bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing a Role for Sarcospan in Immune Function
Authors: Valera Isela C. , Kahmini Aida Rahimi , Smith Kyle A. , Crawford Rhiannon Q. , Parvatiyar Michelle S.
Published: April 2024

Sarcospan (SSPN) is a tetraspanin-like member of the dystrophin-glycoprotein complex (DGC) with expression reported at the transcript level in B cells and several other immune cell populations. SSPN is best known for its expression in skeletal, cardiac, and vascular smooth muscle, however it is expressed in other cell types and its roles in non-muscle cells have not been well described. Analysis of functional interactions of SSPN with effectors of hematopoietic cell lineages uncovered strong associations with several proteins with known roles in hematopoiesis and immune response. In this study, we utilized flow cytometry to uncover SSPN+ immune cell populations expressing the SSPN protein. We performed immunophenotyping of global SSPN-deficient (SSPN-/-) C57BL/6J male and female mice to assess whether SSPN plays an essential role in generation of specific immune cells. By flow cytometry we found that B cells, CD11b+ and CD11c+ (monocytes, tissue macrophages, and a subset of dendritic cells) express the highest levels of SSPN at their cell membranes. To pinpoint potential roles for SSPN in B cell development, SSPN-/-bone marrow cells were isolated and differentiated using phorbol myristate acetate (PMA). To test B cell effector functions, antibody isotype analysis was performed to assess whether SSPN influences antibody class switching. Blood serum of WT and SSPN-/-mice were tested for presence of important developmental signals for B cell maturation, development and isotype switching. Our study is the first to document SSPN protein expression on distinct classes of immune cells including CD11b+, CD11c+ and B cells (CD19+). Immunophenotyping revealed several differences in immune cell populations in the murine spleens: 1) a significant increase in % T cells in SSPN-/-males, 2) slight reduction of % B cells in SSPN-/-females, 3) a significant increase % of dendritic cells in SSPN-/-females, and 4) no significant alterations in NK cells. Under unstimulated conditions, SSPN-/-female mice had a significantly lower IgG2b titers compared to WT. Overall, the observation of SSPN expression in distinct immune cells, potential role(s) in hematopoiesis and B cell effector function is intriguing and warrants further investigation.

Highlights

The sarcospan protein has an established role in stabilization of striated muscle membranes and is an essential member of the dystrophin-glycoprotein complex. This study investigates the reported presence ofSspnin B cells and examines potential roles in immune function including:

Determining a connection with hematopoiesis and establishment of ‘niches’

Impact on immune content in spleens of sarcospan-deficient mice

Identifying a role in B cell effector functions
Extracellular vesicles-based point-of-care testing for the diagnosis and monitoring of Alzheimer’s disease
Authors: Li Xiang , Chen Jie , Yang Yang , Cai Hongwei , Ao Zheng , Xing Yantao , Li Kangle , Yang Kaiyuan , Wallace Abigail , Friend James , Lee Luke P. , Wang Nian , Guo Feng
Published: April 2024

Alzheimer’s disease (AD) is a debilitating condition that affects millions of people worldwide. One promising strategy for detecting and monitoring AD early on is using extracellular vesicles (EVs)-based point-of-care testing; however, diagnosing AD using EVs poses a challenge due to the low abundance of EV-biomarkers. Here, we present a fully integrated organic electrochemical transistor (OECT) that enables high accuracy, speed, and convenience in the detection of EVs from AD patients. We incorporated self-aligned acoustoelectric enhancement of EVs on a chip that rapidly propels, enriches, and specifically binds EVs to the OECT detection area. With our enhancement of pre-concentration, we increased the sensitivity to a limit of detection of 500 EV particles/μL and reduced the required detection time to just two minutes. We also tested the sensor on an AD mouse model to monitor AD progression, examined mouse Aβ EVs at different time courses, and compared them with intraneuronal Aβ cumulation using MRI. This innovative technology has the potential to diagnose Alzheimer’s and other neurodegenerative diseases accurately and quickly, enabling monitoring of disease progression and treatment response.
Comparison of three sequencing methods for identifying and quantifying antibiotic resistance genes (ARGs) in sewage
Authors: Mondhe Divya , Ishtiaq Farah
Published: April 2024

Background

Globally, antimicrobial resistance (AMR) poses a critical threat, requiring robust surveillance methodologies to tackle the growing challenge of drug-resistant microbes. AMR is a huge challenge in India due to high disease burden, lack of etiology-based diagnostic tests and over the counter availability of antibiotics and inadequate treatment of wastewaters are important drivers of AMR in India. There is lack of effective surveillance platforms that monitor health-associated infections. This include developing an understanding on background levels of AMR in the environment and comparison of AMR monitoring methods.

Objectives

This study evaluated the performance of three AMR sequencing methods, Illumina AmpliSeq AMR panel, QIAseq xHYB AMR panel and shotgun sequencing method for the detection of antimicrobial resistance genes (ARGs) in urban sewage. Our goal is to provide insights into the application and robustness of each sequencing method.

Methods

We compare the prevalence, diversity, and composition of ARGs across sequencing method and by sample type (inlet vs outlet) in four sewage treatment plants (STP).

