray squirrels
Authors: Cosentino Bradley J. , Vanek John P. , Gibbs James P.
Published: February 2023

Phenotypic differences between urban and rural populations are well-documented, but the evolutionary processes driving trait variation along urbanization gradients are often unclear. We combined spatial data on abundance, trait variation, and measurements of fitness to understand cline structure and test for natural selection on heritable coat color morphs (melanic, gray) of eastern gray squirrels (Sciurus carolinensis) along an urbanization gradient. Population surveys using remote cameras and visual counts at 76 sites along the urbanization gradient revealed a significant cline in melanism, decreasing from 48% in the city center to <5% in rural woodlands. Among 76 translocated squirrels to test for phenotypic selection, survival was lower for the melanic than gray morph in rural woodlands, whereas there was no difference in survival between color morphs in the city. These results suggest the urban-rural cline in melanism is explained by natural selection favoring the gray morph in rural woodlands combined with relaxed selection in the city. Our study illustrates how trait variation between urban and rural populations can emerge from selection primarily in rural populations rather than adaptation to novel features of the urban environment.
In vivophotopharmacology with light-activated opioid drugs
Authors: McClain Shannan P. , Ma Xiang , Johnson Desiree A. , Johnson Caroline A. , Layden Aryanna E. , Yung Jean C. , Lubejko Susan T. , Livrizzi Giulia , Jenny He X. , Zhou Jingjing , Ventriglia Emilya , Rizzo Arianna , Levinstein Marjorie , Gomez Juan L. , Bonaventura Jordi , Michaelides Michael , Banghart Matthew R.
Published: February 2023

Traditional methods for site-specific drug delivery in the brain are slow, invasive, and difficult to interface with recordings of neural activity. Here, we demonstrate the feasibility and experimental advantages ofin vivophotopharmacology using “caged” opioid drugs that are activated in the brain with light after systemic administration in an inactive form. To enable bidirectional manipulations of endogenous opioid receptorsin vivo, we developed PhOX and PhNX, photoactivatable variants of the mu opioid receptor agonist oxymorphone and the antagonist naloxone. Photoactivation of PhOX in multiple brain areas produced local changes in receptor occupancy, brain metabolic activity, neuronal calcium activity, neurochemical signaling, and multiple pain- and reward-related behaviors. Combining PhOX photoactivation with optical recording of extracellular dopamine revealed adaptations in the opioid sensitivity of mesolimbic dopamine circuitry during chronic morphine administration. This work establishes a general experimental framework for usingin vivophotopharmacology to study the neural basis of drug action.

Highlights

A photoactivatable opioid agonist (PhOX) and antagonist (PhNX) forin vivophotopharmacology.

Systemic pro-drug delivery followed by local photoactivation in the brain.

In vivophotopharmacology produces behavioral changes within seconds of photostimulation.

In vivophotopharmacology enables all-optical pharmacology and physiology.
The double-drift illusion biases the marmoset oculomotor system
Authors: Dotson Nicholas M. , Davis Zachary W. , Salisbury Jared M. , Palmer Stephanie E. , Cavanagh Patrick , Reynolds John H.
Published: February 2023

The double-drift illusion has two unique characteristics: the error between the perceived and physical position of the stimulus grows over time, and saccades to the moving target land much closer to the physical than the perceived location. These results suggest that the perceptual and saccade targeting systems integrate visual information over different timescales. Functional imaging studies in humans have revealed several potential cortical areas of interest, including the prefrontal cortex. However, we currently lack an animal model to study the neural mechanisms of location perception that underlie the double-drift illusion. To fill this gap, we trained two marmoset monkeys to fixate and then saccade to the double drift stimulus. In line with human observers for radial double-drift trajectories, we find that saccade endpoints do show a significant bias that is, as it is in humans, smaller than that seen in perception. This bias is modulated by changes in the external and internal speeds of the stimulus. These results demonstrate that the saccade targeting system of the marmoset monkey is influenced by the double-drift illusion.
Dynamics of brain-muscle networks reveal effects of age and somatosensory function on gait
Authors: Roeder Luisa , Breakspear Michael , Kerr Graham K. , Boonstra Tjeerd W.
Published: February 2023

