bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-inhibiting percolation and viral spreading in epithelial tissue
Authors: Xu Xiaochan , Nielsen Bjarke Frost , Sneppen Kim
Published: December 2023

SARS-CoV-2 induces delayed type-I/III interferon production, allowing it to escape the early innate immune response. The delay has been attributed to a deficiency in the ability of cells to sense viral replication upon infection, which in turn hampers activation of the antiviral state in bystander cells. Here, we introduce a cellular automaton model to investigate the spatiotemporal spreading of viral infection as a function of virus and host-dependent parameters. The model suggests that the considerable person-to-person heterogeneity in SARS-CoV-2 infections is a consequence of high sensitivity to slight variations in biological parameters near a critical threshold. It further suggests that within-host viral proliferation can be curtailed by the presence of remarkably few cells that are primed for IFN production. Thus the observed heterogeneity in defense readiness of cells reflects a remarkably cost-efficient strategy for protection.
Plant plasmodesmata bridges form through ER-dependent incomplete cytokinesis
Authors: Li Ziqiang P. , Moreau Hortense , Petit Jules D. , Souza-Moraes Tatiana , Smokvarska Marija , Perez-Sancho Jessica , Petrel Melina , Decoeur Fanny , Brocard Lysiane , Chambaud Clément , Grison Magali , Paterlini Andrea , Glavier Marie , Hoornaert Lucie , Joshi Amit S. , Gontier Etienne , Prinz William A. , Jaillais Yvon , Taly Antoine , Campelo Felix , Caillaud Marie-Cécile , Bayer Emmanuelle M.
Published: December 2023

Diverging from conventional cell division models, plant cells undergo incomplete division to generate plasmodesmata communication bridges between daughter cells. While fundamental for plant multicellularity, the molecular events leading to bridge stabilization, as opposed to severing, remain unknown. Using electron tomography, we mapped the transition from cell plate fenestrae to plasmodesmata. We show that the ER connects daughter cells across fenestrae, and as the cell plate matures, fenestrae contract, causing the PM to mold around constricted ER tubes. The ER’s presence prevents fenestrae fusion, forming plasmodesmata, while its absence results in closure. The ER-PM tethers MCTP3, 4, and 6 further stabilize nascent plasmodesmata during fenestrae contraction. Genetic deletion inArabidopsisreduces plasmodesmata formation. Our findings reveal how plants undergo incomplete division to promote intercellular communication.

One-Sentence Summary

The ER is important for stabilizing nascent plasmodesmata, a process integral to incomplete cytokinesis in plants.
Contrasting levels of transcriptome-wide SNP diversity and decoupled patterns of molecular and functional adaptive variation in conifers
Authors: Pavy Nathalie , Gérardi Sébastien , Prunier Julien , Rigault Philippe , Laroche Jérôme , Daigle Gaétan , Boyle Brian , Mackay John , Bousquet Jean
Published: December 2023

Adaptive convergence can arise when response to natural selection involves shared molecular or functional mechanisms among multiple taxa. Conifers are of ancient origin with delayed sexual maturity related to their woody perennial nature. Thus, they represent a relevant plant group to assess if convergence from selection may have become disconnected between molecular and functional levels. In this purpose, transcriptome-wide SNP diversity was assessed in seven partially sympatric and reproductively isolated conifer species populating the temperate and boreal forests of northeastern North America. SNP diversity was found highly heterogeneous among species, which would relate to variation in species-specific demography and history. Rapidly evolving genes with signatures of positive selection were identified, and their relative abundance among species reflected differences in transcriptome-wide SNP diversity. Their analysis also revealed very limited convergence among taxa in spite of sampling same tissues at same age. However, convergence increased gradually at the levels of gene families and biological processes, which were largely related to stress response and regulatory mechanisms in all species. Given their multiple small to large gene families and long time since inception, conifers may have had sufficient gene network flexibility and gene functional redundancy for evolving alternative adaptive genes for similar metabolic responses to environmental selection pressures. Despite a long divergence time of ∼350 Mya between conifers and Angiosperms, we also uncovered a set of 20 key genes presumably under positive selection in both lineages.
Human neuron subtype programming through combinatorial patterning with scRNA-seq readouts
Authors: Lin Hsiu-Chuan , Janssens Jasper , Kroell Ann-Sophie , Hornauer Philipp , Santel Malgorzata , Okamoto Ryoko , Karava Kyriaki , Priouret Marthe , Garcia Maria Pascual , Schroeter Manuel , Camp J. Gray , Treutlein Barbara
Published: December 2023

Human neurons programmed through transcription factor (TF) overexpression model neuronal differentiation and neurological diseases. However, programming specific neuron types remains challenging. Here, we modulate developmental signaling pathways combined with TF overexpression to explore the spectrum of neuron subtypes generated from pluripotent stem cells. We screened 480 morphogen signaling modulations coupled with NGN2 or ASCL1/DLX2 induction using a multiplexed single-cell transcriptomic readout. Analysis of 700,000 cells identified diverse excitatory and inhibitory neurons patterned along the anterior-posterior and dorsal-ventral axes of neural tube development. We inferred signaling and TF interaction networks guiding differentiation of forebrain, midbrain, hindbrain, spinal cord, peripheral sympathetic and sensory neurons. Our approach provides a strategy for cell subtype programming and to investigate how cooperative signaling drives neuronal fate.
In vivo mapping of protein-protein interactions of schizophrenia risk factors generates an interconnected disease network
Authors: McClatchy Daniel B. , Powell Susan B. , Yates John R.
Published: December 2023

