bluuebunny/crossref_metadata_2025 huggingface dataset:
Sensory choices as logistic classification
Authors: Carandini Matteo
Published: January 2024

Logistic classification is a simple way to make choices based on a set of factors: give each factor a weight, sum the results, and use the sum to set the log odds of a random draw. This operation is known to describe human and animal choices based on value (economic decisions). There is increasing evidence that it also describes choices based on sensory inputs (perceptual decisions), presented across sensory modalities (multisensory integration) and combined with non-sensory factors such as prior probability, expected value, overall motivation, and recent actions. Logistic classification can also capture the effects of brain manipulations such as local inactivations. The brain may implement by thresholding stochastic inputs (as in signal detection theory) acquired over time (as in the drift diffusion model). It is the optimal strategy under certain conditions, and the brain appears to use it as a heuristic in a wider set of conditions.
The landscape of immune dysregulation in pediatric sepsis at a single-cell resolution
Authors: Alhamdan Fahd , Koutsogiannaki Sophia , Yuki Koichi
Published: January 2024

Recognizing immune dysregulation as a hallmark of sepsis pathophysiology, leukocytes have attracted major attention of investigation. While adult and pediatric sepsis are clinically distinct, their immunological delineation remains limited. Breakthrough of single cell technologies facilitated the characterization of immune signatures. We tackled to delineate immunological profiles of pediatric sepsis at a single-cell level by analyzing blood samples from six septic children, at both acute and recovery phases, and four healthy children. 16 single-cell transcriptomic datasets (96,156 cells) were analyzed and compared to adult sepsis dataset. We showed a unique shift in neutrophil subpopulations and functions between acute and recovery phases, along with examining the regulatory role of resistin. Neutrophil signatures were comparable between adult and pediatric sepsis. Innate-like CD4 T cells were predominantly and uniquely observed in acute phase of pediatric sepsis. Our study provides a thorough and comprehensive understanding of immune dysregulation in pediatric sepsis.
Emergence of neocortical function in heterotopic neurons
Authors: Roig-Puiggros Sergi , Guyoton Maëlle , Suchkov Dmitrii , Fortoul Aurélien , Fièvre Sabine , Matteucci Giulio , Maino Emma , Foucher Charlie G. , Fuciec Daniel , Klingler Esther , Francis Fiona , Minlebaev Marat , El-Boustani Sami , Watrin Françoise , Manent Jean-Bernard , Jabaudon Denis
Published: January 2024

Brains come in various sizes and shapes, yet how neuronal position constrains the type of circuits that they can form remains largely unknown. The spatial layout of anatomical structures with corresponding functions varies widely across species (J-4). Also, during evolution, anatomical structures have duplicated and then diverged to generate new circuits and functions (5,6). Thus, it is critical to understand how the position of neurons constrains their integration into circuits and, ultimately, their function. To address this question, we studiedEmlJknockout mice in which subsets of neocortical neurons form a new structure below the neocortex termed heterotopia (Ht). We examined how this new location affects the molecular identity, topography, input-output circuit connectivity, electrophysiology, and functional properties of these neurons. Our results reveal a striking conservation of the cellular features and circuit properties of Ht neurons, despite their abnormal location and misorientation. Supporting this observation, these neurons were able to functionally substitute for overlying neocortical neurons in a behaviorally relevant task when the latter were optogenetically silenced. Hence, specific neuronal identities and associated function can be reproduced in altered anatomical settings, revealing a remarkable level of self-organization and adaptability of neocortical circuits.
Reduced recruitment of inhibitory control regions in very young children with ADHD during a modified Kiddie Continuous Performance Task: a fMRI study
Authors: Bayat Mohammadreza , Hernandez Melissa , Curzon Madeline , Garic Dea , Graziano Paulo , Dick Anthony Steven
Published: January 2024

Attention-Deficit/Hyperactivity Disorder (ADHD) symptom profiles are known to undergo changes throughout development, rendering the neurobiological assessment of ADHD challenging across different developmental stages. Particularly in young children (ages 4 to 7 years), measuring inhibitory control network activity in the brain has been a formidable task due to the lack of child-friendly functional Magnetic Resonance Imaging (fMRI) paradigms. This study aims to address these difficulties by focusing on measuring inhibitory control in very young children within the MRI environment. A total of 56 children diagnosed with ADHD and 78 typically developing (TD) 4-7-year-old children were examined using a modified version of the Kiddie-Continuous Performance Test (K-CPT) during BOLD fMRI to assess inhibitory control. We concurrently evaluated their performance on the established and standardized K-CPT outside the MRI scanner. Our findings suggest that the modified K-CPT effectively elicited robust and expected brain activity related to inhibitory control in both groups. Comparisons between the two groups revealed subtle differences in brain activity, primarily observed in regions associated with inhibitory control, such as the inferior frontal gyrus, anterior insula, dorsal striatum, medial pre-supplementary motor area (pre-SMA), and cingulate cortex. Notably, increased activity in the right anterior insula was associated with improved response time (RT) and reduced RT variability on the K-CPT administered outside the MRI environment, although this did not survive statistical correction for multiple comparisons. In conclusion, our study successfully overcame the challenges of measuring inhibitory control in very young children within the MRI environment by utilizing a modified K-CPT during BOLD fMRI. These findings shed light on the neurobiological correlates of inhibitory control in ADHD and TD children, provide valuable insights for understanding ADHD across development, and potentially inform ADHD diagnosis and intervention strategies. The research also highlights remaining challenges with task fMRI in very young clinical samples.
Toward subtask decomposition-based learning and benchmarking for genetic perturbation outcome prediction and beyond
Authors: Gao Yicheng , Wei Zhiting , Dong Kejing , Yang Jingya , Chuai Guohui , Liu Qi
Published: January 2024