Walking is a complex motor activity that requires coordinated interactions between sensory and motor systems. We used mobile EEG and EMG to investigate the brain-muscle networks involved in gait control during overground walking in young, older and individuals with Parkinson’s Disease. Dynamic interactions between the sensorimotor cortices and eight leg muscles within a gait cycle were assessed using multivariate analysis. We identified three distinct brain-muscle networks during a gait cycle. These networks include a bilateral network, a left-lateralised network activated during the left swing phase, and a right-lateralised network active during right swing. The trajectories of these networks are contracted in older adults, indicating a reduction in neuromuscular connectivity with age. Individuals with impaired tactile sensitivity of the foot showed a selective enhancement of the bilateral network, possibly reflecting a compensation strategy to maintain gait stability. These findings provide a parsimonious description of interindividual differences in neuromuscular connectivity during gait.

Teaser

Dynamic network analysis shows how brain-muscle connectivity during gait varies with age and somatosensory function.
Optotracers to study biofilms in host-relevant systems and non-conventional treatments usingStaphylococcus aureuswound biofilms as a case study
Authors: Shaikh Nijamuddin , Kaushik Karishma S
Published: February 2023

Optotracers have a wide-range of applications in the detection, visualization, and characterization of biofilms. More recently, optotracers have been used in antibiotic susceptibility assays for biofilms and for the detection of biomarkers in clinical biofilm infections. This is particularly important, given that the field is increasingly focused on the evaluation of novel anti-biofilm agents and the study of biofilms in host-relevant systems. Given this, the possibility of using optotracers for an expanded set of biofilm focus areas is important to explore. In this study, we examine the application of the optotracer EbbaBiolight 680 to study biofilms in a host-relevant system and for the evaluation of a non-conventional anti-biofilm remedy. UsingStaphylococcus aureuswound biofilms as a case study, we leverage a previously builtin vitro4-D wound microenvironment platform and a plant-based wound remedy. We find that EbbaBiolight 680 can be used to visualizeS. aureusbiofilms, likely detecting both bacterial cells and bacterial EPS components. Further, the optotracer can be used to evaluate and quantify the effects of the plant-based wound remedy onS. aureusbiomass formation. However, in the 4-D wound microenvironment, EbbaBiolight 680 detected host cellular and matrix elements, which confounded the detection of biofilms. Taken together, this study opens the possibility of using optotracers as screening tools for the identification of novel anti-biofilm treatments and underscores the need for modifications for their use in host-relevant systems.
Leptin antagonism improves Rett syndrome phenotype in symptomatic maleMecp2-nullmice
Authors: Belaïdouni Yasmine , Diabira Diabe , Brosset-Heckel Mélanie , Valsamides Victoria , Graziano Jean-Charles , Santos Catarina , Menuet Clément , Wayman Gary A. , Gaiarsa Jean-Luc
Published: February 2023

Rett syndrome (RTT) is a severe neurodevelopmental disorder that arise fromde novomutations in the X-linked geneMECP2(methyl-CpG-binding protein 2). Circulating levels of the adipocyte hormone leptin are elevated in RTT patients and rodent models of the disease. Leptin targets a large number of brain structures and regulates a wide range of developmental and physiological functions which are altered in RTT. We hypothesized that elevated leptin levels might contribute to RTT pathogenesis. Accordingly, we show that pharmacological antagonism of leptin or genetic reduction of leptin production prevents the degradation of health status, weight loss and the progression of breathing and locomotor deficits. At the neuronal level, the anti-leptin strategies rescue the hippocampal excitatory/inhibitory imbalance and synaptic plasticity impairment. Targeting leptin might therefore represent a new approach for RTT treatment.
Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics
Authors: Pessi Igor S. , Popin Rafael Vicentini , Durieu Benoit , Lara Yannick , Savaglia Valentina , Roncero-Ramos Beatriz , Hultman Jenni , Verleyen Elie , Vyverman Wim , Wilmotte Annick
Published: February 2023

Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into their diversity, only a handful of genomes of polar Cyanobacteria have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic, and Antarctic microbial mats. We recovered 22 unique metagenome-assembled genomes (MAGs) of Cyanobacteria, most of which are only distantly related to genomes that have been sequenced so far. These include i) lineages that are common in polar microbial mats such as the filamentous taxaPseudanabaena, Leptolyngbya, Microcoleus/Tychonema, andPhormidium; ii) the less common taxaCrinaliumandChamaesiphon; iii) an enigmatic Chroococcales lineage only distantly related toMicrocystis; and iv) an early branching lineage in the order Gloeobacterales that is almost exclusively restricted to the cold biosphere, for which we propose the nameCandidatusSivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments.

Data summary

The sequencing data generated in this study have been submitted to the European Nucleotide Archive (ENA) under the BioProject PRJEB59431. Individual accession numbers for raw reads and genomic bins are listed inTable S1andTable S3, respectively. Genomic bins can also be downloaded from doi.org/10.6084/m9.figshare.22003967. The commands used throughout this study are available ingithub.com/igorspp/polar-cyanobacteria-MAGs.

Impact statement

Cyanobacteria are photosynthetic microorganisms that play important roles in polar lacustrine ecosystems. Many Cyanobacteria are difficult to grow in the laboratory, particularly in isolation from other organisms, which makes it challenging to sequence their genomes. As such, considerably fewer genomes of Cyanobacteria have been sequenced so far compared to other bacteria. In this study, we used a metagenomics approach to recover novel genomes of Cyanobacteria from Arctic and Antarctic microbial mats without the need to isolate the organisms. The community DNA was extracted and sequenced, and the genomes of individual populations were separated using bioinformatics tools. We recovered 22 different genomes of Cyanobacteria, many of which have not been sequenced before. We describe in more detail an interesting lineage of ancestral Cyanobacteria in the order Gloeobacterales, for which we propose the nameCandidatusSivonenia alaskensis. Our study shows that genome-resolved metagenomics is a valuable approach for obtaining novel genomes of Cyanobacteria, which are needed to improve our understanding of life in the polar regions and the planet at large.
Experiment-based Computational Model Predicts that IL-6 Trans-Signaling Plays a Dominant Role in IL-6 mediated signaling in Endothelial Cells
Authors: Song Min , Wang Youli , Annex Brian H. , Popel Aleksander S.
Published: February 2023