Genetic analyses of Schizophrenia (SCZ) patients have identified thousands of risk factors. In silico protein-protein interaction (PPI) network analysis has provided strong evidence that disrupted PPI networks underlie SCZ pathogenesis. In this study, we performedin vivoPPI analysis of several SCZ risk factors in the rodent brain. Using endogenous antibody immunoprecipitations coupled to mass spectrometry (MS) analysis, we constructed a SCZ network comprising 1612 unique PPI with a 5% FDR. Over 90% of the PPI were novel, reflecting the lack of previous PPI MS studies in brain tissue. Our SCZ PPI network was enriched with known SCZ risk factors, which supports the hypothesis that an accumulation of disturbances in selected PPI networks underlies SCZ. We used Stable Isotope Labeling in Mammals (SILAM) to quantitate phencyclidine (PCP) perturbations in the SCZ network and found that PCP weakened most PPI but also led to some enhanced or new PPI. These findings demonstrate that quantitating PPI in perturbed biological states can reveal alterations to network biology.
Simple and Highly Specific Targeting of Resident Microglia with Adeno-Associated Virus
Authors: Serrano Carolina , Cananzi Sergio , Shen Tianjin , Wang Lei-Lei , Zhang Chun-Li
Published: December 2023

Microglia, as the immune cells of the central nervous system (CNS), play dynamic roles in both health and diseased conditions. The ability to genetically target microglia using viruses is crucial for understanding their functions and advancing microglia-based treatments. We here show that resident microglia can be simply and specifically targeted using adeno-associated virus (AAV) vectors containing a 466-bp DNA fragment from the humanIBA1(hIBA1) promoter. This targeting approach is applicable to both resting and reactive microglia. When combining the shorthIBA1promoter with the target sequence of miR124, up to 95% of transduced cells are identified as microglia. Such a simple and highly specific microglia-targeting strategy may be further optimized for research and therapeutics.

Significance Statement

Brain microglia play critical roles in human health and diseases. Genetic manipulation of these cells will offer numerous therapeutic opportunities. However, there is a lack of relevant strategies to target these cells with high specificity since they are traditionally considered to be refractory to virus transduction. Through in vivo screening of many promoters, this study identified a short promoter from the humanIBA1gene. When incorporated into lentivirus or adeno-associated virus vectors, this promoter proves effective in driving gene expression with high specificity for brain microglia. Such a simple strategy will facilitate specific approaches for microglia-based research.
Effects of auditory noise intensity and color on the dynamics of upright stance
Authors: Carey Sam , Ross Jessica M. , Abney Drew , Balasubramaniam Ramesh
Published: December 2023

Previous work assessing the effect of additive noise on the postural control system has found a positive effect of white noise on postural dynamics. This study covers two separate experiments that were run sequentially to better understand how the structure of the additive noise signal affects postural dynamics, while also furthering our knowledge of how the intensity of auditory stimulation of noise may elicit this phenomenon. Across the two experiments, we introduced three auditory noise stimulations of varying structure (white, pink, and brown noise). Experiment 1 presented the stimuli at 35 dB while Experiment 2 was presented at 75 dB. Our findings demonstrate a decrease in variability of the postural control system regardless of the structure of the noise signal presented, but only for high intensity auditory stimulation.
Unfolding and De-confounding: Biologically meaningful causal inference from longitudinal multi-omic networks usingMETALICA
Authors: Ruiz-Perez Daniel , Gimon Isabella , Sazal Musfiqur , Mathee Kalai , Narasimhan Giri
Published: December 2023

A key challenge in the analysis of microbiome data is the integration of multi-omic datasets and the discovery of interactions between microbial taxa, their expressed genes, and the metabolites they consume and/or produce. In an effort to improve the state-of-the-art in inferring biologically meaningful multi-omic interactions, we sought to address some of the most fundamental issues in causal inference from longitudinal multi-omics microbiome data sets. We developed METALICA, a suite of tools and techniques that can infer interactions between microbiome entities. METALICA introduces novelunrollingandde-confoundingtechniques used to uncover multi-omic entities that are believed to act as confounders for some of the relationships that may be inferred using standard causal inferencing tools. The results lend support to predictions about biological models and processes by which microbial taxa interact with each other in a microbiome. Theunrollingprocess helps to identify putative intermediaries (genes and/or metabolites) to explain the interactions between microbes; thede-confoundingprocess identifies putative common causes that may lead to spurious relationships to be inferred. METALICA was applied to the networks inferred by existing causal discovery and network inference algorithms applied to a multi-omics data set resulting from a longitudinal study of IBD microbiomes. The most significant unrollings and de-confoundings were manually validated using the existing literature and databases.