Results

Regardless of the sequencing method used the dominant ARGs remained consistent, and their differential analysis showed consistent trends in detection of epidemiologically relevant ARGs. The cost-effectiveness analysis revealed comparable per-sample costs, with amplicon-based sequencing offering specificity for targeted genes, and shotgun sequencing uses a whole-genome sequencing approach that provides high-resolution taxonomic information for the characterisation of pathogens. This methodology can only detect ARGs that have been annotated in the reference database (e.g., CARD). Therefore, some novel types of ARGs present in the samples may be missed since the analysis is based on a similarity search. Differential abundance analysis to understand change in abundance in dominant ARGs from inlet to outlet of STP showed consistent trends across methods. However, with caution raised regarding potential artifacts introduced by enrichment steps in QIAseq xHYB AMR panel.

Conclusion

The choice of panel used would be governed by the context of the study. Nonetheless, our exploratory study shows that the data gathered using different sequencing pipelines helps in quantifying the ARG burden in the environment. This information is crucial in understanding the spatio-temporal distribution of ARGs in different environment and could help in developing PCR-based approaches for targeted surveillance.
Inferring gene regulatory networks by hypergraph variational autoencoder
Authors: Su Guangxin , Wang Hanchen , Zhang Ying , Coster Adelle CF , Wilkins Marc R. , Canete Pablo F. , Yu Di , Yang Yang , Zhang Wenjie
Published: April 2024

In constructing Gene Regulatory Networks (GRNs), it is crucial to consider cellular heterogeneity and differential gene regulatory modules. However, traditional methods have predominantly focused on cellular heterogeneity, approaching the subject from a relatively narrow scope. We present HyperG-VAE, a Bayesian deep generative model that utilizes a hypergraph to model single-cell RNA sequencing (scRNA-seq) data. HyperG-VAE employs a cell encoder with a Structural Equation Model to address cellular heterogeneity and build GRNs, alongside a gene encoder using hypergraph self-attention to identify gene modules. Encoders are synergistically optimized by a decoder, enabling HyperG-VAE to excel in GRN inference, single-cell clustering, and data visualization, evidenced by benchmarks. Additionally, HyperG-VAE effectively reveals gene regulation patterns and shows robustness in varied downstream analyses, demonstrated using B cell development data in bone marrow. The interplay of encoders by the overlapping genes between predicted GRNs and gene modules is further validated by gene set enrichment analysis, underscoring that the gene encoder boosts the GRN inference. HyperG-VAE proves efficient in scRNA-seq data analysis and GRN inference.
Biotic challenges in the city: Dietary restrictions and body fat content of female sexuals in urban ant populations
Authors: Trigos-Peral Gema , Witek Magdalena , Csata Enikő , Chudzik Paulina , Heinze Jürgen
Published: April 2024

Urban habitats represent an important challenge for many organisms. Besides the abiotic changes, urban habitats are also characterized by changes in the biotic conditions, such as a more uniform species composition and declining population sizes. For urban ants this can result in dietary shortages. In our study, we tested whether urban ant colonies might suffer from dietary restrictions by carrying out a common garden experiment in which ant colonies from urban and rural habitats were exposed to high carbohydrate, protein, and fat / protein diets. We also investigated the body fat content of individuals from both habitat types. Our findings suggest a lower availability of high-quality carbohydrates in urban areas. Additionally, while not statistically significant, rural colonies exhibited a tendency to consume greater quantities of proteins and fat compared to urban colonies. This trend was in line with a higher body fat content observed in female sexuals (gynes) from rural colonies. These results might indicate the outcome of an evolutionary feedback process in which ant colonies adapt to nutritional constraints in urban environments. They achieve this by minimizing the investment in gynes, which might require fewer reserves for survival during colony foundation due to reduced competition for nesting sites within urban green spaces.
Dynamic population coding of social novelty in the insular cortex
Authors: Sato Masaaki , Overton Eric T. N. , Fujima Shuhei , Takumi Toru
Published: April 2024

The familiarity of socially interacting peers has a profound impact on behavior1–3, but little is known about the neuronal representations distinguishing familiar from novel conspecifics. The insular cortex (IC) regulates social behavior4–9, and our previous study revealed that neurons in the agranular IC (aIC) encode ongoing social interactions10. To elucidate how these neurons discriminate between interactions with familiar and novel conspecifics, we monitored neuronal activity in mice by microendoscopic calcium imaging during social recognition memory (SRM) and linear chamber social discrimination (LCSD) tasks. In the SRM task, repeated interactions with the same target activated largely nonoverlapping cells during each session. The fraction of cells associated with social investigation (social cells) decreased as the subject repeatedly interacted with the same target, whereas substitution of a second novel target and subsequent exchange with the first familiar target recruited more new social cells. In the LCSD task, the addition of a novel target to an area containing a familiar target transiently increased the number of cells responding to both targets, followed by an eventual increase in the number of cells responding to the novel target. These results support the view that the aIC dynamically encodes social novelty, rather than consistently encode social identity, by rapidly reorganizing the neural representations of conspecific information.
Computational Mechanisms of Neuroimaging Biomarkers Uncovered by Multicenter Resting-State fMRI Connectivity Variation Profile
Authors: Yamashita Okito , Yamashita Ayumu , Takahara Yuji , Sakai Yuki , Okamoto Yasumasa , Okada Go , Takamura Masahiro , Nakamura Motoaki , Itahashi Takashi , Hanakawa Takashi , Togo Hiroki , Yoshihara Yujiro , Murai Toshiya , Okada Tomohisa , Narumoto Jin , Takahashi Hidehiko , Takagishi Haruto , Hosomi Koichi , Kasai Kiyoto , Okada Naohiro , Abe Osamu , Imamizu Hiroshi , Hayashi Takuya , Koike Shinsuke , Tanaka Saori C. , Kawato Mitsuo ,   Brain/MINDS Beyond Human Brain MRI Group
Published: April 2024