Inflammatory cytokine mediated responses are important in the development of many diseases that are associated with angiogenesis. Targeting angiogenesis as a prominent strategy has shown limited effects in many contexts such as peripheral arterial disease (PAD) and cancer. One potential reason for the unsuccessful outcome is the mutual dependent role between inflammation and angiogenesis. Inflammation-based therapies primarily target inflammatory cytokines such as interleukin-6 (IL-6) in T cells, macrophages, cancer cells, muscle cells, and there is a limited understanding of how these cytokines act on endothelial cells. Thus, we focus on one of the major inflammatory cytokines, IL-6, mediated intracellular signaling in endothelial cells by developing a detailed computational model. Our model quantitatively characterized the effects of IL-6 classic and trans-signaling in activating the signal transducer and activator of transcription 3 (STAT3), phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt), and mitogen-activated protein kinase (MAPK) signaling to phosphorylate STAT3, extracellular regulated kinase (ERK) and Akt, respectively. We applied the trained and validated experiment-based computational model to characterize the dynamics of phosphorylated STAT3 (pSTAT3), Akt (pAkt), and extracellular regulated kinase (pERK) in response to IL-6 classic and/or trans-signaling. The model predicts that IL-6 classic and trans-signaling induced responses are IL-6 and soluble IL-6 receptor (sIL-6R) dose-dependent. Also, IL-6 trans-signaling induces stronger downstream signaling and plays a dominant role in the overall effects from IL-6. In addition, both IL-6 and sIL-6R levels regulate signaling strength. Moreover, our model identifies the influential species and kinetic parameters that specifically modulate the pSTAT3, pAkt, and pERK responses, which represent potential targets for inflammatory cytokine mediated signaling and angiogenesis-based therapies. Overall, the model predicts the effects of IL-6 classic and/or trans-signaling stimulation quantitatively and provides a framework for analyzing and integrating experimental data. More broadly, this model can be utilized to identify targets that influence inflammatory cytokine mediated signaling in endothelial cells and to study the effects of angiogenesis- and inflammation-based therapies.
LDLR-mediated targeting and productive uptake of siRNA-peptide ligand conjugatesin vitroandin vivo
Authors: B. Broc , K. Varini , R. Sonnette , B. Pecqueux , F. Benoist , M. Thomas , M. Masse , Y. Mechioukhi , G. Ferracci , M. David , J. Temsamani , M. Khrestchatisky , G. Jacquot , P. Lécorché
Published: February 2023

siRNAs have become one of the most promising therapeutic agents because of their specificity and their potential to modulate the expression of gene-related diseases. Any gene of interest can be potentially up or down-regulated, making RNA-based technology the healthcare breakthrough of our era. However, the functional and specific delivery of siRNAs into tissues of interest and into the cytosol of target cells remains highly challenging, mainly due to the lack of efficient and selective delivery systems. Among the variety of carriers for siRNA delivery, peptides have become essential candidates because of their high selectivity, stability and conjugation versatility. Here, we describe the development of molecules encompassing siRNAs againstSOD1, conjugated to peptides that target the LDLR, and their biological evaluation bothin vitroandin vivo.

Abstract Figure

GRAPHICAL ABSTRACT
Structure of the ceramide-bound SPOTS complex
Authors: Schäfer Jan-Hannes , Körner Carolin , Esch Bianca M. , Limar Sergej , Parey Kristian , Walter Stefan , Januliene Dovile , Moeller Arne , Fröhlich Florian
Published: February 2023

Sphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyl-transferase (SPT) catalyzes the rate limiting step in sphingolipid biogenesis. Its activity is tightly regulated through multiple binding partners, including Tsc3, Orm proteins, ceramides, and the phosphatidylinositol-4-phosphate (PI4P) phosphatase Sac1. The structural organization and regulatory mechanisms of this complex are not yet understood.

Here, we report the high-resolution cryo-EM structures of the yeast SPT in complex with Tsc3 and Orm1 (SPOT) as dimers and monomers and a monomeric complex further carrying Sac1 (SPOTS). In all complexes, the tight interaction of the downstream metabolite ceramide and Orm1 reveals the ceramide dependent inhibition. Additionally, observation of ceramide and ergosterol binding suggests a co-regulation of sphingolipid biogenesis and sterol metabolism within the SPOTS complex.
Verification of nucleotide sequence reagent identities in original publications in high impact factor cancer research journals
Authors: Pathmendra Pranujan , Park Yasunori , Enguita Francisco J. , Byrne Jennifer A.
Published: February 2023