Importance

We have developed a suite of tools and techniques capable of inferring interactions between microbiome entities. METALICAintroduces novel techniques called unrolling and de-confounding that are employed to uncover multi-omic entities considered to be confounders for some of the relationships that may be inferred using standard causal inferencing tools. To evaluate our method, we conducted tests on the Inflammatory Bowel Disease (IBD) dataset from the iHMP longitudinal study, which we pre-processed in accordance with our previous work.
Seasonal and environmental factors contribute to the variation in the gut microbiome: a large-scale study of a small bird
Authors: Liukkonen Martta , Muriel Jaime , Martínez-Padilla Jesús , Nord Andreas , Pakanen Veli-Matti , Rosivall Balázs , Tilgar Vallo , van Oers Kees , Grond Kirsten , Ruuskanen Suvi
Published: December 2023

Environmental variation can shape the gut microbiome, but majority of studies use captive-bred species, while data on large-scale variation in the gut microbiome and the associated environmental factors is lacking. Furthermore, previous studies have limited taxonomical coverage, and for example knowledge about avian gut microbiomes is still scarce. We investigated large-scale environmental variation in the gut microbiome of wild adult great tits across the species’ European distribution range. Our results show that gut microbiome diversity is higher during winter and that there are compositional differences between winter and summer gut microbiomes. During winter, individuals inhabiting mixed forest habitat show higher gut microbiome diversity, whereas there was no similar association during summer. Also, temperature was found to be a small contributor to compositional differences in the gut microbiome. We did not find significant differences in the gut microbiome among populations, nor any association between latitude, rainfall, and the gut microbiome. The results suggest that there is a seasonal change in wild avian gut microbiomes, but that there are still many unknown factors that shape the gut microbiome of wild bird populations.
Bias-corrected serum creatinine from UK Biobank electronic medical records generates an important data resource for kidney function trajectories
Authors: Gorski Mathias , Wiegrebe Simon , Burkhardt Ralph , Behr Merle , Küchenhoff Helmut , Stark Klaus J. , Böger Carsten A. , Heid Iris M.
Published: December 2023

BACKGROUND

Loss of kidney function is a substantial personal and public health burden. Kidney function is typically assessed as estimated glomerular filtration rate (eGFR) based on serum creatinine. Emerging electronic Medical Records (eMR) in UK Biobank present a promising resource to augment the data on longitudinal eGFR based on study center visits (SC; n=15,000). However, it is unclear whether eMR-based creatinine values can be used for research on eGFR trajectories.

METHODS

We derived eMR-based serum creatinine values (various assays/labs, Jaffe or enzymatic) from UK Biobank “GP-clinical”. We compared these with SC-based creatinine in individuals with both measurements available in the same calendar year (n=70,231; 2007-2012).

RESULTS

We found a multiplicative bias for eMR-based creatinine that was large, factor 0.84, for 2007, and decreased over time (0.97 for 2013). Deriving eGFR based on SC- and bias-corrected eMR-creatinine (CKD-Epi 2021) yielded 454,907 individuals with ≥1eGFR assessment (2,102,174 assessments). This included 206,063 individuals with ≥2 assessments (median=6.00 assessments) for a time between 1stand last assessment of up to 60.2 years (median time=8.7 years). We enriched the dataset with eMR-recorded kidney-relevant events from “GP-clinical” (Acute Kidney Injury, End stage Kidney Disease, Nephrectomy, Dialysis, Kidney Transplant, Pregnancy, and Diabetes). We illustrated the suitability of this data: e.g. we found an annual eGFR decline of 1.04 mL/min/1.73m²/year (95%-CI=1.03-1.05), in line with literature and a four-fold steeper decline following Acute Kidney Injury.

CONCLUSIONS

In summary, our bias-correction of eMR-based creatinine values enabled a 4-fold increase in the number eGFR assessments in UK Biobank suitable for kidney function research.
A plasma peptidomic signature reveals extracellular matrix remodeling and predicts prognosis in alcohol-related hepatitis
Authors: Sayed Khaled , Dolin Christine E. , Wilkey Daniel W. , Li Jiang , Sato Toshifumi , Beier Juliane I , Argemi Josepmaria , Bataller Ramon , Wahed Abdus S , Merchant Michael L , Benos Panayiotis V , Arteel Gavin E
Published: December 2023

Alcohol-related hepatitis (AH) is plagued with high mortality and difficulty in identifying at-risk patients. The extracellular matrix undergoes significant remodeling during inflammatory liver injury that can be detected in biological fluids and potentially used for mortality prediction. EDTA plasma samples were collected from AH patients (n= 62); Model for End-Stage Liver Disease (MELD) score defined AH severity as moderate (12-20; n=28) and severe (>20; n=34). The peptidome data was collected by high resolution, high mass accuracy UPLC-MS. Univariate and multivariate analyses identified differentially abundant peptides, which were used for Gene Ontology, parent protein matrisomal composition and protease involvement. Machine learning methods were used on patient-specific peptidome and clinical data to develop mortality predictors. Analysis of plasma peptides from AH patients and healthy controls identified over 1,600 significant peptide features corresponding to 130 proteins. These were enriched for ECM fragments in AH samples, likely related to turnover of hepatic-derived proteins. Analysis of moderate versus severe AH peptidomes showed a shift in abundance of peptides from collagen 1A1 and fibrinogen A proteins. The dominant proteases for the AH peptidome spectrum appear to be CAPN1 and MMP12. Increase in hepatic expression of these proteases was orthogonally-validated in RNA-seq data of livers from AH patients. Causal graphical modeling identified four peptides directly linked to 90-day mortality in >90% of the learned graphs. These peptides improved the accuracy of mortality prediction over MELD score and were used to create a clinically applicable mortality prediction assay. A signature based on plasma peptidome is a novel, non-invasive method for prognosis stratification in AH patients. Our results could also lead to new mechanistic and/or surrogate biomarkers to identify new AH mechanisms.

