bluuebunny/crossref_metadata_2025 huggingface dataset:
Transverse Aortic COnstriction Multi-omics Analysis (TACOMA) uncovers pathophysiological cardiac molecular mechanisms
Authors: Gjerga Enio , Dewenter Matthias , Britto-Borges Thiago , Grosso Johannes , Stein Frank , Eschenbach Jessica , Rettel Mandy , Backs Johannes , Dieterich Christoph
Published: January 2024

Time-course multi-omics data of a murine model of progressive heart failure induced by transverse aortic constriction (TAC) provide insights into the molecular mechanisms that are causatively involved in contractile failure and structural cardiac remodelling. We employ Illumina-based transcriptomics, Nanopore sequencing, and mass spectrometry-based proteomics on samples from the left ventricle (LV) and right ventricle (RV, RNA only) of the heart at 1, 7, 21, and 56 days following TAC and Sham surgery. Here, we present TACOMA, as an interactive web-application that integrates and visualizes transcriptomics and proteomics data collected in a TAC time-course experiment. TACOMA enables users to visualize the expression profile of known and novel genes and protein products thereof. Importantly, we capture alternative splicing events by assessing differential transcript and exon usage as well. Co-expression-based clustering algorithms and functional enrichment analysis revealed overrepresented annotations of biological processes and molecular functions at the protein and gene levels. To enhance data integration, TACOMA synchronizes transcriptomics and proteomics profiles, enabling cross-omics comparisons. With TACOMA (https://shiny.dieterichlab.org/app/tacoma), we offer a rich web-based resource to uncover molecular events and biological processes implicated in contractile failure and cardiac hypertrophy. For example, we highlight: (i) changes in metabolic genes and proteins in the time course of hypertrophic growth and contractile impairment; (ii) identification of RNA splicing changes in the expression of Tpm2 isoforms between RV and LV; and (iii) novel transcripts and genes likely contributing to the pathogenesis of heart failure. We plan to extend these data with additional environmental and genetic models of heart failure to decipher common and distinct molecular changes in heart diseases of different aetiologies.

Database URL

https://shiny.dieterichlab.org/app/tacoma
Mechanical stability and unfolding pathways of parallel tetrameric G-quadruplexes probed by pulling simulations
Authors: Zhang Zhengyue , Mlýnský Vojtěch , Krepl Miroslav , Šponer Jiří , Stadlbauer Petr
Published: January 2024

Guanine-quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, many aspects of which remain elusive, despite being important for understanding of structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy – Steered Molecular Dynamics (SMD) simulations – combined with standard Molecular Dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. The vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event and it usually started at the 3’-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
Accuracy optimized neural networks do not effectively model optic flow tuning in brain area MSTd
Authors: Layton Oliver W. , Steinmetz Scott T.
Published: January 2024

Accuracy-optimized convolutional neural networks (CNNs) have emerged as highly effective models at predicting neural responses in brain areas along the primate ventral stream, but it is largely unknown whether they effectively model neurons in the complementary primate dorsal stream. We explored how well CNNs model the optic flow tuning properties of neurons in dorsal area MSTd and we compared our results with the Non-Negative Matrix Factorization (NNMF) model proposed by Beyeler, Dutt, & Krichmar (2016), which successfully models many tuning properties of MSTd neurons. To better understand the role of computational properties in the NNMF model that give rise to MSTd-like optic flow tuning, we created additional CNN model variants that implement key NNMF constraints — non-negative weights and sparse coding of optic flow. While the CNNs and NNMF models both accurately estimate the observer’s self-motion from purely translational or rotational optic flow, NNMF and the CNNs with nonnegative weights yield substantially less accurate estimates than the other CNNs when tested on more complex optic flow that combines observer translation and rotation. Despite their poor accuracy, however, neurons in the networks with the nonnegativity constraint give rise to tuning properties that align more closely with those observed in primate MSTd. Interestingly, the addition of the sparsity constraint has a negligible effect on the accuracy of self-motion estimates and model tuning properties. Across all models, we consistently observe the 90-degree offset in the preferred translation and rotation directions found in MSTd neurons, which suggests that this property could emerge through a range of potential computational mechanisms. This work offers a step towards a deeper understanding of the computational properties and constraints that describe optic flow tuning primate area MSTd.

Significance Statement

One of the most exciting developments in visual neuroscience over the past decade is that convolutional artificial neural networks optimized to accurately categorize natural images effectively model neural activity in ventral visual areas of the primate brain. We explored whether accuracy-optimized neural networks account for well-established properties of MSTd, a brain area in the complementary primate dorsal stream that is involved in self-motion perception during navigation. Our findings indicate that such networks depart substantially from MSTd-like tuning, which suggests the computational goal of MSTd may not be to accurately estimate self-motion. We found that adding computational constraints inspired by an existing MSTd model that performs dimensionality reduction on afferent motion signals improves the correspondence with MSTd.
Transient destabilization of whole brain dynamics induced by DMT
Authors: Piccinini Juan Ignacio , Perl Yonatan Sanz , Pallavicini Carla , Deco Gustavo , Kringelbach Morten , Nutt David , Carhart-Harris Robin , Timmermann Christopher , Tagliazucchi Enzo
Published: January 2024