Deciphering cellular responses to genetic perturbations is fundamental for a wide array of biomedical applications, ranging from uncovering gene roles and interactions to unraveling effective therapeutics. Accurately predicting the transcriptional outcomes of genetic perturbations is indispensable for optimizing experimental perturbations and deciphering cellular response mechanisms; however, three scenarios present principal challenges, i.e., predicting single genetic perturbation outcomes, predicting multiple genetic perturbation outcomes and predicting genetic outcomes across cell lines. In this study, we introduceSubTAsk decompositionModeling for geneticPerturbation prediction (STAMP), a conceptually novel computational strategy for genetic perturbation outcome prediction and downstream applications. STAMP innovatively formulates genetic perturbation prediction as a subtask decomposition (STD) problem by resolving three progressive subtasks in a divide-and-conquer manner, i.e., identifying differentially expressed gene (DEG) postperturbations, determining the regulatory directions of DEGs and finally estimating the magnitudes of gene expression changes. In addition to facilitating perturbation prediction, STAMP also serves as a robust and generalizable benchmark guide for evaluating various genetic perturbation prediction models. As a result, STAMP exhibits a substantial improvement in terms of its genetic perturbation prediction ability over the existing approaches on three subtasks and beyond, including revealing the ability to identify key regulatory genes and pathways on small samples and to reveal precise genetic interactions. Overall, STAMP serves as a fundamentally novel and effective prediction and generalizable benchmarking strategy that can facilitate genetic perturbation prediction, guide the design of perturbation experiments, and broaden the understanding of perturbation mechanisms.
In-Depth Mapping of DNA-PKcs Signaling Uncovers Conserved Features of Its Kinase Specificity
Authors: Marshall Shannon , Navarro Marcos V.A.S. , Ascenҫão Carolline F.R. , Smolka Marcus B.
Published: January 2024

DNA-PKcs is a DNA damage sensor kinase with established roles in DNA double-strand break repair via non-homologous end joining. Recent studies have revealed additional roles of DNA-PKcs in the regulation of transcription, translation and DNA replication. However, the substrates through which DNA-PKcs regulates these processes remain largely undefined. Here we utilized quantitative phosphoproteomics to generate a high coverage map of DNA-PKcs signaling in response to ionizing radiation and mapped its interplay with the ATM kinase. Beyond the detection of the canonical S/T-Q phosphorylation motif, we uncovered a non-canonical mode of DNA-PKcs signaling targeting S/T-ψ-D/E motifs. Cross-species analysis in mouse pre-B and human HCT116 cell lines revealed splicing factors and transcriptional regulators phosphorylated at this novel motif, several of which contain SAP domains. These findings expand the list of DNA-PKcs and ATM substrates and establish a novel preferential phosphorylation motif for DNA-PKcs that connects it to proteins involved in nucleotide processes and interactions.
In vivorescue of arboviruses directly from subgenomic DNA fragments
Authors: Cochin Maxime , Driouich Jean-Sélim , Moureau Grégory , Piorkowski Géraldine , de Lamballerie Xavier , Nougairède Antoine
Published: January 2024

Reverse genetic systems are mainly used to study RNA viruses and rescue recombinant strains in cell culture. Here, we provide proof-of-concept for directin vivoviral generation using the ‘Infectious Subgenomic Amplicons’ method. So far, this procedure allowed to rescuein vitroRNA viruses, by the transfection of several overlapping subgenomic DNA fragments encoding the entire virus genome.

We adapted and optimized this technique to generate a pathogenic tick-borne encephalitis virus strain in mice. To define optimal protocol parameters, we injected intramuscularly different amounts of DNA fragments associated, or not, to electroporation. The injection of only 1µg of DNA fragments combined with electroporation resulted in an infection rate of 100%. Then, these parameters were applied to rescue another flavivirus and an alphavirus.

This method provides a novel and efficient strategy forin vivoviral generation, which is typically achieved by injecting infectious clones. Furthermore, as part of the development of DNA- launched live attenuated vaccines, this approach, which also has the advantage of not injecting vector DNA, may simplify the generation of attenuated strainsin vivo.
Low-frequency ERK and Akt activity dynamics are predictive of stochastic cell division events
Authors: Bennett Jamie J. R. , Stern Alan D. , Zhang Xiang , Birtwistle Marc R. , Pandey Gaurav
Published: January 2024