Lay summary

We used degraded proteins found the blood of alcohol-related hepatitis patients to identify new potential mechanisms of injury and to predict 90 day mortality.
Electron-bifurcation and fluoride efflux systems inAcetobacteriumspp. drive defluorination of perfluorinated unsaturated carboxylic acids
Authors: Yu Yaochun , Xu Fengjun , Zhao Weiyang , Thoma Calvin , Che Shun , Richman Jack E. , Jin Bosen , Zhu Yiwen , Xing Yue , Wackett Lawrence , Men Yujie
Published: December 2023

Enzymatic cleavage of C–F bonds in per- and polyfluoroalkyl substances (PFAS) is largely unknown but avidly sought to promote systems biology for PFAS bioremediation. Here, we report the reductive defluorination of α, β-unsaturated per- and polyfluorocarboxylic acids byAcetobacteriumspp. Two critical molecular features inAcetobacteriumspecies enabling reductive defluorination are (i) a functional fluoride efflux transporter (CrcB) and (ii) an electron-bifurcating caffeate reduction pathway (CarABCDE). The fluoride transporter was required for detoxification of released fluoride. Car enzymes were implicated in defluorination by the following evidence: (i) onlyAcetobacteriumspp. withcargenes catalyzed defluorination; (ii) caffeate and PFAS competedin vivo; (iii) models from the X-ray structure of the electron-bifurcating reductase (CarC) positioned the PFAS substrate optimally for reductive defluorination; (iv) products identified by19F-NMR and high-resolution mass spectrometry were consistent with the model. Defluorination biomarkers identified here were found in wastewater treatment plant metagenomes on six continents.
Targeted inCITE-Seq Analysis Identifies the Loss of Nuclear TDP-43 in Endothelium as a Mediator of Blood Brain Barrier Signaling Pathway Dysfunction in Neurodegeneration
Authors: Omar Omar M.F. , Kimble Amy L. , Cheemala Ashok , Tyburski Jordan D. , Pandey Swati , Wu Qian , Reese Bo , Jellison Evan R. , Li Yunfeng , Hao Bing , Yan Riqiang , Murphy Patrick A.
Published: December 2023

Abstract

Despite the importance of the endothelium in the regulation of the blood brain barrier (BBB) in aging and neurodegenerative disease, difficulties in extracting endothelial cell (EC) nuclei have limited analysis of these cells. In addition, nearly all Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Degeneration (FTD), and a large portion of Alzheimer’s Disease (AD) exhibit neuronal TDP-43 aggregation, leading to loss of nuclear function, but whether TDP-43 is similarly altered in human BBB ECs is unknown. Here we utilize a novel technique for the enrichment of endothelial and microglial nuclei from human cortical brain tissues, combined with inCITE-seq, to analyze nuclear proteins and RNA transcripts in a large cohort of healthy and diseased donors. Our findings reveal a unique transcriptional signature in nearly half of the capillary endothelial cells across neurodegenerative states, characterized by reduced levels of nuclear β-Catenin and canonical downstream genes, and an increase in TNF/NF-kB target genes. We demonstrate that this does not correlate with increased nuclear p65/NF-kB, but rather a specific loss of nuclear TDP-43 in these disease associated ECs. Comparative analysis in animal models with targeted disruption of TDP-43 shows that this is sufficient to drive these transcriptional alterations. This work reveals that TDP-43 is a critical governor of the transcriptional output from nuclear p65/NF-kB, which has paradoxical roles in barrier maintenance and also barrier compromising inflammatory responses, and suggests that disease specific loss in ECs contributes to BBB defects observed in the progression of AD, ALS and FTD.
Loss of Endothelial TDP-43 Leads to Blood Brain Barrier Defects in Mouse Models of Amyotrophic Lateral Sclerosis and Frontotemporal Dementia
Authors: Cheemala Ashok , Kimble Amy L. , Tyburski Jordan D. , Leclair Nathan K. , Zuberi Aamir R. , Murphy Melissa , Jellison Evan R. , Reese Bo , Hu Xiangyou , Lutz Cathleen M. , Yan Riqiang , Murphy Patrick A.
Published: December 2023