The transition towards the brain state induced by psychedelic drugs is frequently neglected in favor of a static description of their acute effects. We used a time-dependent whole-brain model to reproduce large-scale brain dynamics measured with fMRI from 15 volunteers under 20 mg intravenous N,N-Dimethyltryptamine (DMT), a short-acting psychedelic. To capture its transient effects, we parametrized the proximity to a global bifurcation using a pharmacokinetic equation. Simulated perturbations revealed a transient of heightened reactivity concentrated in fronto-parietal regions and visual cortices, correlated with serotonin 5HT2a receptor density, the primary target of psychedelics. These advances suggest a mechanism to explain key features of the psychedelic state and also predicts that the temporal evolution of these features aligns with pharmacokinetics. Our results contribute to understanding how psychedelics introduce a transient where minimal perturbations can achieve a maximal effect, shedding light on how short psychedelic episodes may extend an overarching influence over time.
Trajectory inference from single-cell genomics data with a process time model
Authors: Fang Meichen , Gorin Gennady , Pachter Lior
Published: January 2024

Single-cell transcriptomics experiments provide gene expression snapshots of heterogeneous cell populations across cell states. These snapshots have been used to infer trajectories and dynamic information even without intensive, time-series data by ordering cells according to gene expression similarity. However, while single-cell snapshots sometimes offer valuable insights into dynamic processes, current methods for ordering cells are limited by descriptive notions of “pseudotime” that lack intrinsic physical meaning. Instead of pseudotime, we propose inference of “process time” via a principled modeling approach to formulating trajectories and inferring latent variables corresponding to timing of cells subject to a biophysical process. Our implementation of this approach, called Chronocell, provides a biophysical formulation of trajectories built on cell state transitions. The Chronocell model is identifiable, making parameter inference meaningful. Furthermore, Chronocell can interpolate between trajectory inference, when cell states lie on a continuum, and clustering, when cells cluster into discrete states. By using a variety of datasets ranging from cluster-like to continuous, we show that Chronocell enables us to assess the suitability of datasets and reveals distinct cellular distributions along process time that are consistent with biological process times. We also compare our parameter estimates of degradation rates to those derived from metabolic labeling datasets, thereby showcasing the biophysical utility of Chronocell. Nevertheless, based on performance characterization on simulations, we find that process time inference can be challenging, highlighting the importance of dataset quality and careful model assessment.
Modified FRAX Score for Prediction of Fall-induced Hip Fractures; The Added Value of Fall Energy, Number, and Social Vulnerability Index
Authors: Taseh Atta , Sirls Evan , Casey George , Hearns Sarah , Doornberg Job N. , Lozano-Calderon Santiago A. , Harris Mitchel B , Ashkani-Esfahani Soheil
Published: January 2024

Background

The Fracture Risk Assessment Tool (FRAX), widely used for predicting the 10-year likelihood of hip fractures, does not incorporate factors like prior falls and sociodemographic characteristics, notably the Social Vulnerability Index (SVI). Recognizing these limitations, we aim to evaluate the predictive accuracy of FRAX by integrating fall frequency, fall energy, and SVI into the model for assessing the risk of fall-induced hip fractures.

Methods

A retrospective case-control study was conducted, and patients aged ≥ 40 years with a documented diagnosis of a fall-induced hip fracture were age-matched with controls with a history of falls without an associated hip fracture. Basic demographic data, along with information about the number of prior falls and the energy of the current falls, were collected. The FRAX and SVI were calculated accordingly. Logistic regression analysis was employed to identify significant predictors. The performance of the models was evaluated and reported using appropriate metrics. Baseline characteristics of the dataset were presented as medians with interquartile ranges (IQR) or as percentages, where applicable. The significance of the identified variables was quantified using Odds Ratio (OR) along with their 95% Confidence Interval (CI). A p-value threshold of 0.05 was set for statistical significance.

Results

A total of 261 patients per group were included with a median age of 74 (IQR 67-80) and 72 (IQR 62-83) years. The FRAX score was significantly associated with the likelihood of experiencing a fall-induced hip fracture, as indicated by an OR of 1.06 (CI: 1.03-1.09). Participants with a one-time history of falls had an OR of 1.58 (CI: 1.02-2.37), compared to 1.84 (CI: 1.09-3.1) for those with multiple falls. The white race, along with the Housing Type and Transportation domain of the SVI, also demonstrated to play a role (OR= 2.85 (CI: 1.56-5.2) and OR= 0.3 (CI: 0.12-0.8), respectively).