Resting-state functional connectivity (rsFC) is increasingly used to develop biomarkers for psychiatric disorders. Despite progress, development of the reliable and practical FC biomarker remains an unmet goal, particularly one that is clinically predictive at the individual level with generalizability, robustness, and accuracy. In this study, we propose a new approach to profile each connectivity from diverse perspective, encompassing not only disorder-related differences but also disorder-unrelated variations attributed to individual difference, within-subject across-runs, imaging protocol, and scanner factors. By leveraging over 1500 runs of 10-minute resting-state data from 84 traveling-subjects across 29 sites and 900 participants of the case-control study with three psychiatric disorders, the disorder-related and disorder-unrelated FC variations were estimated for each individual FC. Using the FC profile information, we evaluated the effects of the disorder-related and disorder-unrelated variations on the output of the multi-connectivity biomarker trained with ensemble sparse classifiers and generalizable to the multicenter data. Our analysis revealed hierarchical variations in individual functional connectivity, ranging from within-subject across-run variations, individual differences, disease effects, inter-scanner discrepancies, and protocol differences, which were drastically inverted by the sparse machine-learning algorithm. We found this inversion mainly attributed to suppression of both individual difference and within-subject across-runs variations relative to the disorder-related difference by weighted-averaging of the selected FCs and ensemble computing. This comprehensive approach will provide an analytical tool to delineate future directions for developing reliable individual-level biomarkers.
Fur microbiome as a putative source of symbiotic bacteria in sucking lice
Authors: Říhová Jana Martin , Gupta Shruti , Nováková Eva , Hypša Václav
Published: April 2024

Symbiosis between insects and bacteria has been established countless times. While it is well known that the symbionts originated from a variety of different bacterial taxa, it is usually difficult to determine their environmental source and a route of their acquisition by the host. In this study, we address this question using a model of Neisseriaceae symbionts in rodent lice. These bacteria established their symbiosis independently with different louse taxa (Polyplax, Hoplopleura, Neohaematopinus), most likely from the same environmental source. We first applied amplicon analysis to screen for candidate source bacterium in the louse environment, that is, three species of rodents (Microtus arvalis, Clethrionomys glareolus, andApodemus flavicollis). The screened samples included rodent fur, skin, spleen, and ectoparasites sampled from the rodents. The amplicon analysis revealed a Neisseriaceae bacterium, closely related to the known louse symbionts. We assembled genome drafts of this environmental bacterium from all three rodent hosts. The sizes of the three drafts converged to a remarkably small size of approximately 1.4 Mbp, which is even smaller than the genomes of the related symbionts. Based on these findings, we propose a hypothetical scenario of the genome evolution during the transition of a free-living bacterium to the member of the rodent fur-associated microbiome and subsequently to the facultative and obligate louse symbionts.
The Tradeoffs Between Persistence and Mutation Rates at Sub-Inhibitory Antibiotic Concentrations inStaphylococcus aureus
Authors: Ismail Alysha S. , Berryhill Brandon A. , Gil-Gil Teresa , Manuel Joshua A. , Smith Andrew P. , Baquero Fernando , Levin Bruce R.
Published: April 2024

The rational design of the antibiotic treatment of bacterial infections employs these drugs to reach concentrations that exceed the minimum needed to prevent the replication of the target bacteria. However, within a treated patient, spatial and physiological heterogeneity promotes antibiotic gradients such that the concentration of antibiotics at specific sites is below the minimum needed to inhibit bacterial growth. Here, we investigate the effects of sub-inhibitory antibiotic concentrations on three parameters central to bacterial infection and the success of antibiotic treatment, usingin vitroexperiments withStaphylococcus aureusand mathematical-computer simulation models. Our results, using drugs of six different classes, demonstrate that exposure to sub-inhibitory antibiotic concentrations not only alters the dynamics of bacterial growth but also increases the mutation rate to antibiotic resistance and decreases the rate of production of persister cells thereby reducing the persistence level. Understanding this trade-off between mutation rates and persistence levels resulting from sub-inhibitory antibiotic exposure is crucial for optimizing, and mitigating the failure of, antibiotic therapy.
Dissecting Reactive Astrocyte Responses: Lineage Tracing and Morphology-based Clustering
Authors: Delgado-García Lina M. , Ojalvo-Sanz Ana C. , Nakamura Thabatta K. E. , Martín-López Eduardo , Porcionatto Marimelia , Lopez-Mascaraque Laura
Published: April 2024