Loss of nuclear TDP-43 occurs in a wide range of neurodegenerative diseases, and specific mutations in theTARDBPgene that encodes the protein are linked to familial Frontal Temporal Lobar Dementia (FTD), and Amyotrophic Lateral Sclerosis (ALS). Although the focus has been on neuronal cell dysfunction caused by TDP-43 variants,TARDBPmRNA transcripts are expressed at similar levels in brain endothelial cells (ECs). Since increased permeability across the blood brain barrier (BBB) precedes cognitive decline, we postulated that altered functions of TDP-43 in ECs contributes to BBB dysfunction in neurodegenerative disease. To test this hypothesis, we examined EC function and BBB properties in mice with either knock-in mutations found in ALS/FTLD patients (TARDBPG348CandGRNR493X) or EC-specific deletion of TDP-43 throughout the endothelium (Cdh5(PAC)CreERT2; Tardbpff) or restricted to brain endothelium (Slco1c1(BAC)CreERT2; Tardbpff). We found thatTARDBPG348Cmice exhibited increased permeability to 3kDa Texas Red dextran and NHS-biotin, relative to their littermate controls, which could be recapitulated in cultured brain ECs from these mice. Nuclear levels of TDP-43 were reducedin vitroandin vivoin ECs fromTARDBPG348Cmice. This coincided with a reduction in junctional proteins VE-cadherin, claudin-5 and ZO-1 in isolated ECs, supporting a cell autonomous effect on barrier function through a loss of nuclear TDP-43. We further examined two models ofTardbpdeletion in ECs, and found that the loss of TDP-43 throughout the endothelium led to systemic endothelial activation and permeability. Deletion specifically within the brain endothelium acutely increased BBB permeability, and eventually led to hallmarks of FTD, including fibrin deposition, microglial and astrocyte activation, and behavioral defects. Together, these data show that TDP-43 dysfunction specifically within brain ECs would contribute to the BBB defects observed early in the progression of ALS/FTLD.
Stable Cortical Body Maps Before and After Arm Amputation
Authors: Schone Hunter R. , Maimon Mor Roni O. , Kollamkulam Mathew , Szymanska Malgorzata A. , Gerrand Craig , Woollard Alexander , Kang Norbert V. , Baker Chris I. , Makin Tamar R.
Published: December 2023

The adult brain’s capacity for cortical reorganization remains debated. Using longitudinal neuroimaging in three adults, followed up to five years before and after arm amputation, we compared cortical activity elicited by movement of the hand (pre-amputation) versus phantom hand (post-amputation) and lips (pre/post-amputation). We observed stable representations of both hand and lips. By directly quantifying activity changes across amputation, we overturn decades of animal and human research, demonstrating amputation does not trigger large- scale cortical reorganization.
How demography shapes linkage disequilibrium with or without recombination
Authors: Kerdoncuff Elise , Lambert Amaury , Achaz Guillaume
Published: December 2023

Linkage Disequilibrium (LD) is a measure of the statistical association, within a population, between alleles present at different loci. We first briefly explain how LD, and in particular its decay as a function of the genetic distance between the two loci, is expected to be affected by mutation, recombination, selection, drift and demography. We then focus on three specific, widely used measures of LD:D, |D′|, andr2, in three different contexts: absence of recombination, a single recombination event, and an infinite amount of recombination events. We produce detailed characterizations of these three statistics under different demographic scenarios, with simulations, and with analytic results forD. We classify recombination events into four types and rank them according to their respective frequencies and effects. Finally, we provide recommendations for the uses of the different statistics and suggest applications of LD measures in the absence of recombination.
Flexible decision-making is related to strategy learning, vicarious trial and error, and medial prefrontal rhythms during spatial set-shifting
Authors: Miles Jesse T. , Mullins Ginger L. , Mizumori Sheri J. Y.
Published: December 2023

A hallmark of behavioral flexibility is the ability to update behavior in response to changes in context. Most studies tend to rely on error counting around reward contingency or rule switches to measure flexibility, but these measures are difficult to adapt in a way that allows shorter timescale flexibility estimates. Further, choice accuracy does not account for other markers of flexibility, such as the hesitations and decision reversals humans and other animals often exhibit as decisions unfold, a behavior often called vicarious trial and error (VTE). To relate observable information about decision-making to latent aspects like learning and behavioral flexibility, we quantified changes in decision-making strategy using a previously developed, recency-weighted Bayesian inference algorithm. By comparing models of strategy use with decision history to generate strategy likelihood estimates on a trial-by-trial basis, the algorithm enabled us to identify learning points, and served as the basis for the development of a behavioral flexibility score. Aligning flexibility scores to learning points showed that flexibility peaked around estimated learning points and near peaks in VTE rate. However, we occasionally observed VTE during periods of low flexibility, where it often led to incorrect choices, suggesting the likely existence of multiple VTE-types. Additionally, we built on the decades of research suggesting a prominent role for the medial prefrontal cortex in enabling behavioral flexibility by recording field potentials from the medial prefrontal cortex during task performance. We observed changes in different field potential frequency bands that varied with respect to the different behavioral measures we used to characterize learning and decision-making. Overall, we demonstrate the use of multiple measures that jointly assess relationships between learning, behavioral flexibility, and decision-making behaviors. Further, we used these complementary measures to demonstrate that a particular decision-making behavior, VTE, was likely to be a marker of deliberation at some times, and uncertainty at others. Finally, we validate these measures by showing that theta, beta, and gamma rhythms in the medial prefrontal cortex vary with respect to both observable and latent aspects of behavior.
Glucocerebrosidase deficiency leads to neuropathology via cellular immune activation
Authors: Vincow Evelyn S. , Thomas Ruth E. , Milstein Gillian , Pareek Gautam , Bammler Theo , MacDonald James , Pallanck Leo
Published: December 2023