Understanding the dynamics of intracellular signaling pathways, such as ERK1/2 (ERK) and Akt1/2 (Akt), in the context of cell fate decisions is important for advancing our knowledge of cellular processes and diseases, particularly cancer. While previous studies have established associations between ERK and Akt activities and proliferative cell fate, the heterogeneity of single-cell responses adds complexity to this understanding. This study employed a data-driven approach to address this challenge, developing machine learning models trained on a dataset of growth factor-induced ERK and Akt activity time courses in single cells, to predict cell division events. The most effective predictive models were developed by applying discrete wavelet transforms (DWTs) to extract low-frequency features from the time courses, followed by using Ensemble Integration, an effective data integration and predictive modeling framework. The results demonstrated that these models effectively predicted cell division events in MCF10A cells (F-measure=0.524, AUC=0.726). ERK dynamics were found to be more predictive than Akt, but the combination of both measurements further enhanced predictive performance. The ERK model’s performance also generalized to predicting division events in RPE cells, indicating the potential applicability of these models and our data-driven methodology for predicting cell division across different biological contexts. Interpretation of these models suggested that ERK dynamics throughout the cell cycle, rather than immediately after growth factor stimulation, were associated with the likelihood of cell division. Overall, this work contributes insights into the predictive power of intra-cellular signaling dynamics for cell fate decisions, and highlights the potential of machine learning approaches in unraveling complex cellular behaviors.
Pharmacological manipulations of the dorsomedial and dorsolateral striatum during fear extinction have opposing effects on fear renewal
Authors: Tanner Margaret K , Hohorst Alyssa A , Westerman Jessica , Mendoza Carolina Sanchez , Han Rebecca , Moya Nicolette A , Jaime Jennifer , Alvarez Lareina M , Dryden Miles , Balolia Aleezah , Abdul Remla , Loetz Esteban C , Greenwood Benjamin N
Published: January 2024

Systemic manipulations that enhance dopamine (DA) transmission around the time of fear extinction can strengthen fear extinction and reduce conditioned fear relapse. Prior studies investigating the brain regions where DA augments fear extinction focus on targets of mesolimbic and mesocortical DA systems originating in the ventral tegmental area, given the role of these DA neurons in prediction error. The dorsal striatum (DS), a primary target of the nigrostriatal DA system originating in the substantia nigra (SN), is implicated in behaviors beyond its canonical role in movement, such as reward and punishment, goal-directed action, and stimulus-response associations, but whether DS DA contributes to fear extinction is unknown. We have observed that chemogenetic stimulation of SN DA neurons during fear extinction prevents the return of fear in contexts different from the extinction context, a form of relapse called renewal. This effect of SN DA stimulation is mimicked by a DA D1 receptor (D1R) agonist injected into the DS, thus implicating DS DA in fear extinction. Different DS subregions subserve unique functions of the DS, but it is unclear where in the DS D1R agonist acts during fear extinction to reduce renewal. Furthermore, although fear extinction increases neural activity in DS subregions, whether neural activity in DS subregions is causally involved in fear extinction is unknown. To explore the role of DS subregions in fear extinction, adult, male Long-Evans rats received microinjections of either the D1R agonist SKF38393 or a cocktail consisting of GABAA/GABABreceptor agonists muscimol/baclofen selectively into either dorsomedial (DMS) or dorsolateral (DLS) DS subregions immediately prior to fear extinction, and extinction retention and renewal were subsequently assessed drug-free. While increasing D1R signaling in the DMS during fear extinction did not impact fear extinction retention or renewal, DMS inactivation reduced later renewal. In contrast, DLS inactivation had no effect on fear extinction retention or renewal but increasing D1R signaling in the DLS during extinction reduced fear renewal. These data suggest that DMS and DLS activity during fear extinction can have opposing effects on later fear renewal, with the DMS promoting renewal and the DLS opposing renewal. Mechanisms through which the DS could influence the contextual gating of fear extinction are discussed.

Highlights

Dorsolateral striatum D1 receptor signaling during fear extinction reduces renewal

Neural activity in the dorsomedial striatum during fear extinction permits renewal

Dorsal striatum subregions have opposing roles in contextual gating of fear extinction

Graphical Abstract
Group A Streptococcal Collagen-like Protein 1 Restricts Tumor Growth in Murine Pancreatic Adenocarcinoma and Inhibits Cancer-Promoting Neutrophil Extracellular Traps
Authors: Henderson Emily A. , Ivey Abby , Choi Soo , Santiago Stell , McNitt Dudley , Liu Tracy W. , Lukomski Slawomir , Boone Brian A.
Published: January 2024

Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer associated with an immunosuppressive environment. Neutrophil extracellular traps (NETs) were initially described in the context of infection but have more recently been implicated in contributing to the tolerogenic immune response in PDAC. Thus, NETs are an attractive target for new therapeutic strategies. Group A Streptococcus (GAS) has developed defensive strategies to inhibit NETs. In the present work, we propose utilizing intra-tumoral GAS injection to stimulate anti-tumor activity by inhibiting cancer-promoting NETs. Injection of three different M-type GAS strains reduced subcutaneous pancreatic tumor volume compared to control in two different murine PDAC models. Limitation of tumor growth was dependent on streptococcal collagen-like protein 1 (Scl1), as isogenic mutant strain devoid of Scl1 did not reduce tumor size. We further show that Scl1 plays a role in localizing GAS to the tumor site, thereby limiting the systemic spread of bacteria and off-target effects. While mice did elicit a humoral immune response to GAS antigens, tested sera were negative toward Scl1 antigen following intra-tumoral treatment with Scl1-expressing GAS. M1 GAS inhibited NET formation when co-cultured with neutrophils while Scl1-devoid mutant strain did not. Recombinant Scl1 protein inhibited NETsex vivoin a dose-dependent manner by suppressing myeloperoxidase activity. Altogether, we demonstrate that intra-tumoral GAS injections reduce PDAC growth, which is facilitated by Scl1, in part through inhibition of cancer promoting NETs. This work offers a novel strategy by which NETs can be targeted through Scl1 protein and potentiates its use as a cancer therapeutic.
Shared Transcriptomic Signatures of Inflammaging Among Diverse Strains ofDrosophila melanogaster
Authors: Perna Sabrina Isabel , Tang Weihao , Blimbaum Sydney Danielle , Li Andrew , Zhou Lei
Published: January 2024

Background

A prominent hallmark of aging is inflammaging—the increased expression of innate immune genes without identifiable infection. Model organisms with shorter lifespans, such as the fruit fly, provide an essential platform for probing the mechanisms of inflammaging. Multiple groups have reported that, like mammalian models, old flies have significantly higher levels of expression of anti-microbial peptide genes. However, whether some of these genes—or any others—can serve as reliable markers for assessing and comparing inflammaging in different strains remains unclear.

Methods and Results

We compared RNA-Seq datasets generated by different groups. Although the fly strains used in these studies differ significantly, we found that they share a core group of genes with strong aging-associated expression. In addition to anti-microbial peptide genes, we identified other genes that have prominently increased expression in old flies, especiallySPH93. We further showed that machine learning models can be used to predict the “inflammatory age” of the fruit fly.

Conclusion

A core group of genes may serve as markers for studying inflammaging inDrosophila. RNA-Seq profiles, in combination with machine-learning models, can be applied to measure the acceleration or deceleration of inflammaging.
Intestinal barrier function in the naked mole-rat: an emergent model for gastrointestinal insights
Authors: Aguilera-Lizarraga Javier , Ritoux Anne , Bulmer David C. , Smith Ewan St. John
Published: January 2024

The intestinal barrier plays a crucial role in homeostasis, both by facilitating absorption of nutrients and fluids, and providing a tight shield to prevent the invasion by either pathogen or commensal microorganisms. Intestinal barrier malfunction is associated with systemic inflammation, oxidative stress, and decreased insulin sensitivity, which may lead to the dysregulation of other tissues. Therefore, a deeper understanding of physiological aspects related to an enhanced barrier function is of significant scientific and clinical relevance. The naked mole-rat has many unusual biological features, including attenuated colonic neuron sensitivity to acid and bradykinin, and resistance to chemical-induced intestinal damage. However, insight into their intestinal barrier physiology is scarce. Here, we observed notable macroscopic and microscopic differences in intestinal tissue structure between naked mole-rats and mice. Moreover, naked mole-rats showed increased number of larger goblet cells and elevated mucus content. In measuring gut permeability, naked mole-rats showed reduced permeability compared to mice, measured as transepithelial electrical resistance, especially in ileum. Furthermore, intestinal ion secretion induced by serotonin, bradykinin, histamine, and capsaicin was significantly reduced in naked mole-rats compared to mice, despite the expression of receptors for all these agonists. In addition, naked mole-rats exhibited reduced pro-secretory responses to the non-selective adenylate cyclase activator forskolin. Collectively, these findings indicate that naked mole-rats possess a robust and hard-to-penetrate gastrointestinal barrier, that is resistant to environmental and endogenous irritants. Naked mole-rats may therefore provide valuable insights into the physiology of the intestinal barrier and set the stage for the development of innovative and effective therapies.

Graphical abstract
A new class of human CpG island promoters with primate-specific repeats
Authors: Mohan K Naga , Anne Anuhya , Kumar Lov , Chaillet J Richard
Published: January 2024

A subset of imprinting control regions (ICRs) in the human and mouse possess CpG islands associated with imperfect tandem repeats (TRs) that were shown to be essential for genomic imprinting through genetic studies. To identify whether this feature is also present in non-imprinted CpG island promoters, we performed extensive dot plot analyses and identified 365 CpG island gene promoters associated with imperfect TRs of ≥ 400nt. These TRs are absent in the orthologous mouse CGI promoters, and most occur as clusters at the human chromosome ends, distinct from the clusters of imprinted genes. These genes showed an enrichment in neurodevelopmental/behavioral disorders and show interindividual variation in methylation levels. A subset of TR-CGIs is highly methylated and remains so during reprogramming to primed iPSCs, but become unmethylated in naïve iPSCs, as has been shown for the ICRs. Transcript levels correlate with methylation levels for some TR-CGI genes suggesting their gene regulatory potential. Orthologs of the subset of methylated TR-CGIs are unmethylated in mouse, suggesting the role of TRs in imparting methylation in humans. The human TR-CGIs accompanied primate evolution after divergence from the rodent lineage with evidence of recent additions in human evolution. In summary, the incorporation of TRs in certain CGI promoters in primate evolution results in the unique ability to acquire methylation during embryonic development and resist reprogramming to a pluripotent stem cell state with a possible effect on gene expression.
Cholinergic neuromodulation of prefrontal attractor dynamics controls performance in spatial working memory
Authors: Mahrach Alexandre , Bestue David , Qi Xue-Lian , Constantinidis Christos , Compte Albert
Published: January 2024