Human gene research studies that describe wrongly identified nucleotide sequence reagents have been mostly identified in journals of low to moderate impact factor, where unreliable findings could be considered to have limited influence on future research. This study examined whether papers describing wrongly identified nucleotide sequences are also published in high impact factor cancer research journals. We manually verified nucleotide sequence identities in originalMolecular Cancerarticles published in 2014, 2016, 2018 and 2020, including nucleotide sequence reagents that were claimed to target circRNAs. Using keywords identified in problematic 2018 and 2020Molecular Cancerpapers, we also verified nucleotide sequence identities in 2020Oncogenepapers that studied miRNA(s) and/or circRNA(s). Overall, 3.8% (253/6,647) and 4.3% (50/1,165) nucleotide sequences that were verified inMolecular CancerandOncogenepapers, respectively, were found to be wrongly identified. These wrongly identified nucleotide sequences were distributed across 18% (92/500) originalMolecular Cancerpapers, including 38%Molecular Cancerpapers from 2020, and 40% (21/52) selectedOncogenepapers from 2020. Original papers with wrongly identified nucleotide sequences were therefore unexpectedly frequent in two high impact factor cancer research journals, highlighting the risks of employing journal impact factors or citations as proxies for research quality.
IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy
Authors: Tanner Georgette , Barrow Rhiannon , Finetti Martina , Ajaib Shoaib , Ahmed Nazia , Pollock Steven , Rippaus Nora , Bruns Alexander F. , Syed Khaja , Poulter James , Wilson Erica , Johnson Colin , Varn Frederick S. , Brüning-Richardson Anke , Hogg Catherine , Droop Alastair , Gusnanto Arief , Care Matthew A. , Cutillo Luisa , Westhead David , Short Susan C. , Jenkinson Michael D. , Brodbelt Andrew , Chakrabarty Aruna , Ismail Azzam , Verhaak Roel GW , Stead Lucy F.
Published: February 2023

Glioblastoma (GBM) brain tumours lackingIDH1mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumours almost always fatally recur. Using RNAseq data from 107 pairs of pre- and post-standard treatment locally recurrent IDHwt GBM tumours, we identified two responder subtypes based on therapy-driven changes in gene expression. In two thirds of patients a specific subset of genes is up-regulated from primary to recurrence (Up responders) and in one third the same genes are down-regulated (Down responders). Characterisation of the responder subtypes indicates subtype-specific adaptive treatment resistance mechanisms. In Up responders treatment enriches for quiescent proneural GBM stem cells and differentiated neoplastic cells with increased neurotransmitter signalling, whereas Down responders commonly undergo therapy-driven mesenchymal transition. Stratifying GBM tumours by response subtype may lead to more effective treatment. In support of this, modulators of gamma aminobutyric acid (GABA) neurotransmitter signalling differentially sensitise Up and Down responder GBM models to standard treatmentin vitro.
An ULK1/2-PXN mechanotransduction complex suppresses breast cancer cell migration
Authors: Liang Peigang , Zhang Jiaqi , Wu Yuchen , Zheng Shanyuan , Xu Zhaopeng , Yang Shuo , Wang Jinfang , Ma Suibin , Xiao Li , Hu Tianhui , Jiang Wenxue , Xing Qiong , Kundu Mondira , Wang Bo
Published: February 2023

The remodeling and stiffening of the extracellular matrix (ECM) associated with breast cancers is a well-recognized modulator of disease progression. However, how changes in the mechanical properties of the ECM are converted into biochemical signals that direct tumor cell migration and metastasis remains poorly characterized. Here, we describe a new role for the autophagy-inducing serine/threonine kinases ULK1 and ULK2 in mechanotransduction. We demonstrate that ULK1/2 activity inhibits the assembly of actin stress fibers and focal adhesions (FAs), and as a consequence impedes cell contraction and migration. Mechanistically, we identify PXN/paxillin, a key component of the mechanotransducing machinery, as a direct binding partner and substrate of ULK1/2. ULK-mediated phosphorylation of PXN at S32 and S119 weakens homotypic interactions and liquid-liquid phase separation of PXN, impairing FA assembly, which in turn impedes the mechanotransduction of breast cancer cells. ULK1/2 and the well characterized PXN regulator, FAK/Src, have opposing functions on mechanotransduction and compete for phosphorylation of adjacent serine and tyrosine residues. Thus, our study reveals ULK1/2 as important regulators of PXN-dependent mechanotransduction.