Abstract Figure

Graphical Abstract

Brain damage triggers diverse cellular and molecular events, with astrocytes playing a crucial role in activating local neuroprotective and reparative signaling within damaged neuronal circuits. Here, we investigated reactive astrocytes using a multidimensional approach to categorize their responses into different subtypes based on morphology using the StarTrack lineage tracer, single-cell imaging reconstruction and multivariate data analysis. Our findings revealed three profiles of reactive astrocyte responses affecting cell size- and shape-related morphological parameters: “moderate,” “strong,” and “very strong”. We also explored the heterogeneity in astrocyte reactivity, with a particular emphasis in the spatial and clonal distribution. Our research highlights the importance of the relationships between the different astrocyte subpopulations with their reactive responses, showing an enrichment of protoplasmic and fibrous astrocytes within the “strong” and “very strong” subtypes. Overall, our study contributes to a better understanding of astrocyte heterogeneity in response to an injury. By elucidating the diverse reactive responses among astrocyte subpopulations, we pave the way for future research aimed at uncovering novel therapeutic targets for mitigating the effects of brain damage and promoting neural repair.
Dispersal syndromes allow understanding but not predicting dispersal ability across the tree of life
Authors: Fandos Guillermo , Robinson Robert A. , Zurell Damaris
Published: April 2024

Dispersal is fundamental to many ecological and evolutionary processes, yet understanding the determinants and predictability of dispersal remains a crucial challenge. Dispersal syndromes, which describe patterns in the covariation of traits associated with dispersal, can help to gain a deeper understanding of the evolutionary dynamics of dispersal and its implications for range dynamics and ecosystem functioning in the face of global change. However, the extent to which such dispersal syndromes are generalizable across a large taxonomic scale has been hampered by low availability of standardized dispersal data across species. In this study, we used the most comprehensive and up-to-date empirical dispersal dataset for European birds to investigate the formation of dispersal syndromes and their effectiveness in predicting dispersal across species. We found body mass, feeding guild, and life-history traits shape dispersal syndromes in birds. Yet, only body mass and life history accurately predicted dispersal for unassessed species, while even multi-trait dispersal syndromes poorly predicted dispersal for phylogenetically distant species. These results shed light on the complex nature of bird dispersal and emphasize the need for refined approaches in elucidating the mechanisms and constraints underlying dispersal evolution. Our study highlights the importance of considering multiple factors and expanding empirical datasets to enhance our understanding of dispersal in avian populations.
GENOME-WIDE IDENTIFICATION, CHARACTERIZATION AND EXPRESSION ANALYSIS OF NA+/H+EXCHANGER GENE FAMILY IN TWO CORCHORUS SPECIES
Authors: Ahmed Borhan , Tabassum Anika , Bashar Kazi Khayrul , Aktar Nasima , Hossain Sabbir , Mamun Abdullah-Al , Roni Shyduzzaman , Hasan Fakhrul , Alam Mobashwer
Published: April 2024

Na+/H+exchangers (NHXs) are secondary ion transporter to exchange H+ and transfer Na+or K+across membrane plays crucial role in cellular pH and Na+and K+homeostasis in plant. In the present study, we have performed genomewide identification, characterization and comparative analysis of NHXs genes in two cultivated jute species and found seven Co and Cc NHXs in each genome. Subsequently phylogenetic analysis demonstrated that Co and Cc NHXs have three sub-group that correlate with other plant species containing 10-12 transmembrane helices (TMH) and a hydrophilic C-terminal domain in the cytoplasmic region, the TMH compose a hollow cylinder to provide the channel for Na+and H+transport. Promoter profiling of both species NHXs genes revealed in enrichment of cis element involved in stress responsiveness reflecting their potential involvement against abiotic stress. Transcriptome data and real time PCR of Co and Cc NHXs gene expression analysis under saline and drought condition showed significant differences, which suggest their potential role in abiotic stress conditions. This is the first comprehensive analysis providing baseline information of Co and Cc NHXs genes in abiotic stress condition which can be used for the development of abiotic stress tolerant jute variety.
Differential Roles of Kinetic On- and Off-Rates in T-Cell Receptor Signal Integration Revealed with a Modified Fab’-DNA Ligand
Authors: Wilhelm Kiera B. , Vissa Anand , Groves Jay T.
Published: April 2024

Antibody-derived T-cell receptor (TCR) agonists are commonly used to activate T cells. While antibodies can trigger TCRs regardless of clonotype, they bypass native T cell signal integration mechanisms that rely on monovalent, membrane-associated, and relatively weakly-binding ligand in the context of cellular adhesion. Commonly used antibodies and their derivatives bind much more strongly than native peptide-MHC (pMHC) ligands bind their cognate TCRs. Because ligand dwell time is a critical parameter that tightly correlates with physiological function of the TCR signaling system, there is a general need, both in research and therapeutics, for universal TCR ligands with controlled kinetic binding parameters. To this end, we have introduced point mutations into recombinantly expressed α-TCRβ H57 Fab to modulate the dwell time of monovalent Fab binding to TCR. When tethered to a supported lipid bilayer via DNA complementation, these monovalent Fab’-DNA ligands activate T cells with potencies well-correlated with their TCR binding dwell time. Single-molecule tracking studies in live T cells reveal that individual binding events between Fab’-DNA ligands and TCRs elicit local signaling responses closely resembling native pMHC. The unique combination of high on- and off-rate of the H57 R97L mutant enables direct observations of cooperative interplay between ligand binding and TCR-proximal condensation of the linker for activation of T cells (LAT), which is not readily visualized with pMHC. This work provides insights into how T cells integrate kinetic information from synthetic ligands and introduces a method to develop affinity panels for polyclonal T cells, such as cells from a human patient.