The behavioral and neural effects of the endogenous release of acetylcholine following stimulation of the Nucleus Basalis of Meynert (NB) have been recently examined (Qi et al. 2021). Counterintuitively, NB stimulation enhanced behavioral performance while broadening neural tuning in the prefrontal cortex (PFC). The mechanism by which a weaker mnemonic neural code could lead to better performance remains unclear. Here, we show that increased neural excitability in a simple continuous bump attractor model can induce broader neural tuning and decrease bump diffusion, provided neural rates are saturated. Increased memory precision in the model overrides memory accuracy, improving overall task performance. Moreover, we show that bump attractor dynamics can account for the nonuniform impact of neuromodulation on distractibility, depending on distractor distance from the target. Finally, we delve into the conditions under which bump attractor tuning and diffusion balance in biologically plausible heterogeneous network models. In these discrete bump attractor networks, we show that reducing spatial correlations or enhancing excitatory transmission can improve memory precision. Altogether, we provide a mechanistic understanding of how cholinergic neuromodulation controls spatial working memory through perturbed attractor dynamics in PFC.

Significance statement

Acetylcholine has been thought to improve cognitive performance by sharpening neuronal tuning in prefrontal cortex. Recent work has shown that electrical stimulation of the cholinergic forebrain in awake-behaving monkeys induces a reduction in prefrontal neural tuning under stimulation conditions that improve performance. To reconcile these divergent observations, we provide network simulations showing that these derive consistently from specific conditions in prefrontal attractor dynamics: firing rate saturation leads to increased storage precision and reduced neural tuning upon cholinergic activation via an increase in neural excitability, a reduction in neural correlations, and an increase in excitatory transmission. Our study integrates previously reported data into a consistent mechanistic view of how acetylcholine controls spatial working memory via attractor network dynamics in prefrontal cortex.
Niche partitioning in a cyanobacterium through divergence of its novel chlorophylld-based light-harvesting system
Authors: Ulrich Nikea J. , Shen Gaozhong , Bryant Donald A. , Miller Scott R.
Published: January 2024

The evolution of novel traits can have important consequences for biological diversification. New ecological opportunities provided by a novel trait can trigger subsequent trait modification or niche partitioning; however, the underlying mechanisms of novel trait diversification are still poorly understood. Here, we report that the innovation of a new chlorophyll (Chl) pigment, Chld,by the cyanobacteriumAcaryochloris marinawas followed by the functional divergence of its light-harvesting complex. We identified three major photosynthetic spectral types based on Chl fluorescence properties forA. marinalaboratory strains, with shorter and longer wavelength types more recently derived from an ancestral intermediate phenotype. Members of the different spectral types exhibited extensive variation in the Chl-binding proteins as well as the Chl energy levels of their photosynthetic complexes. This spectral type divergence is associated with differences in the wavelength dependence of both growth rate and photosynthetic oxygen evolution. We conclude that the divergence of the light-harvesting apparatus has consequently impactedA. marinaecological diversification through specialization on different far-red photons for photosynthesis.
Spectrally Resolved Localization Microscopy with Ultrahigh-Throughput
Authors: Batey James Ethan , Kim Geun Wan , Yang Meek , Heffer Darby Claire , Pott Elric Dion , Giang Hannah , Dong Bin
Published: January 2024

Single-molecule localization microscopy (SMLM) has become a strong technique in the toolbox of chemists, biologists, physicists, and engineers in recent years for its unique ability to resolve characteristic features quickly and accurately in complex environments at the nanoscopic level. Multicolor super-resolution imaging has seen the greatest advancement among SMLM techniques, drastically improving the differentiation ability of nanostructures beyond the diffraction limit and increasing the resolution with which previously unresolvable structures are studied. However, current multicolor SMLM methodologies present low spatial resolution and throughput and require complex optical systems. Here, we overcome these drawbacks by developing an ultrahigh-throughput SMLM methodology that allows for ultrahigh throughput multicolor imaging at the nanoscopic level using a color glass filter. Our methodology can readily distinguish fluorophores of close spectral emission and achieves sub-10 nm localization and sub-5nm spectral precisions.
Modular Phoneme Processing in Human Superior Temporal Gyrus
Authors: Cleary Daniel R. , Tchoe Youngbin , Bourhis Andrew , Dickey Charles W. , Stedelin Brittany , Ganji Mehran , Lee Sang Hoen , Lee Jihwan , Siler Dominic A. , Brown Erik C. , Rosen Burke Q. , Kaestner Erik , Yang Jimmy C. , Soper Daniel J. , Han Seunggu Jude , Paulk Angelique C. , Cash Sydney S. , Raslan Ahmed M. T. , Dayeh Shadi A. , Halgren Eric
Published: January 2024