Highlights

ULK1/2 interact with PXN and phosphorylate PXN at S32 and S119 in response to mechanical stimuli

ULK1/2-mediated phosphorylation of PXN regulates mechanotransduction and migration of breast cancer cells

ULK1/2 modulate the biomaterial properties of focal adhesions through PXN phosphorylation

ULK1/2 and FAK/Src act antagonistically in mechanotransduction through competitive phosphorylation of PXN
Native Mass Spectrometry of Complexes Formed by Molecular Glues Reveals Stoichiometric Rearrangement of E3 Ligases
Authors: Jackson Cara , Beveridge Rebecca
Published: February 2023

In this application of native mass spectrometry (nMS) to investigate complexes formed by molecular glues (MGs), we have demonstrated its efficiency in delineating stoichiometric rearrangements of E3 ligases that occur during targeted protein degradation (TPD). MGs stabilise interactions between an E3 ligase and a protein of interest (POI) targeted for degradation, and these ternary interactions are challenging to characterise. We have shown that nMS can unambiguously identify complexes formed between the CRBN:DDB1 E3 ligase and the POI GSPT1 upon the addition of lenalidomide, pomalidomide or thalidomide. Ternary complex formation was also identified involving the DCAF15:DDA1:DDB1 E3 ligase in the presence of MG (E7820 or indisulam) and POI RBM39. Moreover, we uncovered that the DCAF15:DDA1:DDB1 E3 ligase self-associates into dimers and trimers when analysed alone at low salt concentrations (100 mM ammonium acetate) which dissociate into single copies of the complex at higher salt concentrations (500 mM ammonium acetate), or upon the addition of MG and POI, forming a 1:1:1 ternary complex. This work demonstrates the strength of nMS in TPD research, reveals novel binding mechanisms of the DCAF15 E3 ligase, and highlights the potential effect of salt concentrations on protein complexes during structural analysis.
An inhibitory circuit-based enhancer of Dyrk1a function reversesDyrk1a-associated impairment in social recognition
Authors: Shih Yu-Tzu , Alipio Jason Bondoc , Sahay Amar
Published: February 2023

Heterozygous mutations in the Dual specificity tyrosine-phosphorylation-regulated kinase 1aDyrk1agene define a syndromic form of Autism Spectrum Disorder. The synaptic and circuit mechanisms mediating Dyrk1a functions in social cognition are unclear. Here, we identify a social experience-sensitive mechanism in hippocampal mossy fiber-parvalbumin interneuron (PV IN) synapses by which Dyrk1a recruits feedforward inhibition of CA3 and CA2 to promote social recognition. We employ genetic epistasis logic to identify a cytoskeletal protein, Ablim3, as a synaptic substrate of Dyrk1a. We demonstrate thatAblim3downregulation in dentate granule cells of adult hemizygousDyrk1amice is sufficient to restore PV IN mediated inhibition of CA3 and CA2 and social recognition. Acute chemogenetic activation of PV INs in CA3/CA2 of adult hemizygousDyrk1amice also rescued social recognition. Together, these findings illustrate how targeting Dyrk1a synaptic and circuit substrates as “enhancers of Dyrk1a function” harbors potential to reverseDyrk1ahaploinsufficiency-associated circuit and cognition impairments.

Highlights

Dyrk1a in mossy fibers recruits PV IN mediated feed-forward inhibition of CA3 and CA2

Dyrk1a-Ablim3 signaling in mossy fiber-PV IN synapses promotes inhibition of CA3 and CA2

DownregulatingAblim3restores PV IN excitability, CA3/CA2 inhibition and social recognition inDyrk1a+/-mice

Chemogenetic activation of PV INs in CA3/CA2 rescues social recognition inDyrk1a+/-mice