STATEMENT OF SIGNIFICANCE

T cells read kinetic information from ligands binding to T-cell receptors (TCRs) to make cell fate decisions. Unique kinetic features of a modified Fab’-DNA ligand enable direct visualization multiple TCR signal coordination through a nascent LAT condensation event. We further observed positive feedback through a kinetic on-rate enhancement in the growing LAT condensate. These observations help unify several seemingly disparate aspects of TCR signaling that have been debated in the literature. Furthermore, calibration of the Fab’-DNA ligand against native agonist pMHC establishes a basis for quantitative analysis of TCR signaling in polyclonal T cell populations.
Changes in taste palatability across the estrous cycle are modulated by hypothalamic estradiol signaling
Authors: Stone Bradly T. , Rahamim Oran M. , Katz Donald B. , Lin Jian-You
Published: April 2024

Food intake varies across the stages of a rat’s estrous cycle. It is reasonable to hypothesize that this cyclic fluctuation in consumption reflects an impact of hormones on taste palatability/preference, but evidence for this hypothesis has been mixed, and critical within-subject experiments in which rats sample multiple tastes during each of the four main estrous phases (metestrus, diestrus, proestrus, and estrus) have been scarce. Here, we assayed licking for pleasant (sucrose, NaCl, saccharin) and aversive (quinine-HCl, citric acid) tastes each day for 5-10 days while tracking rats’ estrous cycles through vaginal cytology. Initial analyses confirmed the previously-described increased consumption of pleasant stimuli 24-48 hours following the time of high estradiol. A closer look, however, revealed this effect to reflect a general magnification of palatability—higher than normal preferences for pleasant tastes and lower than normal preferences for aversive tastes—during metestrus. We hypothesized that this phenomenon might be related to estradiol processing in the lateral hypothalamus (LH), and tested this hypothesis by inhibiting LH estrogen receptor activity with ICI182,780during tasting. Control infusions replicated the metestrus magnification of palatability pattern; ICI infusions blocked this effect as predicted, but failed to render preferences “cycle free,” instead delaying the palatability magnification until diestrus. Clearly, estrous phase mediates details of taste palatability in a manner involving hypothalamic actions of estradiol; further work will be needed to explain the lack of a flat response across the cycle with hypothalamic estradiol binding inhibited, a result which perhaps suggests dynamic interplay between brain regions or hormones.

Significance Statement

Consummatory behaviors are impacted by many variables, including naturally circulating hormones. While it is clear that consumption is particularly high during the stages following the high-estradiol stage of the rodent’s estrous (and human menstrual) cycle, it is as of yet unclear whether this phenomenon reflects cycle stage-specific palatability (i.e., whether pleasant tastes are particularly delicious, and aversive tastes particularly disgusting, at particular phases). Here we show that palatability is indeed modulated by estrous phase, and that this effect is governed, at least in part, by the action of estradiol within the lateral hypothalamus. These findings shed light on the mechanisms underlying the adverse impact on human welfare due to irregularities observed across the otherwise cyclic menstrual process.
A conserved function of corepressors is to nucleate assembly of the transcriptional preinitiation complex
Authors: Leydon Alexander R. , Downing Benjamin , Sanchez Janet Solano , Loll-Krippleber Raphael , Belliveau Nathan M. , Rodriguez-Mias Ricard A , Bauer Andrew , Watson Isabella J. , Bae Lena , Villén Judit , Brown Grant W. , Nemhauser Jennifer L.
Published: April 2024

The plant corepressor TPL is recruited to diverse chromatin contexts, yet its mechanism of repression remains unclear. Previously, we have leveraged the fact that TPL retains its function in a synthetic transcriptional circuit in the yeast modelSaccharomyces cerevisiaeto localize repressive function to two distinct domains. Here, we employed two unbiased whole genome approaches to map the physical and genetic interactions of TPL at a repressed locus. We identified SPT4, SPT5 and SPT6 as necessary for repression with the SPT4 subunit acting as a bridge connecting TPL to SPT5 and SPT6. We also discovered the association of multiple additional constituents of the transcriptional preinitiation complex at TPL-repressed promoters, specifically those involved in early transcription initiation events. These findings were validated in yeast and plants through multiple assays, including a novel method to analyze conditional loss of function of essential genes in plants. Our findings support a model where TPL nucleates preassembly of the transcription activation machinery to facilitate rapid onset of transcription once repression is relieved.
Sonic hedgehog medulloblastoma cells in co-culture with cerebellar organoids converge towardsin vivomalignant cell states
Authors: van Essen Max J. , Nicheperovich Alina , Schuster-Böckler Benjamin , Becker Esther B. E. , Jacob John
Published: April 2024

Background

In the malignant brain tumour sonic hedgehog medulloblastoma (SHH-MB) the properties of cancer cells are influenced by their microenvironment, but the nature of those effects and the phenotypic consequences for the tumour are poorly understood. The aim of this study was to identify phenotypic properties of SHH-MB cells that were driven by the non-malignant tumour microenvironment.