Modular organization is fundamental to cortical processing, but its presence is human association cortex is unknown. We characterized phoneme processing with 128-1024 channel micro-arrays at 50-200μm pitch on superior temporal gyrus of 7 patients. High gamma responses were highly correlated within ∼1.7mm diameter modules, sharply delineated from adjacent modules with distinct time-courses and phoneme-selectivity. We suggest that receptive language cortex may be organized in discrete processing modules.
miRNA family miR-29 inhibits PINK1-PRKN dependent mitophagy via ATG9A
Authors: Markham Briana N , Ramnarine Chloe , Kim Songeun , Grever William E , Soto-Beasley Alexandra I , Heckman Michael , Ren Yingxue , Osborne Andrew C , Bhagwate Aditya V , Liu Yuanhang , Wang Chen , Kim Jungsu , Wszolek Zbigniew K , Ross Owen A , Springer Wolfdieter , Fiesel Fabienne C
Published: January 2024

Loss-of-function mutations in the genes encoding PINK1 and PRKN result in early-onset Parkinson disease (EOPD). Together the encoded enzymes direct a neuroprotective pathway that ensures the elimination of damaged mitochondria via autophagy.

We performed a genome-wide high content imaging miRNA screen for inhibitors of the PINK1-PRKN pathway and identified all three members of the miRNA family 29 (miR-29). Using RNAseq we identified target genes and found that siRNA against ATG9A phenocopied the effects of miR-29 and inhibited the initiation of PINK1-PRKN mitophagy. Furthermore, we discovered two rare, potentially deleterious, missense variants (p.R631W and p.S828L) in our EOPD cohort and tested them experimentally in cells. While expression of wild-type ATG9A was able to rescue the effects of miR-29a, the EOPD-associated variants behaved like loss-of-function mutations.

Together, our study validates miR-29 and its target gene ATG9A as novel regulators of mitophagy initiation. It further serves as proof-of-concept of finding novel, potentially disease-causing EOPD-linked variants specifically in mitophagy regulating genes. The nomination of genetic variants and biological pathways is important for the stratification and treatment of patients that suffer from devastating diseases, such as EOPD.
Acyltransferases in the first step of glycerophospholipid synthesis have redundant and non-redundant roles insn-1 acyl chain regulation, ether lipid levels, and cell survival
Authors: Salame Sarah , Qasmaoui Hasna , Jose Gregor P , Fleuriot Lucile , Debayle Delphine , Harayama Takeshi
Published: January 2024

The increased use of lipidomics analyses in biomedical research made it crucial to understand correctly how lipid compositions are regulated. Lipid acyl chains are important regulators of membrane physicochemical properties, and are incorporated by various acyltransferases. The acyltransferases implicated in the first step of glycerophospholipid synthesis, the GPATs and GNPAT, have distinct localizations and substrate preferences. This suggests that they have distinct roles on lipid regulation, but a complete understanding of their redundant and non-redundant functions is missing. We report here a comprehensive analysis of cells having mutations in GPATs and GNPAT, either alone or in combinations. Our results suggest that the balance between GPATs and GNPAT affect the levels of ether lipids, together with glycerophospholipid acyl chain length and unsaturation. In addition, we found that lipid synthesis initiated at peroxisomes, but not mitochondria, is sufficient to provide the lipid synthesis flux required for normal cell growth. Our study unveils the multifaceted roles of the first step of de novo glycerophospholipid synthesis, thus leading to a better understanding of how lipidomes are shaped.
MetaCompare 2.0: Differential ranking of ecological and human health resistome risks
Authors: Rumi Monjura Afrin , Oh Min , Davis Benjamin C. , Juvekar Adheesh , Brown Connor L. , Vikesland Peter J. , Pruden Amy , Zhang Liqing
Published: January 2024

Background

While there is increasing recognition of numerous environmental contributions to the spread of antibiotic resistance, quantifying the relative contributions of various sources remains a fundamental challenge. Similarly, there is a need to differentiate acute human health risks corresponding to exposure to a given environment, versus broader ecological risk of evolution and spread of antibiotic resistance genes (ARGs) across microbial taxa. Recent studies have proposed various methods of harnessing the rich information housed by metagenomic data for achieving such aims. Here, we introduce MetaCompare 2.0, which improves upon the original MetaCompare pipeline by differentiating indicators of human health resistome risk (i.e., potential for human pathogens to acquire ARGs) from ecological resistome risk (i.e., overall mobility of ARGs across a given microbiome).

Results

To demonstrate the sensitivity of the MetaCompare 2.0 pipeline, we analyzed publicly available metagenomes representing a broad array of environments, including wastewater, surface water, soil, sediment, and human gut. We also assessed the effect of sequence assembly methods on the risk scores. We further evaluated the robustness of the pipeline to sequencing depth, contig count, and metagenomic library coverage bias through comparative analysis of a range of subsamples extracted from a set of deeply sequenced wastewater metagenomes. The analysis utilizing samples from different environments demonstrated that MetaCompare 2.0 consistently produces lower risk scores for environments with little human influence and higher risk scores for human contaminated environments affected by pollution or other stressors. We found that the ranks of risk scores were not measurably affected by different assemblers employed. The Meta-Compare 2.0 risk scores were remarkably consistent despite varying sequencing depth, contig count, and coverage.