Conclusion

This study underscored the significance of factors such as fall frequency, SVI, and race in predicting fall-induced hip fractures. It also highlighted the need for further refinement of the FRAX tool. We recommend that future research should be focused on validating the impact of these sociodemographic and fall characteristics on a broader scale, along with exploring the implications of clinical surrogates related to falls.
Longitudinal Study on Seroprevalence and Immune Response to SARS-CoV-2 in a Population of Food and Retail Workers Through Transformation of ELISA Datasets
Authors: Djaïleb Abdelhadi , Parker Megan-Faye , Lavallée Étienne , Stuible Matthew , Durocher Yves , Thériault Mathieu , Santerre Kim , Gilbert Caroline , Boudreau Denis , Baz Mariana , Masson Jean-Francois , Langlois Marc-André , Trottier Sylvie , Quaglia Daniela , Pelletier Joelle N.
Published: January 2024

Since the onset of the global pandemic caused by the emergence and spread of SARS-CoV-2 in early 2020, numerous studies have been conducted worldwide to understand our immune response to the virus. This study investigates the humoral response elicited by vaccination and by SARS-CoV-2 infection in the poorly studied food and retail workers in the Québec City area. The 1.5-year study period spans from early 2021, when vaccination became available in this region, to mid-2022, following waves of virulence due to the emergence of the first Omicron variants. Cross-correlated with data on workplace protective measures, pre-existing conditions, activities and other potentially relevant factors, this longitudinal study applies recently developed ELISA data transformation to our dataset to obtain normal distribution. This unlocked the possibility to use the ANOVA-Welsh method for statistical analysis to obtain a statistical perspective of the serological response. Our work allows the identification of factors contributing to statistically relevant differences in the humoral response of the cohort and strengthens the utility of the use of decentralized approaches to serological analysis.
Targeting MYCN upregulates L1CAM tumor antigen in MYCN-dysregulated neuroblastoma to increase CAR T cell efficacy
Authors: Grunewald Laura , Andersch Lena , Helmsauer Konstantin , Schwiebert Silke , Klaus Anika , Henssen Anton G. , Straka Teresa , Lodrini Marco , Wicha Sebastian G. , Fuchs Steffen , Hertwig Falk , Westermann Frank , Vitali Alice , Caramel Carlotta , Büchel Gabriele , Eilers Martin , Astrahantseff Kathy , Eggert Angelika , Höpken Uta E. , Schulte Johannes H. , Blankenstein Thomas , Anders Kathleen , Künkele Annette
Published: January 2024

Background

Current treatment protocols have only limited success in pediatric patients with neuroblastomas harboring amplifications of the central oncogene,MYCN. Adoptive T cell therapy presents an innovative strategy to improve cure rates. However, L1CAM-targeting CAR T cells achieved only limited response against refractory/relapsed neuroblastoma in an ongoing phase I trial to date. Here, we investigate how oncogenic MYCN levels influence tumor cell response to CAR T cells, as one possible factor limiting success in trials.

Methods

High MYCN levels were induced in SK-N-AS cells harboring the normal diploidMYCNcomplement using a tetracycline-inducible system. The inducible MYCN cell model orMYCN-amplified neuroblastoma cell lines were cocultured with L1CAM-CAR T cells. CAR T cell effector function was assessed via activation marker expression (flow cytometry), cytokine release and tumor cytotoxicity (biophotonic signal assessment). The cell model was characterized using RNA sequencing, and our data compared to publicly available RNA and proteomic data sets from neuroblastomas. ChIP-sequencing data was used to determine transcriptionalL1CAMregulation by MYCN using public data sets. Synergism between CAR T cells and the MLN8237 AURKA inhibitor, which indirectly inhibits MYCN activity, was assessedin vitrousing the Bliss model andin vivoin an immunocompromised mouse model.

Results

Inducing high MYCN levels in the neuroblastoma cell model reduced L1CAM expression and, consequently, L1CAM-CAR T cell effector function (activation, cytokine release and cytotoxicity)in vitro. Primary neuroblastomas possessing highMYCNlevels expressed lower levels of both theL1CAMtranscript and L1CAM tumor antigen. Indirectly inhibiting MYCN via AURKA using MLN8237 treatment restored L1CAM expression on tumor cellsin vitroand restored L1CAM-CAR T cell effector function. Combining MLN8237 and L1CAM-CAR T cell treatment synergistically increased neuroblastoma-directed killing in MYCN-overexpressing cellsin vitroandin vivoconcomitant with severein vivotoxicity.

Conclusion

We shed new light on a primary resistance mechanism in MYCN-driven neuroblastoma against L1CAM-CAR T cells via target antigen downregulation. These data suggest that combining L1CAM-CAR T cell therapy with pharmacological MYCN inhibition may benefit patients with high-risk neuroblastomas harboringMYCNamplifications.
Brain Vasculature Accumulates Tau and Is Spatially Related to Tau Tangle Pathology in Alzheimer’s Disease
Authors: Hoglund Zachary , Ruiz-Uribe Nancy , del Sastre Eric , Woost Benjamin , Bailey Joshua , Hyman Bradley T. , Zwang Theodore , Bennett Rachel E.
Published: January 2024