Methods

Human induced pluripotent cells (iPSC) were differentiated to cerebellar organoids to simulate the non-malignant tumour microenvironment. Tumour spheroids were generated from two distinct, long-established SHH-MB cell lines which were co-cultured with cerebellar organoids. We profiled the cellular transcriptomes of malignant and non-malignant cells by performing droplet-based single-cell RNA-sequencing (scRNA-seq). The transcriptional profiles of tumour cells in co-culture were compared with those of malignant cells cultured in isolation and with public SHH-MB datasets of patient tumours and patient-derived xenograft (PDX) models.

Results

SHH-MB cell lines in organoid co-culture adopted patient tumour-associated phenotypes and showed increased heterogeneity compared to monocultures. Sub-populations of co-cultured SHH-MB cells activated a key marker of differentiating granule cells,NEUROD1that was not observed in tumour monocultures. Other sub-populations expressed transcriptional determinants consistent with a cancer stem cell (CSC)-like state that resembled cell states identifiedin vivo.

Conclusion

For SHH-MB cell lines in co-culture, there was a convergence of malignant cell states towards patterns of heterogeneity in patient tumours and PDX models implying these states were non-cell autonomously induced by the microenvironment. Therefore, we have generated an advanced, novelin vitromodel of SHH-MB with potential translational applications.
Level Dependent Subcortical EEG Responses to Continuous Speech
Authors: Kulasingham Joshua P. , Innes-Brown Hamish , Enqvist Martin , Alickovic Emina
Published: April 2024

The auditory brainstem response (ABR) is a measure of subcortical activity in response to auditory stimuli. The wave V peak of the ABR depends on stimulus intensity level, and has been widely used for clinical hearing assessment. Conventional methods to estimate the ABR average electroencephalography (EEG) responses to short unnatural stimuli such as clicks. Recent work has moved towards more ecologically relevant continuous speech stimuli using linear deconvolution models called Temporal Response Functions (TRFs). Investigating whether the TRF waveform changes with stimulus intensity is a crucial step towards the use of natural speech stimuli for hearing assessments involving subcortical responses. Here, we develop methods to estimate level-dependent subcortical TRFs using EEG data collected from 21 participants listening to continuous speech presented at 4 different intensity levels. We find that level-dependent changes can be detected in the wave V peak of the subcortical TRF for almost all participants, and are consistent with level-dependent changes in click-ABR wave V. We also investigate the most suitable peripheral auditory model to generate predictors for level-dependent subcortical TRFs and find that simple gammatone filterbanks perform the best. Additionally, around 6 minutes of data may be sufficient for detecting level-dependent effects and wave V peaks above the noise floor for speech segments with higher intensity. Finally, we show a proof-of-concept that level dependent subcortical TRFs can be detected even for the inherent intensity fluctuations in natural continuous speech.

Visual abstract

Significance statement

Subcortical EEG responses to sound depend on the stimulus intensity level and provide a window into the early human auditory pathway. However, current methods detect responses using unnatural transient stimuli such as clicks or chirps. We develop methods for detecting level-dependent responses to continuous speech stimuli, which is more ecologically relevant and may provide several advantages over transient stimuli. Critically, we find consistent patterns of level dependent subcortical responses to continuous speech at an individual level, that are directly comparable to those seen for conventional responses to click stimuli. Our work lays the foundation for the use of subcortical responses to natural speech stimuli in future applications such as clinical hearing assessment and hearing assistive technology.
Prolonged heat stress in Brassica napus during flowering negatively impacts yield and alters glucosinolate and sugars metabolism
Authors: Kourani Mariam , Anastasiadi Maria , Hammond John , Mohareb Fady
Published: April 2024

Oilseed rape (Brassica napus), one of the most important sources of vegetable oil worldwide, is adversely impacted by heat wave-induced temperature stress especially during its yield determining reproductive stages. However, the underlying molecular and biochemical mechanisms are still poorly understood. In this study, we investigated the transcriptomic and metabolomic responses to heat stress in B. napus plants exposed to a gradual increase of temperature reaching 30 °C in the day and 24 °C at night for a period of 6 days. High Performance Liquid Chromatography (HPLC) and Liquid Chromatography-Mass Spectrometry (LC-MS) was used to quantify the content of carbohydrates and glucosinolates respectively. RNA-Seq analysis of flower buds showed a total of 1892, 3253, 4553, 4165 and 1713 genes were differentially expressed at days 0, 1, 2, 6 and 12 after treatment respectively. Results showed that heat stress reduced yield and altered oil composition. Heat stress also increased the content of carbohydrate (Glucose, Fructose and Sucrose) and aliphatic glucosinolates (Gluconapin, Progoitrin) in the leaves but decreased the content of the indolic glucosinolate (Glucobrassicin). Heat treatment resulted in down regulation of genes involved in respiratory metabolism namely Glycolysis, Pentose Phosphate Pathway, Citrate Cycle and Oxidative Phosphorylation especially after 48 hrs of heat stress. Other down regulated genes mapped to sugars transporters, nitrogen transport and storage, cell wall modification and methylation. In contrast, up regulated genes mapped to small heat shock proteins (sHSP20) and other heat shock factors that play important roles in thermotolerance. Furthermore, two genes were chosen from the pathways involved in the heat stress response to further examine their expression using real time RT-qPCR. Taken together, the results of this study demonstrated that the changes in carbohydrates and glucosinolates metabolism and transport under heat stress is one of the response mechanisms employed by the plant under heat stress conditions. Moreover, the transcriptomic data will be useful for further understanding the molecular mechanisms of B. napus plant tolerance to heat stress and provide a basis for breeding heat-tolerant varieties.
Small molecule telomerase inhibitors are also potent inhibitors of telomeric C-strand synthesis
Authors: Johnson Kaitlin , Seidel Julia M. , Cech Thomas R.
Published: April 2024