Conclusion

MetaCompare 2.0 successfully ranked a wide array of environments according to both human health and ecological resistome risks, with both scores being strongly impacted by anthropogenic stress. We packaged the improved pipeline into a publicly-available web service that provides an easy-to-use interface for computing resistome risk scores and visualizing results. The web service is available athttp://metacompare.cs.vt.edu/
Modeling and Correction of Protein Conformational Disease in iPSC-derived Neurons through Personalized Base Editing
Authors: Konishi Colin T , Mulaiese Nancy , Butola Tanvi , Zhang Qinkun , Kagan Dana , Yang Qiaoyan , Pressler Mariel , Dirvin Brooke G , Devinsky Orrin , Basu Jayeeta , Long Chengzu
Published: January 2024

Abstract

Altered protein conformation can cause incurable neurodegenerative disorders. Mutations inSERPINI1, the gene encoding neuroserpin, can alter protein conformation resulting in cytotoxic aggregation leading to neuronal death. Familial encephalopathy with neuroserpin inclusion bodies (FENIB) is a rare autosomal dominant progressive myoclonic epilepsy that progresses to dementia and premature death. We developed HEK293T and induced pluripotent stem cell (iPSC) models of FENIB, harboring a patient-specific pathogenicSERPINI1variant or stably overexpressing mutant neuroserpin fused to GFP (MUT NS-GFP). Here, we utilized a personalized adenine base editor (ABE)-mediated approach to correct the pathogenic variant efficiently and precisely to restore neuronal dendritic morphology. ABE-treated MUT NS-GFP cells demonstrated reduced inclusion size and number. Using an inducible MUT NS-GFP neuron system, we identified early prevention of toxic protein expression allowed aggregate clearance, while late prevention halted further aggregation. To address several challenges for clinical applications of gene correction, we developed a neuron-specific engineered virus-like particle to optimize neuronal ABE delivery, resulting in higher correction efficiency. Our findings provide a targeted strategy which may treat FENIB and potentially other neurodegenerative diseases due to altered protein conformation such as Alzheimer’s and Huntington’s diseases.
Microfluidic platform enables shear-less aerosolization of lipid nanoparticles for messenger RNA inhalation
Authors: Kim Jeonghwan , Jozic Antony , Bloom Elissa , Jones Brian , Marra Michael , Murthy Namratha Turuvekere Vittala , Eygeris Yulia , Sahay Gaurav
Published: January 2024

Leveraging the extensive surface area of the lungs for gene therapy, inhalation route offers distinct advantages for delivery. Clinical nebulizers that employ vibrating mesh technology are the standard choice for converting liquid medicines into aerosols. However, they have limitations when it comes to delivering mRNA through inhalation, including severe damage to nanoparticles due to shearing forces. Here, we introduce a novelmicrofluidic aerosolization platform(MAP) that preserves the structural and physicochemical integrity of lipid nanoparticles, enabling safe and efficient mRNA delivery to the respiratory system. Our results demonstrated the superiority of the novel MAP over the conventional vibrating mesh nebulizer, as it avoided problems such as particle aggregation, loss of mRNA encapsulation, and deformation of nanoparticle morphology. Notably, aerosolized nanoparticles generated by the microfluidic device led to enhanced transfection efficiency across various cell lines.In vivoexperiments with mice that inhaled these aerosolized nanoparticles revealed successful, lung-specific mRNA transfection without observable signs of toxicity. This pioneering MAP represents a significant advancement for the pulmonary gene therapy, enabling precise and effective delivery of aerosolized nanoparticles.
Gut Analysis Toolbox: Automating quantitative analysis of enteric neurons
Authors: Sorensen Luke , Humenick Adam , Poon Sabrina S.B. , Han Myat Noe , Mahdavian Narges Sadat , Hamnett Ryan , Gómez-de-Mariscal Estibaliz , Neckel Peter H. , Saito Ayame , Mutunduwe Keith , Glennan Christie , Haase Robert , McQuade Rachel M. , Foong Jaime P.P. , Brookes Simon J.H. , Kaltschmidt Julia A. , Muñoz-Barrutia Arrate , King Sebastian K. , Veldhuis Nicholas A. , Carbone Simona E. , Poole Daniel P. , Rajasekhar Pradeep
Published: January 2024