Insoluble pathogenic proteins accumulate along blood vessels in conditions of cerebral amyloid angiopathy (CAA), exerting a toxic effect on vascular cells and impacting cerebral homeostasis. In this work we provide new evidence from three-dimensional human brain histology that tau protein, the main component of neurofibrillary tangles, can similarly accumulate along brain vascular segments. We quantitatively assessed n=6 Alzheimer’s disease (AD), and n=6 normal aging control brains and saw that tau-positive blood vessel segments were present in all AD cases. Tau-positive vessels are enriched for tau at levels higher than the surrounding tissue and appear to affect arterioles across cortical layers (I-V). Further, vessels isolated from these AD tissues were enriched for N-terminal tau and tau phosphorylated at T181 and T217. Importantly, tau-positive vessels are associated with local areas of increased tau neurofibrillary tangles. This suggests that accumulation of tau around blood vessels may reflect a local clearance failure. In sum, these data indicate tau, like amyloid beta, accumulates along blood vessels and may exert a significant influence on vasculature in the setting of AD.
Multi-Channel smFRET study reveals a Compact conformation of EF-G on the Ribosome
Authors: Johnson Jordan L. , Steele Jacob H. , Lin Ran , Stepanov Victor G. , Gavriliuc Miriam N. , Wang Yuhong
Published: January 2024

While elongation factor G (EF-G) is crucial for ribosome translocation, the role of its GTP hydrolysis remains ambiguous. EF-G’s indispensability is further exemplified by the phosphorylation of human eukaryotic elongation factor 2 (eEF2) at Thr56, which inhibits protein synthesis globally, but its exact mechanism is not clear. In this study, we developed a multi-channel single-molecule FRET (smFRET) microscopy methodology to examine the conformational changes ofE. coliEF-G induced by mutations that closely aligned with eEF2’s Thr56 residue. We utilized Alexa 488/594 double-labeled EF-G to catalyze the translocation of fMet-Phe-tRNAPhe-Cy3 inside Cy5-L27 labeled ribosomes, allowing us to probe both processes within the same complex. Our findings indicate that in the presence of either GTP or GDPCP, wild-type EF-G undergoes a conformational extension upon binding to the ribosome to promote normal translocation. On the other hand, T48E and T48V mutations did not affect GTP/GDP binding or GTP hydrolysis, but impeded Poly(Phe) synthesis and caused EF-G to adopt a unique compact conformation, which wasn’t observed when the mutants interact solely with the sarcin/ricin loop. This study provides new insights into EF-G’s adaptability and sheds light on the modification mechanism of human eEF2.
Mapping the developmental structure of stereotyped and individual-unique behavioral spaces inC. elegans
Authors: Harel Yuval , Nasser Reemy Ali , Stern Shay
Published: January 2024

Developmental patterns of behavior are variably organized in time and among different individuals. However, long-term behavioral diversity was previously studied using pre-defined behavioral parameters, representing a limited fraction of the full individuality structure. Here, we continuously extracted ∼1.2 billion body postures of ∼2,200 singleC. elegansindividuals throughout their full development time, to create a complete developmental atlas of stereotyped and individual-unique behavioral spaces. Unsupervised inference of low-dimensional movement modes of each single individual revealed a dynamic developmental trajectory of stereotyped behavioral spaces and exposed unique behavioral trajectories of individuals that deviate from the stereotyped patterns. Moreover, classification of behavioral spaces within tens of neuromodulatory- and environmentally-perturbed populations efficiently uncovered plasticity in the temporal structures of stereotyped behavior and individuality. These results present a comprehensive atlas of continuous behavioral dynamics across development time and a general framework for unsupervised dissection of shared and unique developmental signatures of behavior.
Autophagy regulator ATG5 preserves cerebellar function by safeguarding its glycolytic activity
Authors: Tutas J. , Tolve M. , Özer-Yildiz E. , Ickert L. , Klein I , Hosseini M , Liebsch F. , Dethloff F. , Gavalisco P. , Endepols H. , Yang M. , Georgomanolis T. , Neumaier B. , Drzezga A. , Daun S. , Schwarz G. , Thorens B. , Gatto G. , Frezza C. , Kononenko NL
Published: January 2024

Dysfunctions in autophagy, a highly conserved cellular mechanism responsible for the degradation of intracellular components within lysosomes, often result in neurodegeneration. The neuroprotective effect of autophagy varies across neuronal subtypes, and the mechanisms of selective vulnerability of neurons to autophagy dysfunction are currently unknown. Utilizing a mouse model of ATG5 deficiency in inhibitory neurons and a comprehensive approach, including PET imaging, metabolomics, stable-isotope labeling studies, and live cell imaging, we establish that autophagy contributes to the survival of cerebellar Purkinje cells (PCs) by safeguarding their glycolytic activity. We show that the core autophagy protein ATG5 downregulates the levels of the glucose transporter 2 (GLUT2) during brain maturation. Autophagy-deficient PCs exhibit increased glucose uptake, along with elevated levels of glycolytic intermediates and methylglyoxal-modified proteins. We propose lysophosphatidic acid and serine as glycolytic intermediates inducing PC death and demonstrate that deletion of GLUT2 in ATG5-deficient mice mitigates PC neurodegeneration and restores their ataxic gait. Taken together, this study reveals a novel neuroprotective role of autophagy in preventing excessive glycolytic metabolism in the brain.
Visualizing chaperone-mediated multistep assembly of the human 20S proteasome
Authors: Adolf Frank , Du Jiale , Goodall Ellen A. , Walsh Richard M. , Rawson Shaun , von Gronau Susanne , Harper J. Wade , Hanna John , Schulman Brenda A.
Published: January 2024