Telomere replication is essential for continued proliferation of human cells, such as stem cells and cancer cells. Telomerase lengthens the telomeric G-strand, while C-strand replication is accomplished by CST-polymerase α -primase (CST-PP). Replication of both strands is inhibited by formation of G-quadruplex (GQ) structures in the G-rich single-stranded DNA. TMPyP4 and pyridostatin (PDS), which stabilize GQ structures in both DNA and RNA, inhibit telomerasein vitro, and they cause telomere shortening in human cells that has been attributed to telomerase inhibition. Here, we show that TMPyP4 and PDS also inhibit C-strand synthesis by stabilizing DNA secondary structures and thereby preventing CST-PP from binding to telomeric DNA. We also show that these small molecules inhibit CST-PP binding to a DNA sequence containing no consecutive guanine residues, which is unlikely to form GQs. Thus, while these “telomerase inhibitors” indeed inhibit telomerase, they are also robust inhibitors of telomeric C-strand synthesis. Furthermore, given their limited specificity for GQ structures, they may disrupt many other protein-nucleic acid interactions in human cells.
Structural Basis of Non-Latent Signaling by the Anti-Müllerian Hormone Procomplex
Authors: Howard James A , Hok Lucija , Cate Richard L , Sanford Nathaniel J , Hart Kaitlin N , Leach Edmund AE , Bruening Alena S , Pépin David , Donahoe Patricia K , Thompson Thomas B
Published: April 2024

Most TGFβ family ligands exist as procomplexes consisting of a prodomain noncovalently bound to a growth factor (GF); Whereas some prodomains confer latency, the Anti-Müllerian Hormone (AMH) prodomain maintains a remarkably high affinity for the GF yet remains active. Using single particle EM methods, we show the AMH prodomain consists of two subdomains: a vestigial TGFβ prodomain-like fold and a novel, helical bundle GF-binding domain, the result of an exon insertion 450 million years ago, that engages both receptor epitopes. When associated with the prodomain, the AMH GF is distorted into a strained, open conformation whose closure upon bivalent binding of AMHR2 displaces the prodomain through a conformational shift mechanism to allow for signaling.
Characterising Aromatic Side Chains in Proteins through the Synergistic Development of NMR Experiments and Deep Neural Networks
Authors: Shukla Vaibhav Kumar , Karunanithy Gogulan , Vallurupalli Pramodh , Hansen D Flemming
Published: April 2024

Nuclear magnetic resonance (NMR) spectroscopy has become an important technique in structural biology for characterising the structure, dynamics and interactions of macromolecules. While a plethora of NMR methods are now available to inform on backbone and methyl-bearing side-chains of proteins, a characterisation of aromatic side chains is more challenging and often requires specific labelling or13C-detection. Here we present a deep neural network (DNN) named FID-Net-2, which transforms NMR spectra recorded on simple uniformly13C labelled samples to yield high-quality1H-13C correlation spectra of the aromatic side chains. Key to the success of the DNN is the design of a complementary set of NMR experiments that produce spectra with unique features to aid the DNN produce high-resolution aromatic1H-13C correlation spectra with accurate intensities. The reconstructed spectra can be used for quantitative purposes as FID-Net-2 predicts uncertainties in the resulting spectra. We have validated the new methodology experimentally on protein samples ranging from 7 to 40 kDa in size. We demonstrate that the method can accurately reconstruct high resolution two-dimensional aromatic1H-13C correlation maps, high resolution three-dimensional aromatic-methyl NOESY spectra to facilitate aromatic1H-13C assignments, and that the intensities of peaks from the reconstructed aromatic1H-13C correlation maps can be used to quantitatively characterise the kinetics of protein folding. More generally, we believe that this strategy of devising new NMR experiments specifically for analysis using customised DNNs represents a substantial advance that will have a major impact on the study of molecules using NMR in the years to come.
The Role of Cilia in the Development, Survival, and Regeneration of Hair Cells
Authors: Boldizar Hope , Friedman Amanda , Stanley Tess , Padilla María , Galdieri Jennifer , Sclar Arielle , Stawicki Tamara M.
Published: April 2024