The enteric nervous system (ENS) plays an important role in coordinating gut function. The ENS consists of an extensive network of neurons and glial cells within the wall of the gastrointestinal tract. Alterations in neuronal distribution, function, and type are strongly associated with enteric neuropathies and gastrointestinal (GI) dysfunction and can serve as biomarkers for disease. However, current methods for assessing neuronal counts and distribution suffer from undersampling. This is partly due to challenges associated with imaging and analyzing large tissue areas, and operator bias due to manual analysis. Here, we present the Gut Analysis Toolbox (GAT), an image analysis tool designed for characterization of enteric neurons and their neurochemical coding using 2D images of GI wholemount preparations. GAT is developed for the Fiji distribution of ImageJ. It has a user-friendly interface and offers rapid and accurate cell segmentation. Custom deep learning (DL) based cell segmentation models were developed using StarDist. GAT also includes a ganglion segmentation model which was developed using deepImageJ. In addition, GAT allows importing of segmentation generated by other software. DL models have been trained using ZeroCostDL4Mic on diverse datasets sourced from different laboratories. This captures the variability associated with differences in animal species, image acquisition parameters, and sample preparation across research groups. We demonstrate the robustness of the cell segmentation DL models by comparing them against the state-of-the-art cell segmentation software, Cellpose. To quantify neuronal distribution GAT applies proximal neighbor-based spatial analysis. We demonstrate how the proximal neighbor analysis can reveal differences in cellular distribution across gut regions using a published dataset. In summary, GAT provides an easy-to-use toolbox to streamline routine image analysis tasks in ENS research. GAT enhances throughput allowing unbiased analysis of larger tissue areas, multiple neuronal markers and numerous samples rapidly.
Using variable data independent acquisition for capillary electrophoresis-based untargeted metabolomics
Authors: Kiuchi Saki , Otoguro Yasuhiro , Nitta Tomoaki , Chung Mi Hwa , Nakaya Taiki , Matsuzawa Yuki , Oobuchi Katsuya , Sasaki Kazunori , Yamamoto Hiroyuki , Tsugawa Hiroshi
Published: January 2024

Capillary electrophoresis coupled with tandem mass spectrometry (CE-MS/MS) offers advantages in peak capacity and sensitivity for metabolic profiling, owing to the electroosmotic flow-based separation. However, the utilization of data-independent MS/MS acquisition (DIA) is restricted due to the absence of an optimal procedure for analytical chemistry and its related informatics framework. We assessed the mass spectral quality using two DIA techniques, namely, all-ion fragmentation (AIF) and variable DIA (vDIA), to isolate 60∼800 Da precursor ions with respect to annotation rates. Our findings indicate that vDIA, coupled with the updated MS-DIAL chromatogram deconvolution algorithm, yields higher spectral matching scores and annotation rates compared to AIF. Additionally, we evaluated a linear migration time (MT) correction method using internal standards to accurately align chromatographic peaks in a dataset. After the correction, the peaks exhibited less than 0.1 min MT drifts, a difference mostly equivalent to that of conventional reverse-phase liquid chromatography techniques. Moreover, we conducted MT prediction for metabolites recorded in mass spectral libraries and metabolite structure databases containing a total of 469,870 compounds, achieving an accuracy of less than 1.5 min root mean squares. Thus, our platform provides a peak annotation platform utilizing MT information, accurate precursorm/z, and the MS/MS spectrum recommended by the metabolomics standards initiative. Applying this procedure, we investigated metabolic alterations in lipopolysaccharide (LPS)-induced macrophages, characterizing 170 metabolites. Furthermore, we assigned metabolite information to unannotated peaks using anin-silicostructure elucidation tool, MS-FINDER. The results were integrated into the nodes in the molecular spectrum network based on the MS/MS similarity score. Consequently, we identified a significantly increased amount of metabolites in the LPS-administration group, glycinamide ribonucleotide, not present in any spectral libraries. Additionally, we retrieved metabolites of false-negative hits in the initial spectral annotation procedure. Overall, our study underscores the potential of CE-MS/MS with DIA and computational mass spectrometry techniques for metabolic profiling.
Behavioral economic strategies to increase naloxone acquisition and carrying
Authors: Feuerstein-Simon Rachel , Dolan Abby , Sharma Meghana , Lowenstein Margaret W. , Buttenheim Alison M. , Meisel Zachary F. , Cannuscio Carolyn C.
Published: January 2024

Background

The opioid overdose crisis claimed over 80,000 American lives in 2019, with opioids implicated in the majority of these deaths. The COVID-19 pandemic has exacerbated the crisis, with challenges arising from the increased use of fentanyl, synthetic opioids, and combined opioid-stimulant substances. Urgent strategies are required to mitigate drug-related harms in the context of an unsafe drug supply.

Objective

This paper presents the findings of two consecutive randomized controlled trials conducted in Philadelphia, aiming to assess the effectiveness of behavioral economic interventions in promoting naloxone acquisition and carrying among adults.

Methods

The trials focused on increasing naloxone acquisition (Study A) and promoting naloxone carrying (Study B) among participants who completed community-based overdose recognition and reversal training. Participants were randomized into three arms: those receiving text message nudges, those signing commitment contracts, and a control group receiving only in-person overdose reversal training. Data collection utilized a web-based platform, and participants were compensated upon study completion.

Results

In Study A, participants were encouraged to acquire naloxone, and the primary endpoint was naloxone acquisition within four weeks post-training. Results showed that around one in five participants acquired naloxone, regardless of the intervention arm, indicating limited effectiveness of behavioral strategies in promoting naloxone acquisition.

In Study B, where all participants received naloxone by default, the primary endpoint was the consistency of naloxone carrying. Participants had naloxone on hand at approximately half of the eight unannounced check-ins, with no significant differences between intervention groups and the control group.

Conclusion

Naloxone distribution by default emerges as a promising strategy to increase naloxone possession and save lives amidst the opioid overdose crisis. Addressing structural barriers, including cost and pharmacy availability, is essential. Additionally, interventions should consider leveraging motivations such as altruism and regret aversion to encourage naloxone carrying.