Dedicated assembly factors orchestrate stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here, we report cryo-EM reconstructions of seven recombinant human subcomplexes that visualize all five chaperones and the three active site propeptides across a wide swath of the assembly pathway. Comparison of these chaperone-bound intermediates and a matching mature CP reveals molecular mechanisms determining the order of successive subunit additions, and how proteasome subcomplexes and assembly factors structurally adapt upon progressive subunit incorporation to stabilize intermediates, facilitate the formation of subsequent intermediates, and ultimately rearrange to coordinate proteolytic activation with gated access to active sites. The structural findings reported here explain many previous biochemical and genetic observations. This work establishes a methodologic approach for structural analysis of multiprotein complex assembly intermediates, illuminates specific functions of assembly factors, and reveals conceptual principles underlying human proteasome biogenesis.
Turnover of RNA-binding Proteins and MicroRNAs by intrinsically disordered region-directed ZSWIM8 ubiquitin ligase during brain development
Authors: Lei Jing , Zhong Siming , Fan Rong , Shu Xin , Wang Guan , Guo Jiansheng , Xue Shuting , Zheng Luqian , Ren Aiming , Ji Junfang , Yang Bing , Duan Shumin , Wang Zhiping , Guo Xing
Published: January 2024

Widely present in mammalian proteomes, intrinsically disordered regions (IDRs) in proteins play important biological functions by conferring structural flexibility and mediating biomolecular interactions. IDR-containing proteins, including many RNA-binding proteins (RBPs), are prone to misfolding and aggregation and must be constantly monitored. Here we show that the conserved ZSWIM8-type Cullin-RING ubiquitin ligase (CRLZSWIM8) is a master regulator of such proteins during brain development. ZSWIM8 selects its substrates via an IDR-dependent mechanism, and deletion of ZSWIM8 causes aberrant accumulation of numerous RBPs including AGO2 and ELAV1 in neonatal brains. Furthermore, AGO2 ubiquitination by ZSWIM8 is triggered by microRNA binding, leading to target-directed microRNA degradation (TDMD) of MiR7. Dysregulation of MiR7 in the absence of ZSWIM8 results in defects in oligodendrocyte maturation and functions. Together, our findings have demonstrated that, by utilizing variable target-recognition strategies, ZSWIM8 controls the abundance of conformationally flexible RBPs and miRNA metabolism that are essential for brain development.

Teaser

A conserved ubiquitin ligase controls the quality of disordered proteins to ensure brain development.
In vitrosurvival and neurogenic potential of central canal-derived neural stem cells depend on spinal cord injury type
Authors: Schiro Lars Erik , Bauer Ulrich Stefan , Bjorkli Christiana , Sandvig Axel , Sandvig Ioanna
Published: January 2024

The central canal (CC) of the spinal cord is a neurogenic niche consisting of quiescent neural stem cells (NSCs) capable of responding to traumatic damage to the spinal cord by increasing their proliferative activity and sending migrating progeny toward the site of injury, where they contribute to the formation of the glial scar. However, CC NSCs have been demonstrated to have the capability to differentiate into all neural lineage cellsin vitro, but alsoin vivo, in response to infusion of specific growth factors that promote neuronal induction after injury, as well as when transplanted into other neurogenic niches, such as the subgranular zone of the hippocampus. This suggests that CC NSCs may represent a recruitable endogenous source of neural lineage cells that could be harnessed to replenish damaged or lost neural tissue after traumatic spinal cord injury (SCI).

NSCs isolated from the CC neurogenic niche of uninjured rats and mice have been shown to display limited proliferative capacityin vitro, with significantly greater proliferative activity achieved with NSCs isolated from SCI-lesioned rats and mice indicating an injury-specific activation of the quiescent CC NSC pool. A central question that currently remains unanswered is whether, and to what extent the CC niche can spontaneously generate viable neurons, and act as a potential source of new cells to replace lost neuronal populationsin situ, and whether SCI sequalae impact future NSC neurogenic potential. To address this question, we need to understand whether the nature of the injury plays a role in the CC neurogenic niche response. In this study, we compared the intrinsic proliferative response and neurogenic potential of NSCs harvested from the CC neurogenic niche in adult female Sprague Dawley rats by culturing said NSCs across three conditions; (i) control, i.e., uninjured tissue, (ii) afterin vivocompression injury 3 days before harvesting, and (iii) afterin vivosimulated burst fracture injury 3 days before harvestingin vitro. We found that lacerations of the dura mater surrounding the spinal cord during a compression injury resulted in drastically altered and persistentin vitroNSC behavior encompassing both proliferation and development compared to uninjured control and compression injury with the dura intact.
Functional characterization of CCHamides and deorphanization of their receptors in the yellow fever mosquito,Aedes aegypti
Authors: Tan Jinghan , Neupert Susanne , Paluzzi Jean-Paul
Published: January 2024