Mutations impacting cilia genes lead to a class of human diseases known as ciliopathies. This is due to the role of cilia in the development, survival, and regeneration of many cell types. We investigated the extent to which disrupting cilia impacted these processes in hair cells. We found that mutations in two intraflagellar transport (IFT) genes,ift88anddync2h1,which lead to the loss of kinocilia, caused increased hair cell apoptosis in the zebrafish lateral line. IFT gene mutants also have a decreased mitochondrial membrane potential, and blocking the mitochondrial uniporter causes a loss of hair cells in wild-type zebrafish but not mutants, suggesting mitochondria dysfunction may contribute to the apoptosis seen in these mutants. These mutants also showed decreased proliferation during hair cell regeneration, but did not show consistent changes in support cell number or proliferation during hair cell development. These results show that disruption of the cilia through either mutations in anterograde or retrograde IFT genes appear to impact hair cell survival but not necessarily development in the lateral line.
Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine
Authors: He Yongqun Oliver , Barisoni Laura , Rosenberg Avi Z , Robinson Peter N. , Diehl Alexander D. , Chen Yichao , Phuong Jimmy P. , Hansen Jens , Herr Bruce W. , Börner Katy , Bonevich Nikki , Arnous Ghida , Boddapati Saketh , Zheng Jie , Alakwaa Fadhl , Sardar Pinaki , Duncan William D. , Liang Chen , Valerius M. Todd , Jain Sanjay , Iyengar Ravi , Himmelfarb Jonathan , Kretzler Matthias ,   the Kidney Precision Medicine Project
Published: April 2024

Many resources are now generating, processing, storing, or providing kidney-related molecular, pathological, and clinical data. Reference ontologies offer an opportunity to support knowledge and data organization and integration. The Kidney Precision Medicine Project (KPMP) team contributed to the representation and addition of 329 kidney phenotype terms to the Human Phenotype Ontology (HPO) and identified many subcategories of acute kidney injury (AKI) or chronic kidney disease (CKD). The Kidney Tissue Atlas Ontology (KTAO) imports and integrates kidney-related terms from existing ontologies (e.g., HPO, CL, and Uberon) and represents 259 kidney-related biomarkers. We also developed a precision medicine metadata ontology (PMMO) to integrate 50 variables from KPMP and CellxGene resources and applied PMMO for integrative analysis. The gene expression profiles of kidney gene biomarkers were specifically analyzed in healthy controls or AKI/CKD disease states. This work demonstrates how ontology-based approaches support multi-domain data and knowledge organization and integration to advance precision medicine.
During haptic communication, the central nervous system compensates distinctly for delay and noise
Authors: Eden Jonathan , Ivanova Ekaterina , Burdet Etienne
Published: April 2024

Connected humans have been previously shown to exploit the exchange of haptic forces and tactile information to improve their performance in joint action tasks. As human interactions are increasingly mediated through robots and networks it is important to understand the impact that network features such as lag and noise may have on human behaviour. In this paper, we investigated the interaction with a human-like robot controller that provides similar haptic communication behaviour as human-human interaction and examined the influence and compensation mechanisms for delay and noise on haptic communication. The results of our experiments show that participants can distinguish between noise and delay, and make use of compensation mechanisms to preserve performance in both cases. However, while noise is compensated for by increasing co-contraction, delay compensation could not be explained by this strategy. Instead, computational modelling suggested that a feed-forward prediction mechanism is used to compensate for the temporal delay and yield an efficient haptic communication.

Author summary

Increasingly humans are making use of networks and robots to coordinate haptic interactions through teleoperation. However, with networks comes delays and noise that can change both the force that is transmitted and how we perceive that force. The haptic communication involved in joint actions, such as moving a piano or performing a pair spin, has been shown to improve performance, but how does delay affect this behaviour? We tested how participants tracked a moving target with their right hand when connected to a human-like robotic partner, when perturbed by delay or noise.

Through a comparison between noise and delay perturbation in experimental performance and in simulation with a computational model, we found that participants could from small values of perturbation identify if the perturbation was from delay or noise and that they adopted different compensation strategies in each case.
A short sequence targets transmembrane proteins to primary cilia
Authors: Macarelli Viviana , Harding Edward , Gershlick David C. , Merkle Florian T.
Published: April 2024

Primary cilia are finger-like sensory organelles that extend from the bodies of most cell types and have a distinct lipid and protein composition from the plasma membrane. This partitioning is maintained by a diffusion barrier that restricts the entry of non-ciliary proteins, and allows the selective entry of proteins harboring a ciliary targeting sequence (CTS). However, CTSs are not stereotyped, and previously-reported sequences are insufficient to drive efficient ciliary localization across diverse cell types. Here, we describe a short peptide sequence that efficiently targets transmembrane proteins to primary cilia in all tested cell types, including human neurons. We generate human induced pluripotent stem cell (hiPSC) lines stably expressing a transmembrane construct bearing an extracellular HaloTag and intracellular fluorescent protein, that enables bright, specific labeling of primary cilia in neurons and other cell types. We demonstrate the utility of this resource by developing an image analysis pipeline for the automated measurement of primary cilia to detect changes in their length.