Mutations inGBA(glucosylceramidase beta), which encodes the lysosomal enzyme glucocerebrosidase (GCase), are the strongest genetic risk factor for the neurodegenerative disorders Parkinson’s disease (PD) and Lewy body dementia. Recent work has suggested that neuroinflammation may be an important factor in the risk conferred byGBAmutations. We therefore systematically tested the contributions of immune-related genes to neuropathology in aDrosophilamodel of GCase deficiency. We identified target immune factors via RNA-Seq and proteomics on heads from GCase-deficient flies, which revealed both increased abundance of humoral factors and increased macrophage activation. We then manipulated the identified immune factors and measured their effect on head protein aggregates, a hallmark of neurodegenerative disease. Genetic ablation of humoral (secreted) immune factors did not suppress the development of protein aggregation. By contrast, re-expressingGba1bin activated macrophages suppressed head protein aggregation inGba1bmutants and rescued their lifespan and behavioral deficits. Moreover, reducing the GCase substrate glucosylceramide in activated macrophages also amelioratedGba1bmutant phenotypes. Taken together, our findings show that glucosylceramide accumulation due to GCase deficiency leads to macrophage activation, which in turn promotes the development of neuropathology.

Author Summary

Mutations in the geneGBAare the largest risk factor for developing Parkinson’s disease and Lewy body dementia, diseases in which important brain cells die. We know that the immune system can be involved in these diseases, and thatGBAmutations cause immune changes. We did experiments to learn how the immune system changes could make brain cells more likely to die. Using a fruit fly that was missing the fly version ofGBA, we found out that inappropriately activated immune cells, but not secreted immune proteins, were important in the development of brain problems. We also learned that the abnormal activation was triggered by the lack ofGBAfunction in the immune cells, not by signals from the brain or other parts of the body. We would like to find out next whether the immune cells get inside the brain or cause harm from a distance. What we learned matters because it could help us prevent or cure brain diseases associated withGBAmutations. Treating the abnormal activation of immune cells in people with these mutations might help prevent damage to the brain.
Examining the potential involvement of NONO in TDP-43 proteinopathy inDrosophila
Authors: Koch Rafael , Nagoshi Emi
Published: December 2023

The misfolding and aggregation of TAR DNA binding protein-43 (TDP-43), leading to the formation of cytoplasmic inclusions, emerge as a key pathological feature in a spectrum of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). TDP-43 shuttles between the nucleus and cytoplasm but forms nuclear bodies (NBs) in response to stress. These NBs partially colocalize with nuclear speckles and paraspeckles that sequester RNAs and proteins, thereby regulating many cellular functions. The laboratory of Steven Brown has recently found that the non-POU domain-containing octamer-binding protein (NONO), a component of paraspeckles, forms novel nuclear speckle-like structures in mouse cortical neurons in response to stress and sleep deprivation. These findings suggest the possibility of a functional link between NONO and TDP-43, potentially contributing to TDP-43 proteinopathy. Here, we demonstrate that loss of function in theDrosophilahomolog ofNONO, no on or off transient A(NonA), exacerbates pathological phenotypes caused byTDP-43gain of function, leading to locomotor defects and life span shortening. These results provide supporting evidence for the functional link between NONO and TDP-43 and lay the foundation for dissecting underlying mechanisms.
Battery-Free Optoelectronic Patch for Photodynamic and Light Therapies in Treating Bacteria-Infected Wounds
Authors: Xue Zhao , Chou Wenxin , Xu Yixuan , Cheng ZiYi , Ren Xuechun , Sun Tianzhen , Tong Wenbin , Xie Yang , Chen Junyu , Zhang Nuohan , Sheng Xing , Wang Yongtian , Zhao Hongyou , Yang Jian , Ding He
Published: December 2023

Light therapy is an effective approach for the treatment of a variety of challenging dermatological conditions. In contrast to existing methods involving high doses and large areas of illumination, alternative strategies based on wearable designs that utilize a low light dose over an extended period provide a precise and convenient treatment. In this study, we present a battery-free, skin-integrated optoelectronic patch that incorporates a coil-powered circuit, an array of microscale violet and red light emitting diodes (LEDs), and polymer microneedles (MNs) loaded with 5-aminolevulinic acid (5-ALA). This polymer MNs, based on the biodegradable composite materials of polyvinyl alcohol (PVA) and hyaluronic acid (HA), serves as light waveguides for optical access and a medium for drug release into deeper skin layers. Unlike conventional clinical photomedical appliances with a rigid and fixed light source, this flexible design allows for a conformable light source that can be applied directly to the skin. In animal models with bacterial-infected wounds, the experimental group with the combination treatment of metronomic photodynamic and light therapies reduced 2.48 log10CFU mL−1in bactericidal level compared to the control group, indicating an effective anti-infective response. Furthermore, post-treatment analysis revealed the activation of proregenerative genes in monocyte and macrophage cell populations, suggesting enhanced tissue regeneration, neovascularization, and dermal recovery. Overall, this optoelectronic patch design broadens the scope for targeting deep skin lesions, and provides an alternative with the functionality of standard clinical light therapy methods.
Determining glycosyltransferase functional order via lethality due to accumulated O-antigen intermediates, exemplified withShigella flexneriO-antigen biosynthesis
Authors: Qin Jilong , Hong Yaoqin , Totsika Makrina
Published: December 2023