As a widely distributed anthropophilic mosquito species and vector of various arboviruses,Aedes aegyptiposes a significant threat to human health on a global scale. Investigating mosquito neuropeptides allows us to better understand their physiology. The neuropeptides CCHamide1 (CCHa-1) and CCHamide-2 (CCHa-2) and their associated G protein-coupled receptors (CCHa-1R and CCHa-2R) were recently identified and studied across insects. However, expression profiles and physiological roles of CCHamides and their receptors in many other insects, includingA. aegypti, remain unclear. This research aimed to quantify and localize the expression of CCHamides along with their receptors and to elucidate their physiological function in the yellow fever mosquito. RT-qPCR analysis revealed transcript abundance of CCHamides and receptors changes over development. Differential expression was also observed in tissues/organs of adult mosquitoes indicatingCCHa-1andCCHa-2transcripts are most highly enriched in the midgut, while receptors are expressed across various tissues. Further, CCHamides were immunolocalized in neurons in the brain and ventral nerve cord along with enteroendocrine cells in the posterior midgut adjacent to the midgut-hindgut junction, corroborating their transcript expression profiles. Using different mass spectrometrical approaches, presence of CCHamides were confirmed in the brain of both sexes, including thepars intercerebralisof female mosquitoes, as well as in the gut of adult mosquitoes. For chemical identification of predicted CCHamides, we analyzed brain and gut extracts by ESI-Q Exactive Orbitrap MS and resulting fragmentations confirmed CCHa1 and CCHa2 in brain and midgut samples of both male and female mosquitoes. A heterologous functional assay was used to confirm the specificity and sensitivity of the two CCHamide receptors by assessing their activation in response to diverse mosquito peptides, which confirmed CCHa-1 and CCHa-2 as the natural ligands. Finally, using a capillary feeder (CAFE) bioassay, our results suggest that CCHa-2 modulates feeding behaviour in female mosquitoes.
Disruption of autism-associatedPcdh9gene leads to transcriptional alterations, synapses overgrowth and aberrant excitatory transmission in the CA1
Authors: Miozzo Federico , Murru Luca , Maiellano Greta , Zippo Antonio , Moretto Edoardo , Avendano Annalaura Zambrano , Metodieva Verjinia D. , Riccardi Sara , D’Aliberti Deborah , Spinelli Silvia , Canu Tamara , Chaabane Linda , Hirano Shinji , Kas Martien J. H. , Francolini Maura , Piazza Rocco , Passafaro Maria
Published: January 2024

Protocadherins are cell adhesion molecules with crucial role in cell-cell contacts, whose mutations or altered expression have been implicated in multiple brain disorders. In particular, growing evidence links genetic alterations inProtocadherin 9(PCDH9) gene with Autism Spectrum Disorder (ASD) and Major Depression Disorder (MDD). Furthermore,Pcdh9deletion induces neuronal defects in the mouse somatosensory cortex, accompanied by sensorimotor and memory impairment. However, the synaptic and molecular mechanisms underlyingPcdh9physiological function and its involvement in brain pathology remain largely unknown. To this aim, we conducted a comprehensive investigation of PCDH9 role in the mouse hippocampus at the ultrastructural, biochemical, transcriptomic, electrophysiological and network level. We show that PCDH9 mainly localizes at glutamatergic synapses and its expression peaks in the first week after birth, a crucial time window for synaptogenesis. Strikingly,Pcdh9KO neurons exhibit oversized presynaptic terminal and postsynaptic density (PSD) in the CA1. Synapse overgrowth is sustained by the broad up-regulation of synaptic genes and the dysregulation of key drivers of synapse morphogenesis, as revealed by single-nucleus RNAseq. Synaptic and transcriptional defects are accompanied by increased EPSC frequency and disturbances in the hippocampal network activity ofPcdh9KO mice. In conclusion, our work indicates thatPcdh9regulates the morphology and function of excitatory synapses in the CA1, thereby affecting glutamatergic transmission in hippocampal circuitries.
Analyzing the Usage of the GIM-COVID-19 Long-Term Sequelae Rapid Access to Consultative Expertise (RACE) Line
Authors: Kaushal Saniya , Birks Peter , Greiner Jesse , Levin Adeera , Malbeuf Michelle , Schwartz Zachary
Published: January 2024

Real time access to guidance for physicians has been offered through Rapid Access to Consultative Expertise (RACE) in British Columbia (BC) for the past 12 years.1In the context of the novel coronavirus (COVID-19), the service for RACE was expanded to include a Long-COVID RACE line.1We report here the types and frequencies of questions asked to General Internal Medicine (GIM) experts in Long-COVID, by general practitioners in BC. 149 calls over an 11-month period were tracked by GIM experts, and analysis of the call themes was undertaken. These calls mainly involved consults regarding the post-infection COVID-19 symptoms being experienced by Primary Care Practitioners’ patients. Respiratory symptoms were the leading type of symptoms reported, with shortness of breath, cough, fatigue, and fevers being the most common, respectively. This data will be used to inform future resource utilization and provide insights on the usage of the Long-COVID RACE line.
Practical Challenges for Commercial Enterprises in the Ethics Review Process for Digital Health Research: Document Analysis and Interview Study
Authors: Yang Katherine , Potts Henry W W
Published: January 2024

Introduction

The rapid evolution of digital health interventions has created challenges in navigating the ethics approval process for commercial enterprises. Recognising the need for processes that balance ethical considerations with the specifics of digital health research, this study aimed to describe what happens when enterprises seek ethical review in the UK and propose strategies for a smoother process.