The O antigen (OAg) polysaccharide is one of the most diverse surface molecules of Gram-negative bacterial pathogens. The structural classification of OAg based on serological typing and sequence analysis is important in epidemiology and surveillance of outbreaks of bacterial infections. Despite the diverse chemical structures of OAg repeating units (RUs) described, the genetic basis of the assembly of these RUs remains poorly understood and represents a major limitation in our understanding of the gene functions in the polysaccharide biosynthesis. Here we describe a genetic approach to interrogate the functional order of glycosyltransferases (GTs). UsingShigella flexnerias a model, we established an initial glycosyltransferase (IT) controlled system to allocate the functional order of the subsequent GT in a two-fold manner. First by reporting the growth defects caused by the sequestration of UndP through disruption of late GTs, and second by comparing the molecular sizes of stalled OAg intermediates when each putative GT is disrupted. Using this approach, we demonstrate that for RfbF and RfbG, the GTs involved in the assembly ofS. flexneribackbone OAg RU, RfbG is responsible for both the committed step of OAg synthesis, as well as the third transferase for the second L-Rha. We also show that RfbF functions as the last GT to complete theS. flexneriOAg RU backbone. We propose that this simple and effective genetic approach can be also extended to define the functional order of enzymatic synthesis of other diverse polysaccharides produced both by Gram-negative and Gram-positive bacteria.

Importance

The genetic basis of enzymatic assembly of structurally diverse OAg repeating units in Gram-negative pathogens is poorly understood, representing a major limitation in our understanding of gene functions for the synthesis of bacterial polysaccharides. We present a simple genetic approach to assigning glycosyltransferase (GT) functions and the order in which they act in the assembly of the OAg RU in their native background strain with reasonable confidence. We demonstrated with this approach the functional allocation of GTs forShigella flexneriO antigen assembly. This approach can be generally applied in interrogating GT functions encoded by other bacterial polysaccharides to advance our understanding of diverse gene functions in the biosynthesis of polysaccharides, key knowledge in advancing biosynthetic polysaccharide production.
Human Trophoblast Stem Cells Restrict Human Cytomegalovirus Replication
Authors: Rollman Tyler B. , Berkebile Zachary W. , Okae Hiroaki , Bardwell Vivian J. , Gearhart Micah D. , Bierle Craig J.
Published: December 2023

Placental infection plays a central role in the pathogenesis of congenital human cytomegalovirus (HCMV) infections and is a cause of fetal growth restriction and pregnancy loss. HCMV can replicate in some trophoblast cell types, but it remains unclear how the virus evades antiviral immunity in the placenta and how infection compromises placental development and function. Human trophoblast stem cells (TSCs) can be differentiated into extravillous trophoblasts (EVTs), syncytiotrophoblasts (STBs), and organoids, and this study assessed the utility of TSCs as a model of HCMV infection in the first trimester placenta. HCMV was found to non-productively infect TSCs, EVTs, and STBs. Immunofluorescence assays and flow cytometry experiments further revealed that infected TSCs frequently only express immediate early viral gene products. Similarly, RNA-sequencing found that viral gene expression in TSCs does not follow the kinetic patterns observed during lytic infection in fibroblasts. Canonical antiviral responses were largely not observed in HCMV-infected TSCs and TSC-derived trophoblasts. Rather, infection dysregulated factors involved in cell identity, differentiation, and WNT signaling. Thus, while HCMV does not replicate in TSCs, infection may perturb trophoblast differentiation in ways that could interfere with placental function.

Importance

Placental infection plays a central role in HCMV pathogenesis during pregnancy, but the species-specificity of HCMV and the limited availability and lifespan of primary trophoblasts have been persistent barriers to understanding how infection impacts this vital organ. Human TSCs represent a new approach to modeling viral infection early in placental development. This study reveals that TSCs, like other stem cell types, restrict HCMV replication. However, infection perturbs the expression of genes involved in differentiation and cell fate determination, pointing to a mechanism by which HCMV could cause placental injury.
A Novel Classification System for Prokaryotic DNA Methyltransferases Based on 3D Catalytic Domain Topology
Authors: Samokhina Maria , Alexeevski A.
Published: December 2023

Prokaryotic DNA methyltransferases (MTases) are essential enzymes that play a crucial role in restriction-modification systems, preventing the degradation of self DNA by restriction enzymes. In addition, they contribute to the regulation of gene expression, DNA repair, DNA replication, and other processes.

We propose a novel classification of prokaryotic MTases that addresses a longstanding deficiency in the previous classification scheme developed by Malone and Bujnicki. The latter classification, which grouped MTases into categories such as α, β, γ, etc., has been in use for over 20 years.

Our approach involves identifying 6 classes of MTases based on the 3D topology of the catalytic domain. This was achieved by analyzing the available 3D structures and certain predicted 3D structures of MTases from the AlfaFold database. The catalytic domains of each class of MTase exhibit homology not only in structure but also in conserved motifs. To develop this classification algorithm, we utilized a set of MTases from the gold standard REBASE database.

Our new classification system facilitates the recovery of MTase evolution and MTase annotations in both existing and new sequence data sets. This is particularly important for understanding the complex relationships between MTases and their roles in various biological processes.

GRAPHICAL ABSTRACT
Collaborative metabolic curation of an emerging model marine bacterium,Alteromonas macleodiiATCC 27126
Authors: Sher Daniel , George Emma E. , Wietz Matthias , Gifford Scott , Zoccaratto Luca , Weissberg Osnat , Koedooder Coco , Waseem Bashir VK , Filho Marcelo Malisano Barreto , Mireles Raul , Malavin Stas , Naim Michal Liddor , Idan Tal , Shrivastava Vibhaw , Itelson Lynne , Sade Dagan , Hamoud Alhan Abu , Soussan Yara , Barak Noga , Karp Peter , Moore Lisa
Published: December 2023

Inferring the metabolic capabilities of an organism from its genome is a challenging process, relying on computationally-derived or manually curated metabolic networks. Manual curation can correct mistakes in the draft network and add missing reactions based on the literature, but requires significant expertise and is often the bottleneck for high-quality metabolic reconstructions. Here, we present a synopsis of a community curation workshop for the emerging model marine bacteriumAlteromonas macleodiiATCC 27126 and its genome database in BioCyc, focusing on pathways for utilizing organic carbon and nitrogen sources. Due to the scarcity of biochemical information or gene knock-outs, the curation process relied primarily on published growth phenotypes and bioinformatic analyses, including comparisons with relatedAlteromonasstrains. We report full pathways for the utilization of the algal polysaccharides alginate and pectin in contrast to inconclusive evidence for one carbon metabolism and mixed acid fermentation, in accordance with the lack of growth on methanol and formate. Pathways for amino acid degradation are ubiquitous acrossAlteromonas macleodiistrains, yet enzymes in the pathways for the degradation of threonine, tryptophan and tyrosine were not identified. Nucleotide degradation pathways are also partial in ATCC 27126. We postulate that demonstrated growth on nitrate as sole N source proceeds via a nitrate reductase pathway that is a hybrid of known pathways. Our evidence highlights the value of joint and interactive curation efforts, but also shows major knowledge gaps regardingAlteromonasmetabolism. The manually-curated metabolic reconstruction is available as a “Tier-2” database on BioCyc.

Importance

Metabolic reconstructions are vital for the systemic understanding of an organism’s ecology. Here, we report the outcome of a collaborative, interactive curation workshop to build a curated “metabolic encyclopedia” forAlteromonas macleodiiATCC 27126, a marine heterotrophic bacterium with widespread occurrence. Curating pathways for polysaccharide degradation, one-carbon metabolism, and others closed major knowledge gaps, and identified further avenues of research. Our study highlights how the combination of bioinformatic, genomic and physiological evidence can be harvested into a detailed metabolic model, but also identifies challenges if little experimental data is available for support. Overall, we show how an interactive get-together by a diverse group of scientists can advance the ecological understanding of emerging model bacteria, with relevance for the entire scientific community.
Isolation and Lipidomic Profiling of Neuronal Lipid Droplets: Unveiling the Lipid Landscape for insights into Neurodegenerative Disorders
Authors: Kumar Mukesh , Knapp Justin A , Gupta Kallol , Ryan Timothy A.
Published: December 2023

Recent advances have expanded the role of lipid droplets (LDs) beyond passive lipid storage, implicating their involvement in various metabolic processes across mammalian tissues. Neuronal LDs, long debated in existence, have been identified in several neural structures, raising questions about their contribution to neurodegenerative disorders. Elucidating the specific chemical makeup of these organelles within neurons is critical for understanding their implication in neural pathologies. This study outlines an improved methodology to stimulate and isolate mature LDs from cultured primary neurons, offering insights into their unique lipid-protein composition. Integrating this method with high-throughput techniques may unveil disease-specific alterations in lipid metabolism, providing avenues for potential therapeutic interventions.
A protective and broadly binding antibody class engages the influenza virus hemagglutinin head at its stem interface
Authors: Simmons Holly C. , Finney Joel , Kotaki Ryutaro , Adachi Yu , Moseman Annie Park , Watanabe Akiko , Song Shengli , Robinson-McCarthy Lindsey R. , Le Sage Valerie , Kuraoka Masayuki , Moseman E. Ashley , Kelsoe Garnett , Takahashi Yoshimasa , McCarthy Kevin R.
Published: December 2023

Influenza infection and vaccination impart strain-specific immunity that protects against neither seasonal antigenic variants nor the next pandemic. However, antibodies directed to conserved sites can confer broad protection. Here we identify and characterize a class of human antibodies that engage a previously undescribed, conserved epitope on the influenza hemagglutinin (HA) protein. Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head-stem interface epitope are non-neutralizingin vitrobut protect against lethal influenza infection in mice. Antibody isotypes that direct clearance of infected cells enhance this protection. Head-stem interface antibodies bind to most influenza A serotypes and seasonal human variants, and are present at low frequencies in the memory B cell populations of multiple human donors. Vaccines designed to elicit these antibodies might contribute to “universal” influenza immunity.