Methods

Inductive thematic analysis was conducted on thirty-two ethics review documents (29 to an NHS Research Ethics Committee, 3 to an ethics committee at a higher education institution) submitted by digital health developers with commercial sponsors and ten semi-structured interviews with digital health enterprise representatives.

Results

Ethics committees raised an average of 4.3 action points per submission. We identified five broad themes around committees’ concerns: ethical commitments in care; study design; digital health research peculiarities; data governance; document quality and completeness. Interviewees reported a range of experiences. Here, we identified six broad themes: submission and protocol revisions; the dynamic between parties; application time and procedures; acumen and practicality in digital health; support and guidance from RECs; enterprise expertise and resources.

Conclusion

We suggest strategies for applicants to achieve a favourable decision, such as evidence-based study designs and participant support for better inclusion and equity, and identified specific pitfalls to avoid, such as lack of justification for data governance procedures. We recommend that UK research ethics committees provide adapted guidance and foster collaboration through open communication and mutual understanding, to facilitate a smoother approval process in digital health research.
Validity of a Common Measure of Intimate Partner Violence Perpetration: Impact on Study Inference in Trials in Low- and Middle-Income Countries
Authors: Clark Cari Jo , Bergenfeld Irina , Shervinskie Abbie , Johnson Erin R. , Cheong Yuk Fai , Kaslow Nadine J , Yount Kathryn M
Published: January 2024

Background

In lower-and middle-income countries (LMICs), studies of interventions to reduce intimate partner violence (IPV) perpetration are expanding, yet measurement equivalence of the IPV perpetration construct that is the primary outcome in these investigations has not been established. We assessed the measurement equivalence of physical and sexual IPV perpetration item sets used in recent trials in LMICs and tested the impact of non-invariance on trial inference.

Methods

With data from three intervention trials among men (sample size 505-1537 across studies) completed in 2019, we calculated tetrachoric correlations among items and used multiple-group confirmatory factor analysis to assess invariance across arms and over time. We also assessed treatment effects adjusting for covariate imbalance and using inverse probability to treatment weights to assess concordance of invariant measures with published results, where warranted.

Findings

The average correlation among items measuring IPV perpetration was high and increased by 0.03 to 0.15 for physical IPV and 0.07 to 0.17 for sexual IPV over time with several items in two studies showing correlations ≥ 0.85 at endline. Increases in the degree of correlation for physical IPV were concentrated in the treatment arm in two of the studies. The increase in correlation in sexual IPV differed by arm across studies. Across all studies, a correlated two-factor solution was the best fitting model according to the EFAs and CFAs. One study demonstrated measurement invariance across arms and over time. In two of the studies, longitudinal measurement non-invariance was detected in the intervention arms. In post hoc testing, one study attained invariance with a one-factor model and study inference was concordant with published findings. The other study did not attain even partial invariance.

Conclusion

Common measures of physical and sexual IPV perpetration cannot be used validly for comparisons across treatment versus control groups over time without further refinement. The study highlights the need for an expanded item set, content validity assessments, further measurement invariance testing, and then consistent use of the item sets in future intervention trials to ensure valid inferences regarding the effectiveness of IPV perpetration prevention interventions within and across trials.
Multi-conflict islands are a widespread trend withinSerratiaspp
Authors: Cummins Thomas , Garrett Stephen R. , Blower Tim R. , Mariano Giuseppina
Published: January 2024

Bacteria carry numerous anti-phage systems in ‘defence islands’ or hotspots. Recent studies have delineated the content and boundaries of these islands in various species, revealing instances of islands that encode additional factors, including antibiotic resistance, stress genes, Type VI Secretion System (T6SS)-dependent effectors, and virulence factors.

Our study identifies three defence islands in theSerratiagenus with a mixed cargo of anti-phage systems, virulence factors and different types of anti-bacterial modules, revealing a widespread trend of co-accumulation that extends beyond T6SS-dependent effectors to colicins and contact-dependent inhibition systems. We report the identification of four distinct anti-phage system/subtypes, including a previously unreported Toll/IL-1 receptor (TIR)-domain-containing system with population-wide immunity, and two loci co-opting a predicted T6SS-related protein for phage defence. This study enhances our understanding of the protein domains that can be co-opted for phage defence and of the diverse combinations in which known anti-phage proteins can be assembled, resulting in a highly diversified anti-phage arsenal.
Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother’s milk
Authors: Allert Mattea , Ferretti Pamela , Johnson Kelsey E. , Heisel Timothy , Gonia Sara , Knights Dan , Fields David A. , Albert Frank W. , Demerath Ellen W. , Gale Cheryl A. , Blekhman Ran
Published: January 2024

The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as the sole source of nutrition for the human infant, little is known about how variation in milk composition, and especially the milk microbiome, shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiome using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. We found that the microbial taxonomic overlap between milk and the infant gut was driven by bifidobacteria, in particular byB. longum. Infant stool samples dominated byB. longumalso showed higher temporal stability compared to samples dominated by other species. We identified two instances of strain sharing between maternal milk and the infant gut, one involving a commensal (B. longum) and one a pathobiont (K. pneumoniae). In addition, strain sharing between unrelated infants was higher among infants born at the same hospital compared to infants born in different hospitals, suggesting a potential role of the hospital environment in shaping the infant gut microbiome composition. The infant gut microbiome at one month compared to six months of age was enriched in metabolic pathways associated withde-novomolecule biosynthesis, suggesting that early colonisers might be more versatile and metabolically independent compared to later colonizers. Lastly, we found a significant overlap in antimicrobial resistance genes carriage between the mother’s milk and their infant’s gut microbiome. Taken together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.
Hypoxia-induced Complement Component 3 Promotes Aggressive Tumor Growth in the Glioblastoma Microenvironment
Authors: Rosberg Rebecca , Smolag Karolina I. , Sjölund Jonas , Johansson Elinn , Bergelin Christina , Wahldén Julia , Pantazopoulou Vasiliki , Ceberg Crister , Pietras Kristian , Blom Anna M. , Pietras Alexander
Published: January 2024

Glioblastoma (GBM) is the most aggressive form of glioma with a high rate of relapse despite intensive treatment. Tumor recurrence is tightly linked to radio-resistance, which in turn is associated with hypoxia. Here, we discovered a strong link between hypoxia and local complement signaling using publicly available bulk, single cell, and spatially resolved transcriptomic data from human GBM patients. Complement component 3 (C3) and the receptorC3AR1were both associated with aggressive disease and shorter survival in human glioma. In a genetically engineered mouse model of GBM, we found C3 specifically in hypoxic tumor areas. In vitro, we found an oxygen level-dependent increase inC3andC3AR1expression in response to hypoxia in several GBM and stromal cell types. Presence of C3 increased proliferation of GBM cells under hypoxic conditions, as well as clonal survival of GBM cells following radiation. Targeting C3aR using the antagonist SB290157 decreased GBM cell self-renewal in vitro, and prolonged survival of glioma bearing mice both alone and in combination with radiotherapy while reducing the number of M2-polarized macrophages. Our findings establish a strong link between hypoxia and complement pathways in GBM, and support a role of hypoxia-induced C3a-C3aR signaling as a contributor to glioma aggressiveness.
Temporal epigenome modulation enables efficient bacteriophage engineering and functional analysis of phage DNA modifications
Authors: Pozhydaieva Nadiia , Billau Franziska Anna , Wolfram-Schauerte Maik , Rojas Adán Andrés Ramírez , Paczia Nicole , Schindler Daniel , Höfer Katharina
Published: January 2024

Lytic bacteriophages hold substantial promise in medical and biotechnological applications. CRISPR-Cas systems offer a way to explore these mechanisms via site-specific phage mutagenesis. However, phages can resist Cas-mediated cleavage through extensive DNA modifications like cytosine glycosylation, hindering mutagenesis efficiency. Our study utilizes the eukaryotic enzyme NgTET to temporarily reduce phage DNA modifications, facilitating Cas nuclease cleavage and enhancing mutagenesis efficiency. This approach enables precise DNA targeting and seamless point mutation integration, exemplified by deactivating specific ADP-ribosyltransferases crucial for phage infection. Furthermore, by temporally removing DNA modifications, we elucidated the effects of these modifications on T4 phage infections without necessitating gene deletions.

Our results present a strategy enabling the investigation of phage epigenome functions and streamlining the engineering of phages with cytosine DNA modifications. The described temporal modulation of the phage epigenome is valuable for synthetic biology and fundamental research to comprehend phage infection mechanisms through the generation of mutants.
Rapid and objective assessment of auditory temporal processing using dynamic amplitude-modulated stimuli
Authors: Parida Satyabrata , Yurasits Kimberly , Cancel Victoria E. , Zink Maggie E. , Mitchell Claire , Ziliak Meredith C. , Harrison Audrey V. , Bartlett Edward L. , Parthasarathy Aravindakshan
Published: January 2024

Auditory neural coding of speech-relevant temporal cues can be noninvasively probed using envelope following responses (EFRs), neural ensemble responses phase-locked to the stimulus amplitude envelope. EFRs emphasize different neural generators, such as the auditory brainstem or auditory cortex, by altering the temporal modulation rate of the stimulus. EFRs can be an important diagnostic tool to assess auditory neural coding deficits that go beyond traditional audiometric estimations. Existing approaches to measure EFRs use discrete amplitude modulated (AM) tones of varying modulation frequencies, which is time consuming and inefficient, impeding clinical translation. Here we present a faster and more efficient framework to measure EFRs across a range of AM frequencies using stimuli that dynamically vary in modulation rates, combined with spectrally specific analyses that offer optimal spectrotemporal resolution. EFRs obtained from several species (humans, Mongolian gerbils, Fischer-344 rats, and Cba/CaJ mice) showed robust, high-SNR tracking of dynamic AM trajectories (up to 800Hz in humans, and 1.4 kHz in rodents), with a fivefold decrease in recording time and thirtyfold increase in spectrotemporal resolution. EFR amplitudes between dynamic AM stimuli and traditional discrete AM tokens within the same subjects were highly correlated (94% variance explained) across species. Hence, we establish a time-efficient and spectrally specific approach to measure EFRs. These results could yield novel clinical diagnostics for precision audiology approaches by enabling rapid, objective assessment of temporal processing along the entire auditory neuraxis.